Removes some unused imports and formats DatasetManager.

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

@@ -4,8 +4,6 @@ package eu.eudat.data.entities;
 import eu.eudat.data.converters.DateToUTCConverter;
 import eu.eudat.queryable.queryableentity.DataEntity;
 import org.hibernate.annotations.GenericGenerator;
-import org.hibernate.annotations.ManyToAny;
-import org.hibernate.annotations.Type;
 
 import javax.persistence.*;
 import java.util.*;

dmp-backend/web/src/main/java/eu/eudat/controllers/DMPProfileController.java

@@ -1,9 +1,7 @@
 package eu.eudat.controllers;
 
 import eu.eudat.data.entities.DMPProfile;
-import eu.eudat.data.query.items.item.dmpprofile.DataManagementPlanProfileCriteriaRequest;
 import eu.eudat.data.query.items.table.dmpprofile.DataManagementPlanProfileTableRequest;
-import eu.eudat.logic.managers.AdminManager;
 import eu.eudat.logic.managers.DataManagementProfileManager;
 import eu.eudat.logic.security.claims.ClaimedAuthorities;
 import eu.eudat.logic.services.ApiContext;

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

@@ -11,7 +11,6 @@ import eu.eudat.logic.managers.UserManager;
 import eu.eudat.logic.security.claims.ClaimedAuthorities;
 import eu.eudat.logic.services.ApiContext;
 import eu.eudat.logic.services.forms.VisibilityRuleService;
-import eu.eudat.logic.utilities.documents.helpers.FileEnvelope;
 import eu.eudat.models.data.datasetwizard.DataManagentPlanListingModel;
 import eu.eudat.models.data.datasetwizard.DatasetWizardModel;
 import eu.eudat.models.data.dmp.AssociatedProfile;
@@ -29,14 +28,11 @@ import org.springframework.http.ResponseEntity;
 import org.springframework.web.bind.annotation.*;
 import org.springframework.web.multipart.MultipartFile;
 
-import javax.activation.MimetypesFileTypeMap;
 import javax.transaction.Transactional;
-import javax.xml.bind.JAXBException;
 import java.io.File;
 import java.io.FileInputStream;
 import java.io.IOException;
 import java.io.InputStream;
-import java.nio.file.Files;
 import java.util.List;
 import java.util.UUID;
 

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

@@ -5,9 +5,9 @@ import eu.eudat.configurations.dynamicproject.DynamicProjectConfiguration;
 import eu.eudat.configurations.dynamicproject.entities.Property;
 import eu.eudat.data.dao.criteria.*;
 import eu.eudat.data.dao.entities.*;
-import eu.eudat.data.entities.*;
 import eu.eudat.data.entities.Organisation;
 import eu.eudat.data.entities.Researcher;
+import eu.eudat.data.entities.*;
 import eu.eudat.data.query.items.item.dmp.DataManagementPlanCriteriaRequest;
 import eu.eudat.data.query.items.table.dmp.DataManagementPlanTableRequest;
 import eu.eudat.data.query.items.table.dmp.DataManagmentPlanPublicTableRequest;
@@ -40,7 +40,6 @@ import eu.eudat.models.data.security.Principal;
 import eu.eudat.models.data.user.composite.PagedDatasetProfile;
 import eu.eudat.models.data.userinfo.UserListingModel;
 import eu.eudat.queryable.QueryableList;
-import org.apache.poi.xwpf.usermodel.ParagraphAlignment;
 import org.apache.poi.xwpf.usermodel.XWPFDocument;
 import org.apache.poi.xwpf.usermodel.XWPFParagraph;
 import org.apache.poi.xwpf.usermodel.XWPFRun;
@@ -53,10 +52,7 @@ import org.springframework.web.client.RestTemplate;
 import org.springframework.web.multipart.MultipartFile;
 import org.w3c.dom.Document;
 import org.w3c.dom.Element;
-import org.w3c.dom.Node;
-import org.w3c.dom.NodeList;
 
-import javax.activation.MimetypesFileTypeMap;
 import javax.xml.bind.JAXBContext;
 import javax.xml.bind.JAXBException;
 import javax.xml.bind.Unmarshaller;

