Merge branch 'Development'

dmp-backend/data/src/main/java/eu/eudat/data/converters/DateToUTCConverter.java

 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;
     }

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

@@ -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;
+    }
 }

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

@@ -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;
+    }
 }

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

@@ -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;
+    }
 }

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

@@ -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);
 

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

@@ -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;

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

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

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

@@ -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;
     }

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

@@ -281,20 +281,41 @@ public class Dataset implements DataEntity<Dataset, UUID> {
 		this.setLabel(entity.getLabel());
 		this.setProperties(entity.getProperties());
 
-		this.getDatasetDataRepositories().removeAll(this.getDatasetDataRepositories());
-		if (entity.getDatasetDataRepositories() != null)
-			this.getDatasetDataRepositories().addAll(entity.getDatasetDataRepositories());
+		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());
+			} 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());
+			} else {
+				this.setDatasetExternalDatasets(new HashSet<>());
+			}
+			this.getDatasetExternalDatasets().addAll(entity.getDatasetExternalDatasets().stream().peek(item -> item.setDataset(this)).collect(Collectors.toList()));
+		}
 
-		this.getDatasetExternalDatasets().removeAll(this.getDatasetExternalDatasets());
-		if (entity.getDatasetExternalDatasets() != null)
-			this.getDatasetExternalDatasets().addAll(entity.getDatasetExternalDatasets());
+		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());

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

@@ -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;
 

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

@@ -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;
 

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

@@ -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;
 

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

@@ -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;
 

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

@@ -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;
         }

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

@@ -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;
     }
 

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

 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();

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

@@ -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;
     }

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

@@ -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();

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

@@ -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()));

dmp-backend/web/src/main/java/eu/eudat/cache/ResponsesCache.java

@@ -2,6 +2,8 @@ package eu.eudat.cache;
 
 
 import com.google.common.cache.CacheBuilder;
+import org.slf4j.Logger;