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Merge branch 'Development'

This commit is contained in:
Diamantis Tziotzios 2020-01-31 18:26:27 +02:00
parent 3ada5a0d3d f5de71d0ad
commit 1b4952a909
439 changed files with 8116 additions and 3512 deletions
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7
dmp-backend/data/src/main/java/eu/eudat/data/converters/DateToUTCConverter.java
View File

@ -1,5 +1,7 @@
package eu.eudat.data.converters;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.format.datetime.DateFormatter;
import javax.persistence.AttributeConverter;
@ -15,6 +17,7 @@ import java.util.TimeZone;
*/
@Converter
public class DateToUTCConverter implements AttributeConverter<Date, Date> {
private static final Logger logger = LoggerFactory.getLogger(DateToUTCConverter.class);
@Override
public Date convertToDatabaseColumn(Date attribute) {
@ -25,7 +28,7 @@ public class DateToUTCConverter implements AttributeConverter<Date, Date> {
String date = formatterIST.format(attribute);
return formatterIST.parse(date);
} catch (ParseException e) {
e.printStackTrace();
logger.error(e.getMessage(), e);
}
return null;
}
@ -39,7 +42,7 @@ public class DateToUTCConverter implements AttributeConverter<Date, Date> {
String date = formatterIST.format(dbData);
return formatterIST.parse(date);
} catch (ParseException e) {
e.printStackTrace();
logger.error(e.getMessage(), e);
}
return null;
}

16
dmp-backend/data/src/main/java/eu/eudat/data/dao/criteria/DataManagementPlanPublicCriteria.java
View File

@ -12,6 +12,8 @@ public class DataManagementPlanPublicCriteria extends Criteria<DMP> {
public List<UUID> datasetProfile;
private List<String> dmpOrganisations;
private Integer role;
private boolean allVersions;
private List<UUID> groupIds;
public GrantStateType getGrantStatus() {
return grantStatus;
@ -47,4 +49,18 @@ public class DataManagementPlanPublicCriteria extends Criteria<DMP> {
public void setRole(Integer role) {
this.role = role;
}
public boolean getAllVersions() {
return allVersions;
}
public void setAllVersions(boolean allVersions) {
this.allVersions = allVersions;
}
public List<UUID> getGroupIds() {
return groupIds;
}
public void setGroupIds(List<UUID> groupIds) {
this.groupIds = groupIds;
}
}

8
dmp-backend/data/src/main/java/eu/eudat/data/dao/criteria/DatasetCriteria.java
View File

@ -21,6 +21,7 @@ public class DatasetCriteria extends Criteria<Dataset> {
private List<UUID> grants;
private List<UUID> collaborators;
private List<UUID> datasetTemplates;
private List<UUID> groupIds;
public boolean getAllVersions() {
return allVersions;
@ -105,4 +106,11 @@ public class DatasetCriteria extends Criteria<Dataset> {
public void setDatasetTemplates(List<UUID> datasetTemplates) {
this.datasetTemplates = datasetTemplates;
}
public List<UUID> getGroupIds() {
return groupIds;
}
public void setGroupIds(List<UUID> groupIds) {
this.groupIds = groupIds;
}
}

8
dmp-backend/data/src/main/java/eu/eudat/data/dao/criteria/DatasetProfileCriteria.java
View File

@ -32,6 +32,7 @@ public class DatasetProfileCriteria extends Criteria<DatasetProfile> {
private List<UUID> groupIds;
private Short filter;
private UUID userId;
private boolean finalized;
public boolean getAllVersions() { return allVersions; }
public void setAllVersions(boolean allVersions) { this.allVersions = allVersions; }
@ -52,4 +53,11 @@ public class DatasetProfileCriteria extends Criteria<DatasetProfile> {
public void setUserId(UUID userId) {
this.userId = userId;
}
public boolean getFinalized() {
return finalized;
}
public void setFinalized(boolean finalized) {
this.finalized = finalized;
}
}

3
dmp-backend/data/src/main/java/eu/eudat/data/dao/entities/DatasetDao.java
View File

@ -6,13 +6,14 @@ import eu.eudat.data.entities.Dataset;
import eu.eudat.data.entities.UserInfo;
import eu.eudat.queryable.QueryableList;
import java.util.List;
import java.util.UUID;
public interface DatasetDao extends DatabaseAccessLayer<Dataset, UUID> {
QueryableList<Dataset> getWithCriteria(DatasetCriteria criteria);
QueryableList<Dataset> getAuthenticated(QueryableList<Dataset> query, UserInfo principal);
QueryableList<Dataset> getAuthenticated(QueryableList<Dataset> query, UserInfo principal, List<Integer> roles);
Dataset isPublicDataset(UUID id);

18
dmp-backend/data/src/main/java/eu/eudat/data/dao/entities/DatasetDaoImpl.java
View File

@ -13,8 +13,10 @@ import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.scheduling.annotation.Async;
import org.springframework.stereotype.Component;
import javax.persistence.criteria.Join;
import javax.persistence.criteria.JoinType;
import java.util.Arrays;
import java.util.List;
import java.util.UUID;
import java.util.concurrent.CompletableFuture;
@ -41,13 +43,15 @@ public class DatasetDaoImpl extends DatabaseAccess<Dataset> implements DatasetDa
query.where((builder, root) -> builder.greaterThan(root.get("created"), criteria.getPeriodStart()));
if (!criteria.getAllVersions())
query.initSubQuery(String.class).where((builder, root) -> builder.equal(root.get("dmp").get("version"), query.<String>subQueryMax((builder1, externalRoot, nestedRoot) -> builder1.equal(externalRoot.get("dmp").get("groupId"), nestedRoot.get("dmp").get("groupId")), Arrays.asList(new SelectionField(FieldSelectionType.COMPOSITE_FIELD, "dmp:version")), String.class)));
if (criteria.getGroupIds() != null && !criteria.getGroupIds().isEmpty())
query.where((builder, root) -> root.get("dmp").get("groupId").in(criteria.getGroupIds()));
if (criteria.getDmpIds() != null && !criteria.getDmpIds().isEmpty())
query.where((builder, root) -> root.get("dmp").get("id").in(criteria.getDmpIds()));
if (criteria.getRole() != null) {
/*if (criteria.getRole() != null) {
query.where((builder, root) -> builder.equal(root.join("dmp").join("users").get("role"), criteria.getRole()));
} else {
query.where((builder, root) -> root.join("dmp").join("users").get("role").in(UserDMP.UserDMPRoles.getAllValues()));
}
}*/
if (criteria.getOrganisations() != null && !criteria.getOrganisations().isEmpty())
query.where((builder, root) -> root.join("dmp").join("organisations").get("reference").in(criteria.getOrganisations()));
if (criteria.getGrants() != null && !criteria.getGrants().isEmpty())
@ -87,9 +91,13 @@ public class DatasetDaoImpl extends DatabaseAccess<Dataset> implements DatasetDa
}
@Override
public QueryableList<Dataset> getAuthenticated(QueryableList<Dataset> query, UserInfo principal) {
if (principal.getId() == null) query.where((builder, root) -> builder.equal(root.get("isPublic"), true));
else {
public QueryableList<Dataset> getAuthenticated(QueryableList<Dataset> query, UserInfo principal, List<Integer> roles) {
if (roles != null && !roles.isEmpty()) {
query.where((builder, root) -> {
Join userJoin = root.join("dmp", JoinType.LEFT).join("users", JoinType.LEFT);
return builder.and(builder.equal(userJoin.join("user", JoinType.LEFT).get("id"), principal.getId()), userJoin.get("role").in(roles));
});
} else {
query.where((builder, root) -> builder.equal(root.join("dmp", JoinType.LEFT).join("users", JoinType.LEFT).join("user", JoinType.LEFT).get("id"), principal.getId()));
}
return query;

4
dmp-backend/data/src/main/java/eu/eudat/data/dao/entities/DatasetProfileDaoImpl.java
View File

@ -52,7 +52,11 @@ public class DatasetProfileDaoImpl extends DatabaseAccess<DatasetProfile> implem
builder.notEqual(root.get("id"), criteria.getUserId())));
}
}
if (criteria.getFinalized()) {
query.where(((builder, root) -> builder.equal(root.get("status"), DatasetProfile.Status.FINALIZED.getValue())));
} else {
query.where(((builder, root) -> builder.notEqual(root.get("status"), DatasetProfile.Status.DELETED.getValue())));
}
return query;
}

2
dmp-backend/data/src/main/java/eu/eudat/data/dao/entities/GrantDaoImpl.java
View File

@ -53,7 +53,7 @@ public class GrantDaoImpl extends DatabaseAccess<Grant> implements GrantDao {
if (criteria.getFunderId() != null && !criteria.getFunderId().trim().isEmpty())
query.where((builder, root) -> builder.equal(root.get("funder").get("id"), UUID.fromString(criteria.getFunderId())));
if (criteria.getFunderReference() != null && !criteria.getFunderReference().isEmpty())
query.where((builder, root) -> builder.equal(root.join("funder", JoinType.LEFT).get("reference"), criteria.getFunderReference()));
query.where((builder, root) -> builder.or(builder.like(root.join("funder", JoinType.LEFT).get("reference"), "%" + criteria.getFunderReference())));
query.where((builder, root) -> builder.notEqual(root.get("status"), Grant.Status.DELETED.getValue()));
return query;
}

37
dmp-backend/data/src/main/java/eu/eudat/data/entities/Dataset.java
View File

@ -281,20 +281,41 @@ public class Dataset implements DataEntity<Dataset, UUID> {
this.setLabel(entity.getLabel());
this.setProperties(entity.getProperties());
if (entity.getDatasetDataRepositories() == null || entity.getDatasetDataRepositories().size() < 1) {
if (this.getDatasetDataRepositories() != null) this.getDatasetDataRepositories().removeAll(this.getDatasetDataRepositories());
} else {
if (this.getDatasetDataRepositories() != null) {
this.getDatasetDataRepositories().removeAll(this.getDatasetDataRepositories());
if (entity.getDatasetDataRepositories() != null)
this.getDatasetDataRepositories().addAll(entity.getDatasetDataRepositories());
} else {
this.setDatasetDataRepositories(new HashSet<>());
}
this.getDatasetDataRepositories().addAll(entity.getDatasetDataRepositories().stream().peek(item -> item.setDataset(this)).collect(Collectors.toList()));
}
if (entity.getDatasetExternalDatasets() == null || entity.getDatasetExternalDatasets().size() < 1) {
if (this.getDatasetExternalDatasets() != null) this.getDatasetExternalDatasets().removeAll(this.getDatasetExternalDatasets());
} else {
if (this.getDatasetExternalDatasets() != null) {
this.getDatasetExternalDatasets().removeAll(this.getDatasetExternalDatasets());
if (entity.getDatasetExternalDatasets() != null)
this.getDatasetExternalDatasets().addAll(entity.getDatasetExternalDatasets());
} else {
this.setDatasetExternalDatasets(new HashSet<>());
}
this.getDatasetExternalDatasets().addAll(entity.getDatasetExternalDatasets().stream().peek(item -> item.setDataset(this)).collect(Collectors.toList()));
}
if (entity.getServices() == null || entity.getServices().size() < 1) {
if (this.getServices() != null) this.getServices().removeAll(this.getServices());
} else {
if (this.getServices() != null) {
this.getServices().removeAll(this.getServices());
} else {
this.setServices(new HashSet<>());
}
this.getServices().addAll(entity.getServices().stream().peek(item -> item.setDataset(this)).collect(Collectors.toList()));
}
this.setRegistries(entity.getRegistries());
this.getServices().removeAll(this.getServices());
if (entity.getServices() != null)
this.getServices().addAll(entity.getServices());
this.setDmp(entity.getDmp());
this.setStatus(entity.getStatus());
this.setProfile(entity.getProfile());

4
dmp-backend/data/src/main/java/eu/eudat/data/entities/Funder.java
View File

@ -66,8 +66,8 @@ public class Funder implements DataEntity<Funder, UUID> {
}
@Id
@GeneratedValue
@GenericGenerator(name = "uuid2", strategy = "uuid2")
//@GeneratedValue
//@GenericGenerator(name = "uuid2", strategy = "uuid2")
@Column(name = "\"ID\"", updatable = false, nullable = false, columnDefinition = "BINARY(16)")
private UUID id;

4
dmp-backend/data/src/main/java/eu/eudat/data/entities/Grant.java
View File

@ -81,8 +81,8 @@ public class Grant implements DataEntity<Grant, UUID> {
}
@Id
@GeneratedValue
@GenericGenerator(name = "uuid2", strategy = "uuid2")
//@GeneratedValue
//@GenericGenerator(name = "uuid2", strategy = "uuid2")
@Column(name = "\"ID\"", updatable = false, nullable = false, columnDefinition = "BINARY(16)")
private UUID id;

4
dmp-backend/data/src/main/java/eu/eudat/data/entities/Project.java
View File

@ -67,8 +67,8 @@ public class Project implements DataEntity<Project, UUID> {
}
@Id
@GeneratedValue
@GenericGenerator(name = "uuid2", strategy = "uuid2")
//@GeneratedValue
//@GenericGenerator(name = "uuid2", strategy = "uuid2")
@Column(name = "\"ID\"", updatable = false, nullable = false, columnDefinition = "BINARY(16)")
private UUID id;

4
dmp-backend/data/src/main/java/eu/eudat/data/entities/Researcher.java
View File

@ -19,8 +19,8 @@ import java.util.UUID;
public class Researcher implements DataEntity<Researcher, UUID> {
@Id
@GeneratedValue
@GenericGenerator(name = "uuid2", strategy = "uuid2")
/*@GeneratedValue
@GenericGenerator(name = "uuid2", strategy = "uuid2")*/
@Column(name = "\"ID\"", updatable = false, nullable = false, columnDefinition = "BINARY(16)")
private UUID id;

9
dmp-backend/data/src/main/java/eu/eudat/data/query/definition/Query.java
View File

@ -3,8 +3,11 @@ package eu.eudat.data.query.definition;
import eu.eudat.data.dao.criteria.Criteria;
import eu.eudat.queryable.QueryableList;
import eu.eudat.queryable.queryableentity.DataEntity;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
public abstract class Query<C extends Criteria<T>, T extends DataEntity> implements CriteriaQuery<C, T> {
private static final Logger logger = LoggerFactory.getLogger(Query.class);
private C criteria;
private QueryableList<T> query;
@ -33,10 +36,8 @@ public abstract class Query<C extends Criteria<T>, T extends DataEntity> impleme
q.setCriteria(criteria);
q.setQuery(query);
return q;
} catch (InstantiationException e) {
e.printStackTrace();
} catch (IllegalAccessException e) {
e.printStackTrace();
} catch (InstantiationException | IllegalAccessException e) {
logger.error (e.getMessage(), e);
}
return null;
}

11
dmp-backend/data/src/main/java/eu/eudat/data/query/items/table/dmp/DataManagmentPlanPublicTableRequest.java
View File

@ -5,8 +5,11 @@ import eu.eudat.data.entities.DMP;
import eu.eudat.data.query.PaginationService;
import eu.eudat.data.query.definition.TableQuery;
import eu.eudat.queryable.QueryableList;
import eu.eudat.queryable.types.FieldSelectionType;
import eu.eudat.queryable.types.SelectionField;
import eu.eudat.types.grant.GrantStateType;
import java.util.Arrays;
import java.util.Date;
import java.util.UUID;
@ -33,6 +36,14 @@ public class DataManagmentPlanPublicTableRequest extends TableQuery<DataManageme
query.where((builder, root) -> root.join("associatedDmps").get("id").in(this.getCriteria().datasetProfile));
if (this.getCriteria().getDmpOrganisations() != null && !this.getCriteria().getDmpOrganisations().isEmpty())
query.where(((builder, root) -> root.join("organisations").get("reference").in(this.getCriteria().getDmpOrganisations())));
if (!this.getCriteria().getAllVersions()) {
query.initSubQuery(String.class).where((builder, root) -> builder.equal(root.get("version"),
query.<String>subQueryMax((builder1, externalRoot, nestedRoot) -> builder1.and(builder1.equal(externalRoot.get("groupId"),
nestedRoot.get("groupId")), builder1.equal(nestedRoot.get("isPublic"), true)), Arrays.asList(new SelectionField(FieldSelectionType.FIELD, "version")), String.class)));
}
if (this.getCriteria().getGroupIds() != null && !this.getCriteria().getGroupIds().isEmpty()) {
query.where((builder, root) -> root.get("groupId").in(this.getCriteria().getGroupIds()));
}
return query;
}

5
dmp-backend/elastic/src/main/java/eu/eudat/elastic/entities/Dataset.java
View File

@ -1,6 +1,8 @@
package eu.eudat.elastic.entities;
import org.elasticsearch.common.xcontent.XContentBuilder;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.io.IOException;
import java.util.LinkedList;
@ -11,6 +13,7 @@ import java.util.Map;
* Created by ikalyvas on 7/5/2018.
*/
public class Dataset implements ElasticEntity<Dataset> {
private static final Logger logger = LoggerFactory.getLogger(Dataset.class);
private String id;
private List<Tag> tags = new LinkedList<>();
@ -40,7 +43,7 @@ public class Dataset implements ElasticEntity<Dataset> {
try {
x.toElasticEntity(builder);
} catch (IOException e) {
e.printStackTrace();
logger.error(e.getMessage(), e);
}
});
builder.endArray();

5
dmp-backend/elastic/src/main/java/eu/eudat/elastic/repository/ElasticRepository.java
View File

@ -6,6 +6,8 @@ import eu.eudat.elastic.entities.ElasticEntity;
import org.elasticsearch.client.Client;
import org.elasticsearch.client.RestClient;
import org.elasticsearch.client.RestHighLevelClient;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.io.IOException;
@ -13,6 +15,7 @@ import java.io.IOException;
* Created by ikalyvas on 7/5/2018.
*/
public abstract class ElasticRepository<T extends ElasticEntity,C extends Criteria> implements Repository<T,C> {
private static final Logger logger = LoggerFactory.getLogger(ElasticRepository.class);
private RestHighLevelClient client;
public RestHighLevelClient getClient() {
@ -29,7 +32,7 @@ public abstract class ElasticRepository<T extends ElasticEntity,C extends Criter
try {
item = mapper.readValue(value, tClass);
} catch (IOException e) {
e.printStackTrace();
logger.error(e.getMessage(), e);
}
return item;
}

4
dmp-backend/logging/src/main/java/eu/eudat/core/logger/remote/http/HttpRemoteLogger.java
View File

@ -28,14 +28,14 @@ import java.util.Map;
* Created by ikalyvas on 5/30/2018.
*/
@Service("logger")
//@Service("logger")
public class HttpRemoteLogger extends AbstractBatchLogger implements Logger {
private RestTemplate rest;
private HttpHeaders headers;
private Environment environment;
@Autowired
//@Autowired
public HttpRemoteLogger(Environment environment) {
super(environment);
this.rest = new RestTemplate();

5
dmp-backend/queryable/src/main/java/eu/eudat/queryable/jpa/hibernatequeryablelist/QueryableHibernateList.java
View File

@ -7,6 +7,8 @@ import eu.eudat.queryable.jpa.predicates.*;
import eu.eudat.queryable.queryableentity.DataEntity;
import eu.eudat.queryable.types.FieldSelectionType;
import eu.eudat.queryable.types.SelectionField;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.scheduling.annotation.Async;
import javax.persistence.EntityManager;
@ -18,6 +20,7 @@ import java.util.concurrent.CompletableFuture;
import java.util.stream.Collectors;
public class QueryableHibernateList<T extends DataEntity> implements QueryableList<T> {
private static final Logger logger = LoggerFactory.getLogger(QueryableHibernateList.class);
private Collector collector = new Collector();
private EntityManager manager;
@ -264,7 +267,7 @@ public class QueryableHibernateList<T extends DataEntity> implements QueryableLi
try {
return (T) this.tClass.newInstance().buildFromTuple(groupedResults.get(x.get("id")), this.fields, "");
} catch (InstantiationException | IllegalAccessException e) {
e.printStackTrace();
logger.error(e.getMessage(), e);
}
return null;
}).collect(Collectors.toList()));

7
dmp-backend/web/src/main/java/eu/eudat/cache/ResponsesCache.java vendored
View File

@ -2,6 +2,8 @@ package eu.eudat.cache;
import com.google.common.cache.CacheBuilder;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.cache.CacheManager;
import org.springframework.cache.annotation.EnableCaching;
import org.springframework.cache.guava.GuavaCache;
@ -17,6 +19,7 @@ import java.util.concurrent.TimeUnit;
@Component
@EnableCaching
public class ResponsesCache {
private static final Logger logger = LoggerFactory.getLogger(ResponsesCache.class);
public static long HOW_MANY = 30;
public static TimeUnit TIME_UNIT = TimeUnit.MINUTES;
@ -24,7 +27,7 @@ public class ResponsesCache {
@Bean
public CacheManager cacheManager() {
System.out.print("Loading ResponsesCache...");
logger.info("Loading ResponsesCache...");
SimpleCacheManager simpleCacheManager = new SimpleCacheManager();
List<GuavaCache> caches = new ArrayList<GuavaCache>();
caches.add(new GuavaCache("repositories", CacheBuilder.newBuilder().expireAfterAccess(HOW_MANY, TIME_UNIT).build()));
@ -38,7 +41,7 @@ public class ResponsesCache {
caches.add(new GuavaCache("researchers", CacheBuilder.newBuilder().expireAfterAccess(HOW_MANY, TIME_UNIT).build()));
caches.add(new GuavaCache("externalDatasets", CacheBuilder.newBuilder().expireAfterAccess(HOW_MANY, TIME_UNIT).build()));
simpleCacheManager.setCaches(caches);
System.out.println("OK");
logger.info("OK");
return simpleCacheManager;
}

2
dmp-backend/web/src/main/java/eu/eudat/configurations/WebMVCConfiguration.java
View File

@ -37,6 +37,6 @@ public class WebMVCConfiguration extends WebMvcConfigurerAdapter {
@Override
public void addInterceptors(InterceptorRegistry registry) {
registry.addInterceptor(new RequestInterceptor(this.apiContext.getHelpersService().getLoggerService()));
// registry.addInterceptor(new RequestInterceptor(this.apiContext.getHelpersService().getLoggerService()));
}
}

10
dmp-backend/web/src/main/java/eu/eudat/configurations/dynamicfunder/DynamicFunderConfigurationDevelImpl.java
View File

@ -4,6 +4,8 @@ import eu.eudat.configurations.dynamicfunder.entities.Configuration;
import eu.eudat.configurations.dynamicfunder.entities.Property;
import eu.eudat.models.data.dynamicfields.Dependency;
import eu.eudat.models.data.dynamicfields.DynamicField;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.context.annotation.Profile;
import org.springframework.core.env.Environment;
import org.springframework.stereotype.Service;
@ -19,6 +21,7 @@ import java.util.List;
@Service("dynamicFunderConfiguration")
@Profile("devel")
public class DynamicFunderConfigurationDevelImpl implements DynamicFunderConfiguration {
private static final Logger logger = LoggerFactory.getLogger(DynamicFunderConfigurationDevelImpl.class);
private Configuration configuration;
private List<DynamicField> fields;
@ -32,7 +35,7 @@ public class DynamicFunderConfigurationDevelImpl implements DynamicFunderConfigu
public Configuration getConfiguration() {
if (this.configuration != null) return this.configuration;
String fileUrl = this.environment.getProperty("configuration.dynamicFunderUrl");
System.out.println("Loaded also config file: " + fileUrl);
logger.info("Loaded also config file: " + fileUrl);
String current = null;
InputStream is = null;
try {
@ -43,13 +46,12 @@ public class DynamicFunderConfigurationDevelImpl implements DynamicFunderConfigu
is = new URL("file:///"+ current + "/web/src/main/resources/FunderConfiguration.xml").openStream();
this.configuration = (Configuration) jaxbUnmarshaller.unmarshal(is);
} catch (Exception ex) {
ex.printStackTrace();
System.out.println("Cannot find in folder" + current);
logger.error("Cannot find in folder" + current, ex);
} finally {
try {
if (is != null) is.close();
} catch (IOException e) {
System.out.println("Warning: Could not close a stream after reading from file: " + fileUrl);
logger.warn("Warning: Could not close a stream after reading from file: " + fileUrl, e);
}
}
return this.configuration;

