Merge branch 'Development' of https://code-repo.d4science.org/MaDgiK-CITE/argos into Development

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

@@ -15,6 +15,7 @@ import eu.eudat.logic.proxy.config.configloaders.ConfigLoader;
 import eu.eudat.logic.security.claims.ClaimedAuthorities;
 import eu.eudat.logic.services.ApiContext;
 import eu.eudat.logic.services.forms.VisibilityRuleService;
+import eu.eudat.logic.services.forms.VisibilityRuleServiceImpl;
 import eu.eudat.logic.utilities.documents.helpers.FileEnvelope;
 import eu.eudat.logic.utilities.documents.pdf.PDFUtils;
 import eu.eudat.models.data.dataset.DatasetOverviewModel;
@@ -126,11 +127,11 @@ public class Datasets extends BaseController {
     public @ResponseBody
     ResponseEntity getSingle(@PathVariable String id, @RequestHeader("Content-Type") String contentType, @ClaimedAuthorities(claims = {Authorities.ADMIN, Authorities.MANAGER, Authorities.USER, Authorities.ANONYMOUS}) Principal principal) throws IllegalAccessException, IOException, InstantiationException {
         try {
+            VisibilityRuleService visibilityRuleService = new VisibilityRuleServiceImpl();
             if (contentType.equals("application/xml")) {
-                VisibilityRuleService visibilityRuleService = this.getApiContext().getUtilitiesService().getVisibilityRuleService();
                 return this.datasetManager.getDocument(id, visibilityRuleService, contentType, principal);
             } else if (contentType.equals("application/msword")) {
-                FileEnvelope file = datasetManager.getWordDocumentFile(this.configLoader, id, this.getApiContext().getUtilitiesService().getVisibilityRuleService(), principal);
+                FileEnvelope file = datasetManager.getWordDocumentFile(this.configLoader, id, visibilityRuleService, principal);
                 InputStream resource = new FileInputStream(file.getFile());
                 HttpHeaders responseHeaders = new HttpHeaders();
                 responseHeaders.setContentLength(file.getFile().length());
@@ -218,7 +219,7 @@ public class Datasets extends BaseController {
     @RequestMapping(method = RequestMethod.GET, value = {"/getPDF/{id}"})
     public @ResponseBody
     ResponseEntity<byte[]> getPDFDocument(@PathVariable String id, @ClaimedAuthorities(claims = {Authorities.ADMIN, Authorities.MANAGER, Authorities.USER, Authorities.ANONYMOUS}) Principal principal) throws IllegalAccessException, IOException, InstantiationException, InterruptedException {
-        FileEnvelope file = datasetManager.getWordDocumentFile(this.configLoader, id, this.getApiContext().getUtilitiesService().getVisibilityRuleService(), principal);
+        FileEnvelope file = datasetManager.getWordDocumentFile(this.configLoader, id, new VisibilityRuleServiceImpl(), principal);
         String fileName = file.getFilename().replace(" ", "_").replace(",", "_");
         if (fileName.endsWith(".docx")){
             fileName = fileName.substring(0, fileName.length() - 5);

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

@@ -1,7 +1,5 @@
 package eu.eudat.logic.managers;
 
-import com.fasterxml.jackson.core.JsonParser;
-import com.fasterxml.jackson.databind.JsonNode;
 import com.fasterxml.jackson.databind.ObjectMapper;
 import eu.eudat.configurations.dynamicgrant.DynamicGrantConfiguration;
 import eu.eudat.configurations.dynamicgrant.entities.Property;
@@ -33,6 +31,7 @@ import eu.eudat.logic.mapper.elastic.criteria.DmpCriteriaMapper;
 import eu.eudat.logic.proxy.config.configloaders.ConfigLoader;
 import eu.eudat.logic.services.ApiContext;
 import eu.eudat.logic.services.forms.VisibilityRuleService;
+import eu.eudat.logic.services.forms.VisibilityRuleServiceImpl;
 import eu.eudat.logic.services.operations.DatabaseRepository;
 import eu.eudat.logic.services.utilities.UtilitiesService;
 import eu.eudat.logic.utilities.builders.XmlBuilder;
@@ -106,7 +105,6 @@ public class DataManagementPlanManager {
 