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

@@ -1,7 +1,9 @@
 package eu.eudat.logic.managers;
 
 import eu.eudat.data.dao.criteria.*;
-import eu.eudat.data.dao.entities.*;
+import eu.eudat.data.dao.entities.DataRepositoryDao;
+import eu.eudat.data.dao.entities.DatasetDao;
+import eu.eudat.data.dao.entities.RegistryDao;
 import eu.eudat.data.entities.*;
 import eu.eudat.data.query.items.table.dataset.DatasetPublicTableRequest;
 import eu.eudat.data.query.items.table.dataset.DatasetTableRequest;
@@ -17,13 +19,13 @@ import eu.eudat.logic.utilities.documents.types.ParagraphStyle;
 import eu.eudat.logic.utilities.documents.word.WordBuilder;
 import eu.eudat.logic.utilities.documents.xml.ExportXmlBuilder;
 import eu.eudat.models.HintedModelFactory;
-import eu.eudat.models.data.datasetImport.*;
+import eu.eudat.models.data.datasetImport.DatasetImportField;
+import eu.eudat.models.data.datasetImport.DatasetImportPagedDatasetProfile;
 import eu.eudat.models.data.datasetwizard.DatasetWizardModel;
 import eu.eudat.models.data.dmp.AssociatedProfile;
 import eu.eudat.models.data.helpers.common.DataTableData;
 import eu.eudat.models.data.listingmodels.DatasetListingModel;
 import eu.eudat.models.data.security.Principal;
-import eu.eudat.models.data.user.composite.DatasetProfilePage;
 import eu.eudat.models.data.user.composite.PagedDatasetProfile;
 import eu.eudat.queryable.QueryableList;
 import org.apache.commons.io.IOUtils;
@@ -33,20 +35,15 @@ import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.core.env.Environment;
 import org.springframework.core.io.FileSystemResource;
 import org.springframework.http.*;
-import org.springframework.http.converter.ByteArrayHttpMessageConverter;
-import org.springframework.http.converter.HttpMessageConverter;
-import org.springframework.http.converter.json.MappingJackson2HttpMessageConverter;
 import org.springframework.stereotype.Component;
 import org.springframework.util.LinkedMultiValueMap;
 import org.springframework.web.client.RestTemplate;
+import org.springframework.web.multipart.MultipartFile;
 
 import javax.activation.MimetypesFileTypeMap;
-import javax.mail.Multipart;
 import javax.xml.bind.JAXBContext;
 import javax.xml.bind.JAXBException;
 import javax.xml.bind.Unmarshaller;
-
-import org.springframework.web.multipart.MultipartFile;
 import java.io.*;
 import java.math.BigInteger;
 import java.net.URL;
@@ -84,19 +81,17 @@ public class DatasetManager {
         try {
             datasets = datasetCriteria.getTags() != null && datasetCriteria.getTags().size() > 0 && datasetRepository.exists() ?
                     datasetRepository.query(datasetCriteria) : new LinkedList<>();
-        }
+        } catch (Exception ex) {
-        catch (Exception ex){
             datasets = null;
         }
 
         UserInfo userInfo = builderFactory.getBuilder(UserInfoBuilder.class).id(principal.getId()).build();
         QueryableList<eu.eudat.data.entities.Dataset> items = databaseRepository.getDatasetDao().getWithCriteria(datasetTableRequest.getCriteria()).withHint(HintedModelFactory.getHint(DatasetListingModel.class));
         if (datasets != null && datasetTableRequest.getCriteria().getTags() != null && !datasetTableRequest.getCriteria().getTags().isEmpty()) {
-            if (!datasets.isEmpty()){
+            if (!datasets.isEmpty()) {
                 List<eu.eudat.elastic.entities.Dataset> finalDatasets = datasets;
                 items.where((builder, root) -> root.get("id").in(finalDatasets.stream().map(x -> UUID.fromString(x.getId())).collect(Collectors.toList())));
-            }
+            } else
-            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);
@@ -121,11 +116,10 @@ public class DatasetManager {
         DatasetCriteria datasetCriteria = new DatasetCriteria();
         datasetCriteria.setTags(datasetTableRequest.getCriteria().getTags());
         List<eu.eudat.elastic.entities.Dataset> datasets;
-        try{
+        try {
             datasets = datasetCriteria.getTags() != null && datasetCriteria.getTags().size() > 0 && datasetRepository.exists() ?
                     datasetRepository.query(datasetCriteria) : new LinkedList<>();
-        }
+        } catch (Exception ex) {
-        catch (Exception ex){
             datasets = null;
         }
         datasetTableRequest.setQuery(databaseRepository.getDatasetDao().asQueryable().withHint(HintedModelFactory.getHint(DatasetListingModel.class)));
@@ -134,8 +128,7 @@ public class DatasetManager {
             if (!datasets.isEmpty()) {
                 List<eu.eudat.elastic.entities.Dataset> finalDatasets = datasets;
                 items.where((builder, root) -> root.get("id").in(finalDatasets.stream().map(x -> UUID.fromString(x.getId())).collect(Collectors.toList())));
-            }
+            } else
-            else
                 items.where((builder, root) -> root.get("id").in(new UUID[]{UUID.randomUUID()}));
         }
         QueryableList<eu.eudat.data.entities.Dataset> pagedItems = PaginationManager.applyPaging(items, datasetTableRequest);
@@ -158,11 +151,10 @@ public class DatasetManager {
         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;
-        try{
+        try {
             datasetElastic = datasetRepository.exists() ?
                     datasetRepository.findDocument(id) : new eu.eudat.elastic.entities.Dataset();
-        }
+        } catch (Exception ex) {
-        catch (Exception ex){
             datasetElastic = new eu.eudat.elastic.entities.Dataset();
         }
         dataset.setDatasetProfileDefinition(getPagedProfile(dataset, datasetEntity));
@@ -182,9 +174,9 @@ public class DatasetManager {
         List<DatasetProfile> profileVersionsIncluded = new LinkedList<>();
 