10
dmp-backend/web/src/main/java/eu/eudat/configurations/dynamicfunder/DynamicFunderConfigurationProdImpl.java
View File

@ -4,6 +4,8 @@ import eu.eudat.configurations.dynamicfunder.entities.Configuration;
import eu.eudat.configurations.dynamicfunder.entities.Property;
import eu.eudat.models.data.dynamicfields.Dependency;
import eu.eudat.models.data.dynamicfields.DynamicField;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.context.annotation.Profile;
import org.springframework.core.env.Environment;
import org.springframework.stereotype.Service;
@ -20,6 +22,7 @@ import java.util.List;
@Service("dynamicFunderConfiguration")
@Profile({ "production", "staging" })
public class DynamicFunderConfigurationProdImpl implements DynamicFunderConfiguration {
private static final Logger logger = LoggerFactory.getLogger(DynamicFunderConfigurationProdImpl.class);
private Configuration configuration;
private List<DynamicField> fields;
@ -33,7 +36,7 @@ public class DynamicFunderConfigurationProdImpl implements DynamicFunderConfigur
public Configuration getConfiguration() {
if (this.configuration != null) return this.configuration;
String fileUrl = this.environment.getProperty("configuration.dynamicFunderUrl");
System.out.println("Loaded also config file: " + fileUrl);
logger.info("Loaded also config file: " + fileUrl);
String current = null;
InputStream is = null;
try {
@ -44,13 +47,12 @@ public class DynamicFunderConfigurationProdImpl implements DynamicFunderConfigur
is = new URL(Paths.get(fileUrl).toUri().toURL().toString()).openStream();
this.configuration = (Configuration) jaxbUnmarshaller.unmarshal(is);
} catch (Exception ex) {
ex.printStackTrace();
System.out.println("Cannot find in folder" + current);
logger.error("Cannot find in folder" + current, ex);
} finally {
try {
if (is != null) is.close();
} catch (IOException e) {
System.out.println("Warning: Could not close a stream after reading from file: " + fileUrl);
logger.warn("Warning: Could not close a stream after reading from file: " + fileUrl, e);
}
}
return this.configuration;

10
dmp-backend/web/src/main/java/eu/eudat/configurations/dynamicgrant/DynamicGrantConfigurationDevelImpl.java
View File

@ -4,6 +4,8 @@ import eu.eudat.configurations.dynamicgrant.entities.Configuration;
import eu.eudat.configurations.dynamicgrant.entities.Property;
import eu.eudat.models.data.dynamicfields.Dependency;
import eu.eudat.models.data.dynamicfields.DynamicField;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.context.annotation.Profile;
import org.springframework.core.env.Environment;
@ -24,6 +26,7 @@ import java.util.List;
@Service("dynamicGrantConfiguration")
@Profile("devel")
public class DynamicGrantConfigurationDevelImpl implements DynamicGrantConfiguration {
private static final Logger logger = LoggerFactory.getLogger(DynamicGrantConfigurationDevelImpl.class);
private Configuration configuration;
@ -40,7 +43,7 @@ public class DynamicGrantConfigurationDevelImpl implements DynamicGrantConfigura
public Configuration getConfiguration() {
if (this.configuration != null) return this.configuration;
String fileUrl = this.environment.getProperty("configuration.dynamicGrantUrl");
System.out.println("Loaded also config file: " + fileUrl);
logger.info("Loaded also config file: " + fileUrl);
String current = null;
InputStream is = null;
try {
@ -51,13 +54,12 @@ public class DynamicGrantConfigurationDevelImpl implements DynamicGrantConfigura
is = new URL("file:///"+ current + "/web/src/main/resources/GrantConfiguration.xml").openStream();
this.configuration = (Configuration) jaxbUnmarshaller.unmarshal(is);
} catch (Exception ex) {
ex.printStackTrace();
System.out.println("Cannot find in folder" + current);
logger.error("Cannot find in folder" + current, ex);
} finally {
try {
if (is != null) is.close();
} catch (IOException e) {
System.out.println("Warning: Could not close a stream after reading from file: " + fileUrl);
logger.warn("Warning: Could not close a stream after reading from file: " + fileUrl, e);
}
}
return this.configuration;

10
dmp-backend/web/src/main/java/eu/eudat/configurations/dynamicgrant/DynamicGrantConfigurationProdImpl.java
View File

@ -4,6 +4,8 @@ import eu.eudat.configurations.dynamicgrant.entities.Configuration;
import eu.eudat.configurations.dynamicgrant.entities.Property;
import eu.eudat.models.data.dynamicfields.Dependency;
import eu.eudat.models.data.dynamicfields.DynamicField;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.context.annotation.Profile;
import org.springframework.core.env.Environment;
@ -24,6 +26,7 @@ import java.util.List;
@Service("dynamicGrantConfiguration")
@Profile({ "production", "staging" })
public class DynamicGrantConfigurationProdImpl implements DynamicGrantConfiguration {
private static final Logger logger = LoggerFactory.getLogger(DynamicGrantConfigurationProdImpl.class);
private Configuration configuration;
@ -40,7 +43,7 @@ public class DynamicGrantConfigurationProdImpl implements DynamicGrantConfigurat
public Configuration getConfiguration() {
if (this.configuration != null) return this.configuration;
String fileUrl = this.environment.getProperty("configuration.dynamicGrantUrl");
System.out.println("Loaded also config file: " + fileUrl);
logger.info("Loaded also config file: " + fileUrl);
String current = null;
InputStream is = null;
try {
@ -51,13 +54,12 @@ public class DynamicGrantConfigurationProdImpl implements DynamicGrantConfigurat
is = new URL(Paths.get(fileUrl).toUri().toURL().toString()).openStream();
this.configuration = (Configuration) jaxbUnmarshaller.unmarshal(is);
} catch (Exception ex) {
ex.printStackTrace();
System.out.println("Cannot find in folder" + current);
logger.error("Cannot find in folder" + current, ex);
} finally {
try {
if (is != null) is.close();
} catch (IOException e) {
System.out.println("Warning: Could not close a stream after reading from file: " + fileUrl);
logger.warn("Warning: Could not close a stream after reading from file: " + fileUrl, e);
}
}
return this.configuration;

10
dmp-backend/web/src/main/java/eu/eudat/configurations/dynamicproject/DynamicProjectConfigurationDevelImpl.java
View File

@ -4,6 +4,8 @@ import eu.eudat.configurations.dynamicproject.entities.Configuration;
import eu.eudat.configurations.dynamicproject.entities.Property;
import eu.eudat.models.data.dynamicfields.Dependency;
import eu.eudat.models.data.dynamicfields.DynamicField;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.context.annotation.Profile;
import org.springframework.core.env.Environment;
@ -20,6 +22,7 @@ import java.util.List;
@Service("dynamicProjectConfiguration")
@Profile("devel")
public class DynamicProjectConfigurationDevelImpl implements DynamicProjectConfiguration{
private static final Logger logger = LoggerFactory.getLogger(DynamicProjectConfigurationDevelImpl.class);
private Configuration configuration;
private List<DynamicField> fields;
@ -34,7 +37,7 @@ public class DynamicProjectConfigurationDevelImpl implements DynamicProjectConfi
public Configuration getConfiguration() {
if (this.configuration != null) return this.configuration;
String fileUrl = this.environment.getProperty("configuration.dynamicProjectUrl");
System.out.println("Loaded also config file: " + fileUrl);
logger.info("Loaded also config file: " + fileUrl);
String current = null;
InputStream is = null;
try {
@ -45,13 +48,12 @@ public class DynamicProjectConfigurationDevelImpl implements DynamicProjectConfi
is = new URL("file:///"+ current + "/web/src/main/resources/ProjectConfiguration.xml").openStream();
this.configuration = (Configuration) jaxbUnmarshaller.unmarshal(is);
} catch (Exception ex) {
ex.printStackTrace();
System.out.println("Cannot find in folder" + current);
logger.error("Cannot find in folder" + current, ex);
} finally {
try {
if (is != null) is.close();
} catch (IOException e) {
System.out.println("Warning: Could not close a stream after reading from file: " + fileUrl);
logger.warn("Warning: Could not close a stream after reading from file: " + fileUrl, e);
}
}
return this.configuration;

10
dmp-backend/web/src/main/java/eu/eudat/configurations/dynamicproject/DynamicProjectConfigurationProdImpl.java
View File

@ -4,6 +4,8 @@ import eu.eudat.configurations.dynamicproject.entities.Configuration;
import eu.eudat.configurations.dynamicproject.entities.Property;
import eu.eudat.models.data.dynamicfields.Dependency;
import eu.eudat.models.data.dynamicfields.DynamicField;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.context.annotation.Profile;
import org.springframework.core.env.Environment;
@ -21,6 +23,7 @@ import java.util.List;
@Service("dynamicProjectConfiguration")
@Profile({ "production", "staging" })
public class DynamicProjectConfigurationProdImpl implements DynamicProjectConfiguration{
private static final Logger logger = LoggerFactory.getLogger(DynamicProjectConfigurationProdImpl.class);
private Configuration configuration;
@ -37,7 +40,7 @@ public class DynamicProjectConfigurationProdImpl implements DynamicProjectConfig
public Configuration getConfiguration() {
if (this.configuration != null) return this.configuration;
String fileUrl = this.environment.getProperty("configuration.dynamicProjectUrl");
System.out.println("Loaded also config file: " + fileUrl);
logger.info("Loaded also config file: " + fileUrl);
String current = null;
InputStream is = null;
try {
@ -48,13 +51,12 @@ public class DynamicProjectConfigurationProdImpl implements DynamicProjectConfig
is = new URL(Paths.get(fileUrl).toUri().toURL().toString()).openStream();
this.configuration = (Configuration) jaxbUnmarshaller.unmarshal(is);
} catch (Exception ex) {
ex.printStackTrace();
System.out.println("Cannot find in folder" + current);
logger.error("Cannot find in folder" + current, ex);
} finally {
try {
if (is != null) is.close();
} catch (IOException e) {
System.out.println("Warning: Could not close a stream after reading from file: " + fileUrl);
logger.warn("Warning: Could not close a stream after reading from file: " + fileUrl, e);
}
}
return this.configuration;

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

@ -42,7 +42,7 @@ public class Admin extends BaseController {
private ConfigLoader configLoader;
@Autowired
public Admin(ApiContext apiContext, DatasetProfileManager datasetProfileManager, UserManager userManager, Logger logger, ConfigLoader configLoader) {
public Admin(ApiContext apiContext, DatasetProfileManager datasetProfileManager, UserManager userManager/*, Logger logger*/, ConfigLoader configLoader) {
super(apiContext);
this.datasetProfileManager = datasetProfileManager;
this.userManager = userManager;

6
dmp-backend/web/src/main/java/eu/eudat/controllers/BaseController.java
View File

@ -9,7 +9,7 @@ import org.springframework.web.bind.annotation.InitBinder;
public abstract class BaseController {
private Logger logger;
/*private Logger logger;*/
private ApiContext apiContext;
@ -17,9 +17,9 @@ public abstract class BaseController {
return apiContext;
}
public Logger getLoggerService() {
/*public Logger getLoggerService() {
return logger;
}
}*/
public BaseController(ApiContext apiContext) {

5
dmp-backend/web/src/main/java/eu/eudat/controllers/ContactEmail.java
View File

@ -5,6 +5,8 @@ import eu.eudat.models.data.ContactEmail.ContactEmailModel;
import eu.eudat.models.data.helpers.responses.ResponseItem;
import eu.eudat.models.data.security.Principal;
import eu.eudat.types.ApiMessageCode;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.http.HttpStatus;
import org.springframework.http.ResponseEntity;
import org.springframework.web.bind.annotation.*;
@ -15,6 +17,7 @@ import javax.transaction.Transactional;
@CrossOrigin
@RequestMapping(value = "api/contactEmail")
public class ContactEmail {
private static final Logger logger = LoggerFactory.getLogger(ContactEmail.class);
private ContactEmailManager contactEmailManager;
@ -31,7 +34,7 @@ public class ContactEmail {
this.contactEmailManager.sendContactEmail(contactEmailModel, principal);
return ResponseEntity.status(HttpStatus.OK).body(new ResponseItem().status(ApiMessageCode.SUCCESS_MESSAGE));
} catch (Exception ex) {
ex.printStackTrace();
logger.error(ex.getMessage(), ex);
return ResponseEntity.status(HttpStatus.BAD_REQUEST).body(new ResponseItem().status(ApiMessageCode.ERROR_MESSAGE).message(ex.getMessage()));
}
}

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

@ -29,6 +29,8 @@ import eu.eudat.models.data.security.Principal;
import eu.eudat.query.DMPQuery;
import eu.eudat.types.ApiMessageCode;
import eu.eudat.types.Authorities;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.core.env.Environment;
import org.springframework.http.HttpHeaders;
@ -55,6 +57,7 @@ import java.util.UUID;
@CrossOrigin
@RequestMapping(value = {"/api/dmps/"})
public class DMPs extends BaseController {
private static final Logger logger = LoggerFactory.getLogger(DMPs.class);
private DynamicGrantConfiguration dynamicGrantConfiguration;
private Environment environment;
@ -95,7 +98,7 @@ public class DMPs extends BaseController {
if (contentType.equals("application/xml") || contentType.equals("application/msword")) {
return this.dataManagementPlanManager.getDocument(id, contentType, principal, this.configLoader);
} else {
eu.eudat.models.data.dmp.DataManagementPlan dataManagementPlan = this.dataManagementPlanManager.getSingle(id, principal, this.dynamicGrantConfiguration);
eu.eudat.models.data.dmp.DataManagementPlan dataManagementPlan = this.dataManagementPlanManager.getSingle(id, principal);
return ResponseEntity.status(HttpStatus.OK).body(new ResponseItem<DataManagementPlan>().status(ApiMessageCode.NO_MESSAGE).payload(dataManagementPlan));
}
}
@ -110,14 +113,18 @@ public class DMPs extends BaseController {
@RequestMapping(method = RequestMethod.GET, value = {"rda/{id}"})
public @ResponseBody
ResponseEntity getRDAJsonDocument(@PathVariable String id, @ClaimedAuthorities(claims = {Authorities.ADMIN, Authorities.MANAGER, Authorities.USER, Authorities.ANONYMOUS}) Principal principal) throws IOException {
return this.dataManagementPlanManager.getRDAJsonDocument(id, principal);
return this.dataManagementPlanManager.getRDAJsonDocument(id, datasetManager, principal);
}
@RequestMapping(method = RequestMethod.GET, value = {"/overview/{id}"})
public @ResponseBody
ResponseEntity getOverviewSingle(@PathVariable String id, Principal principal) throws IllegalAccessException, InstantiationException {
ResponseEntity getOverviewSingle(@PathVariable String id, Principal principal) {
try {
DataManagementPlanOverviewModel dataManagementPlan = this.dataManagementPlanManager.getOverviewSingle(id, principal);
return ResponseEntity.status(HttpStatus.OK).body(new ResponseItem<DataManagementPlanOverviewModel>().status(ApiMessageCode.NO_MESSAGE).payload(dataManagementPlan));
} catch (Exception e) {
return ResponseEntity.status(HttpStatus.NOT_FOUND).body(new ResponseItem<DataManagementPlanOverviewModel>().status(ApiMessageCode.ERROR_MESSAGE));
}
}
@RequestMapping(method = RequestMethod.GET, value = {"/public/{id}"})
@ -195,7 +202,7 @@ public class DMPs extends BaseController {
String name = file.getName().substring(0, file.getName().length() - 5);
File pdffile = datasetManager.convertToPDF(file, environment, name);
InputStream resource = new FileInputStream(pdffile);
System.out.println("Mime Type of " + file.getName() + " is " +
logger.info("Mime Type of " + file.getName() + " is " +
new MimetypesFileTypeMap().getContentType(file));
HttpHeaders responseHeaders = new HttpHeaders();
responseHeaders.setContentLength(pdffile.length());
@ -269,7 +276,7 @@ public class DMPs extends BaseController {
String zenodoDOI = this.dataManagementPlanManager.createZenodoDoi(UUID.fromString(id), principal, configLoader);
return ResponseEntity.status(HttpStatus.OK).body(new ResponseItem<String>().status(ApiMessageCode.SUCCESS_MESSAGE).message("Successfully created DOI for Data Datamanagement Plan in question.").payload(zenodoDOI));
} catch (Exception e) {
e.printStackTrace();
logger.error(e.getMessage(), e);
return ResponseEntity.status(HttpStatus.BAD_REQUEST).body(new ResponseItem<String>().status(ApiMessageCode.ERROR_MESSAGE).message(e.getMessage()));
}
}

5
dmp-backend/web/src/main/java/eu/eudat/controllers/DashBoardController.java
View File

@ -1,6 +1,7 @@
package eu.eudat.controllers;
import eu.eudat.logic.managers.DashBoardManager;
import eu.eudat.logic.security.claims.ClaimedAuthorities;
import eu.eudat.logic.services.ApiContext;
import eu.eudat.models.data.dashboard.recent.RecentActivity;
import eu.eudat.models.data.dashboard.searchbar.SearchBarItem;
@ -8,6 +9,7 @@ import eu.eudat.models.data.dashboard.statistics.DashBoardStatistics;
import eu.eudat.models.data.helpers.responses.ResponseItem;
import eu.eudat.models.data.security.Principal;
import eu.eudat.types.ApiMessageCode;
import eu.eudat.types.Authorities;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.http.HttpStatus;
import org.springframework.http.ResponseEntity;
@ -46,7 +48,8 @@ public class DashBoardController extends BaseController {
}
@RequestMapping(method = RequestMethod.GET, value = {"/dashboard/search"}, produces = "application/json")
public ResponseEntity<ResponseItem<List<SearchBarItem>>> search(@RequestParam(name = "like") String like, Principal principal) {
public ResponseEntity<ResponseItem<List<SearchBarItem>>> search(@RequestParam(name = "like") String like,
@ClaimedAuthorities(claims = {Authorities.ADMIN, Authorities.MANAGER, Authorities.USER, Authorities.ANONYMOUS}) Principal principal) {
List<SearchBarItem> searchBarItemList = dashBoardManager.searchUserData(like, principal);
return ResponseEntity.status(HttpStatus.OK).body(new ResponseItem<List<SearchBarItem>>().status(ApiMessageCode.NO_MESSAGE).payload(searchBarItemList));
}

6
dmp-backend/web/src/main/java/eu/eudat/controllers/DataRepositories.java
View File

@ -43,10 +43,10 @@ public class DataRepositories extends BaseController {
@Transactional
@RequestMapping(method = RequestMethod.POST, consumes = "application/json", produces = "application/json")
public @ResponseBody
ResponseEntity<ResponseItem<DataRepository>> create(@RequestBody eu.eudat.models.data.datarepository.DataRepositoryModel dataRepositoryModel, Principal principal) throws Exception {
ResponseEntity<ResponseItem<DataRepositoryModel>> create(@RequestBody eu.eudat.models.data.datarepository.DataRepositoryModel dataRepositoryModel, Principal principal) throws Exception {
DataRepository dataRepository = this.dataRepositoryManager.create(dataRepositoryModel, principal);
return ResponseEntity.status(HttpStatus.OK).body(new ResponseItem<DataRepository>().payload(dataRepository).status(ApiMessageCode.SUCCESS_MESSAGE));
DataRepositoryModel dataRepositoryModel1 = new DataRepositoryModel().fromDataModel(dataRepository);
return ResponseEntity.status(HttpStatus.OK).body(new ResponseItem<DataRepositoryModel>().payload(dataRepositoryModel1).status(ApiMessageCode.SUCCESS_MESSAGE));
}
}

5
dmp-backend/web/src/main/java/eu/eudat/controllers/DatasetWizardController.java
View File

@ -19,6 +19,8 @@ import eu.eudat.models.data.security.Principal;
import eu.eudat.models.data.user.composite.PagedDatasetProfile;
import eu.eudat.types.ApiMessageCode;
import org.apache.poi.util.IOUtils;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.core.env.Environment;
import org.springframework.http.HttpHeaders;
@ -44,6 +46,7 @@ import static eu.eudat.types.Authorities.ANONYMOUS;
@CrossOrigin
@RequestMapping(value = {"api/datasetwizard"})
public class DatasetWizardController extends BaseController {
private static final Logger logger = LoggerFactory.getLogger(DatasetWizardController.class);
private Environment environment;
private DatasetManager datasetManager;
@ -191,7 +194,7 @@ public class DatasetWizardController extends BaseController {
return ResponseEntity.status(HttpStatus.BAD_REQUEST).body(new ResponseItem().status(ApiMessageCode.NO_MESSAGE).message("Import was unsuccessful."));
}
} catch (Exception e) {
e.printStackTrace();
logger.error(e.getMessage(), e);
return ResponseEntity.status(HttpStatus.BAD_REQUEST).body(new ResponseItem().status(ApiMessageCode.NO_MESSAGE).message("Import was unsuccessful."));
}
}

7
dmp-backend/web/src/main/java/eu/eudat/controllers/EmailConfirmation.java
View File

@ -36,7 +36,11 @@ public class EmailConfirmation {
return ResponseEntity.status(HttpStatus.OK).body(new ResponseItem().status(ApiMessageCode.SUCCESS_MESSAGE));
} catch
(HasConfirmedEmailException | TokenExpiredException ex) {
if (ex instanceof TokenExpiredException) {
return ResponseEntity.status(HttpStatus.BAD_REQUEST).body(new ResponseItem().status(ApiMessageCode.NO_MESSAGE));
} else {
return ResponseEntity.status(HttpStatus.FOUND).body(new ResponseItem().status(ApiMessageCode.WARN_MESSAGE));
}
}
}
@ -48,6 +52,9 @@ public class EmailConfirmation {
this.emailConfirmationManager.sendConfirmationEmail(email, principal);
return ResponseEntity.status(HttpStatus.OK).body(new ResponseItem().status(ApiMessageCode.SUCCESS_MESSAGE));
} catch (Exception ex) {
if (ex instanceof HasConfirmedEmailException) {
return ResponseEntity.status(HttpStatus.FOUND).body(new ResponseItem().status(ApiMessageCode.WARN_MESSAGE));
}
return ResponseEntity.status(HttpStatus.BAD_REQUEST).body(new ResponseItem().status(ApiMessageCode.NO_MESSAGE));
}
}

5
dmp-backend/web/src/main/java/eu/eudat/controllers/ExternalDatasets.java
View File

@ -62,8 +62,9 @@ public class ExternalDatasets extends BaseController {
@Transactional
@RequestMapping(method = RequestMethod.POST, value = {"/externaldatasets"}, consumes = "application/json", produces = "application/json")
public @ResponseBody
ResponseEntity<ResponseItem<ExternalDataset>> create(@RequestBody eu.eudat.models.data.externaldataset.ExternalDatasetModel externalDatasetModel, Principal principal) throws Exception {
ResponseEntity<ResponseItem<ExternalDatasetListingModel>> create(@RequestBody eu.eudat.models.data.externaldataset.ExternalDatasetModel externalDatasetModel, Principal principal) throws Exception {
ExternalDataset externalDataset = this.externalDatasetManager.create(externalDatasetModel, principal);
return ResponseEntity.status(HttpStatus.OK).body(new ResponseItem<ExternalDataset>().payload(externalDataset).status(ApiMessageCode.SUCCESS_MESSAGE));
ExternalDatasetListingModel externalDatasetListingModel = new ExternalDatasetListingModel().fromDataModel(externalDataset);
return ResponseEntity.status(HttpStatus.OK).body(new ResponseItem<ExternalDatasetListingModel>().payload(externalDatasetListingModel).status(ApiMessageCode.SUCCESS_MESSAGE));
}
}