     private ApiContext apiContext;
     private DatasetManager datasetManager;
-    private UtilitiesService utilitiesService;
     private DatabaseRepository databaseRepository;
     private Environment environment;
     private RDAManager rdaManager;
@@ -117,7 +115,6 @@ public class DataManagementPlanManager {
     public DataManagementPlanManager(ApiContext apiContext, DatasetManager datasetManager, Environment environment, RDAManager rdaManager, UserManager userManager, MetricsManager metricsManager) {
         this.apiContext = apiContext;
         this.datasetManager = datasetManager;
-        this.utilitiesService = apiContext.getUtilitiesService();
         this.databaseRepository = apiContext.getOperationsContext().getDatabaseRepository();
         this.environment = environment;
         this.rdaManager = rdaManager;
@@ -1172,7 +1169,7 @@ public class DataManagementPlanManager {
 
     public FileEnvelope getWordDocument(String id, Principal principal, ConfigLoader configLoader, Boolean versioned) throws IOException {
         WordBuilder wordBuilder = new WordBuilder();
-        VisibilityRuleService visibilityRuleService = this.utilitiesService.getVisibilityRuleService();
+        VisibilityRuleService visibilityRuleService = new VisibilityRuleServiceImpl();
         DatasetWizardModel dataset = new DatasetWizardModel();
         XWPFDocument document = configLoader.getDocument();
 
@@ -1341,7 +1338,7 @@ public class DataManagementPlanManager {
 
     private FileEnvelope getXmlDocument(String id, Principal principal) throws InstantiationException, IllegalAccessException, IOException {
         ExportXmlBuilder xmlBuilder = new ExportXmlBuilder();
-        VisibilityRuleService visibilityRuleService = utilitiesService.getVisibilityRuleService();
+        VisibilityRuleService visibilityRuleService = new VisibilityRuleServiceImpl();
         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)
             throw new UnauthorisedException();

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

@@ -26,6 +26,7 @@ import eu.eudat.logic.mapper.elastic.criteria.DmpCriteriaMapper;
 import eu.eudat.logic.proxy.config.configloaders.ConfigLoader;
 import eu.eudat.logic.services.ApiContext;
 import eu.eudat.logic.services.forms.VisibilityRuleService;
+import eu.eudat.logic.services.forms.VisibilityRuleServiceImpl;
 import eu.eudat.logic.services.operations.DatabaseRepository;
 import eu.eudat.logic.utilities.documents.helpers.FileEnvelope;
 import eu.eudat.logic.utilities.documents.types.ParagraphStyle;
@@ -49,7 +50,6 @@ import eu.eudat.models.data.user.composite.PagedDatasetProfile;
 import eu.eudat.queryable.QueryableList;
 import eu.eudat.types.Authorities;
 import eu.eudat.types.MetricNames;
-import org.apache.commons.io.IOUtils;
 import org.apache.poi.xwpf.extractor.XWPFWordExtractor;
 import org.apache.poi.xwpf.usermodel.XWPFDocument;
 import org.apache.poi.xwpf.usermodel.XWPFParagraph;
@@ -60,11 +60,11 @@ 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;
+import org.springframework.http.HttpHeaders;
-import org.springframework.http.*;
+import org.springframework.http.HttpStatus;
+import org.springframework.http.MediaType;
+import org.springframework.http.ResponseEntity;
 import org.springframework.stereotype.Component;
-import org.springframework.util.LinkedMultiValueMap;
-import org.springframework.web.client.RestTemplate;
 import org.springframework.web.multipart.MultipartFile;
 import org.w3c.dom.Document;
 import org.w3c.dom.Element;
@@ -91,8 +91,6 @@ import java.time.temporal.ChronoUnit;
 import java.util.*;
 import java.util.stream.Collectors;
 import java.util.stream.Stream;
-import java.util.zip.ZipEntry;
-import java.util.zip.ZipInputStream;
 
