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@ -1,7 +1,7 @@
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package eu.eudat.logic.managers;
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import com.fasterxml.jackson.core.JsonProcessingException;
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import com.fasterxml.jackson.databind.JsonNode;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import eu.eudat.data.dao.criteria.*;
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import eu.eudat.data.dao.entities.DataRepositoryDao;
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import eu.eudat.data.dao.entities.DatasetDao;
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@ -49,22 +49,22 @@ import eu.eudat.models.data.user.composite.PagedDatasetProfile;
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import eu.eudat.queryable.QueryableList;
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import eu.eudat.types.Authorities;
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import eu.eudat.types.MetricNames;
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import org.apache.commons.io.IOUtils;
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import jakarta.xml.bind.JAXBContext;
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import jakarta.xml.bind.JAXBException;
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import jakarta.xml.bind.Unmarshaller;
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import org.apache.poi.xwpf.extractor.XWPFWordExtractor;
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import org.apache.poi.xwpf.usermodel.XWPFDocument;
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import org.apache.poi.xwpf.usermodel.XWPFParagraph;
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import org.apache.poi.xwpf.usermodel.XWPFRun;
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import org.json.JSONArray;
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import org.json.JSONObject;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import org.springframework.beans.factory.annotation.Autowired;
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import org.springframework.core.env.Environment;
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import org.springframework.core.io.FileSystemResource;
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import org.springframework.http.*;
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import org.springframework.http.HttpHeaders;
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import org.springframework.http.HttpStatus;
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import org.springframework.http.MediaType;
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import org.springframework.http.ResponseEntity;
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import org.springframework.stereotype.Component;
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import org.springframework.util.LinkedMultiValueMap;
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import org.springframework.web.client.RestTemplate;
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import org.springframework.web.multipart.MultipartFile;
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import org.w3c.dom.Document;
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import org.w3c.dom.Element;
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@ -75,9 +75,6 @@ import javax.activation.MimetypesFileTypeMap;
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import javax.persistence.criteria.Join;
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import javax.persistence.criteria.JoinType;
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import javax.transaction.Transactional;
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import javax.xml.bind.JAXBContext;
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import javax.xml.bind.JAXBException;
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import javax.xml.bind.Unmarshaller;
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import javax.xml.parsers.DocumentBuilder;
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import javax.xml.parsers.DocumentBuilderFactory;
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import javax.xml.xpath.XPath;
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@ -91,8 +88,6 @@ import java.time.temporal.ChronoUnit;
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import java.util.*;
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import java.util.stream.Collectors;
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import java.util.stream.Stream;
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import java.util.zip.ZipEntry;
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import java.util.zip.ZipInputStream;
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@Component
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public class DatasetManager {
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@ -279,7 +274,7 @@ public class DatasetManager {
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return dataTable;
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}
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public DatasetWizardModel getSingle(String id, Principal principal) {
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public DatasetWizardModel getSingle(String id, Principal principal) throws JsonProcessingException {
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DatasetWizardModel dataset = new DatasetWizardModel();
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eu.eudat.data.entities.Dataset datasetEntity = databaseRepository.getDatasetDao().find(UUID.fromString(id), HintedModelFactory.getHint(DatasetWizardModel.class));
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if (datasetEntity.getDmp().getUsers()
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@ -380,12 +375,11 @@ public class DatasetManager {
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return databaseRepository.getDatasetDao().find(id);
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}
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public PagedDatasetProfile getPagedProfile(DatasetWizardModel dataset, eu.eudat.data.entities.Dataset datasetEntity) {
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public PagedDatasetProfile getPagedProfile(DatasetWizardModel dataset, eu.eudat.data.entities.Dataset datasetEntity) throws JsonProcessingException {
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eu.eudat.models.data.user.composite.DatasetProfile datasetprofile = userManager.generateDatasetProfileModel(datasetEntity.getProfile());
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datasetprofile.setStatus(dataset.getStatus());
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if (datasetEntity.getProperties() != null) {
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JSONObject jObject = new JSONObject(datasetEntity.getProperties());
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Map<String, Object> properties = jObject.toMap();