58
dmp-backend/web/src/main/java/eu/eudat/controllers/LanguageController.java Normal file
View File

@ -0,0 +1,58 @@
package eu.eudat.controllers;
import eu.eudat.models.data.helpers.responses.ResponseItem;
import eu.eudat.models.data.security.Principal;
import eu.eudat.types.ApiMessageCode;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.core.env.Environment;
import org.springframework.http.HttpHeaders;
import org.springframework.http.HttpStatus;
import org.springframework.http.MediaType;
import org.springframework.http.ResponseEntity;
import org.springframework.web.bind.annotation.*;
import java.io.*;
import java.util.UUID;
@RestController
@CrossOrigin
@RequestMapping(value = {"/api/language/"})
public class LanguageController {
Environment environment;
@Autowired
public LanguageController(Environment environment) {
this.environment = environment;
}
@RequestMapping(value = "{lang}", method = RequestMethod.GET)
public ResponseEntity getLanguage(@PathVariable String lang) throws IOException {
String fileName = this.environment.getProperty("language.path") + lang + ".json";
InputStream is = new FileInputStream(fileName);
HttpHeaders responseHeaders = new HttpHeaders();
responseHeaders.setContentLength(is.available());
responseHeaders.setContentType(MediaType.APPLICATION_JSON);
responseHeaders.set("Content-Disposition", "attachment;filename=" + fileName);
responseHeaders.set("Access-Control-Expose-Headers", "Content-Disposition");
responseHeaders.get("Access-Control-Expose-Headers").add("Content-Type");
byte[] content = new byte[is.available()];
is.read(content);
is.close();
return new ResponseEntity<>(content, responseHeaders, HttpStatus.OK);
}
@RequestMapping(value = "update/{lang}", method = RequestMethod.POST)
public @ResponseBody
ResponseEntity<ResponseItem<String>> updateLang(@PathVariable String lang, @RequestBody String json) throws Exception {
String fileName = this.environment.getProperty("language.path") + lang + ".json";
OutputStream os = new FileOutputStream(fileName);
os.write(json.getBytes());
os.close();
return ResponseEntity.status(HttpStatus.OK).body(new ResponseItem<String>().status(ApiMessageCode.SUCCESS_MESSAGE).message("Updated").payload("Updated"));
}
}

19
dmp-backend/web/src/main/java/eu/eudat/controllers/Login.java
View File

@ -1,6 +1,6 @@
package eu.eudat.controllers;
import eu.eudat.core.logger.Logger;
import eu.eudat.exceptions.security.NullEmailException;
import eu.eudat.logic.managers.UserManager;
import eu.eudat.logic.proxy.config.configloaders.ConfigLoader;
@ -28,6 +28,8 @@ import eu.eudat.models.data.login.Credentials;
import eu.eudat.models.data.login.LoginInfo;
import eu.eudat.models.data.security.Principal;
import eu.eudat.types.ApiMessageCode;
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;
@ -42,6 +44,7 @@ import java.security.GeneralSecurityException;
@CrossOrigin
@RequestMapping(value = "api/auth")
public class Login {
private static final Logger logger = LoggerFactory.getLogger(Login.class);
private CustomAuthenticationProvider customAuthenticationProvider;
private AuthenticationService nonVerifiedUserAuthenticationService;
@ -53,13 +56,13 @@ public class Login {
private ConfigurableProviderTokenValidator configurableProviderTokenValidator;
private ConfigLoader configLoader;
private Logger logger;
// private Logger logger;
private UserManager userManager;
@Autowired
public Login(CustomAuthenticationProvider customAuthenticationProvider, AuthenticationService nonVerifiedUserAuthenticationService,
TwitterTokenValidator twitterTokenValidator, LinkedInTokenValidator linkedInTokenValidator, B2AccessTokenValidator b2AccessTokenValidator,
ORCIDTokenValidator orcidTokenValidator, OpenAIRETokenValidator openAIRETokenValidator, ConfigurableProviderTokenValidator configurableProviderTokenValidator, ConfigLoader configLoader, UserManager userManager, Logger logger) {
ORCIDTokenValidator orcidTokenValidator, OpenAIRETokenValidator openAIRETokenValidator, ConfigurableProviderTokenValidator configurableProviderTokenValidator, ConfigLoader configLoader, UserManager userManager/*, Logger logger*/) {
this.customAuthenticationProvider = customAuthenticationProvider;
this.nonVerifiedUserAuthenticationService = nonVerifiedUserAuthenticationService;
this.twitterTokenValidator = twitterTokenValidator;
@ -69,7 +72,7 @@ public class Login {
this.openAIRETokenValidator = openAIRETokenValidator;
this.configurableProviderTokenValidator = configurableProviderTokenValidator;
this.configLoader = configLoader;
this.logger = logger;
// this.logger = logger;
this.userManager = userManager;
}
@ -77,7 +80,7 @@ public class Login {
@RequestMapping(method = RequestMethod.POST, value = {"/externallogin"}, consumes = "application/json", produces = "application/json")
public @ResponseBody
ResponseEntity<ResponseItem<Principal>> externallogin(@RequestBody LoginInfo credentials) throws GeneralSecurityException, NullEmailException {
this.logger.info(credentials, "Trying To Login With " + credentials.getProvider());
logger.info("Trying To Login With " + credentials.getProvider());
return ResponseEntity.status(HttpStatus.OK).body(new ResponseItem<Principal>().payload(customAuthenticationProvider.authenticate(credentials)).status(ApiMessageCode.SUCCESS_MESSAGE));
}
@ -85,7 +88,7 @@ public class Login {
@RequestMapping(method = RequestMethod.POST, value = {"/nativelogin"}, consumes = "application/json", produces = "application/json")
public @ResponseBody
ResponseEntity<ResponseItem<Principal>> nativelogin(@RequestBody Credentials credentials) throws NullEmailException {
this.logger.info(credentials.getUsername(), "Trying To Login");
logger.info(credentials.getUsername() + " Trying To Login");
return ResponseEntity.status(HttpStatus.OK).body(new ResponseItem<Principal>().payload(userManager.authenticate(this.nonVerifiedUserAuthenticationService, credentials)).status(ApiMessageCode.SUCCESS_MESSAGE));
}
@ -128,7 +131,7 @@ public class Login {
@RequestMapping(method = RequestMethod.POST, value = {"/me"}, consumes = "application/json", produces = "application/json")
public @ResponseBody
ResponseEntity<ResponseItem<Principal>> authMe(Principal principal) throws NullEmailException {
this.logger.info(principal, "Getting Me");
logger.info(principal + " Getting Me");
return ResponseEntity.status(HttpStatus.OK).body(new ResponseItem<Principal>().payload(this.nonVerifiedUserAuthenticationService.Touch(principal.getToken())).status(ApiMessageCode.NO_MESSAGE));
}
@ -137,7 +140,7 @@ public class Login {
public @ResponseBody
ResponseEntity<ResponseItem<Principal>> logout(Principal principal) {
this.nonVerifiedUserAuthenticationService.Logout(principal.getToken());
this.logger.info(principal, "Logged Out");
logger.info(principal + " Logged Out");
return ResponseEntity.status(HttpStatus.OK).body(new ResponseItem<Principal>().status(ApiMessageCode.NO_MESSAGE));
}

13
dmp-backend/web/src/main/java/eu/eudat/controllers/Organisations.java
View File

@ -2,12 +2,10 @@ package eu.eudat.controllers;
import eu.eudat.data.query.items.table.organisations.OrganisationsTableRequest;
import eu.eudat.logic.managers.OrganisationsManager;
import eu.eudat.logic.proxy.config.ExternalUrlCriteria;
import eu.eudat.logic.proxy.config.exceptions.HugeResultSet;
import eu.eudat.logic.proxy.config.exceptions.NoURLFound;
import eu.eudat.logic.services.ApiContext;
import eu.eudat.models.data.dmp.Organisation;
import eu.eudat.models.data.external.OrganisationsExternalSourcesModel;
import eu.eudat.models.data.helpers.common.DataTableData;
import eu.eudat.models.data.helpers.responses.ResponseItem;
import eu.eudat.models.data.security.Principal;
@ -19,7 +17,6 @@ import org.springframework.web.bind.annotation.*;
import javax.validation.Valid;
import java.util.List;
import java.util.Map;
@RestController
@ -28,6 +25,8 @@ import java.util.Map;
public class Organisations extends BaseController {
private OrganisationsManager organisationsManager;
private ApiContext apiContext;
@Autowired
public Organisations(ApiContext apiContext, OrganisationsManager organisationsManager) {
super(apiContext);
@ -36,13 +35,11 @@ public class Organisations extends BaseController {
@RequestMapping(method = RequestMethod.GET, value = {"/external/organisations"}, produces = "application/json")
public @ResponseBody
ResponseEntity<ResponseItem<OrganisationsExternalSourcesModel>> listExternalOrganisations(
ResponseEntity<ResponseItem<List<Organisation>>> listExternalOrganisations(
@RequestParam(value = "query", required = false) String query, @RequestParam(value = "type", required = false) String type
) throws HugeResultSet, NoURLFound {
ExternalUrlCriteria externalUrlCriteria = new ExternalUrlCriteria(query);
List<Map<String, String>> remoteRepos = this.getApiContext().getOperationsContext().getRemoteFetcher().getOrganisations(externalUrlCriteria, type);
OrganisationsExternalSourcesModel organisationsExternalSourcesModel = new OrganisationsExternalSourcesModel().fromExternalItem(remoteRepos);
return ResponseEntity.status(HttpStatus.OK).body(new ResponseItem<OrganisationsExternalSourcesModel>().payload(organisationsExternalSourcesModel).status(ApiMessageCode.NO_MESSAGE));
List<Organisation> organisations = organisationsManager.getCriteriaWithExternal(query, type);
return ResponseEntity.status(HttpStatus.OK).body(new ResponseItem<List<Organisation>>().payload(organisations).status(ApiMessageCode.NO_MESSAGE));
}
@RequestMapping(method = RequestMethod.POST, value = {"/internal/organisations"}, produces = "application/json")

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

@ -3,11 +3,13 @@ package eu.eudat.controllers;
import eu.eudat.data.entities.Funder;
import eu.eudat.data.entities.Project;
import eu.eudat.logic.managers.*;
import eu.eudat.logic.managers.DatasetManager;
import eu.eudat.logic.managers.QuickWizardManager;
import eu.eudat.logic.services.ApiContext;
import eu.eudat.models.data.datasetwizard.DatasetWizardModel;
import eu.eudat.models.data.dmp.DataManagementPlan;
import eu.eudat.models.data.helpers.responses.ResponseItem;
import eu.eudat.models.data.quickwizard.DatasetCreateWizardModel;
import eu.eudat.models.data.quickwizard.DatasetDescriptionQuickWizardModel;
import eu.eudat.models.data.quickwizard.QuickWizardModel;
import eu.eudat.models.data.security.Principal;
@ -16,7 +18,6 @@ import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.http.HttpStatus;
import org.springframework.http.ResponseEntity;
import org.springframework.web.bind.annotation.*;
import eu.eudat.models.data.quickwizard.DatasetCreateWizardModel;
import javax.transaction.Transactional;
import javax.validation.Valid;
@ -47,7 +48,6 @@ public class QuickWizardController extends BaseController {
if (quickWizard.getFunder() == null) {
throw new Exception("Funder is a mandatory entity");
} else if (quickWizard.getFunder().getExistFunder() == null && quickWizard.getFunder().getLabel() == null) {
// funderEntity = null;
throw new Exception("Funder is a mandatory entity");
} else if (quickWizard.getFunder().getExistFunder() == null && quickWizard.getFunder().getLabel() != null) {
funderEntity = this.quickWizardManager.createOrUpdate(quickWizard.getFunder().toDataFunder(), principal);
@ -57,7 +57,11 @@ public class QuickWizardController extends BaseController {
eu.eudat.data.entities.Grant grantEntity;
//Create Grant
if (quickWizard.getGrant().getExistGrant() == null) {
if (quickWizard.getGrant() == null) {
throw new Exception("Grant is a mandatory entity");
} else if (quickWizard.getGrant().getExistGrant() == null && quickWizard.getGrant().getLabel() == null) {
throw new Exception("Grant is a mandatory entity");
} else if (quickWizard.getGrant().getExistGrant() == null) {
grantEntity = this.quickWizardManager.createOrUpdate(quickWizard.getGrant().toDataGrant(), principal);
} else {
grantEntity = quickWizard.getGrant().getExistGrant().toDataModel();
@ -68,17 +72,15 @@ public class QuickWizardController extends BaseController {
if (quickWizard.getProject().getExistProject() == null
&& quickWizard.getProject().getLabel() == null) {
projectEntity = null;
} else if (quickWizard.getProject().getExistProject() == null && quickWizard.getProject().getLabel() != null){
} else if (quickWizard.getProject().getExistProject() == null && quickWizard.getProject().getLabel() != null) {
projectEntity = this.quickWizardManager.createOrUpdate(quickWizard.getProject().toDataProject(), principal);
} else {
projectEntity = quickWizard.getProject().getExistProject().toDataModel();
}
//Create Dmp
eu.eudat.data.entities.DMP dmpEntity = this.quickWizardManager.createOrUpdate(
quickWizard.getDmp().toDataDmp(grantEntity, projectEntity, principal),
funderEntity,
principal);
DataManagementPlan dataManagementPlan = quickWizard.getDmp().toDataDmp(grantEntity, projectEntity, principal);
eu.eudat.data.entities.DMP dmpEntity = this.quickWizardManager.createOrUpdate(dataManagementPlan, funderEntity, principal);
//Create Datasets
quickWizard.getDmp().setId(dmpEntity.getId());

6
dmp-backend/web/src/main/java/eu/eudat/controllers/Registries.java
View File

@ -42,10 +42,10 @@ public class Registries extends BaseController {
@Transactional
@RequestMapping(method = RequestMethod.POST, value = {"/registries"}, consumes = "application/json", produces = "application/json")
public @ResponseBody
ResponseEntity<ResponseItem<Registry>> create(@RequestBody RegistryModel registryModel, Principal principal) throws Exception {
ResponseEntity<ResponseItem<RegistryModel>> create(@RequestBody RegistryModel registryModel, Principal principal) throws Exception {
Registry registry = this.registryManager.create(registryModel, principal);
return ResponseEntity.status(HttpStatus.OK).body(new ResponseItem<Registry>().payload(registry).status(ApiMessageCode.SUCCESS_MESSAGE));
RegistryModel registryModel1 = new RegistryModel().fromDataModel(registry);
return ResponseEntity.status(HttpStatus.OK).body(new ResponseItem<RegistryModel>().payload(registryModel1).status(ApiMessageCode.SUCCESS_MESSAGE));
}
}

5
dmp-backend/web/src/main/java/eu/eudat/controllers/Services.java
View File

@ -43,9 +43,10 @@ public class Services extends BaseController {
@Transactional
@RequestMapping(method = RequestMethod.POST, value = {"/services"}, consumes = "application/json", produces = "application/json")
public @ResponseBody
ResponseEntity<ResponseItem<Service>> create(@RequestBody ServiceModel serviceModel, Principal principal) throws Exception {
ResponseEntity<ResponseItem<ServiceModel>> create(@RequestBody ServiceModel serviceModel, Principal principal) throws Exception {
Service service = serviceManager.create(serviceModel, principal);
return ResponseEntity.status(HttpStatus.OK).body(new ResponseItem<Service>().payload(service).status(ApiMessageCode.SUCCESS_MESSAGE));
ServiceModel serviceModel1 = new ServiceModel().fromDataModel(service);
return ResponseEntity.status(HttpStatus.OK).body(new ResponseItem<ServiceModel>().payload(serviceModel1).status(ApiMessageCode.SUCCESS_MESSAGE));
}
}

15
dmp-backend/web/src/main/java/eu/eudat/controllers/controllerhandler/ControllerErrorHandler.java
View File

@ -4,11 +4,12 @@ import com.fasterxml.jackson.core.JsonProcessingException;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.fasterxml.jackson.databind.ObjectWriter;
import com.fasterxml.jackson.databind.SerializationFeature;
import eu.eudat.core.logger.Logger;
import eu.eudat.core.models.exception.ApiExceptionLoggingModel;
import eu.eudat.models.data.helpers.responses.ResponseItem;
import eu.eudat.models.data.security.Principal;
import eu.eudat.types.ApiMessageCode;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.http.HttpStatus;
import org.springframework.web.bind.annotation.ControllerAdvice;
@ -27,13 +28,14 @@ import java.util.Map;
@ControllerAdvice
@Priority(5)
public class ControllerErrorHandler {
private static final Logger logger = LoggerFactory.getLogger(ControllerErrorHandler.class);
private Logger logger;
// private Logger logger;
@Autowired
/*@Autowired
public ControllerErrorHandler(Logger logger) {
this.logger = logger;
}
}*/
@ExceptionHandler(Exception.class)
@ResponseStatus(HttpStatus.BAD_REQUEST)
@ -49,12 +51,11 @@ public class ControllerErrorHandler {
exceptionMap.put("exception", json);
apiExceptionLoggingModel.setData(ow.writeValueAsString(exceptionMap));
} catch (JsonProcessingException e) {
e.printStackTrace();
logger.error(e.getMessage(), e);
}
apiExceptionLoggingModel.setMessage(ex.getMessage());
apiExceptionLoggingModel.setType(LoggingType.ERROR);
ex.printStackTrace();
this.logger.error(apiExceptionLoggingModel);
logger.error(ex.getMessage(), ex);
return new ResponseItem<Exception>().message(ex.getMessage()).status(ApiMessageCode.DEFAULT_ERROR_MESSAGE);
}
}

13
dmp-backend/web/src/main/java/eu/eudat/controllers/controllerhandler/ControllerUnauthorisedHandler.java
View File

@ -1,7 +1,8 @@
package eu.eudat.controllers.controllerhandler;
import eu.eudat.core.logger.Logger;
import eu.eudat.exceptions.security.UnauthorisedException;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.core.annotation.Order;
import org.springframework.http.HttpStatus;
@ -18,19 +19,19 @@ import javax.annotation.Priority;
@ControllerAdvice
@Priority(4)
public class ControllerUnauthorisedHandler {
private Logger logger;
private static final Logger logger = LoggerFactory.getLogger(ControllerUnauthorisedHandler.class);
// private Logger logger;
@Autowired
public ControllerUnauthorisedHandler(Logger logger) {
this.logger = logger;
public ControllerUnauthorisedHandler(/*Logger logger*/) {
// this.logger = logger;
}
@ExceptionHandler(UnauthorisedException.class)
@ResponseStatus(HttpStatus.UNAUTHORIZED)
@ResponseBody
public void processValidationError(UnauthorisedException ex) {
this.logger.error(ex, ex.getMessage());
logger.error(ex.getMessage(), ex);
return;
}
}

12
dmp-backend/web/src/main/java/eu/eudat/controllers/interceptors/RequestInterceptor.java
View File

@ -2,6 +2,8 @@ package eu.eudat.controllers.interceptors;
import eu.eudat.logic.services.helpers.LoggerService;
import eu.eudat.types.WarningLevel;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Component;
import org.springframework.web.servlet.handler.HandlerInterceptorAdapter;
@ -15,19 +17,19 @@ import java.util.Date;
*/
@Component
public class RequestInterceptor extends HandlerInterceptorAdapter {
private LoggerService loggerService;
private static final Logger logger = LoggerFactory.getLogger(RequestInterceptor.class);
// private LoggerService loggerService;
@Autowired
public RequestInterceptor(LoggerService loggerService) {
this.loggerService = loggerService;
public RequestInterceptor(/*LoggerService loggerService*/) {
// this.loggerService = loggerService;
}
@Override
public boolean preHandle(HttpServletRequest request,
HttpServletResponse response, Object handler) throws Exception {
String reqUri = request.getRequestURI();
this.loggerService.log("Call to " + reqUri + " method: " + request.getMethod() + " at: " + new Date(), WarningLevel.INFO);
logger.info("Call to " + reqUri + " method: " + request.getMethod() + " at: " + new Date(), WarningLevel.INFO);
return super.preHandle(request, response, handler);
}
}

5
dmp-backend/web/src/main/java/eu/eudat/logic/builders/BuilderFactoryImpl.java
View File

@ -7,9 +7,7 @@ import eu.eudat.logic.builders.model.criteria.RegistryCriteriaBuilder;
import eu.eudat.logic.builders.model.models.*;
import org.springframework.stereotype.Service;
/**
* Created by ikalyvas on 2/15/2018.
*/
@Service("builderFactory")
public class BuilderFactoryImpl implements BuilderFactory {
@ -29,6 +27,7 @@ public class BuilderFactoryImpl implements BuilderFactory {
if (tClass.equals(ResearcherBuilder.class)) return (T) new ResearcherBuilder();
if (tClass.equals(ExternalDatasetCriteriaBuilder.class)) return (T) new ExternalDatasetCriteriaBuilder();
if (tClass.equals(RecentActivityDataBuilder.class)) return (T) new RecentActivityDataBuilder();
if (tClass.equals(OrganisationBuilder.class)) return (T) new OrganisationBuilder();
return null;
}

7
dmp-backend/web/src/main/java/eu/eudat/logic/builders/model/models/FunderBuilder.java
View File

@ -17,6 +17,7 @@ public class FunderBuilder extends Builder<Funder> {
private Date modified;
private Integer type;
private String source;
private String key;
public FunderBuilder id(UUID id) {
this.id = id;
@ -63,6 +64,11 @@ public class FunderBuilder extends Builder<Funder> {
return this;
}
public FunderBuilder key(String key) {
this.key = key;
return this;
}
@Override
public Funder build() {
Funder funder = new Funder();
@ -75,6 +81,7 @@ public class FunderBuilder extends Builder<Funder> {
funder.setModified(modified);
funder.setType(type);
funder.setSource(source);
funder.setKey(key);
return funder;
}
}

11
dmp-backend/web/src/main/java/eu/eudat/logic/builders/model/models/GrantBuilder.java
View File

@ -9,9 +9,6 @@ import java.util.Date;
import java.util.List;
import java.util.UUID;
/**
* Created by ikalyvas on 2/15/2018.
*/
public class GrantBuilder extends Builder<Grant> {
private UUID id;
@ -44,6 +41,8 @@ public class GrantBuilder extends Builder<Grant> {
private String source;
private String key;
public GrantBuilder id(UUID id) {
this.id = id;
return this;
@ -119,6 +118,11 @@ public class GrantBuilder extends Builder<Grant> {
return this;
}
public GrantBuilder key(String key) {
this.key = key;
return this;
}
@Override
public Grant build() {
Grant grant = new Grant();
@ -137,6 +141,7 @@ public class GrantBuilder extends Builder<Grant> {
grant.setCreationUser(creationUser);
grant.setStartDate(startDate);
grant.setSource(source);
grant.setKey(key);
return grant;
}
}

88
dmp-backend/web/src/main/java/eu/eudat/logic/builders/model/models/OrganisationBuilder.java Normal file
View File

@ -0,0 +1,88 @@
package eu.eudat.logic.builders.model.models;
import eu.eudat.logic.builders.Builder;
import eu.eudat.models.data.dmp.Organisation;
public class OrganisationBuilder extends Builder<Organisation> {
private String label;
private String name;
private String id;
private String reference;
private int status;
private String tag;
private String key;
public String getLabel() {
return label;
}
public OrganisationBuilder label(String label) {
this.label = label;
return this;
}
public String getName() {
return name;
}
public OrganisationBuilder name(String name) {
this.name = name;
return this;
}
public String getId() {
return id;
}
public OrganisationBuilder id(String id) {
this.id = id;
return this;
}
public String getReference() { return reference; }
public OrganisationBuilder reference(String reference) {
this.reference = reference;
return this;
}
public int getStatus() {
return status;
}
public OrganisationBuilder status(int status) {
this.status = status;
return this;
}
public String getTag() {
return tag;
}
public OrganisationBuilder tag(String tag) {
this.tag = tag;
return this;
}
public String getKey() {
return key;
}
public OrganisationBuilder key(String key) {
this.key = key;
return this;
}
@Override
public Organisation build() {
Organisation Organisation = new Organisation();
Organisation.setId(id);
Organisation.setReference(reference);
Organisation.setLabel(label);
Organisation.setName(name);
Organisation.setStatus(status);
Organisation.setTag(tag);
Organisation.setKey(key);
return Organisation;
}
}