         // Iterate through the versions and remove those that are not included in the DMP of the dataset in question.
-        for(DatasetProfile version : profileVersions) {
+        for (DatasetProfile version : profileVersions) {
-            for(AssociatedProfile p : dataset.getDmp().getProfiles()){
+            for (AssociatedProfile p : dataset.getDmp().getProfiles()) {
-                if(version.getId().toString().equals(p.getId().toString())) {
+                if (version.getId().toString().equals(p.getId().toString())) {
                     profileVersionsIncluded.add(version);
                 }
             }
@@ -208,12 +200,11 @@ public class DatasetManager {
         DatasetWizardModel dataset = new DatasetWizardModel();
         eu.eudat.data.entities.Dataset datasetEntity = databaseRepository.getDatasetDao().isPublicDataset(UUID.fromString(id));
 
-        if (datasetEntity != null && datasetEntity.getStatus() == 1 && datasetEntity.getDmp().getStatus() == 1){
+        if (datasetEntity != null && datasetEntity.getStatus() == 1 && datasetEntity.getDmp().getStatus() == 1) {
             dataset.setDatasetProfileDefinition(getPagedProfile(dataset, datasetEntity));
             dataset.fromDataModel(datasetEntity);
             return dataset;
-        }
+        } else {
-        else {
             throw new Exception("Selected dataset is not public");
         }
     }
@@ -465,7 +456,7 @@ public class DatasetManager {
             InputStream in = importFile.getInputStream();
             jaxbContext = JAXBContext.newInstance(DatasetImportPagedDatasetProfile.class);
             Unmarshaller jaxbUnmarshaller = jaxbContext.createUnmarshaller();
-            DatasetImportPagedDatasetProfile datasetImport = (DatasetImportPagedDatasetProfile)jaxbUnmarshaller.unmarshal(in);
+            DatasetImportPagedDatasetProfile datasetImport = (DatasetImportPagedDatasetProfile) jaxbUnmarshaller.unmarshal(in);
             importModel = datasetImport;
         } catch (IOException e) {
             e.printStackTrace();
@@ -487,12 +478,12 @@ public class DatasetManager {
         Map<String, String> importMap = importModel.getPages().stream()
                 .flatMap(s -> s.getSections().getSection().stream()
                         .flatMap(cFields -> cFields.getCompositeFields().stream()
-                        .flatMap(cField -> cField.getCompositeField().stream()
+                                .flatMap(cField -> cField.getCompositeField().stream()
-                                .filter(Objects::nonNull)
+                                        .filter(Objects::nonNull)
-                        .flatMap(fields -> fields.getFields().stream()
+                                        .flatMap(fields -> fields.getFields().stream()
-                        .flatMap(field -> field.getField().stream()
+                                                .flatMap(field -> field.getField().stream()
-                                .filter(f -> f.getValue() != null)
+                                                        .filter(f -> f.getValue() != null)
-                        )))))
+                                                )))))
                 .collect(Collectors.toMap(DatasetImportField::getId, DatasetImportField::getValue));
 
         // Transforms map into json file.
@@ -533,11 +524,10 @@ public class DatasetManager {
         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;
-        try{
+        try {
             datasetElastic = datasetRepository.exists() ?
                     datasetRepository.findDocument(id) : new eu.eudat.elastic.entities.Dataset();
-        }
+        } catch (Exception ex) {
-        catch (Exception ex){
             datasetElastic = new eu.eudat.elastic.entities.Dataset();
         }
         dataset.setDatasetProfileDefinition(getPagedProfile(dataset, datasetEntity));

dmp-backend/web/src/main/java/eu/eudat/models/data/dmp/DmpRDAExportModel.java

@@ -2,7 +2,6 @@ package eu.eudat.models.data.dmp;
 
 import eu.eudat.data.entities.DMP;
 import eu.eudat.data.entities.UserDMP;
-import eu.eudat.models.DataModel;
 
 import java.util.Date;
 import java.util.UUID;