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Map<String, Object> properties = apiContext.getObjectMapper().readValue(datasetEntity.getProperties(), HashMap.class);
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datasetprofile.fromJsonObject(properties);
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}
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PagedDatasetProfile pagedDatasetProfile = new PagedDatasetProfile();
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@ -451,8 +445,7 @@ public class DatasetManager {
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Map<String, Object> properties = new HashMap<>();
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if (datasetEntity.getProperties() != null) {
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JSONObject jObject = new JSONObject(datasetEntity.getProperties());
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properties = jObject.toMap();
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properties = apiContext.getObjectMapper().readValue(datasetEntity.getProperties(), HashMap.class);
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}
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wordBuilder.addParagraphContent("Dataset Description", document, ParagraphStyle.HEADER2, BigInteger.ZERO);
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@ -484,8 +477,7 @@ public class DatasetManager {
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Map<String, Object> properties = new HashMap<>();
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if (dataset.getDatasetProfileDefinition() != null) {
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JSONObject jObject = new JSONObject(propertiesModelToString(dataset.getDatasetProfileDefinition()));
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properties = jObject.toMap();
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properties = apiContext.getObjectMapper().readValue(propertiesModelToString(dataset.getDatasetProfileDefinition()), HashMap.class);
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}
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wordBuilder.addParagraphContent("Dataset Description", document, ParagraphStyle.HEADER2, BigInteger.ZERO);
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@ -542,8 +534,7 @@ public class DatasetManager {
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throw new UnauthorisedException();
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Map<String, Object> properties = new HashMap<>();
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if (datasetEntity.getProperties() != null) {
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JSONObject jobject = new JSONObject(datasetEntity.getProperties());
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properties = jobject.toMap();
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properties = apiContext.getObjectMapper().readValue(datasetEntity.getProperties(), HashMap.class);
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}
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PagedDatasetProfile pagedDatasetProfile = getPagedProfile(dataset, datasetEntity);
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visibilityRuleService.setProperties(properties);
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@ -656,9 +647,9 @@ public class DatasetManager {
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nodeList = (NodeList) xPath.compile(expression).evaluate(xmlDocument, XPathConstants.NODESET);
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JSONObject obj = new JSONObject(dataset.getProperties());
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Map<String, Object> obj = apiContext.getObjectMapper().readValue(dataset.getProperties(), HashMap.class);
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VisibilityRuleService visibilityRuleService = this.apiContext.getUtilitiesService().getVisibilityRuleService();
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visibilityRuleService.setProperties(obj.toMap());
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visibilityRuleService.setProperties(obj);
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dataset.setProfile(profile);
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PagedDatasetProfile pagedDatasetProfile = this.getPagedProfile(new DatasetWizardModel(), dataset);
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@ -666,7 +657,7 @@ public class DatasetManager {
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for (String validator : datasetProfileValidators) {
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if ((obj.has(validator) && (obj.getString(validator) == null || obj.getString(validator).trim().isEmpty())) && isElementVisible(nodeList, validator, visibilityRuleService)) {
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if ((obj.containsKey(validator) && (obj.get(validator) == null || obj.get(validator).toString().trim().isEmpty())) && isElementVisible(nodeList, validator, visibilityRuleService)) {
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throw new Exception("Field value of " + validator + " must be filled.");
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}
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}
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@ -695,11 +686,10 @@ public class DatasetManager {
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}
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}
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private String propertiesModelToString(PagedDatasetProfile pagedDatasetProfile) {
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private String propertiesModelToString(PagedDatasetProfile pagedDatasetProfile) throws JsonProcessingException {
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Map<String, Object> values = new LinkedHashMap<>();
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pagedDatasetProfile.toMap(values);
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JSONObject jobject = new JSONObject(values);
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return jobject.toString();
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return apiContext.getObjectMapper().writeValueAsString(values);
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}
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public void updateTags(Dataset datasetEntity, List<Tag> tags) throws Exception {
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@ -908,12 +898,9 @@ public class DatasetManager {
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)))))
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.collect(Collectors.toMap(DatasetImportField::getId, DatasetImportField::getValue));
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// Transforms map into json file.
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JSONObject jsonDatasetProperties = new JSONObject(importMap);
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// Creates the entity data set to save.