7
dmp-backend/web/src/main/java/eu/eudat/logic/builders/model/models/ProjectBuilder.java
View File

@ -28,6 +28,7 @@ public class ProjectBuilder extends Builder<Project> {
private Date modified;
private String description;
private String source;
private String key;
public ProjectBuilder id(UUID id) {
this.id = id;
@ -109,6 +110,11 @@ public class ProjectBuilder extends Builder<Project> {
return this;
}
public ProjectBuilder key(String key) {
this.key = key;
return this;
}
@Override
public Project build() {
Project project = new Project();
@ -127,6 +133,7 @@ public class ProjectBuilder extends Builder<Project> {
project.setCreationUser(creationUser);
project.setStartDate(startDate);
project.setSource(source);
project.setKey(key);
return project;
}
}

23
dmp-backend/web/src/main/java/eu/eudat/logic/builders/model/models/ResearcherBuilder.java
View File

@ -3,15 +3,14 @@ package eu.eudat.logic.builders.model.models;
import eu.eudat.logic.builders.Builder;
import eu.eudat.models.data.dmp.Researcher;
/**
* Created by ikalyvas on 3/6/2018.
*/
public class ResearcherBuilder extends Builder<Researcher> {
private String label;
private String name;
private String id;
private String reference;
private int status;
private String tag;
private String key;
public String getLabel() {
return label;
@ -40,6 +39,13 @@ public class ResearcherBuilder extends Builder<Researcher> {
return this;
}
public String getReference() { return reference; }
public ResearcherBuilder reference(String reference) {
this.reference = reference;
return this;
}
public int getStatus() {
return status;
}
@ -58,14 +64,25 @@ public class ResearcherBuilder extends Builder<Researcher> {
return this;
}
public String getKey() {
return key;
}
public ResearcherBuilder key(String key) {
this.key = key;
return this;
}
@Override
public Researcher build() {
Researcher researcher = new Researcher();
researcher.setId(id);
researcher.setReference(reference);
researcher.setLabel(label);
researcher.setName(name);
researcher.setStatus(status);
researcher.setTag(tag);
researcher.setKey(key);
return researcher;
}
}

41
dmp-backend/web/src/main/java/eu/eudat/logic/managers/DashBoardManager.java
View File

@ -80,7 +80,7 @@ public class DashBoardManager {
List<Integer> roles = new LinkedList<>();
CompletableFuture dmpFuture = dataManagementPlanRepository.getAuthenticated(dataManagementPlanRepository.getWithCriteria(dataManagementPlanCriteria), principal.getId(), roles).countAsync()
.whenComplete((dmpsStats, throwable) -> statistics.setTotalDataManagementPlanCount(dmpsStats));
CompletableFuture datasetFuture = datasetRepository.getAuthenticated(datasetRepository.getWithCriteria(datasetCriteria), user).countAsync()
CompletableFuture datasetFuture = datasetRepository.getAuthenticated(datasetRepository.getWithCriteria(datasetCriteria), user, roles).countAsync()
.whenComplete((datasetsStats, throwable) -> statistics.setTotalDataSetCount(datasetsStats));
CompletableFuture grantFuture = grantRepository.getAuthenticated(grantRepository.getWithCriteria(grantCriteria), user).countAsync()
.whenComplete((grantsStats, throwable) -> statistics.setTotalGrantCount(grantsStats));
@ -113,7 +113,7 @@ public class DashBoardManager {
.selectAsync(item -> recentActivityDataBuilder.label(item.getLabel()).timestamp(item.getModified()).id(item.getId().toString()).build())
.whenComplete((dmpActivities, throwable) -> activity.setRecentDmpActivities(dmpActivities));
CompletableFuture<List<RecentActivityData>> datasets = datasetRepository.getAuthenticated(datasetRepository.getWithCriteria(datasetCriteria), user)
CompletableFuture<List<RecentActivityData>> datasets = datasetRepository.getAuthenticated(datasetRepository.getWithCriteria(datasetCriteria), user, roles)
.withHint("datasetRecentActivity")
.orderBy((builder, root) -> builder.desc(root.get("modified")))
.take(numberofactivities)
@ -132,7 +132,6 @@ public class DashBoardManager {
}
public List<SearchBarItem> searchUserData(String like, Principal principal) {
RecentActivity activity = new RecentActivity();
UserInfo user = new UserInfo();
user.setId(principal.getId());
DMPDao dataManagementPlanRepository = databaseRepository.getDmpDao();
@ -141,29 +140,53 @@ public class DashBoardManager {
List<Integer> roles = new LinkedList<>();
List<SearchBarItem> searchBarItems = new LinkedList<>();
CompletableFuture<List<SearchBarItem>> publicDmps = dataManagementPlanRepository.asQueryable()
.where((builder, root) -> builder.like(builder.upper(root.get("label")), "%" + like.toUpperCase() + "%"))
.where((builder, root) -> builder.notEqual(root.get("status"), DMP.DMPStatus.DELETED.getValue()))
.where((builder, root) -> builder.equal(root.get("isPublic"), true))
.orderBy((builder, root) -> builder.desc(root.get("modified")))
.selectAsync(item -> new SearchBarItem(item.getId().toString(), item.getLabel(), SearchBarItemType.DMP.getValue(), true))
.whenComplete((dmpItems, throwable) -> searchBarItems.addAll(dmpItems));
CompletableFuture<List<SearchBarItem>> publicDatasets = datasetRepository.asQueryable()
.where((builder, root) -> builder.like(builder.upper(root.get("label")), "%" + like.toUpperCase() + "%"))
.where((builder, root) -> builder.equal(root.get("status"), Dataset.Status.FINALISED.getValue()))
.where((builder, root) -> builder.equal(root.get("dmp").get("isPublic"), true))
.orderBy((builder, root) -> builder.desc(root.get("modified")))
.selectAsync(item -> new SearchBarItem(item.getId().toString(), item.getLabel(), SearchBarItemType.DATASET.getValue(), true))
.whenComplete((dataSetItems, throwable) -> searchBarItems.addAll(dataSetItems));
if (principal.getId() != null) {
CompletableFuture<List<SearchBarItem>> dmps = dataManagementPlanRepository.getAuthenticated(dataManagementPlanRepository.asQueryable(), principal.getId(), roles)
.withHint("dmpRecentActivity")
.where((builder, root) -> builder.like(builder.upper(root.get("label")), "%" + like.toUpperCase() + "%"))
.where((builder, root) -> builder.notEqual(root.get("status"), DMP.DMPStatus.DELETED.getValue()))
.orderBy((builder, root) -> builder.desc(root.get("modified")))
.selectAsync(item -> new SearchBarItem(item.getId().toString(), item.getLabel(), SearchBarItemType.DMP.getValue()))
.selectAsync(item -> new SearchBarItem(item.getId().toString(), item.getLabel(), SearchBarItemType.DMP.getValue(), false))
.whenComplete((dmpItems, throwable) -> searchBarItems.addAll(dmpItems));
CompletableFuture<List<SearchBarItem>> datasets = datasetRepository.getAuthenticated(datasetRepository.asQueryable(), user)
CompletableFuture<List<SearchBarItem>> datasets = datasetRepository.getAuthenticated(datasetRepository.asQueryable(), user, roles)
.withHint("datasetRecentActivity")
.where((builder, root) -> builder.like(builder.upper(root.get("label")), "%" + like.toUpperCase() + "%"))
.where((builder, root) -> builder.notEqual(root.get("status"), Dataset.Status.DELETED.getValue()))
.where((builder, root) -> builder.notEqual(root.get("status"), Dataset.Status.CANCELED.getValue()))
.orderBy((builder, root) -> builder.desc(root.get("modified")))
.selectAsync(item -> new SearchBarItem(item.getId().toString(), item.getLabel(), SearchBarItemType.DATASET.getValue()))
.selectAsync(item -> new SearchBarItem(item.getId().toString(), item.getLabel(), SearchBarItemType.DATASET.getValue(), false))
.whenComplete((dataSetItems, throwable) -> searchBarItems.addAll(dataSetItems));
CompletableFuture<List<SearchBarItem>> grants = grantRepository.getAuthenticated(grantRepository.asQueryable(), user)
.withHint("grantRecentActivity")
.where((builder, root) -> builder.like(builder.upper(root.get("label")), "%" + like.toUpperCase() + "%"))
.orderBy((builder, root) -> builder.desc(root.get("modified")))
.selectAsync(item -> new SearchBarItem(item.getId().toString(), item.getLabel(), SearchBarItemType.GRANT.getValue()))
.selectAsync(item -> new SearchBarItem(item.getId().toString(), item.getLabel(), SearchBarItemType.GRANT.getValue(), false))
.whenComplete((grantItems, throwable) -> searchBarItems.addAll(grantItems));
CompletableFuture.allOf(grants, dmps, datasets).join();
return searchBarItems;
CompletableFuture.allOf(grants, dmps, datasets, publicDmps, publicDatasets).join();
} else {
CompletableFuture.allOf(publicDmps, publicDatasets).join();
}
return searchBarItems;
}
}

111
dmp-backend/web/src/main/java/eu/eudat/logic/managers/DataManagementPlanManager.java
View File

@ -1,5 +1,6 @@
package eu.eudat.logic.managers;
import com.fasterxml.jackson.annotation.JsonInclude;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.eudat.configurations.dynamicgrant.DynamicGrantConfiguration;
import eu.eudat.configurations.dynamicgrant.entities.Property;
@ -49,6 +50,8 @@ import org.apache.poi.xwpf.usermodel.XWPFDocument;
import org.apache.poi.xwpf.usermodel.XWPFParagraph;
import org.apache.poi.xwpf.usermodel.XWPFRun;
import org.json.JSONObject;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.core.env.Environment;
import org.springframework.core.io.FileSystemResource;
@ -68,15 +71,14 @@ import javax.xml.bind.JAXBException;
import javax.xml.bind.Unmarshaller;
import java.io.*;
import java.math.BigInteger;
import java.net.URL;
import java.nio.file.Files;
import java.nio.file.Paths;
import java.util.*;
import java.util.concurrent.CompletableFuture;
import java.util.stream.Collectors;
@Component
public class DataManagementPlanManager {
private static final Logger logger = LoggerFactory.getLogger(DataManagementPlanManager.class);
private ApiContext apiContext;
private DatasetManager datasetManager;
@ -105,7 +107,6 @@ public class DataManagementPlanManager {
CompletableFuture itemsFuture;
if (fieldsGroup.equals("listing")) {
itemsFuture = pagedItems.withHint(HintedModelFactory.getHint(DataManagementPlanListingModel.class))
.selectAsync(item -> {
item.setDataset(
@ -119,15 +120,17 @@ public class DataManagementPlanManager {
return new DataManagementPlanListingModel().fromDataModelDatasets(item);
})
.whenComplete((resultList, throwable) -> dataTable.setData(resultList));
} else if (fieldsGroup.equals("autocomplete")) {
itemsFuture = pagedItems
.selectAsync(item -> new DataManagementPlanListingModel().fromDataModelAutoComplete(item))
.whenComplete((resultList, throwable) -> dataTable.setData(resultList));
} else {
itemsFuture = pagedItems
.selectAsync(item -> new DataManagementPlanListingModel().fromDataModelAssociatedProfiles(item))
.whenComplete((resultList, throwable) -> dataTable.setData(resultList));
}
CompletableFuture countFuture = authItems.countAsync().whenComplete((count, throwable) ->
dataTable.setTotalCount(count)
);
CompletableFuture countFuture = authItems.countAsync().whenComplete((count, throwable) -> dataTable.setTotalCount(count));
CompletableFuture.allOf(itemsFuture, countFuture).join();
return dataTable;
}
@ -311,7 +314,7 @@ public class DataManagementPlanManager {
try {
wordBuilder.build(document, pagedDatasetProfile, visibilityRuleService);
} catch (IOException e) {
e.printStackTrace();
logger.error(e.getMessage(), e);
}
// Page break at the end of the Dataset.
XWPFParagraph parBreakDataset = document.createParagraph();
@ -341,34 +344,31 @@ public class DataManagementPlanManager {
return this.datasetManager.convertToPDF(file, environment, fileName);
}*/
public eu.eudat.models.data.dmp.DataManagementPlan getSingle(String id, Principal principal, DynamicGrantConfiguration dynamicGrantConfiguration) throws InstantiationException, IllegalAccessException {
public eu.eudat.models.data.dmp.DataManagementPlan getSingle(String id, Principal principal) {
DMP dataManagementPlanEntity = databaseRepository.getDmpDao().find(UUID.fromString(id));
if (dataManagementPlanEntity.getUsers().stream().filter(userInfo -> userInfo.getUser().getId() == principal.getId()).collect(Collectors.toList()).size() == 0)
if (dataManagementPlanEntity.getUsers().stream().noneMatch(userInfo -> userInfo.getUser().getId() == principal.getId())) {
if (!dataManagementPlanEntity.isPublic()) {
throw new UnauthorisedException();
eu.eudat.models.data.dmp.DataManagementPlan datamanagementPlan = new eu.eudat.models.data.dmp.DataManagementPlan();
datamanagementPlan.fromDataModel(dataManagementPlanEntity);
}
}
eu.eudat.models.data.dmp.DataManagementPlan dataManagementPlan = new eu.eudat.models.data.dmp.DataManagementPlan();
dataManagementPlan.fromDataModel(dataManagementPlanEntity);
Map dmpProperties = dataManagementPlanEntity.getDmpProperties() != null ? new org.json.JSONObject(dataManagementPlanEntity.getDmpProperties()).toMap() : null;
// datamanagementPlan.setDynamicFields(dynamicGrantConfiguration.getFields().stream().map(item -> {
// DynamicFieldWithValue fieldWithValue = new DynamicFieldWithValue();
// fieldWithValue.setId(item.getId());
// fieldWithValue.setDependencies(item.getDependencies());
// fieldWithValue.setName(item.getName());
// fieldWithValue.setQueryProperty(item.getQueryProperty());
// fieldWithValue.setRequired(item.getRequired());
// return fieldWithValue;
// }).collect(Collectors.toList()));
if (dmpProperties != null && datamanagementPlan.getDynamicFields() != null)
datamanagementPlan.getDynamicFields().forEach(item -> {
if (dmpProperties != null && dataManagementPlan.getDynamicFields() != null)
dataManagementPlan.getDynamicFields().forEach(item -> {
Map<String, String> properties = (Map<String, String>) dmpProperties.get(item.getId());
if (properties != null)
item.setValue(new Tuple<>(properties.get("id"), properties.get("label")));
});
return datamanagementPlan;
return dataManagementPlan;
}
public DataManagementPlanOverviewModel getOverviewSingle(String id, Principal principal) throws InstantiationException, IllegalAccessException {
public DataManagementPlanOverviewModel getOverviewSingle(String id, Principal principal) throws Exception {
DMP dataManagementPlanEntity = databaseRepository.getDmpDao().find(UUID.fromString(id));
if (dataManagementPlanEntity.getStatus() == DMP.DMPStatus.DELETED.getValue()) {
throw new Exception("DMP is deleted.");
}
if (dataManagementPlanEntity.getUsers()
.stream().filter(userInfo -> userInfo.getUser().getId() == principal.getId())
.collect(Collectors.toList()).size() == 0)
@ -478,10 +478,13 @@ public class DataManagementPlanManager {
if (dataManagementPlan.getId() != null) {
DMP dmp1 = apiContext.getOperationsContext().getDatabaseRepository().getDmpDao().find(dataManagementPlan.getId());
if (!isUserOwnerOfDmp(dmp1, principal)) {
throw new Exception("User not being the creator is not authorized to edit this DMP.");
}
List<Dataset> datasetList = new ArrayList<>(dmp1.getDataset());
for (Dataset dataset : datasetList) {
if (dataManagementPlan.getProfiles().stream().filter(associatedProfile -> dataset.getProfile().getId().equals(associatedProfile.getId())).findAny().orElse(null) == null)
throw new Exception("Dataset Template for Dataest Description is missing from the DMP.");
throw new Exception("Dataset Template for Dataset Description is missing from the DMP.");
}
if (dataManagementPlan.getStatus() == (int) DMP.DMPStatus.FINALISED.getValue() && dmp1.getStatus().equals(DMP.DMPStatus.FINALISED.getValue()))
throw new Exception("DMP is finalized, therefore cannot be edited.");
@ -566,7 +569,7 @@ public class DataManagementPlanManager {
}
public void assignUser(DMP dmp, UserInfo userInfo) {
private void assignUser(DMP dmp, UserInfo userInfo) {
UserDMP userDMP = new UserDMP();
userDMP.setDmp(dmp);
userDMP.setUser(userInfo);
@ -576,7 +579,9 @@ public class DataManagementPlanManager {
public void newVersion(UUID uuid, DataManagementPlanNewVersionModel dataManagementPlan, Principal principal) throws Exception {
DMP oldDmp = databaseRepository.getDmpDao().find(uuid);
if (!isUserOwnerOfDmp(oldDmp, principal)) {
throw new Exception("User not being the creator is not authorized to perform this action.");
}
DataManagementPlanCriteria criteria = new DataManagementPlanCriteria();
LinkedList<UUID> list = new LinkedList<>();
list.push(oldDmp.getGroupId());
@ -587,7 +592,6 @@ public class DataManagementPlanManager {
if (latestVersionDMP.get(0).getVersion().equals(oldDmp.getVersion())) {
DMP newDmp = dataManagementPlan.toDataModel();
UserInfo user = apiContext.getOperationsContext().getBuilderFactory().getBuilder(UserInfoBuilder.class).id(principal.getId()).build();
createOrganisationsIfTheyDontExist(newDmp, databaseRepository.getOrganisationDao());
createResearchersIfTheyDontExist(newDmp, databaseRepository.getResearcherDao(), user);
@ -644,7 +648,6 @@ public class DataManagementPlanManager {
databaseRepository.getGrantDao().createOrUpdate(newDmp.getGrant());
newDmp = databaseRepository.getDmpDao().createOrUpdate(newDmp);
// Assign creator.
assignUser(newDmp, user);
copyDatasets(newDmp, databaseRepository.getDatasetDao());
}
@ -696,6 +699,7 @@ public class DataManagementPlanManager {
if (grantEntity != null) grant.setId(grantEntity.getId());
else {
grant.setType(Grant.GrantType.EXTERNAL.getValue());
grant.setCreationUser(null);
grantDao.createOrUpdate(grant);
}
}
@ -723,6 +727,7 @@ public class DataManagementPlanManager {
if (projectEntity != null) project.setId(projectEntity.getId());
else {
project.setType(Project.ProjectType.EXTERNAL.getValue());
if (project.getId() == null) project.setId(UUID.randomUUID());
projectDao.createOrUpdate(project);
}
}
@ -785,11 +790,12 @@ public class DataManagementPlanManager {
if (newDataset.getDatasetDataRepositories() != null) {
newDataset.setDatasetDataRepositories(newDataset.getDatasetDataRepositories().stream().map(item -> {
DataRepository dataRepository = new DataRepository();
dataRepository.setId(item.getId());
dataRepository.setId(item.getDataRepository().getId());
DatasetDataRepository datasetDataRepository = new DatasetDataRepository();
datasetDataRepository.setDataRepository(dataRepository);
datasetDataRepository.setDataset(newDataset);
datasetDataRepository.setData(item.getData());
return datasetDataRepository;
}).collect(Collectors.toSet()));
}
@ -797,10 +803,11 @@ public class DataManagementPlanManager {
if (newDataset.getDatasetExternalDatasets() != null) {
newDataset.setDatasetExternalDatasets(newDataset.getDatasetExternalDatasets().stream().map(item -> {
ExternalDataset externalDataset = new ExternalDataset();
externalDataset.setId(item.getId());
externalDataset.setId(item.getExternalDataset().getId());
DatasetExternalDataset datasetExternalDataset = new DatasetExternalDataset();
datasetExternalDataset.setExternalDataset(externalDataset);
datasetExternalDataset.setDataset(newDataset);
datasetExternalDataset.setData(item.getData());
return datasetExternalDataset;
}).collect(Collectors.toSet()));
}
@ -820,6 +827,7 @@ public class DataManagementPlanManager {
DatasetService datasetService = new DatasetService();
datasetService.setService(service);
datasetService.setDataset(newDataset);
datasetService.setData(item.getData());
return datasetService;
}).collect(Collectors.toSet()));
}
@ -833,7 +841,7 @@ public class DataManagementPlanManager {
}
}
public FileEnvelope getXmlDocument(String id, Principal principal) throws InstantiationException, IllegalAccessException, IOException {
private FileEnvelope getXmlDocument(String id, Principal principal) throws InstantiationException, IllegalAccessException, IOException {
ExportXmlBuilder xmlBuilder = new ExportXmlBuilder();
VisibilityRuleService visibilityRuleService = utilitiesService.getVisibilityRuleService();
eu.eudat.data.entities.DMP dmp = databaseRepository.getDmpDao().find(UUID.fromString(id));
@ -868,14 +876,34 @@ public class DataManagementPlanManager {
}
dmpElement.appendChild(dmpProfileElement);
// Funder.
Element funder = xmlDoc.createElement("funder");
Element funderLabel = xmlDoc.createElement("label");
Element funderId = xmlDoc.createElement("id");
funderLabel.setTextContent(dmp.getGrant().getFunder().getLabel());
funderId.setTextContent(dmp.getGrant().getFunder().getId().toString());
funder.appendChild(funderLabel);
funder.appendChild(funderId);
dmpElement.appendChild(funder);
// Grant.
Element grant = xmlDoc.createElement("grant");
Element label = xmlDoc.createElement("label");
label.setTextContent(dmp.getGrant().getLabel());
grant.appendChild(label);
Element grantLabel = xmlDoc.createElement("label");
Element grantId = xmlDoc.createElement("id");
grantLabel.setTextContent(dmp.getGrant().getLabel());
grantId.setTextContent(dmp.getGrant().getId().toString());
grant.appendChild(grantLabel);
grant.appendChild(grantId);
dmpElement.appendChild(grant);
// Project.
Element project = xmlDoc.createElement("project");
Element projectLabel = xmlDoc.createElement("label");
Element projectId = xmlDoc.createElement("id");
projectLabel.setTextContent(dmp.getProject().getLabel());
projectId.setTextContent(dmp.getProject().getId().toString());
project.appendChild(projectLabel);
project.appendChild(projectId);
dmpElement.appendChild(project);
Element organisationsElement = xmlDoc.createElement("organisations");
for (Organisation organisation : dmp.getOrganisations()) {
Element organisationElement = xmlDoc.createElement("organisation");
@ -944,20 +972,21 @@ public class DataManagementPlanManager {
return fileEnvelope;
}
public ResponseEntity<byte[]> getRDAJsonDocument(String id, Principal principal) throws IOException {
public ResponseEntity<byte[]> getRDAJsonDocument(String id, DatasetManager datasetManager, Principal principal) throws IOException {
eu.eudat.data.entities.DMP dmp = databaseRepository.getDmpDao().find(UUID.fromString(id));
if (!dmp.isPublic() && dmp.getUsers().stream().filter(userInfo -> userInfo.getUser().getId() == principal.getId()).collect(Collectors.toList()).size() == 0)
if (!dmp.isPublic() && dmp.getUsers().stream().noneMatch(userInfo -> userInfo.getUser().getId() == principal.getId()))
throw new UnauthorisedException();
RDAExportModel rdaExportModel = new RDAExportModel().fromDataModel(dmp);
RDAExportModel rdaExportModel = new RDAExportModel().fromDataModel(dmp, datasetManager);
ObjectMapper mapper = new ObjectMapper();
mapper.setSerializationInclusion(JsonInclude.Include.NON_NULL);
String fileName = dmp.getLabel();
fileName = fileName.replaceAll("[^a-zA-Z0-9+ ]", "");
File file = new File(fileName);
try {
mapper.writeValue(file, rdaExportModel);
} catch (IOException e) {
e.printStackTrace();
logger.error(e.getMessage(), e);
}
InputStream resource = new FileInputStream(file);
@ -1015,7 +1044,7 @@ public class DataManagementPlanManager {
DmpImportModel dmpImportModel = (DmpImportModel) jaxbUnmarshaller.unmarshal(in);
dataManagementPlans.add(dmpImportModel);
} catch (IOException | JAXBException ex) {
ex.printStackTrace();
logger.error(ex.getMessage(), ex);
}
// TODO Iterate through the list of dataManagementPlans.
// Creates new dataManagementPlan to fill it with the data model that was parsed from the xml.
@ -1078,7 +1107,7 @@ public class DataManagementPlanManager {
//createOrUpdate(apiContext, dm, principal);
System.out.println(dm);
logger.info(dm.toString());
}
return dataManagementPlans;

