diff --git a/dmp-backend/data/src/main/java/eu/eudat/data/entities/DMP.java b/dmp-backend/data/src/main/java/eu/eudat/data/entities/DMP.java index b385401ae..05b14d287 100644 --- a/dmp-backend/data/src/main/java/eu/eudat/data/entities/DMP.java +++ b/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.*; diff --git a/dmp-backend/web/src/main/java/eu/eudat/controllers/DMPProfileController.java b/dmp-backend/web/src/main/java/eu/eudat/controllers/DMPProfileController.java index 1214ac615..2d83fc918 100644 --- a/dmp-backend/web/src/main/java/eu/eudat/controllers/DMPProfileController.java +++ b/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; diff --git a/dmp-backend/web/src/main/java/eu/eudat/controllers/DatasetWizardController.java b/dmp-backend/web/src/main/java/eu/eudat/controllers/DatasetWizardController.java index 9b84ab024..e3184cbf8 100644 --- a/dmp-backend/web/src/main/java/eu/eudat/controllers/DatasetWizardController.java +++ b/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; diff --git a/dmp-backend/web/src/main/java/eu/eudat/logic/managers/DataManagementPlanManager.java b/dmp-backend/web/src/main/java/eu/eudat/logic/managers/DataManagementPlanManager.java index 68f31faa2..ba5eaa2e5 100644 --- a/dmp-backend/web/src/main/java/eu/eudat/logic/managers/DataManagementPlanManager.java +++ b/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; diff --git a/dmp-backend/web/src/main/java/eu/eudat/logic/managers/DatasetManager.java b/dmp-backend/web/src/main/java/eu/eudat/logic/managers/DatasetManager.java index ddd04ebfc..26a57542a 100644 --- a/dmp-backend/web/src/main/java/eu/eudat/logic/managers/DatasetManager.java +++ b/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 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 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 authItems = databaseRepository.getDatasetDao().getAuthenticated(items, userInfo); @@ -121,11 +116,10 @@ public class DatasetManager { DatasetCriteria datasetCriteria = new DatasetCriteria(); datasetCriteria.setTags(datasetTableRequest.getCriteria().getTags()); List 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 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 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 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(AssociatedProfile p : dataset.getDmp().getProfiles()){ - if(version.getId().toString().equals(p.getId().toString())) { + for (DatasetProfile version : profileVersions) { + for (AssociatedProfile p : dataset.getDmp().getProfiles()) { + 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 importMap = importModel.getPages().stream() .flatMap(s -> s.getSections().getSection().stream() .flatMap(cFields -> cFields.getCompositeFields().stream() - .flatMap(cField -> cField.getCompositeField().stream() - .filter(Objects::nonNull) - .flatMap(fields -> fields.getFields().stream() - .flatMap(field -> field.getField().stream() - .filter(f -> f.getValue() != null) - ))))) + .flatMap(cField -> cField.getCompositeField().stream() + .filter(Objects::nonNull) + .flatMap(fields -> fields.getFields().stream() + .flatMap(field -> field.getField().stream() + .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)); diff --git a/dmp-backend/web/src/main/java/eu/eudat/models/data/dmp/DmpRDAExportModel.java b/dmp-backend/web/src/main/java/eu/eudat/models/data/dmp/DmpRDAExportModel.java index e472df57a..10942dbe1 100644 --- a/dmp-backend/web/src/main/java/eu/eudat/models/data/dmp/DmpRDAExportModel.java +++ b/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;