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eu.eudat.data.entities.Dataset entity = new Dataset();
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entity.setProperties(jsonDatasetProperties.toString());
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entity.setProperties(apiContext.getObjectMapper().writeValueAsString(importMap));
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entity.setLabel(importFile.getOriginalFilename());
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DMP dmp = new DMP();
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dmp.setId(UUID.fromString(dmpId));
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@ -942,7 +929,7 @@ public class DatasetManager {
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// TODO: When tags functionality return.
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}
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public DatasetWizardModel datasetUpdateProfile(String id) {
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public DatasetWizardModel datasetUpdateProfile(String id) throws JsonProcessingException {
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DatasetWizardModel dataset = new DatasetWizardModel();
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eu.eudat.data.entities.Dataset datasetEntity = databaseRepository.getDatasetDao().find(UUID.fromString(id), HintedModelFactory.getHint(DatasetWizardModel.class));
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eu.eudat.elastic.entities.Dataset datasetElastic;
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@ -982,12 +969,11 @@ public class DatasetManager {
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return dataset;
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}
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public PagedDatasetProfile getLatestDatasetProfile(Dataset datasetEntity, DatasetProfile profile) {
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public PagedDatasetProfile getLatestDatasetProfile(Dataset datasetEntity, DatasetProfile profile) throws JsonProcessingException {
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eu.eudat.models.data.user.composite.DatasetProfile datasetprofile = userManager.generateDatasetProfileModel(profile);
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datasetprofile.setStatus(datasetEntity.getStatus());
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if (datasetEntity.getProperties() != null) {
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JSONObject jobject = new JSONObject(datasetEntity.getProperties());
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Map<String, Object> properties = jobject.toMap();
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Map<String, Object> properties = apiContext.getObjectMapper().readValue(datasetEntity.getProperties(), HashMap.class);
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datasetprofile.fromJsonObject(properties);
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}
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PagedDatasetProfile pagedDatasetProfile = new PagedDatasetProfile();
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@ -1039,9 +1025,8 @@ public class DatasetManager {
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public void getTagsFromProfile(DatasetWizardModel wizardModel, Dataset dataset) throws IOException {
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dataset.setProfile(apiContext.getOperationsContext().getDatabaseRepository().getDatasetProfileDao().find(dataset.getProfile().getId()));
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wizardModel.setDatasetProfileDefinition(this.getPagedProfile(wizardModel, dataset));
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ObjectMapper mapper = new ObjectMapper();
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String json = mapper.writeValueAsString(wizardModel.getDatasetProfileDefinition());
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JsonNode propertiesJson = mapper.readTree(json);
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String json = apiContext.getObjectMapper().writeValueAsString(wizardModel.getDatasetProfileDefinition());
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JsonNode propertiesJson = apiContext.getObjectMapper().readTree(json);
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DatasetCriteria criteria = new DatasetCriteria();
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criteria.setHasTags(true);
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List<Tag> tags = apiContext.getOperationsContext().getElasticRepository().getDatasetRepository().query(criteria).stream().map(eu.eudat.elastic.entities.Dataset::getTags).flatMap(Collection::stream).filter(StreamDistinctBy.distinctByKey(Tag::getId)).collect(Collectors.toList());
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@ -1053,11 +1038,20 @@ public class DatasetManager {
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JsonNode value = node.get("value");
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if (!value.toString().equals("\"\"")) {
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String stringValue = value.toString().replaceAll("=", ":");
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JSONArray values = new JSONArray(stringValue);
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values.iterator().forEachRemaining(element -> {
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Map<String, Object> data = ((JSONObject) element).toMap();
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this.addTag(tags, wizardModel.getTags(), data.get("id").toString(), data.get("name").toString());
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});
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List<Map<String, Object>> values = null;
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try {
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values = apiContext.getObjectMapper().readValue(stringValue, LinkedList.class);
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} catch (JsonProcessingException e) {
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logger.error(e.getLocalizedMessage(), e);
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}
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if (values != null) {
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values.iterator().forEachRemaining(element -> {
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Map<String, Object> data = element;
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this.addTag(tags, wizardModel.getTags(), data.get("id").toString(), data.get("name").toString());
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});
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} else {
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this.addTag(tags, wizardModel.getTags(), "", value.asText());
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}
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}
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});
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}
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George Kalampokis