7
dmp-backend/web/src/main/java/eu/eudat/logic/managers/DataManagementProfileManager.java
View File

@ -21,6 +21,8 @@ import eu.eudat.models.data.listingmodels.DataManagementPlanProfileListingModel;
import eu.eudat.models.data.security.Principal;
import eu.eudat.queryable.QueryableList;
import eu.eudat.logic.services.ApiContext;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.http.ResponseEntity;
import org.springframework.stereotype.Component;
@ -43,6 +45,7 @@ import org.w3c.dom.Element;
*/
@Component
public class DataManagementProfileManager {
private static final Logger logger = LoggerFactory.getLogger(DataManagementProfileManager.class);
private ApiContext apiContext;
private DatabaseRepository databaseRepository;
@ -93,7 +96,7 @@ public class DataManagementProfileManager {
public ResponseEntity<byte[]> getDocument(DataManagementPlanProfileListingModel dmpProfile, String label) throws IllegalAccessException, IOException, InstantiationException {
FileEnvelope envelope = getXmlDocument(dmpProfile, label);
InputStream resource = new FileInputStream(envelope.getFile());
System.out.println("Mime Type of " + envelope.getFilename() + " is " +
logger.info("Mime Type of " + envelope.getFilename() + " is " +
new MimetypesFileTypeMap().getContentType(envelope.getFile()));
HttpHeaders responseHeaders = new HttpHeaders();
responseHeaders.setContentLength(envelope.getFile().length());
@ -124,7 +127,7 @@ public class DataManagementProfileManager {
try {
return xmlBuilder.build(convert(multiPartFile));
} catch (IOException e) {
e.printStackTrace();
logger.error(e.getMessage(), e);
}
return null;
}

15
dmp-backend/web/src/main/java/eu/eudat/logic/managers/DatasetManager.java
View File

@ -36,6 +36,8 @@ import org.apache.poi.xwpf.usermodel.XWPFDocument;
import org.apache.poi.xwpf.usermodel.XWPFParagraph;
import org.apache.poi.xwpf.usermodel.XWPFRun;
import org.json.JSONObject;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.core.env.Environment;
import org.springframework.core.io.FileSystemResource;
@ -73,6 +75,7 @@ import java.util.zip.ZipInputStream;
@Component
public class DatasetManager {
private static final Logger logger = LoggerFactory.getLogger(DatasetManager.class);
private ApiContext apiContext;
private DatabaseRepository databaseRepository;
@ -109,7 +112,9 @@ public class DatasetManager {
} else
items.where((builder, root) -> root.get("id").in(new UUID[]{UUID.randomUUID()}));
}
QueryableList<eu.eudat.data.entities.Dataset> authItems = databaseRepository.getDatasetDao().getAuthenticated(items, userInfo);
List<Integer> roles = new LinkedList<>();
if (datasetTableRequest.getCriteria().getRole() != null) roles.add(datasetTableRequest.getCriteria().getRole());
QueryableList<eu.eudat.data.entities.Dataset> authItems = databaseRepository.getDatasetDao().getAuthenticated(items, userInfo, roles);
QueryableList<eu.eudat.data.entities.Dataset> pagedItems = PaginationManager.applyPaging(authItems, datasetTableRequest);
DataTableData<DatasetListingModel> dataTable = new DataTableData<DatasetListingModel>();
@ -172,7 +177,7 @@ public class DatasetManager {
return dataTable;
}
public DatasetWizardModel getSingle(String id) throws InstantiationException, IllegalAccessException, IOException {
public DatasetWizardModel getSingle(String id) {
DatasetWizardModel dataset = new DatasetWizardModel();
eu.eudat.data.entities.Dataset datasetEntity = databaseRepository.getDatasetDao().find(UUID.fromString(id), HintedModelFactory.getHint(DatasetWizardModel.class));
eu.eudat.elastic.entities.Dataset datasetElastic;
@ -542,7 +547,7 @@ public class DatasetManager {
public ResponseEntity<byte[]> getDocument(String id, VisibilityRuleService visibilityRuleService, String contentType) throws IllegalAccessException, IOException, InstantiationException {
FileEnvelope envelope = getXmlDocument(id, visibilityRuleService);
InputStream resource = new FileInputStream(envelope.getFile());
System.out.println("Mime Type of " + envelope.getFilename() + " is " +
logger.info("Mime Type of " + envelope.getFilename() + " is " +
new MimetypesFileTypeMap().getContentType(envelope.getFile()));
HttpHeaders responseHeaders = new HttpHeaders();
responseHeaders.setContentLength(envelope.getFile().length());
@ -572,7 +577,7 @@ public class DatasetManager {
DatasetImportPagedDatasetProfile datasetImport = (DatasetImportPagedDatasetProfile) jaxbUnmarshaller.unmarshal(in);
importModel = datasetImport;
} catch (IOException e) {
e.printStackTrace();
logger.error(e.getMessage(), e);
}
// Checks if XML datasetProfileId GroupId matches the one selected.
@ -583,7 +588,7 @@ public class DatasetManager {
throw new Exception();
}
} catch (Exception e) {
e.printStackTrace();
logger.error(e.getMessage(), e);
return null;
}

7
dmp-backend/web/src/main/java/eu/eudat/logic/managers/DatasetProfileManager.java
View File

@ -22,6 +22,8 @@ import eu.eudat.models.data.externaldataset.ExternalAutocompleteFieldModel;
import eu.eudat.models.data.helpers.common.DataTableData;
import eu.eudat.queryable.QueryableList;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.http.*;
import org.springframework.stereotype.Component;
@ -41,6 +43,7 @@ import java.io.*;
@Component
public class DatasetProfileManager {
private static final Logger logger = LoggerFactory.getLogger(DatasetProfileManager.class);
private ApiContext apiContext;
private DatabaseRepository databaseRepository;
@ -119,7 +122,7 @@ public class DatasetProfileManager {
public ResponseEntity<byte[]> getDocument(eu.eudat.models.data.user.composite.DatasetProfile datasetProfile, String label) throws IllegalAccessException, IOException, InstantiationException {
FileEnvelope envelope = getXmlDocument(datasetProfile, label);
InputStream resource = new FileInputStream(envelope.getFile());
System.out.println("Mime Type of " + envelope.getFilename() + " is " +
logger.info("Mime Type of " + envelope.getFilename() + " is " +
new MimetypesFileTypeMap().getContentType(envelope.getFile()));
HttpHeaders responseHeaders = new HttpHeaders();
responseHeaders.setContentLength(envelope.getFile().length());
@ -151,7 +154,7 @@ public class DatasetProfileManager {
try {
return xmlBuilder.build(convert(multiPartFile));
} catch (IOException e) {
e.printStackTrace();
logger.error(e.getMessage(), e);
}
return null;
}

7
dmp-backend/web/src/main/java/eu/eudat/logic/managers/DocumentManager.java
View File

@ -13,6 +13,8 @@ import eu.eudat.models.data.user.composite.PagedDatasetProfile;
import org.apache.commons.io.IOUtils;
import org.apache.poi.xwpf.usermodel.XWPFDocument;
import org.json.JSONObject;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.core.env.Environment;
import org.springframework.core.io.FileSystemResource;
import org.springframework.http.*;
@ -36,6 +38,7 @@ import java.util.zip.ZipInputStream;
*/
@Service
public class DocumentManager {
private static final Logger logger = LoggerFactory.getLogger(DocumentManager.class);
private ApiContext context;
private DatasetManager datasetManager;
@ -104,12 +107,12 @@ public class DocumentManager {
Map mediaResult = new RestTemplate().getForObject(environment.getProperty("pdf.converter.url") +
"/api/v1/" + queueResult.get("id"), Map.class);
System.out.println("Status: " + mediaResult.get("status"));
logger.info("Status: " + mediaResult.get("status"));
while (!mediaResult.get("status").equals("finished")) {
Thread.sleep(500);
mediaResult = new RestTemplate().getForObject(environment.getProperty("pdf.converter.url") +
"api/v1/" + queueResult.get("id"), Map.class);
System.out.println("Polling");
logger.info("Polling");
}
RestTemplate restTemplate = new RestTemplate();
restTemplate.getMessageConverters().add(new ByteArrayHttpMessageConverter());

9
dmp-backend/web/src/main/java/eu/eudat/logic/managers/EmailConfirmationManager.java
View File

@ -34,20 +34,21 @@ public class EmailConfirmationManager {
.getDatabaseRepository().getLoginConfirmationEmailDao().asQueryable()
.where((builder, root) -> builder.equal(root.get("token"), UUID.fromString(token))).getSingle();
if (loginConfirmationEmail.getExpiresAt().compareTo(new Date()) < 0)
throw new TokenExpiredException("Token has expired.");
UserInfo user = databaseRepository.getUserInfoDao().asQueryable()
.where((builder, root) -> builder.equal(root.get("id"), loginConfirmationEmail.getUserId())).getSingle();
if (user.getEmail() != null)
throw new HasConfirmedEmailException("User already has confirmed his Email.");
if (loginConfirmationEmail.getExpiresAt().compareTo(new Date()) < 0)
throw new TokenExpiredException("Token has expired.");
loginConfirmationEmail.setIsConfirmed(true);
// Checks if mail is used by another user. If it is, merges the new the old.
Long existingUsers = databaseRepository.getUserInfoDao().asQueryable().where((builder, root) -> builder.equal(root.get("email"), loginConfirmationEmail.getEmail())).count();
if (existingUsers > 0) {
UserInfo oldUser = databaseRepository.getUserInfoDao().asQueryable().where((builder, root) -> builder.equal(root.get("email"), loginConfirmationEmail.getEmail())).getSingle();
if (oldUser != null) {
mergeNewUserToOld(user, oldUser);
expireUserToken(user);
databaseRepository.getLoginConfirmationEmailDao().createOrUpdate(loginConfirmationEmail);

3
dmp-backend/web/src/main/java/eu/eudat/logic/managers/FunderManager.java
View File

@ -3,6 +3,7 @@ package eu.eudat.logic.managers;
import eu.eudat.data.query.items.item.funder.FunderCriteriaRequest;
import eu.eudat.logic.builders.model.models.FunderBuilder;
import eu.eudat.logic.proxy.config.ExternalUrlCriteria;
import eu.eudat.logic.proxy.config.configloaders.ConfigLoader;
import eu.eudat.logic.proxy.config.exceptions.HugeResultSet;
import eu.eudat.logic.proxy.config.exceptions.NoURLFound;
import eu.eudat.logic.proxy.fetching.RemoteFetcher;
@ -47,6 +48,8 @@ public class FunderManager {
eu.eudat.models.data.funder.Funder funder = apiContext.getOperationsContext().getBuilderFactory().getBuilder(FunderBuilder.class)
.reference(externalListingItem.getRemoteId()).label(externalListingItem.getName())
.status(eu.eudat.data.entities.Funder.Status.fromInteger(0))
.key(externalListingItem.getKey())
.source(externalListingItem.getTag())
.build();
if (externalListingItem.getSource() != null) {
funder.setSource(externalListingItem.getSource());

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

@ -109,21 +109,24 @@ public class GrantManager {
public List<eu.eudat.models.data.grant.Grant> getCriteriaWithExternal(GrantCriteriaRequest grantCriteria, Principal principal) throws HugeResultSet, NoURLFound {
eu.eudat.data.entities.UserInfo userInfo = new eu.eudat.data.entities.UserInfo();
userInfo.setId(principal.getId());
if (grantCriteria.getCriteria().getFunderReference() != null && !grantCriteria.getCriteria().getFunderReference().trim().isEmpty()) {
/*if (grantCriteria.getCriteria().getFunderReference() != null && !grantCriteria.getCriteria().getFunderReference().trim().isEmpty()) {
FunderCriteria funderCriteria = new FunderCriteria();
funderCriteria.setReference(grantCriteria.getCriteria().getFunderReference());
Funder funder = apiContext.getOperationsContext().getDatabaseRepository().getFunderDao().getWithCritetia(funderCriteria).getSingleOrDefault();
if (funder != null) {
grantCriteria.getCriteria().setFunderId(funder.getId().toString());
}
}*/
ExternalUrlCriteria externalUrlCriteria = new ExternalUrlCriteria(grantCriteria.getCriteria().getLike());
if (grantCriteria.getCriteria().getFunderReference() != null) {
externalUrlCriteria.setFunderId(grantCriteria.getCriteria().getFunderReference());
grantCriteria.getCriteria().setFunderReference(null);
}
grantCriteria.getCriteria().setReference("dmp:");
QueryableList<eu.eudat.data.entities.Grant> items = apiContext.getOperationsContext().getDatabaseRepository().getGrantDao().getWithCriteria(grantCriteria.getCriteria());
QueryableList<eu.eudat.data.entities.Grant> authItems = apiContext.getOperationsContext().getDatabaseRepository().getGrantDao().getAuthenticated(items, userInfo);
List<eu.eudat.models.data.grant.Grant> grants = authItems.select(item -> new Grant().fromDataModel(item));
ExternalUrlCriteria externalUrlCriteria = new ExternalUrlCriteria(grantCriteria.getCriteria().getLike());
if (grantCriteria.getCriteria().getFunderReference() != null) externalUrlCriteria.setFunderId(grantCriteria.getCriteria().getFunderReference());
List<Map<String, String>> remoteRepos = remoteFetcher.getGrants(externalUrlCriteria);
GrantsExternalSourcesModel grantsExternalSourcesModel = new GrantsExternalSourcesModel().fromExternalItem(remoteRepos);
@ -131,6 +134,7 @@ public class GrantManager {
eu.eudat.models.data.grant.Grant grant = apiContext.getOperationsContext().getBuilderFactory().getBuilder(GrantBuilder.class)
.reference(externalListingItem.getRemoteId()).label(externalListingItem.getName())
.description(externalListingItem.getDescription()).uri(externalListingItem.getUri())
.key(externalListingItem.getKey())
.abbreviation(externalListingItem.getAbbreviation()).status(eu.eudat.data.entities.Grant.Status.fromInteger(0))
.source(externalListingItem.getTag())
.build();

30
dmp-backend/web/src/main/java/eu/eudat/logic/managers/OrganisationsManager.java
View File

@ -1,24 +1,25 @@
package eu.eudat.logic.managers;
import eu.eudat.data.dao.criteria.OrganisationCriteria;
import eu.eudat.data.dao.entities.OrganisationDao;
import eu.eudat.data.entities.DMP;
import eu.eudat.data.query.items.table.dmp.DataManagmentPlanPublicTableRequest;
import eu.eudat.data.query.items.table.organisations.OrganisationsTableRequest;
import eu.eudat.logic.builders.model.models.OrganisationBuilder;
import eu.eudat.logic.proxy.config.ExternalUrlCriteria;
import eu.eudat.logic.proxy.config.exceptions.HugeResultSet;
import eu.eudat.logic.proxy.config.exceptions.NoURLFound;
import eu.eudat.logic.services.ApiContext;
import eu.eudat.logic.services.operations.DatabaseRepository;
import eu.eudat.models.HintedModelFactory;
import eu.eudat.models.data.dmp.Organisation;
import eu.eudat.models.data.external.ExternalSourcesItemModel;
import eu.eudat.models.data.external.OrganisationsExternalSourcesModel;
import eu.eudat.models.data.helpers.common.DataTableData;
import eu.eudat.models.data.listingmodels.DataManagementPlanListingModel;
import eu.eudat.models.data.security.Principal;
import eu.eudat.queryable.QueryableList;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Component;
import java.util.ArrayList;
import java.util.LinkedList;
import java.util.List;
import java.util.Map;
import java.util.stream.Collectors;
@Component
@ -64,4 +65,21 @@ public class OrganisationsManager {
return organisationDataTableData;
}
public List<Organisation> getCriteriaWithExternal(String query, String type) throws HugeResultSet, NoURLFound {
ExternalUrlCriteria externalUrlCriteria = new ExternalUrlCriteria(query);
List<Map<String, String>> remoteRepos = apiContext.getOperationsContext().getRemoteFetcher().getOrganisations(externalUrlCriteria, type);
OrganisationsExternalSourcesModel organisationsExternalSourcesModel = new OrganisationsExternalSourcesModel().fromExternalItem(remoteRepos);
List<Organisation> organisations = new LinkedList<>();
for (ExternalSourcesItemModel externalListingItem : organisationsExternalSourcesModel) {
Organisation organisation = apiContext.getOperationsContext().getBuilderFactory().getBuilder(OrganisationBuilder.class)
.name(externalListingItem.getName())
.reference(externalListingItem.getRemoteId())
.tag(externalListingItem.getTag())
.key(externalListingItem.getKey())
.build();
organisations.add(organisation);
}
return organisations.stream().distinct().collect(Collectors.toList());
}
}

1
dmp-backend/web/src/main/java/eu/eudat/logic/managers/ProjectManager.java
View File

@ -48,6 +48,7 @@ public class ProjectManager {
.reference(externalListingItem.getRemoteId()).label(externalListingItem.getName())
.description(externalListingItem.getDescription()).uri(externalListingItem.getUri())
.abbreviation(externalListingItem.getAbbreviation()).status(eu.eudat.data.entities.Project.Status.fromInteger(0))
.key(externalListingItem.getKey())
.source(externalListingItem.getTag())
.build();

2
dmp-backend/web/src/main/java/eu/eudat/logic/managers/QuickWizardManager.java
View File

@ -13,6 +13,7 @@ import org.springframework.stereotype.Component;
import java.io.IOException;
import java.text.ParseException;
import java.util.UUID;
@Component
public class QuickWizardManager {
@ -109,6 +110,7 @@ public class QuickWizardManager {
eu.eudat.data.entities.Project projectEntity = databaseRepository.getProjectDao().getWithCritetia(criteria).getSingleOrDefault();
if (projectEntity != null) project.setId(projectEntity.getId());
else {
if (project.getId() == null) project.setId(UUID.randomUUID());
project.setType(Project.ProjectType.EXTERNAL.getValue());
databaseRepository.getProjectDao().createOrUpdate(project);
}

16
dmp-backend/web/src/main/java/eu/eudat/logic/managers/ResearcherManager.java
View File

@ -3,6 +3,8 @@ package eu.eudat.logic.managers;
import eu.eudat.logic.builders.model.models.ResearcherBuilder;
import eu.eudat.data.entities.Researcher;
import eu.eudat.logic.proxy.config.ExternalUrlCriteria;
import eu.eudat.logic.proxy.config.configloaders.ConfigLoader;
import eu.eudat.logic.utilities.helpers.ListHelper;
import eu.eudat.models.data.external.ExternalSourcesItemModel;
import eu.eudat.models.data.external.ResearchersExternalSourcesModel;
import eu.eudat.data.query.items.item.researcher.ResearcherCriteriaRequest;
@ -17,7 +19,6 @@ import org.springframework.stereotype.Component;
import java.util.List;
import java.util.Map;
import java.util.UUID;
import java.util.stream.Collectors;
/**
@ -28,11 +29,13 @@ public class ResearcherManager {
private ApiContext apiContext;
private RemoteFetcher remoteFetcher;
private ConfigLoader configLoader;
@Autowired
public ResearcherManager(ApiContext apiContext) {
public ResearcherManager(ApiContext apiContext, ConfigLoader configLoader) {
this.apiContext = apiContext;
this.remoteFetcher = apiContext.getOperationsContext().getRemoteFetcher();
this.configLoader = configLoader;
}
public Researcher create(eu.eudat.models.data.researcher.Researcher researcher, Principal principal) throws Exception {
@ -46,6 +49,13 @@ public class ResearcherManager {
QueryableList<eu.eudat.data.entities.Researcher> items = apiContext.getOperationsContext().getDatabaseRepository().getResearcherDao().getWithCriteria(researcherCriteriaRequest.getCriteria());
items.where((builder, root) -> builder.equal(root.get("creationUser").get("id"), principal.getId()));
List<eu.eudat.models.data.dmp.Researcher> researchers = items.select(item -> new eu.eudat.models.data.dmp.Researcher().fromDataModel(item));
Map<String, String> keyToSourceMap = configLoader.getKeyToSourceMap();
for (eu.eudat.models.data.dmp.Researcher item : researchers) {
if (item.getKey().equals("Internal"))
item.setTag(item.getKey());
else
item.setTag(keyToSourceMap.get(item.getKey()));
}
ExternalUrlCriteria externalUrlCriteria = new ExternalUrlCriteria(researcherCriteriaRequest.getCriteria().getName());
List<Map<String, String>> remoteRepos = remoteFetcher.getResearchers(externalUrlCriteria,null);
ResearchersExternalSourcesModel researchersExternalSourcesModel = new ResearchersExternalSourcesModel().fromExternalItem(remoteRepos);
@ -53,8 +63,10 @@ public class ResearcherManager {
eu.eudat.models.data.dmp.Researcher researcher = apiContext.getOperationsContext().getBuilderFactory().getBuilder(ResearcherBuilder.class)
.label(externalListingItem.getAbbreviation())
.id(externalListingItem.getId())
.reference(externalListingItem.getRemoteId())
.name(externalListingItem.getName())
.tag(externalListingItem.getTag())
.key(externalListingItem.getKey())
.build();
researchers.add(researcher);
}

2
dmp-backend/web/src/main/java/eu/eudat/logic/proxy/config/configloaders/ConfigLoader.java
View File

@ -5,10 +5,12 @@ import eu.eudat.logic.security.customproviders.ConfigurableProvider.entities.Con
import org.apache.poi.xwpf.usermodel.XWPFDocument;
import java.util.List;
import java.util.Map;
public interface ConfigLoader {
ExternalUrls getExternalUrls();
List<String> getRdaProperties();
XWPFDocument getDocument();
ConfigurableProviders getConfigurableProviders();
Map<String, String> getKeyToSourceMap();
}

140
dmp-backend/web/src/main/java/eu/eudat/logic/proxy/config/configloaders/DevelConfigLoader.java
View File

@ -5,73 +5,81 @@ import com.fasterxml.jackson.databind.ObjectMapper;
import eu.eudat.logic.proxy.config.ExternalUrls;
import eu.eudat.logic.security.customproviders.ConfigurableProvider.entities.ConfigurableProviders;
import org.apache.poi.xwpf.usermodel.XWPFDocument;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.context.annotation.Profile;
import org.springframework.core.env.Environment;
import org.springframework.stereotype.Service;
import org.w3c.dom.Document;
import org.w3c.dom.Node;
import org.w3c.dom.NodeList;
import org.xml.sax.SAXException;
import javax.xml.bind.JAXBContext;
import javax.xml.bind.Unmarshaller;
import java.io.BufferedReader;
import java.io.FileReader;
import java.io.IOException;
import java.io.InputStream;
import java.net.URL;
import javax.xml.parsers.DocumentBuilder;
import javax.xml.parsers.DocumentBuilderFactory;
import javax.xml.parsers.ParserConfigurationException;
import javax.xml.xpath.XPath;
import javax.xml.xpath.XPathConstants;
import javax.xml.xpath.XPathExpressionException;
import javax.xml.xpath.XPathFactory;
import java.io.*;
import java.util.HashMap;
import java.util.LinkedList;
import java.util.List;
import java.util.Map;
import java.util.stream.Collectors;
@Service("configLoader")
@Profile("devel")
public class DevelConfigLoader implements ConfigLoader {
private static final Logger logger = LoggerFactory.getLogger(DevelConfigLoader.class);
private ExternalUrls externalUrls;
private List<String> rdaProperties;
private XWPFDocument document;
private ConfigurableProviders configurableProviders;
private Map<String, String> keyToSourceMap;
@Autowired
private Environment environment;
private void setExternalUrls() {
String fileUrl = this.environment.getProperty("configuration.externalUrls");
System.out.println("Loaded also config file: " + fileUrl);
String current = null;
logger.info("Loaded also config file: " + fileUrl);
InputStream is = null;
try {
current = new java.io.File(".").getCanonicalPath();
JAXBContext jaxbContext = JAXBContext.newInstance(ExternalUrls.class);
Unmarshaller jaxbUnmarshaller = jaxbContext.createUnmarshaller();
is = new URL("file:///" + current + fileUrl).openStream();
is = getClass().getClassLoader().getResource(fileUrl).openStream();
externalUrls = (ExternalUrls) jaxbUnmarshaller.unmarshal(is);
} catch (Exception ex) {
ex.printStackTrace();
System.out.println("Cannot find in folder" + current);
logger.error("Cannot find resource in classpath", ex);
} finally {
try {
if (is != null) is.close();
} catch (IOException e) {
System.out.println("Warning: Could not close a stream after reading from file: " + fileUrl);
} catch (IOException | NullPointerException e) {
logger.warn("Warning: Could not close a stream after reading from file: " + fileUrl, e);
}
}
}
private void setRdaProperties() {
String filePath = environment.getProperty("configuration.rda");
String current = null;
BufferedReader reader;
List<String> rdaList = new LinkedList<>();
try {
current = new java.io.File(".").getCanonicalPath();
reader = new BufferedReader(new FileReader(current + filePath));
reader = new BufferedReader(new FileReader(getClass().getClassLoader().getResource(filePath).getFile()));
String line = reader.readLine();
while (line != null) {
rdaList.add(line);
line = reader.readLine();
}
reader.close();
} catch (IOException e) {
e.printStackTrace();
} catch (IOException | NullPointerException e) {
logger.error(e.getMessage(), e);
}
rdaProperties = rdaList;
@ -79,43 +87,63 @@ public class DevelConfigLoader implements ConfigLoader {
private void setDocument() {
String filePath = environment.getProperty("configuration.h2020template");
String current = null;
InputStream is = null;
try {
current = new java.io.File(".").getCanonicalPath();
is = new URL("file:///" + current + filePath).openStream();
is = getClass().getClassLoader().getResource(filePath).openStream();
this.document = new XWPFDocument(is);
} catch (IOException e) {
e.printStackTrace();
} catch (IOException | NullPointerException e) {
logger.error(e.getMessage(), e);
} finally {
try {
if (is != null) is.close();
} catch (IOException e) {
System.out.println("Warning: Could not close a stream after reading from file: " + filePath);
logger.warn("Warning: Could not close a stream after reading from file: " + filePath, e);
}
}
}
public void setConfigurableProviders() {
private void setConfigurableProviders() {
String filePath = environment.getProperty("configuration.configurable_login_providers");
String current = null;
InputStream is = null;
try {
current = new java.io.File(".").getCanonicalPath();
is = new URL("file:///" + current + filePath).openStream();
is = getClass().getClassLoader().getResource(filePath).openStream();
ObjectMapper mapper = new ObjectMapper().configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
this.configurableProviders = mapper.readValue(is, ConfigurableProviders.class);
} catch (IOException e) {
e.printStackTrace();
} catch (IOException | NullPointerException e) {
logger.error(e.getMessage(), e);
} finally {
try {
if (is != null) is.close();
} catch (IOException e) {
System.out.println("Warning: Could not close a stream after reading from file: " + filePath);
logger.warn("Warning: Could not close a stream after reading from file: " + filePath, e);
}
}
}
private void setKeyToSourceMap() {
String filePath = this.environment.getProperty("configuration.externalUrls");
logger.info("Loaded also config file: " + filePath);
Document doc = getXmlDocumentFromFilePath(filePath);
if (doc == null) {
this.keyToSourceMap = null;
return;
}
String xpathExpression = "//key";
Map<String, String> keysToSourceMap = new HashMap<>();
List<String> keys = getXmlValuesFromXPath(doc, xpathExpression);
keys = keys.stream().distinct().collect(Collectors.toList());
for (String key : keys) {
String sourceExpression = String.format("//urlConfig[key='%s']/label", key);
List<String> sources = getXmlValuesFromXPath(doc, sourceExpression);
if (sources.size() != 0) {
keysToSourceMap.put(key, sources.get(0));
}
}
this.keyToSourceMap = keysToSourceMap;
}
public ExternalUrls getExternalUrls() {
this.setExternalUrls();
return externalUrls;
@ -135,4 +163,52 @@ public class DevelConfigLoader implements ConfigLoader {
this.setConfigurableProviders();
return configurableProviders;
}
public Map<String, String> getKeyToSourceMap() {
this.setKeyToSourceMap();
return keyToSourceMap;
}
private Document getXmlDocumentFromFilePath(String filePath) {
InputStream is = null;
Document doc;
try {
is = getClass().getClassLoader().getResource(filePath).openStream();
DocumentBuilderFactory documentBuilderFactory = DocumentBuilderFactory.newInstance();
DocumentBuilder documentBuilder = documentBuilderFactory.newDocumentBuilder();
doc = documentBuilder.parse(is);
return doc;
} catch (IOException | ParserConfigurationException | SAXException | NullPointerException e) {
logger.error(e.getMessage(), e);
} finally {
try {
if (is != null) {
is.close();
}
} catch (IOException e) {
logger.warn("Warning: Could not close a stream after reading from file: " + filePath, e);
}
}
return null;
}
private List<String> getXmlValuesFromXPath(Document doc, String expression) {
XPath xPath = XPathFactory.newInstance().newXPath();
NodeList nodeList = null;
List<String> values = new LinkedList<>();
try {
nodeList = (NodeList) xPath.compile(expression).evaluate(doc, XPathConstants.NODESET);
} catch (XPathExpressionException e) {
logger.error(e.getMessage(), e);
}
if (nodeList != null) {
for (int i = 0; i < nodeList.getLength(); i++) {
Node node = nodeList.item(i);
if (node.hasChildNodes()) {
values.add(nodeList.item(i).getChildNodes().item(0).getNodeValue());
}
}
}
return values;
}
}

137
dmp-backend/web/src/main/java/eu/eudat/logic/proxy/config/configloaders/ProductionConfigLoader.java
View File

@ -4,55 +4,68 @@ import com.fasterxml.jackson.databind.ObjectMapper;
import eu.eudat.logic.proxy.config.ExternalUrls;
import eu.eudat.logic.security.customproviders.ConfigurableProvider.entities.ConfigurableProviders;
import org.apache.poi.xwpf.usermodel.XWPFDocument;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.context.annotation.Profile;
import org.springframework.core.env.Environment;
import org.springframework.stereotype.Service;
import org.w3c.dom.Document;
import org.w3c.dom.Node;
import org.w3c.dom.NodeList;
import org.xml.sax.SAXException;
import javax.xml.bind.JAXBContext;
import javax.xml.bind.Unmarshaller;
import java.io.BufferedReader;
import java.io.FileReader;
import java.io.IOException;
import java.io.InputStream;
import javax.xml.parsers.DocumentBuilder;
import javax.xml.parsers.DocumentBuilderFactory;
import javax.xml.parsers.ParserConfigurationException;
import javax.xml.xpath.XPath;
import javax.xml.xpath.XPathConstants;
import javax.xml.xpath.XPathExpressionException;
import javax.xml.xpath.XPathFactory;
import java.io.*;
import java.net.URL;
import java.nio.file.Paths;
import java.util.HashMap;
import java.util.LinkedList;
import java.util.List;
import java.util.Map;
import java.util.stream.Collectors;
@Service("configLoader")
@Profile({ "production", "staging" })
public class ProductionConfigLoader implements ConfigLoader {
private static final Logger logger = LoggerFactory.getLogger(ProductionConfigLoader.class);
private ExternalUrls externalUrls;
private List<String> rdaProperties;
private XWPFDocument document;
private ConfigurableProviders configurableProviders;
private Map<String, String> keyToSourceMap;
@Autowired
private Environment environment;
private void setExternalUrls() {
String fileUrl = this.environment.getProperty("configuration.externalUrls");
System.out.println("Loaded also config file: " + fileUrl);
logger.info("Loaded also config file: " + fileUrl);
String current = null;
InputStream is = null;
try {
current = new java.io.File(".").getCanonicalPath();
JAXBContext jaxbContext = JAXBContext.newInstance(ExternalUrls.class);
Unmarshaller jaxbUnmarshaller = jaxbContext.createUnmarshaller();
is = new URL(Paths.get(fileUrl).toUri().toURL().toString()).openStream();
externalUrls = (ExternalUrls) jaxbUnmarshaller.unmarshal(is);
} catch (Exception ex) {
ex.printStackTrace();
System.out.println("Cannot find in folder" + current);
logger.error("Cannot find in folder" + current, ex);
} finally {
try {
if (is != null) is.close();
} catch (IOException e) {
System.out.println("Warning: Could not close a stream after reading from file: " + fileUrl);
logger.warn("Warning: Could not close a stream after reading from file: " + fileUrl, e);
}
}
}
@ -70,7 +83,7 @@ public class ProductionConfigLoader implements ConfigLoader {
}
reader.close();
} catch (IOException e) {
e.printStackTrace();
logger.error(e.getMessage(), e);
}
rdaProperties = rdaList;
@ -78,27 +91,63 @@ public class ProductionConfigLoader implements ConfigLoader {
private void setDocument() {
String filePath = environment.getProperty("configuration.h2020template");
String current = null;
InputStream is = null;
try {
current = new java.io.File(".").getCanonicalPath();
InputStream is = new URL(Paths.get(filePath).toUri().toURL().toString()).openStream();
is = new URL(Paths.get(filePath).toUri().toURL().toString()).openStream();
this.document = new XWPFDocument(is);
} catch (IOException e) {
e.printStackTrace();
logger.error(e.getMessage(), e);
} finally {
try {
if (is != null) is.close();
} catch (IOException e) {
logger.warn("Warning: Could not close a stream after reading from file: " + filePath, e);
}
}
}
public void setConfigurableProviders() {
private void setConfigurableProviders() {
String filePath = environment.getProperty("configuration.configurable_login_providers");
String current = null;
InputStream is = null;
try {
current = new java.io.File(".").getCanonicalPath();
InputStream is = new URL(Paths.get(filePath).toUri().toURL().toString()).openStream();
File tempFile = new File(filePath);
if (tempFile.exists()) {
is = new URL(Paths.get(filePath).toUri().toURL().toString()).openStream();
ObjectMapper objectMapper = new ObjectMapper();
this.configurableProviders = objectMapper.readValue(is, ConfigurableProviders.class);
} catch (IOException e) {
e.printStackTrace();
} else {
this.configurableProviders = new ConfigurableProviders();
}
} catch (IOException e) {
logger.error(e.getMessage(), e);
} finally {
try {
if (is != null) is.close();
} catch (IOException e) {
logger.warn("Warning: Could not close a stream after reading from file: " + filePath, e);
}
}
}
private void setKeyToSourceMap() {
String filePath = this.environment.getProperty("configuration.externalUrls");
logger.info("Loaded also config file: " + filePath);
Document doc = getXmlDocumentFromFilePath(filePath);
if (doc == null) {
this.keyToSourceMap = null;
return;
}
String xpathExpression = "//key";
Map<String, String> keysToSourceMap = new HashMap<>();
List<String> keys = getXmlValuesFromXPath(doc, xpathExpression);
keys = keys.stream().distinct().collect(Collectors.toList());
for (String key : keys) {
String sourceExpression = String.format("//urlConfig[key='%s']/label", key);
List<String> sources = getXmlValuesFromXPath(doc, sourceExpression);
if (sources.size() != 0) {
keysToSourceMap.put(key, sources.get(0));
}
}
this.keyToSourceMap = keysToSourceMap;
}
public ExternalUrls getExternalUrls() {
@ -120,4 +169,52 @@ public class ProductionConfigLoader implements ConfigLoader {
this.setConfigurableProviders();
return configurableProviders;
}
public Map<String, String> getKeyToSourceMap() {
this.setKeyToSourceMap();
return keyToSourceMap;
}
private Document getXmlDocumentFromFilePath(String filePath) {
InputStream is = null;
Document doc;
try {
is = new URL(Paths.get(filePath).toUri().toURL().toString()).openStream();
DocumentBuilderFactory documentBuilderFactory = DocumentBuilderFactory.newInstance();
DocumentBuilder documentBuilder = documentBuilderFactory.newDocumentBuilder();
doc = documentBuilder.parse(is);
return doc;
} catch (IOException | ParserConfigurationException | SAXException e) {
logger.error(e.getMessage(), e);
} finally {
try {
if (is != null) {
is.close();
}
} catch (IOException e) {
logger.warn("Warning: Could not close a stream after reading from file: " + filePath, e);
}
}
return null;
}
private List<String> getXmlValuesFromXPath(Document doc, String expression) {
XPath xPath = XPathFactory.newInstance().newXPath();
NodeList nodeList = null;
List<String> values = new LinkedList<>();
try {
nodeList = (NodeList) xPath.compile(expression).evaluate(doc, XPathConstants.NODESET);
} catch (XPathExpressionException e) {
logger.error(e.getMessage(), e);
}
if (nodeList != null) {
for (int i = 0; i < nodeList.getLength(); i++) {
Node node = nodeList.item(i);
if (node.hasChildNodes()) {
values.add(nodeList.item(i).getChildNodes().item(0).getNodeValue());
}
}
}
return values;
}
}

37
dmp-backend/web/src/main/java/eu/eudat/logic/proxy/fetching/RemoteFetcher.java
View File

@ -8,6 +8,8 @@ import eu.eudat.logic.proxy.config.*;
import eu.eudat.logic.proxy.config.configloaders.ConfigLoader;
import eu.eudat.logic.proxy.config.exceptions.HugeResultSet;
import eu.eudat.logic.proxy.config.exceptions.NoURLFound;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.cache.annotation.Cacheable;
import org.springframework.stereotype.Service;
@ -25,6 +27,7 @@ import java.util.stream.Collectors;
@Service
public class RemoteFetcher {
private static final Logger logger = LoggerFactory.getLogger(RemoteFetcher.class);
private ConfigLoader configLoader;
@ -120,15 +123,16 @@ public class RemoteFetcher {
private List<Map<String, String>> getAll(List<UrlConfiguration> urlConfigs, FetchStrategy fetchStrategy, ExternalUrlCriteria externalUrlCriteria) throws NoURLFound, HugeResultSet {
if (urlConfigs == null || urlConfigs.isEmpty())
throw new NoURLFound("No Repository urls found in configuration");
List<Map<String, String>> results = new LinkedList<>();
if (urlConfigs == null || urlConfigs.isEmpty()) return results;
// throw new NoURLFound("No Repository urls found in configuration");
urlConfigs.sort(Comparator.comparing(UrlConfiguration::getOrdinal));
List<Map<String, String>> results = new LinkedList<>();
for (UrlConfiguration urlConfig : urlConfigs) {
ifFunderQueryExist(urlConfig, externalUrlCriteria);
if (urlConfig.getType() == null || urlConfig.getType().equals("External")) {
results.addAll(getAllResultsFromUrl(urlConfig.getUrl(), fetchStrategy, urlConfig.getData(), urlConfig.getPaginationPath(), externalUrlCriteria, urlConfig.getLabel(), urlConfig.getContentType(), urlConfig.getFirstpage()));
results.addAll(getAllResultsFromUrl(urlConfig.getUrl(), fetchStrategy, urlConfig.getData(), urlConfig.getPaginationPath(), externalUrlCriteria, urlConfig.getLabel(), urlConfig.getKey(), urlConfig.getContentType(), urlConfig.getFirstpage()));
} else if (urlConfig.getType() != null && urlConfig.getType().equals("Internal")) {
results.addAll(getAllResultsFromMockUpJson(urlConfig.getUrl(), externalUrlCriteria.getLike()));
}
@ -138,7 +142,7 @@ public class RemoteFetcher {
private void ifFunderQueryExist(UrlConfiguration urlConfiguration, ExternalUrlCriteria externalUrlCriteria) {
if (urlConfiguration.getFunderQuery() != null) {
if (externalUrlCriteria.getFunderId() != null && urlConfiguration.getFunderQuery().startsWith("dmp:")) {
if (externalUrlCriteria.getFunderId() != null && !urlConfiguration.getFunderQuery().startsWith("dmp:")) {
urlConfiguration.setUrl(urlConfiguration.getUrl().replace("{funderQuery}", urlConfiguration.getFunderQuery()));
}
else {
@ -162,7 +166,7 @@ public class RemoteFetcher {
try {
funderId = URLEncoder.encode(externalUrlCriteria.getFunderId(), "UTF-8");
} catch (UnsupportedEncodingException e) {
e.printStackTrace();
logger.error(e.getMessage(), e);
}
completedPath = completedPath.replace("{funderId}", funderId);
}
@ -178,19 +182,19 @@ public class RemoteFetcher {
if (externalUrlCriteria.getPageSize() != null) {
completedPath = completedPath.replace("{pageSize}", externalUrlCriteria.getPageSize());
} else {
completedPath = completedPath.replace("{pageSize}", "10");
completedPath = completedPath.replace("{pageSize}", "60");
}
return completedPath;
}
private List<Map<String, String>> getAllResultsFromUrl(String path, FetchStrategy fetchStrategy, final DataUrlConfiguration jsonDataPath, final String jsonPaginationPath, ExternalUrlCriteria externalUrlCriteria, String key, String contentType, String firstPage) throws HugeResultSet {
private List<Map<String, String>> getAllResultsFromUrl(String path, FetchStrategy fetchStrategy, final DataUrlConfiguration jsonDataPath, final String jsonPaginationPath, ExternalUrlCriteria externalUrlCriteria, String tag, String key, String contentType, String firstPage) throws HugeResultSet {
Set<Integer> pages = new HashSet<>();
String replacedPath = replaceCriteriaOnUrl(path, externalUrlCriteria, firstPage);
Results results = getResultsFromUrl(replacedPath, jsonDataPath, jsonPaginationPath, contentType);
if (fetchStrategy == FetchStrategy.FIRST)
return results == null ? new LinkedList<>() : results.getResults().stream().peek(x -> x.put("tag", key)).collect(Collectors.toList());
return results == null ? new LinkedList<>() : results.getResults().stream().peek(x -> x.put("tag", tag)).peek(x -> x.put("key", key)).collect(Collectors.toList());
if (results != null && results.getPagination() != null && results.getPagination().get("pages") != null) //if has more pages, add them to the pages set
for (int i = 2; i <= results.getPagination().get("pages"); i++)
@ -209,7 +213,7 @@ public class RemoteFetcher {
Results remainingResults = optionalResults.orElseGet(Results::new);
remainingResults.getResults().addAll(results.getResults());
return remainingResults.getResults().stream().peek(x -> x.put("tag", key)).collect(Collectors.toList());
return remainingResults.getResults().stream().peek(x -> x.put("tag", tag)).collect(Collectors.toList());
}
@ -243,20 +247,20 @@ public class RemoteFetcher {
results = new Results(jsonContext.read(jsonDataPath.getPath()
+ "[" + jsonDataPath.getFieldsUrlConfiguration().getName() + "," + jsonDataPath.getFieldsUrlConfiguration().getDescription()
+ "," + jsonDataPath.getFieldsUrlConfiguration().getUri() + "," + jsonDataPath.getFieldsUrlConfiguration().getId() + "]"),
jsonContext.read(jsonPaginationPath));
new HashMap<>(1, 1));
}
results.results = results.results.stream().map(e -> e.entrySet().stream().collect(Collectors.toMap(x -> this.transformKey(jsonDataPath,x.getKey()), Map.Entry::getValue)))
.collect(Collectors.toList());
return results;
}
} catch (MalformedURLException e1) {
e1.printStackTrace();
logger.error(e1.getMessage(), e1);
} //maybe print smth...
catch (IOException e2) {
e2.printStackTrace();
logger.error(e2.getMessage(), e2);
} //maybe print smth...
catch (Exception exception) {
exception.printStackTrace();
logger.error(exception.getMessage(), exception);
} //maybe print smth...
finally {
}
@ -270,10 +274,9 @@ public class RemoteFetcher {
String filePath = Paths.get(path).toUri().toURL().toString();
ObjectMapper mapper = new ObjectMapper();
internalResults = mapper.readValue(new File(filePath), new TypeReference<List<Map<String, Object>>>(){});
searchListMap(internalResults, query);
return internalResults;
return searchListMap(internalResults, query);
} catch (Exception e) {
e.printStackTrace();
logger.error(e.getMessage(), e);
return new LinkedList<>();
}
}

10
dmp-backend/web/src/main/java/eu/eudat/logic/security/CustomAuthenticationProvider.java
View File

@ -6,6 +6,8 @@ import eu.eudat.exceptions.security.UnauthorisedException;
import eu.eudat.models.data.login.LoginInfo;
import eu.eudat.models.data.security.Principal;
import eu.eudat.logic.security.validators.TokenValidatorFactory;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Component;
@ -14,6 +16,7 @@ import java.security.GeneralSecurityException;
@Component
public class CustomAuthenticationProvider {
private static final Logger logger = LoggerFactory.getLogger(CustomAuthenticationProvider.class);
@Autowired
@ -25,14 +28,13 @@ public class CustomAuthenticationProvider {
Principal principal = this.tokenValidatorFactory.getProvider(credentials.getProvider()).validateToken(credentials);
return principal;
} catch (NonValidTokenException e) {
e.printStackTrace();
System.out.println("Could not validate a user by his token! Reason: " + e.getMessage());
logger.error("Could not validate a user by his token! Reason: " + e.getMessage(), e);
throw new UnauthorisedException("Token validation failed - Not a valid token");
} catch (IOException e) {
e.printStackTrace();
logger.error(e.getMessage(), e);
throw new UnauthorisedException("IO Exeption");
} catch (NullEmailException e) {
e.printStackTrace();
logger.error(e.getMessage(), e);
throw new NullEmailException();
}
}

5
dmp-backend/web/src/main/java/eu/eudat/logic/services/helpers/FileStorageServiceImpl.java
View File

@ -2,6 +2,8 @@ package eu.eudat.logic.services.helpers;
import eu.eudat.exceptions.files.TempFileNotFoundException;
import eu.eudat.models.data.files.ContentFile;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.core.env.Environment;
import org.springframework.core.io.Resource;
@ -22,6 +24,7 @@ import java.util.UUID;
*/
@Service("fileStorageService")
public class FileStorageServiceImpl implements FileStorageService {
private static final Logger logger = LoggerFactory.getLogger(FileStorageServiceImpl.class);
private Environment environment;
@ -68,7 +71,7 @@ public class FileStorageServiceImpl implements FileStorageService {
Files.createDirectory(Paths.get(environment.getProperty("files.storage.final")));
}
} catch (IOException e) {
e.printStackTrace();
logger.error(e.getMessage(), e);
}
}

2
dmp-backend/web/src/main/java/eu/eudat/logic/services/helpers/HelpersService.java
View File

@ -9,5 +9,5 @@ public interface HelpersService {
MessageSource getMessageSource();
LoggerService getLoggerService();
// LoggerService getLoggerService();
}

10
dmp-backend/web/src/main/java/eu/eudat/logic/services/helpers/HelpersServiceImpl.java
View File

@ -11,12 +11,12 @@ import org.springframework.stereotype.Service;
public class HelpersServiceImpl implements HelpersService {
private MessageSource messageSource;
private LoggerService loggerService;
// private LoggerService loggerService;
@Autowired
public HelpersServiceImpl(MessageSource messageSource, LoggerService loggerService) {
public HelpersServiceImpl(MessageSource messageSource/*, LoggerService loggerService*/) {
this.messageSource = messageSource;
this.loggerService = loggerService;
// this.loggerService = loggerService;
}
@Override
@ -24,8 +24,8 @@ public class HelpersServiceImpl implements HelpersService {
return messageSource;
}
@Override
/*@Override
public LoggerService getLoggerService() {
return loggerService;
}
}*/
}

4
dmp-backend/web/src/main/java/eu/eudat/logic/services/helpers/LoggerServiceImpl.java
View File

@ -12,7 +12,7 @@ import java.util.Map;
/**
* Created by ikalyvas on 3/1/2018.
*/
@Service("loggerService")
//@Service("loggerService")
public class LoggerServiceImpl implements LoggerService {
private Logger logger;
private WarningLevel level;
@ -22,7 +22,7 @@ public class LoggerServiceImpl implements LoggerService {
this.level = level;
}
@Autowired
// @Autowired
public LoggerServiceImpl(Logger logger) {
this.logger = logger;
this.options.put(WarningLevel.DEBUG, (log, message) -> log.debug(message));

5
dmp-backend/web/src/main/java/eu/eudat/logic/services/operations/authentication/AbstractAuthenticationService.java
View File

@ -15,12 +15,15 @@ import eu.eudat.models.data.loginprovider.LoginProviderUser;
import eu.eudat.models.data.security.Principal;
import eu.eudat.types.Authorities;
import org.json.JSONObject;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.core.env.Environment;
import org.springframework.transaction.annotation.Transactional;
import java.util.*;
public abstract class AbstractAuthenticationService implements AuthenticationService {
private static final Logger logger = LoggerFactory.getLogger(AbstractAuthenticationService.class);
protected ApiContext apiContext;
protected Environment environment;
@ -86,7 +89,7 @@ public abstract class AbstractAuthenticationService implements AuthenticationSer
try {
credential = this.autoCreateUser(credentials.getUsername(), credentials.getSecret());
} catch (Exception e) {
e.printStackTrace();
logger.error(e.getMessage(), e);
return null;
}
}

13
dmp-backend/web/src/main/java/eu/eudat/logic/services/utilities/ConfirmationEmailServiceImpl.java
View File

@ -1,9 +1,10 @@
package eu.eudat.logic.services.utilities;
import eu.eudat.core.logger.Logger;
import eu.eudat.data.dao.entities.LoginConfirmationEmailDao;
import eu.eudat.data.entities.LoginConfirmationEmail;
import eu.eudat.models.data.mail.SimpleMail;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.core.env.Environment;
import org.springframework.stereotype.Service;
@ -13,11 +14,12 @@ import java.util.concurrent.CompletableFuture;
@Service("ConfirmationEmailService")
public class ConfirmationEmailServiceImpl implements ConfirmationEmailService {
private Logger logger;
private static final Logger logger = LoggerFactory.getLogger(ConfirmationEmailServiceImpl.class);
//private Logger logger;
private Environment environment;
public ConfirmationEmailServiceImpl(Logger logger, Environment environment) {
this.logger = logger;
public ConfirmationEmailServiceImpl(/*Logger logger,*/ Environment environment) {
// this.logger = logger;
this.environment = environment;
}
@ -48,8 +50,7 @@ public class ConfirmationEmailServiceImpl implements ConfirmationEmailService {
try {
mailService.sendSimpleMail(mail);
} catch (Exception ex) {
ex.printStackTrace();
this.logger.error(ex, ex.getMessage());
logger.error(ex.getMessage(), ex);
}
});
}

14
dmp-backend/web/src/main/java/eu/eudat/logic/services/utilities/InvitationServiceImpl.java
View File

@ -1,6 +1,5 @@
package eu.eudat.logic.services.utilities;
import eu.eudat.core.logger.Logger;
import eu.eudat.core.models.exception.ApiExceptionLoggingModel;
import eu.eudat.data.dao.entities.DMPDao;
import eu.eudat.data.dao.entities.InvitationDao;
@ -8,6 +7,8 @@ import eu.eudat.data.entities.DMP;
import eu.eudat.data.entities.Invitation;
import eu.eudat.data.entities.UserInfo;
import eu.eudat.models.data.mail.SimpleMail;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.core.env.Environment;
import org.springframework.http.HttpStatus;
@ -25,13 +26,13 @@ import java.util.stream.Collectors;
@Service("invitationService")
public class InvitationServiceImpl implements InvitationService {
private Logger logger;
private static final Logger logger = LoggerFactory.getLogger(InvitationServiceImpl.class);
// private Logger logger;
private Environment environment;
@Autowired
public InvitationServiceImpl(Logger logger, Environment environment) {
this.logger = logger;
public InvitationServiceImpl(/*Logger logger,*/ Environment environment) {
// this.logger = logger;
this.environment = environment;
}
@ -75,8 +76,7 @@ public class InvitationServiceImpl implements InvitationService {
try {
mailService.sendSimpleMail(mail);
} catch (Exception ex) {
ex.printStackTrace();
this.logger.error(ex, ex.getMessage());
logger.error(ex.getMessage(), ex);
}
});
}

5
dmp-backend/web/src/main/java/eu/eudat/logic/services/utilities/MailServiceImpl.java
View File

@ -2,6 +2,8 @@ package eu.eudat.logic.services.utilities;
import eu.eudat.models.data.mail.SimpleMail;
import org.apache.commons.io.IOUtils;
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;
@ -17,6 +19,7 @@ import java.io.*;
@Service("mailService")
public class MailServiceImpl implements MailService {
private static final Logger logger = LoggerFactory.getLogger(MailServiceImpl.class);
private Environment env;
@ -54,7 +57,7 @@ public class MailServiceImpl implements MailService {
IOUtils.copy(inputStream, writer, "UTF-8");
return writer.toString();
} catch (IOException e) {
e.printStackTrace();
logger.error(e.getMessage(), e);
}
return "";
}

15
dmp-backend/web/src/main/java/eu/eudat/logic/utilities/builders/ModelBuilder.java
View File

@ -5,6 +5,8 @@ import eu.eudat.models.data.components.commons.datafield.*;
import eu.eudat.models.data.entities.xmlmodels.modeldefinition.DatabaseModelDefinition;
import eu.eudat.logic.utilities.interfaces.ModelDefinition;
import eu.eudat.logic.utilities.interfaces.ViewStyleDefinition;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.w3c.dom.Element;
import java.util.LinkedList;
@ -12,15 +14,16 @@ import java.util.List;
import java.util.Map;
public class ModelBuilder {
private static final Logger logger = LoggerFactory.getLogger(ModelBuilder.class);
public <U extends ModelDefinition<T>, T extends DatabaseModelDefinition> List<T> toModelDefinition(List<U> items, Class<T> clazz) {
List<T> list = new LinkedList<T>();
for (U item : items) {
try {
list.add(item.toDatabaseDefinition(clazz.newInstance()));
} catch (InstantiationException e) {
e.printStackTrace();
logger.error(e.getMessage(), e);
} catch (IllegalAccessException e) {
e.printStackTrace();
logger.error(e.getMessage(), e);
}
}
return list;
@ -32,9 +35,9 @@ public class ModelBuilder {
try {
list.add(item.toDatabaseDefinition(clazz.newInstance()));
} catch (InstantiationException e) {
e.printStackTrace();
logger.error(e.getMessage(), e);
} catch (IllegalAccessException e) {
e.printStackTrace();
logger.error(e.getMessage(), e);
}
}
return list;
@ -48,9 +51,9 @@ public class ModelBuilder {
modelItem.fromDatabaseDefinition(item);
list.add(modelItem);
} catch (InstantiationException e) {
e.printStackTrace();
logger.error(e.getMessage(), e);
} catch (IllegalAccessException e) {
e.printStackTrace();
logger.error(e.getMessage(), e);
}
}
return list;

9
dmp-backend/web/src/main/java/eu/eudat/logic/utilities/builders/XmlBuilder.java
View File

@ -1,5 +1,7 @@
package eu.eudat.logic.utilities.builders;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.w3c.dom.Document;
import org.w3c.dom.Element;
import org.w3c.dom.Node;
@ -21,6 +23,7 @@ import java.io.StringWriter;
public class XmlBuilder {
private static final Logger logger = LoggerFactory.getLogger(XmlBuilder.class);
public static Document getDocument() {
DocumentBuilderFactory docFactory = DocumentBuilderFactory.newInstance();
@ -31,7 +34,7 @@ public class XmlBuilder {
return doc;
} catch (ParserConfigurationException e) {
// TODO Auto-generated catch block
e.printStackTrace();
logger.error(e.getMessage(), e);
return null;
}
}
@ -48,7 +51,7 @@ public class XmlBuilder {
return writer.toString();
} catch (TransformerException e) {
// TODO Auto-generated catch block
e.printStackTrace();
logger.error(e.getMessage(), e);
return null;
}
}
@ -63,7 +66,7 @@ public class XmlBuilder {
return doc;
} catch (ParserConfigurationException | SAXException | IOException e) {
// TODO Auto-generated catch block
e.printStackTrace();
logger.error(e.getMessage(), e);
return null;
}
}

38
dmp-backend/web/src/main/java/eu/eudat/logic/utilities/documents/word/WordBuilder.java
View File

@ -19,15 +19,17 @@ import org.openxmlformats.schemas.wordprocessingml.x2006.main.CTAbstractNum;
import org.openxmlformats.schemas.wordprocessingml.x2006.main.CTDecimalNumber;
import org.openxmlformats.schemas.wordprocessingml.x2006.main.CTLvl;
import org.openxmlformats.schemas.wordprocessingml.x2006.main.STNumberFormat;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.io.IOException;
import java.math.BigInteger;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.Objects;
public class WordBuilder {
private static final Logger logger = LoggerFactory.getLogger(WordBuilder.class);
private Map<ParagraphStyle, ApplierWithValue<XWPFDocument, String, XWPFParagraph>> options = new HashMap<>();
private CTAbstractNum cTAbstractNum;
@ -132,13 +134,13 @@ public class WordBuilder {
return document;
}
public void createPages(List<DatasetProfilePage> datasetProfilePages, XWPFDocument mainDocumentPart, Boolean createListing, VisibilityRuleService visibilityRuleService) {
private void createPages(List<DatasetProfilePage> datasetProfilePages, XWPFDocument mainDocumentPart, Boolean createListing, VisibilityRuleService visibilityRuleService) {
datasetProfilePages.forEach(item -> {
createSections(item.getSections(), mainDocumentPart, ParagraphStyle.HEADER4, 0, createListing, visibilityRuleService);
});
}
public void createSections(List<Section> sections, XWPFDocument mainDocumentPart, ParagraphStyle style, Integer indent, Boolean createListing, VisibilityRuleService visibilityRuleService) {
private void createSections(List<Section> sections, XWPFDocument mainDocumentPart, ParagraphStyle style, Integer indent, Boolean createListing, VisibilityRuleService visibilityRuleService) {
if (createListing) this.addListing(mainDocumentPart, indent, false, true);
sections.forEach(section -> {
if (visibilityRuleService.isElementVisible(section.getId())) {
@ -153,7 +155,7 @@ public class WordBuilder {
});
}
public void createCompositeFields(List<FieldSet> compositeFields, XWPFDocument mainDocumentPart, Integer indent, Boolean createListing, VisibilityRuleService visibilityRuleService) {
private void createCompositeFields(List<FieldSet> compositeFields, XWPFDocument mainDocumentPart, Integer indent, Boolean createListing, VisibilityRuleService visibilityRuleService) {
if (createListing) this.addListing(mainDocumentPart, indent, true, true);
compositeFields.forEach(compositeField -> {
if (visibilityRuleService.isElementVisible(compositeField.getId()) && hasVisibleFields(compositeField, visibilityRuleService)) {
@ -177,7 +179,7 @@ public class WordBuilder {
});
}
public void createFields(List<Field> fields, XWPFDocument mainDocumentPart, Integer indent, Boolean createListing, VisibilityRuleService visibilityRuleService) {
private void createFields(List<Field> fields, XWPFDocument mainDocumentPart, Integer indent, Boolean createListing, VisibilityRuleService visibilityRuleService) {
if (createListing) this.addListing(mainDocumentPart, indent, false, false);
fields.forEach(field -> {
if (visibilityRuleService.isElementVisible(field.getId())) {
@ -187,7 +189,7 @@ public class WordBuilder {
CTDecimalNumber number = paragraph.getCTP().getPPr().getNumPr().addNewIlvl();
number.setVal(BigInteger.valueOf(indent));
} catch (IOException e) {
e.printStackTrace();
logger.error(e.getMessage(), e);
}
}
}
@ -202,7 +204,7 @@ public class WordBuilder {
return paragraph;
}
public void addListing(XWPFDocument document, int indent, Boolean question, Boolean hasIndication) {
private void addListing(XWPFDocument document, int indent, Boolean question, Boolean hasIndication) {
CTLvl cTLvl = this.cTAbstractNum.addNewLvl();
String textLevel = "";
@ -222,7 +224,7 @@ public class WordBuilder {
}
}
public String formatter(Field field) throws IOException {
private String formatter(Field field) throws IOException {
switch (field.getViewStyle().getRenderStyle()) {
case "combobox": {
String comboboxType = ((ComboBoxData) field.getData()).getType();
@ -232,7 +234,7 @@ public class WordBuilder {
Map<String, String> map = new HashMap<>();
if (!field.getValue().equals("")) {
try {
JSONArray jsonarray = new JSONArray(field.getValue());
JSONArray jsonarray = new JSONArray(field.getValue().toString());
for (int i = 0; i < jsonarray.length(); i++) {
JSONObject jsonobject = jsonarray.getJSONObject(i);
String id = jsonobject.getString("id");
@ -241,37 +243,39 @@ public class WordBuilder {
map.put(id, label);
}
}
} catch (Exception e){
Map<String, String> exMap = mapper.readValue(field.getValue(), new TypeReference<Map<String, String>>() {
} catch (Exception e) {
Map<String, String> exMap = mapper.readValue(field.getValue().toString(), new TypeReference<Map<String, String>>() {
});
return exMap.get("label");
}
}
StringBuilder sb = new StringBuilder();
int index = 0;
for (Map.Entry<String, String> entry : map.entrySet()) {
sb.append("\n");
sb.append(entry.getValue());
if (index != map.size() - 1) sb.append(", ");
index++;
}
return sb.toString();
} else if (comboboxType.equals("wordlist")) {
return field.getValue();
return field.getValue().toString();
}
}
case "booleanDecision":
if (field.getValue() != null && field.getValue().equals("true")) return "Yes";
else return "No";
case "radiobox":
return field.getValue();
return field.getValue().toString();
case "checkBox":
CheckBoxData data = (CheckBoxData) field.getData();
if (field.getValue() == null || field.getValue().equals("false")) return null;
return data.getLabel();
case "freetext":
return field.getValue();
return field.getValue().toString();
case "textarea":
return field.getValue();
return field.getValue().toString();
case "datepicker":
return field.getValue();
return field.getValue().toString();
}
return null;
}

25
dmp-backend/web/src/main/java/eu/eudat/logic/utilities/documents/xml/ExportXmlBuilder.java
View File

@ -7,6 +7,8 @@ import eu.eudat.models.data.user.components.datasetprofile.FieldSet;
import eu.eudat.models.data.user.components.datasetprofile.Section;
import eu.eudat.models.data.user.composite.DatasetProfilePage;
import eu.eudat.models.data.user.composite.PagedDatasetProfile;
import org.json.JSONArray;
import org.json.JSONException;
import org.w3c.dom.Document;
import org.w3c.dom.Element;
@ -17,9 +19,6 @@ import java.io.IOException;
import java.util.List;
import java.util.UUID;
/**
* Created by ikalyvas on 3/5/2018.
*/
public class ExportXmlBuilder {
public File build(PagedDatasetProfile pagedDatasetProfile, UUID datasetProfileId, VisibilityRuleService visibilityRuleService) throws IOException {
@ -49,7 +48,7 @@ public class ExportXmlBuilder {
return pages;
}
public Element createSections(List<Section> sections, VisibilityRuleService visibilityRuleService, Document element) {
private Element createSections(List<Section> sections, VisibilityRuleService visibilityRuleService, Document element) {
Element elementSections = element.createElement("sections");
sections.forEach(section -> {
Element elementSection = element.createElement("section");
@ -62,7 +61,7 @@ public class ExportXmlBuilder {
return elementSections;
}
public Element createCompositeFields(List<FieldSet> compositeFields, VisibilityRuleService visibilityRuleService, Document element) {
private Element createCompositeFields(List<FieldSet> compositeFields, VisibilityRuleService visibilityRuleService, Document element) {
Element elementComposites = element.createElement("composite-fields");
compositeFields.forEach(compositeField -> {
if (visibilityRuleService.isElementVisible(compositeField.getId()) && hasVisibleFields(compositeField, visibilityRuleService)) {
@ -86,15 +85,25 @@ public class ExportXmlBuilder {
return elementComposites;
}
public Element createFields(List<Field> fields, VisibilityRuleService visibilityRuleService, Document element) {
private Element createFields(List<Field> fields, VisibilityRuleService visibilityRuleService, Document element) {
Element elementFields = element.createElement("fields");
fields.forEach(field -> {
if (visibilityRuleService.isElementVisible(field.getId())) {
Element elementField = element.createElement("field");
elementField.setAttribute("id", field.getId());
if (field.getValue() != null && !field.getValue().isEmpty()) {
if (field.getValue() != null) {
Element valueField = element.createElement("value");
valueField.setTextContent(field.getValue());
try {
JSONArray jsonArray = new JSONArray(field.getValue().toString());
StringBuilder sb = new StringBuilder();
for (int i = 0; i < jsonArray.length(); i++) {
sb.append(jsonArray.getJSONObject(i).get("label").toString());
if (i != jsonArray.length() - 1) sb.append(", ");
}
valueField.setTextContent(sb.toString());
} catch (JSONException ex) {
valueField.setTextContent(field.getValue().toString());
}
elementField.appendChild(valueField);
}
elementFields.appendChild(elementField);

5
dmp-backend/web/src/main/java/eu/eudat/logic/utilities/documents/xml/datasetProfileXml/ImportXmlBuilderDatasetProfile.java
View File

@ -1,5 +1,7 @@
package eu.eudat.logic.utilities.documents.xml.datasetProfileXml;
import eu.eudat.logic.utilities.documents.xml.datasetProfileXml.datasetProfileModel.DatasetProfile;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import javax.xml.bind.JAXBContext;
import javax.xml.bind.JAXBException;
@ -7,6 +9,7 @@ import javax.xml.bind.Unmarshaller;
import java.io.*;
public class ImportXmlBuilderDatasetProfile {
private static final Logger logger = LoggerFactory.getLogger(ImportXmlBuilderDatasetProfile.class);
public DatasetProfile build(File xmlFile) throws IOException {
DatasetProfile datasetProfile = new DatasetProfile();
@ -16,7 +19,7 @@ public class ImportXmlBuilderDatasetProfile {
Unmarshaller unmarshaller = jaxbContext.createUnmarshaller();
datasetProfile = (DatasetProfile) unmarshaller.unmarshal(xmlFile);
} catch (JAXBException e) {
e.printStackTrace();
logger.error(e.getMessage(), e);
}
return datasetProfile;

5
dmp-backend/web/src/main/java/eu/eudat/logic/utilities/documents/xml/dmpXml/ImportXmlBuilderDmpProfile.java
View File

@ -1,6 +1,8 @@
package eu.eudat.logic.utilities.documents.xml.dmpXml;
import eu.eudat.logic.utilities.documents.xml.dmpXml.dmpProfileModel.DmpProfile;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import javax.xml.bind.JAXBContext;
import javax.xml.bind.JAXBException;
@ -9,6 +11,7 @@ import java.io.File;
import java.io.IOException;
public class ImportXmlBuilderDmpProfile {
private static final Logger logger = LoggerFactory.getLogger(ImportXmlBuilderDmpProfile.class);
public DmpProfile build(File xmlFile) throws IOException {
DmpProfile dmpProfile = new DmpProfile();
@ -18,7 +21,7 @@ public class ImportXmlBuilderDmpProfile {
Unmarshaller unmarshaller = jaxbContext.createUnmarshaller();
dmpProfile = (DmpProfile) unmarshaller.unmarshal(xmlFile);
} catch (JAXBException e) {
e.printStackTrace();
logger.error(e.getMessage(), e);
}
return dmpProfile;

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

@ -1,16 +1,20 @@
package eu.eudat.models;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
public class HintedModelFactory {
private static final Logger logger = LoggerFactory.getLogger(HintedModelFactory.class);
public static <T extends DataModel> String getHint(Class<T> clazz) {
try {
return clazz.newInstance().getHint();
} catch (InstantiationException e) {
e.printStackTrace();
logger.error(e.getMessage(), e);
return null;
} catch (IllegalAccessException e) {
e.printStackTrace();
logger.error(e.getMessage(), e);
return null;
}
}

15
dmp-backend/web/src/main/java/eu/eudat/models/data/dashboard/searchbar/SearchBarItem.java
View File

@ -1,17 +1,16 @@
package eu.eudat.models.data.dashboard.searchbar;
/**
* Created by ikalyvas on 7/26/2018.
*/
public class SearchBarItem {
private String id;
private String label;
private int type;
private boolean isPublished;
public SearchBarItem(String id, String label, int type) {
public SearchBarItem(String id, String label, int type, boolean isPublished) {
this.id = id;
this.label = label;
this.type = type;
this.isPublished = isPublished;
}
public String getId() {
@ -37,4 +36,12 @@ public class SearchBarItem {
public void setType(int type) {
this.type = type;
}
public boolean getIsPublished() {
return isPublished;
}
public void setPublished(boolean published) {
isPublished = published;
}
}

26
dmp-backend/web/src/main/java/eu/eudat/models/data/datarepository/DataRepositoryModel.java
View File

@ -1,6 +1,5 @@
package eu.eudat.models.data.datarepository;
import com.fasterxml.jackson.annotation.JsonProperty;
import eu.eudat.data.entities.DataRepository;
import eu.eudat.data.entities.UserInfo;
import eu.eudat.models.DataModel;
@ -8,13 +7,9 @@ import eu.eudat.models.DataModel;
import java.util.Date;
import java.util.UUID;
/**
* Created by ikalyvas on 9/3/2018.
*/
public class DataRepositoryModel implements DataModel<DataRepository, DataRepositoryModel> {
private UUID id;
@JsonProperty("name")
private String label;
private String name;
private String pid;
private String abbreviation;
private String uri;
@ -30,11 +25,11 @@ public class DataRepositoryModel implements DataModel<DataRepository, DataReposi
this.id = id;
}
public String getLabel() {
return label;
public String getName() {
return name;
}
public void setLabel(String label) {
this.label = label;
public void setName(String name) {
this.name = name;
}
public String getPid() {
@ -89,9 +84,10 @@ public class DataRepositoryModel implements DataModel<DataRepository, DataReposi
@Override
public DataRepositoryModel fromDataModel(DataRepository entity) {
this.setAbbreviation(entity.getAbbreviation());
this.setLabel(entity.getLabel());
this.setName(entity.getLabel());
this.setUri(entity.getUri());
this.setId(entity.getId());
this.setPid(entity.getReference());
String source1 = entity.getReference().substring(0, entity.getReference().indexOf(":"));
if (source1.equals("dmp")) {
this.source = "Internal";
@ -108,11 +104,15 @@ public class DataRepositoryModel implements DataModel<DataRepository, DataReposi
dataRepository.setAbbreviation(this.abbreviation);
dataRepository.setCreated(this.created != null ? this.created : new Date());
dataRepository.setModified(new Date());
dataRepository.setLabel(this.label);
dataRepository.setLabel(this.name);
if (this.source != null) {
if (this.source.equals("Internal") || this.source.equals(this.id.toString().substring(0, this.source.length()))) {
dataRepository.setReference(this.id.toString());
} else {
dataRepository.setReference(this.source + ":" + this.id);
dataRepository.setReference(this.source + ":" + dataRepository.getId());
}
} else {
dataRepository.setReference("dmp:" + dataRepository.getId());
}
dataRepository.setUri(this.uri);
dataRepository.setStatus((short) 0);

42
dmp-backend/web/src/main/java/eu/eudat/models/data/dataset/DataRepository.java
View File

@ -4,16 +4,26 @@ import eu.eudat.models.DataModel;
import eu.eudat.logic.utilities.helpers.LabelGenerator;
import java.util.Date;
import java.util.UUID;
public class DataRepository implements DataModel<eu.eudat.data.entities.DataRepository, DataRepository>, LabelGenerator {
private String id;
private String pid;
private String label;
private String name;
private String uri;
private String info;
private String reference;
private String abbreviation;
private String tag;
private String source;
public String getId() {
return id;
}
public void setId(String id) {
this.id = id;
}
public String getPid() {
return pid;
}
@ -21,11 +31,11 @@ public class DataRepository implements DataModel<eu.eudat.data.entities.DataRepo
this.pid = pid;
}
public String getLabel() {
return label;
public String getName() {
return name;
}
public void setLabel(String label) {
this.label = label;
public void setName(String name) {
this.name = name;
}
public String getUri() {
@ -49,6 +59,13 @@ public class DataRepository implements DataModel<eu.eudat.data.entities.DataRepo
this.reference = reference;
}
public String getAbbreviation() {
return abbreviation;
}
public void setAbbreviation(String abbreviation) {
this.abbreviation = abbreviation;
}
public String getTag() {
return tag;
}
@ -64,9 +81,11 @@ public class DataRepository implements DataModel<eu.eudat.data.entities.DataRepo
}
public DataRepository fromDataModel(eu.eudat.data.entities.DataRepository entity) {
this.id = entity.getId().toString();
this.pid = entity.getReference();
this.label = entity.getLabel();
this.name = entity.getLabel();
this.uri = entity.getUri();
this.abbreviation = entity.getAbbreviation();
this.reference = entity.getReference();
String source1 = entity.getReference().substring(0, entity.getReference().indexOf(":"));
if (source1.equals("dmp")) {
@ -79,8 +98,11 @@ public class DataRepository implements DataModel<eu.eudat.data.entities.DataRepo
public eu.eudat.data.entities.DataRepository toDataModel() {
eu.eudat.data.entities.DataRepository entity = new eu.eudat.data.entities.DataRepository();
if (this.id != null) {
entity.setId(UUID.fromString(this.id));
}
entity.setReference(this.pid);
entity.setLabel(this.label);
entity.setLabel(this.name);
entity.setUri(this.uri);
entity.setCreated(new Date());
entity.setModified(new Date());
@ -94,12 +116,16 @@ public class DataRepository implements DataModel<eu.eudat.data.entities.DataRepo
entity.setReference(this.source.toLowerCase() + ":" + this.reference);
}
}
if (this.abbreviation != null)
entity.setAbbreviation(this.abbreviation);
return entity;
}
@Override
public String generateLabel() {
return this.getLabel();
return this.getName();
}
@Override

12
dmp-backend/web/src/main/java/eu/eudat/models/data/datasetwizard/DatasetWizardModel.java
View File

@ -159,7 +159,7 @@ public class DatasetWizardModel implements DataModel<Dataset, DatasetWizardModel
this.registries = entity.getRegistries().stream().map(item -> new Registry().fromDataModel(item)).collect(Collectors.toList());
this.dataRepositories = entity.getDatasetDataRepositories().stream().map(item -> {
DataRepository dataRepository = new DataRepository().fromDataModel(item.getDataRepository());
if(item.getData()!=null) {
if (item.getData() != null) {
Map<String, Map<String, String>> data = (Map<String, Map<String, String>>) JSONValue.parse(item.getData());
Map<String, String> values = data.get("data");
dataRepository.setInfo(values.get("info"));
@ -171,7 +171,7 @@ public class DatasetWizardModel implements DataModel<Dataset, DatasetWizardModel
this.dmp = new DataManagementPlan().fromDataModelNoDatasets(entity.getDmp());
this.externalDatasets = entity.getDatasetExternalDatasets().stream().map(item -> {
ExternalDatasetListingModel externalDatasetListingModel = new ExternalDatasetListingModel().fromDataModel(item.getExternalDataset());
if(item.getData()!= null) {
if (item.getData() != null) {
Map<String, Map<String, String>> data = (Map<String, Map<String, String>>) JSONValue.parse(item.getData());
Map<String, String> values = data.get("data");
externalDatasetListingModel.setInfo(values.get("info"));
@ -214,10 +214,10 @@ public class DatasetWizardModel implements DataModel<Dataset, DatasetWizardModel
eu.eudat.data.entities.DataRepository dataRepository = dataRepositoryModel.toDataModel();
DatasetDataRepository datasetDataRepository = new DatasetDataRepository();
datasetDataRepository.setDataRepository(dataRepository);
Map<String,Map<String,String>> data = new HashMap<>();
Map<String,String> values = new HashMap<>();
values.put("info",dataRepositoryModel.getInfo());
data.put("data",values);
Map<String, Map<String, String>> data = new HashMap<>();
Map<String, String> values = new HashMap<>();
values.put("info", dataRepositoryModel.getInfo());
data.put("data", values);
datasetDataRepository.setData(JSONValue.toJSONString(data));
entity.getDatasetDataRepositories().add(datasetDataRepository);
}

10
dmp-backend/web/src/main/java/eu/eudat/models/data/dmp/DataManagementPlan.java
View File

@ -28,7 +28,7 @@ public class DataManagementPlan implements DataModel<DMP, DataManagementPlan> {
private String description;
private List<DatasetListingModel> datasets;
private List<AssociatedProfile> profiles;
private eu.eudat.models.data.grant.Grant grant;
private Grant grant;
private List<Organisation> organisations;
private List<Researcher> researchers;
private List<UserListingModel> associatedUsers;
@ -218,7 +218,7 @@ public class DataManagementPlan implements DataModel<DMP, DataManagementPlan> {
this.organisations = entity.getOrganisations().stream().map(item -> new Organisation().fromDataModel(item)).collect(Collectors.toList());
this.researchers = entity.getResearchers().stream().map(item -> new Researcher().fromDataModel(item)).collect(Collectors.toList());
this.version = entity.getVersion();
this.groupId = this.groupId == null ? null : this.groupId;
this.groupId = this.groupId == null ? null : entity.getGroupId();
this.label = entity.getLabel();
this.grant = new Grant();
this.properties = entity.getProperties() != null ? new org.json.JSONObject(entity.getProperties()).toMap() : null;
@ -243,9 +243,15 @@ public class DataManagementPlan implements DataModel<DMP, DataManagementPlan> {
this.profiles.add(associatedProfile);
}
}
if (entity.isPublic()) {
this.datasets = entity.getDataset().stream()
.filter(dataset -> !dataset.getStatus().equals(Dataset.Status.DELETED.getValue()) && !dataset.getStatus().equals(Dataset.Status.CANCELED.getValue()) && !dataset.getStatus().equals(Dataset.Status.SAVED.getValue()))
.map(x-> new DatasetListingModel().fromDataModel(x)).collect(Collectors.toList());
} else {
this.datasets = entity.getDataset().stream()
.filter(dataset -> !dataset.getStatus().equals(Dataset.Status.DELETED.getValue()) && !dataset.getStatus().equals(Dataset.Status.CANCELED.getValue()))
.map(x-> new DatasetListingModel().fromDataModel(x)).collect(Collectors.toList());
}
this.modified = entity.getModified();
this.created = entity.getCreated();
this.description = entity.getDescription();

12
dmp-backend/web/src/main/java/eu/eudat/models/data/dmp/DataManagementPlanEditorModel.java
View File

@ -218,11 +218,12 @@ public class DataManagementPlanEditorModel implements DataModel<DMP, DataManagem
this.organisations = entity.getOrganisations().stream().map(item -> new Organisation().fromDataModel(item)).collect(Collectors.toList());
this.researchers = entity.getResearchers().stream().map(item -> new Researcher().fromDataModel(item)).collect(Collectors.toList());
this.version = entity.getVersion();
this.groupId = this.groupId == null ? null : this.groupId;
this.groupId = this.groupId == null ? null : entity.getGroupId();
this.label = entity.getLabel();
this.grant = new GrantDMPEditorModel();
this.properties = entity.getProperties() != null ? new org.json.JSONObject(entity.getProperties()).toMap() : null;
this.grant.getExistGrant().fromDataModel(entity.getGrant());
this.grant.getExistGrant().setSource("");
this.creator = new eu.eudat.models.data.userinfo.UserInfo();
this.groupId = entity.getGroupId();
this.lockable = entity.getDataset().stream().findAny().isPresent();
@ -278,10 +279,11 @@ public class DataManagementPlanEditorModel implements DataModel<DMP, DataManagem
dataManagementPlanEntity.setGrant(this.grant.getExistGrant().toDataModel());
else {
Grant grant = new Grant();
grant.setId(UUID.randomUUID());
grant.setAbbreviation("");
grant.setLabel(this.grant.getLabel());
grant.setType(Grant.GrantType.INTERNAL.getValue());
grant.setReference("dmp:" + this.grant.getLabel());
grant.setReference("dmp:" + grant.getId());
grant.setUri("");
grant.setDefinition("");
grant.setCreated(new Date());
@ -302,9 +304,10 @@ public class DataManagementPlanEditorModel implements DataModel<DMP, DataManagem
} else {
if (this.funder.getLabel() != null) {
Funder funder = new Funder();
funder.setId(UUID.randomUUID());
funder.setLabel(this.funder.getLabel());
funder.setType(Funder.FunderType.INTERNAL.getValue());
funder.setReference("dmp:" + this.funder.getLabel());
funder.setReference("dmp:" + funder.getId());
funder.setDefinition("");
funder.setCreated(new Date());
funder.setStatus(Funder.Status.ACTIVE.getValue());
@ -322,10 +325,11 @@ public class DataManagementPlanEditorModel implements DataModel<DMP, DataManagem
dataManagementPlanEntity.setProject(this.project.getExistProject().toDataModel());
else {
Project project = new Project();
project.setId(UUID.randomUUID());
project.setAbbreviation("");
project.setLabel(this.project.getLabel());
project.setType(Project.ProjectType.INTERNAL.getValue());
project.setReference("dmp:" + this.project.getLabel());
project.setReference("dmp:" + project.getId());
project.setUri("");
project.setDefinition("");
project.setCreated(new Date());

27
dmp-backend/web/src/main/java/eu/eudat/models/data/dmp/DataManagementPlanNewVersionModel.java
View File

@ -182,10 +182,11 @@ public class DataManagementPlanNewVersionModel implements DataModel<DMP, DataMan
entity.setGrant(this.grant.getExistGrant().toDataModel());
else {
eu.eudat.data.entities.Grant grant = new eu.eudat.data.entities.Grant();
grant.setId(UUID.randomUUID());
grant.setAbbreviation("");
grant.setLabel(this.grant.getLabel());
grant.setType(eu.eudat.data.entities.Grant.GrantType.INTERNAL.getValue());
grant.setReference("dmp:" + this.grant.getLabel());
grant.setReference("dmp:" + grant.getId());
grant.setUri("");
grant.setDefinition("");
grant.setCreated(new Date());
@ -197,27 +198,28 @@ public class DataManagementPlanNewVersionModel implements DataModel<DMP, DataMan
}
}
if(this.funder == null && this.funder.getExistFunder() == null && this.funder.getLabel() == null) {
entity.getGrant().setFunder(null);
}
else if (this.funder != null && this.funder.getExistFunder() == null && this.funder.getLabel() == null) {
entity.getGrant().setFunder(null);
}
else {
if (this.funder == null) {
// dataManagementPlanEntity.getGrant().setFunder(null);
throw new Exception("Funder is a mandatory entity");
} else if (this.funder.getExistFunder() == null && this.funder.getLabel() == null) {
// dataManagementPlanEntity.getGrant().setFunder(null);
throw new Exception("Funder is a mandatory entity");
} else {
if (this.funder.getLabel() != null) {
Funder funder = new Funder();
funder.setId(UUID.randomUUID());
funder.setLabel(this.funder.getLabel());
funder.setType(Funder.FunderType.INTERNAL.getValue());
funder.setReference("dmp:" + this.funder.getLabel());
funder.setReference("dmp:" + funder.getId());
funder.setDefinition("");
funder.setCreated(new Date());
funder.setStatus(Funder.Status.ACTIVE.getValue());
funder.setModified(new Date());
entity.getGrant().setFunder(funder);
}
else if (this.funder.getExistFunder() != null && this.funder.getLabel() == null){
} else if (this.funder.getExistFunder() != null && this.funder.getLabel() == null){
entity.getGrant().setFunder(this.funder.getExistFunder().toDataModel());
entity.getGrant().getFunder().setType(Funder.FunderType.EXTERNAL.getValue());
}
}
@ -226,10 +228,11 @@ public class DataManagementPlanNewVersionModel implements DataModel<DMP, DataMan
entity.setProject(this.project.getExistProject().toDataModel());
else {
Project project = new Project();
project.setId(UUID.randomUUID());
project.setAbbreviation("");
project.setLabel(this.project.getLabel());
project.setType(Project.ProjectType.INTERNAL.getValue());
project.setReference("dmp:" + this.project.getLabel());
project.setReference("dmp:" + project.getId());
project.setUri("");
project.setDefinition("");
project.setCreated(new Date());

33
dmp-backend/web/src/main/java/eu/eudat/models/data/dmp/Organisation.java
View File

@ -9,8 +9,10 @@ public class Organisation implements DataModel<eu.eudat.data.entities.Organisati
private String label;
private String name;
private String id;
private String reference;
private int status;
private String tag;
private String tag; // how the external source is displayed. ex: "Cristin".
private String key; // the external source. ex: "cristin".
public String getLabel() {
return label;
@ -33,6 +35,13 @@ public class Organisation implements DataModel<eu.eudat.data.entities.Organisati
this.id = id;
}
public String getReference() {
return reference;
}
public void setReference(String reference) {
this.reference = reference;
}
public int getStatus() {
return status;
}
@ -47,26 +56,30 @@ public class Organisation implements DataModel<eu.eudat.data.entities.Organisati
this.tag = tag;
}
public String getKey() {
return key;
}
public void setKey(String key) {
this.key = key;
}
@Override
public Organisation fromDataModel(eu.eudat.data.entities.Organisation entity) {
this.id = entity.getReference();
this.id = entity.getId().toString();
this.name = entity.getLabel();
this.label = entity.getUri();
if (entity.getReference().contains(":cristin")) {
this.tag = "cristin";
} else {
this.tag = entity.getReference().substring(0, entity.getReference().indexOf(":"));
}
this.reference = entity.getReference();
this.key = entity.getReference().substring(0, entity.getReference().indexOf(":"));
return this;
}
@Override
public eu.eudat.data.entities.Organisation toDataModel() {
eu.eudat.data.entities.Organisation organisationEntity = new eu.eudat.data.entities.Organisation();
if (this.tag.equals(this.id.substring(0, this.tag.length()))) {
organisationEntity.setReference(this.id);
if ((this.key + ":").equals(this.reference.substring(0, this.key.length() + 1))) {
organisationEntity.setReference(this.reference);
} else {
organisationEntity.setReference(this.tag + ":" + this.id);
organisationEntity.setReference(this.key + ":" + this.reference);
}
organisationEntity.setLabel(this.name);
organisationEntity.setUri(this.label);

68
dmp-backend/web/src/main/java/eu/eudat/models/data/dmp/Researcher.java
View File

@ -2,20 +2,25 @@ package eu.eudat.models.data.dmp;
import eu.eudat.models.DataModel;
import eu.eudat.logic.utilities.helpers.LabelGenerator;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.util.Date;
import java.util.UUID;
public class Researcher implements DataModel<eu.eudat.data.entities.Researcher, Researcher>, LabelGenerator {
private static final Logger logger = LoggerFactory.getLogger(Researcher.class);
private String label;
private String name;
private String id;
private String reference;
private int status;
private String tag;
private String key;
public String getLabel() {
return label;
}
public void setLabel(String label) {
this.label = label;
}
@ -23,7 +28,6 @@ public class Researcher implements DataModel<eu.eudat.data.entities.Researcher,
public String getName() {
return name;
}
public void setName(String name) {
this.name = name;
}
@ -31,15 +35,20 @@ public class Researcher implements DataModel<eu.eudat.data.entities.Researcher,
public String getId() {
return id;
}
public void setId(String id) {
this.id = id;
}
public String getReference() {
return reference;
}
public void setReference(String reference) {
this.reference = reference;
}
public int getStatus() {
return status;
}
public void setStatus(int status) {
this.status = status;
}
@ -47,38 +56,61 @@ public class Researcher implements DataModel<eu.eudat.data.entities.Researcher,
public String getTag() {
return tag;
}
public void setTag(String tag) {
this.tag = tag;
}
public String getKey() {
return key;
}
public void setKey(String key) {
this.key = key;
}
@Override
public Researcher fromDataModel(eu.eudat.data.entities.Researcher entity) {
this.id = entity.getReference();
this.id = entity.getId().toString();
this.label = entity.getUri();
this.name = entity.getLabel();
this.status = entity.getStatus();
if (entity.getReference().contains(":cristin")) {
this.tag = "cristin";
} else {
this.reference = entity.getReference();
String source = entity.getReference().substring(0, entity.getReference().indexOf(":"));
if (source.equals("dmp"))
this.tag = "Internal";
this.key = "Internal";
else
this.tag = source;
}
this.key = source;
return this;
}
@Override
public eu.eudat.data.entities.Researcher toDataModel() {
eu.eudat.data.entities.Researcher researcher = new eu.eudat.data.entities.Researcher();
if (this.tag.equals("Internal") || this.tag.equals(this.id.substring(0, this.tag.length()))) {
researcher.setReference(this.id);
} else {
researcher.setReference(this.tag + ":" + this.id);
if (this.id == null) {
this.id = UUID.randomUUID().toString();
}
researcher.setId(UUID.fromString(this.id));
if (this.key != null) {
if (this.key.toLowerCase().equals("internal")) {
if (this.reference != null && "dmp".equals(this.reference.substring(0, 3))) {
researcher.setReference(this.reference);
} else {
researcher.setReference("dmp:" + this.id);
}
} else {
if ((this.key + ":").equals(this.reference.substring(0, this.key.length() + 1))) {
researcher.setReference(this.reference);
} else {
researcher.setReference(this.key + ":" + this.reference);
}
}
} else {
try {
throw new Exception("Researcher has no key value");
} catch (Exception e) {
logger.error(e.getMessage(), e);
}
}
researcher.setLabel(this.name);
researcher.setUri(this.label);
researcher.setCreated(new Date());
@ -108,6 +140,6 @@ public class Researcher implements DataModel<eu.eudat.data.entities.Researcher,
@Override
public int hashCode() {
return id.hashCode();
return reference.hashCode();
}
}

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

@ -11,6 +11,7 @@ public class ExternalSourcesItemModel {
private String abbreviation;
private String tag;
private String source;
private String key;
public String getId() {
return id;
@ -74,4 +75,11 @@ public class ExternalSourcesItemModel {
public void setSource(String source) {
this.source = source;
}
public String getKey() {
return key;
}
public void setKey(String key) {
this.key = key;
}
}

1
dmp-backend/web/src/main/java/eu/eudat/models/data/external/FundersExternalSourcesModel.java vendored
View File

@ -15,6 +15,7 @@ public class FundersExternalSourcesModel extends ExternalListingItem<FundersExte
model.setDescription(item.get("description"));
model.setSource(item.get("source"));
model.setTag(item.get("tag"));
model.setKey(item.get("key"));
this.add(model);
}
return this;

1
dmp-backend/web/src/main/java/eu/eudat/models/data/external/GrantsExternalSourcesModel.java vendored
View File

@ -14,6 +14,7 @@ public class GrantsExternalSourcesModel extends ExternalListingItem<GrantsExtern
model.setName(item.get("name"));
model.setDescription(item.get("description"));
model.setTag(item.get("tag"));
model.setKey(item.get("key"));
this.add(model);
}
return this;

3
dmp-backend/web/src/main/java/eu/eudat/models/data/external/OrganisationsExternalSourcesModel.java vendored
View File

@ -11,10 +11,11 @@ public class OrganisationsExternalSourcesModel extends ExternalListingItem<Organ
public OrganisationsExternalSourcesModel fromExternalItem(List<Map<String, String>> values) {
for (Map<String, String> item : values) {
ExternalSourcesItemModel model = new ExternalSourcesItemModel();
model.setId(item.get("pid"));
model.setRemoteId(item.get("pid"));
model.setUri(item.get("uri"));
model.setName(item.get("name"));
model.setTag(item.get("tag"));
model.setKey(item.get("key"));
this.add(model);
}
return this;

12
dmp-backend/web/src/main/java/eu/eudat/models/data/external/ProjectsExternalSourcesModel.java vendored
View File

@ -2,12 +2,15 @@ package eu.eudat.models.data.external;
import com.fasterxml.jackson.databind.JsonNode;
import com.fasterxml.jackson.databind.ObjectMapper;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.io.IOException;
import java.util.List;
import java.util.Map;
public class ProjectsExternalSourcesModel extends ExternalListingItem<ProjectsExternalSourcesModel> {
private static final Logger logger = LoggerFactory.getLogger(ProjectsExternalSourcesModel.class);
private static final ObjectMapper mapper = new ObjectMapper();
@Override
@ -51,10 +54,17 @@ public class ProjectsExternalSourcesModel extends ExternalListingItem<ProjectsEx
model.setTag(item.get("tag"));
}
JsonNode key = node.get("key");
if (key != null && !key.isNull() && key.isObject()) {
model.setKey(node.get("key").get("$").asText());
} else {
model.setKey(item.get("key"));
}
this.add(model);
} catch (IOException e) {
e.printStackTrace();
logger.error(e.getMessage(), e);
}
}
return this;

3
dmp-backend/web/src/main/java/eu/eudat/models/data/external/ResearchersExternalSourcesModel.java vendored
View File

@ -9,10 +9,11 @@ public class ResearchersExternalSourcesModel extends ExternalListingItem<Researc
public ResearchersExternalSourcesModel fromExternalItem(List<Map<String, String>> values) {
for (Map<String, String> item : values) {
ExternalSourcesItemModel model = new ExternalSourcesItemModel();
model.setId(item.get("pid"));
model.setRemoteId(item.get("pid"));
model.setUri(item.get("uri"));
model.setName(item.get("name"));
model.setTag(item.get("tag"));
model.setKey(item.get("key"));
this.add(model);
}
return this;

3
dmp-backend/web/src/main/java/eu/eudat/models/data/externaldataset/ExternalDatasetListingModel.java
View File

@ -140,6 +140,9 @@ public class ExternalDatasetListingModel implements DataModel<ExternalDataset, E
externalDataset.setReference(this.source.toLowerCase() + ":" + this.reference);
}
}
if (externalDataset.getReference() == null) {
externalDataset.setReference(this.pid);
}
externalDataset.setModified(new Date());
return externalDataset;
}

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