 @Component
 public class DatasetManager {
@@ -527,7 +525,7 @@ public class DatasetManager {
     public String getWordDocumentText (Dataset datasetEntity) throws Exception {
         DatasetWizardModel datasetWizardModel = new DatasetWizardModel().fromDataModel(datasetEntity);
         datasetWizardModel.setDatasetProfileDefinition(this.getPagedProfile(datasetWizardModel, datasetEntity));
-        XWPFDocument document = getLightWordDocument(this.configLoader, datasetWizardModel, this.apiContext.getUtilitiesService().getVisibilityRuleService());
+        XWPFDocument document = getLightWordDocument(this.configLoader, datasetWizardModel, new VisibilityRuleServiceImpl());
         XWPFWordExtractor extractor = new XWPFWordExtractor(document);
         return extractor.getText();/*.replaceAll("\n\\s*", " ");*/
     }
@@ -657,7 +655,7 @@ public class DatasetManager {
 
 
         JSONObject obj = new JSONObject(dataset.getProperties());
-        VisibilityRuleService visibilityRuleService = this.apiContext.getUtilitiesService().getVisibilityRuleService();
+        VisibilityRuleService visibilityRuleService = new VisibilityRuleServiceImpl();
         visibilityRuleService.setProperties(obj.toMap());
 
         dataset.setProfile(profile);
@@ -666,12 +664,16 @@ public class DatasetManager {
 
 
         for (String validator : datasetProfileValidators) {
-            if ((obj.has(validator) && (obj.getString(validator) == null || obj.getString(validator).trim().isEmpty())) && isElementVisible(nodeList, validator, visibilityRuleService)) {
+            if (obj.has(validator) && isNullOrEmpty(obj.getString(validator)) && isElementVisible(nodeList, validator, visibilityRuleService)) {
                 throw new Exception("Field value of " + validator + " must be filled.");
             }
         }
     }
 
+    private boolean isNullOrEmpty(String value) {
+        return value == null || value.trim().isEmpty();
+    }
+
     private boolean isElementVisible(NodeList nodeList, String id, VisibilityRuleService visibilityRuleService) {
         Element fieldSet = null;
         for (int i = 0; i < nodeList.getLength(); i++) {

dmp-backend/web/src/main/java/eu/eudat/logic/services/forms/VisibilityRuleServiceImpl.java

@@ -1,30 +1,26 @@
 package eu.eudat.logic.services.forms;
 
 import eu.eudat.models.data.user.components.commons.Rule;
-import org.springframework.stereotype.Service;
 
 import java.util.*;
 
 /**
  * Created by ikalyvas on 3/5/2018.
  */
-@Service("visibilityRuleService")
 public class VisibilityRuleServiceImpl implements VisibilityRuleService {
-    private Map<String, Boolean> elementVisibility = new HashMap<>();
+    private final Map<String, Boolean> elementVisibility = new HashMap<>();
-    private VisibilityContext visibilityContext;
     private Map<String, Object> properties;
 
     public boolean isElementVisible(String id) {
-        if (!this.elementVisibility.containsKey(id) || this.elementVisibility.get(id)) return true;
+        return !this.elementVisibility.containsKey(id) || this.elementVisibility.get(id);
-        return false;
     }
 
     public void setProperties(Map<String, Object> properties) {
         this.properties = properties;
         this.properties.entrySet().stream()
-                .filter(stringObjectEntry -> stringObjectEntry.getValue() instanceof String && ((String) stringObjectEntry.getValue()).startsWith("[") && ((String) stringObjectEntry.getValue()).endsWith("]")).forEach(stringObjectEntry -> {
+                .filter(stringObjectEntry -> stringObjectEntry.getValue() instanceof String && ((String) stringObjectEntry.getValue()).startsWith("[")
-            stringObjectEntry.setValue(parseArray((String) stringObjectEntry.getValue()));
+                        && ((String) stringObjectEntry.getValue()).endsWith("]"))
-        });
+                .forEach(stringObjectEntry -> stringObjectEntry.setValue(parseArray((String) stringObjectEntry.getValue())));
     }
 
     private List<String> parseArray(String original) {
@@ -33,22 +29,20 @@ public class VisibilityRuleServiceImpl implements VisibilityRuleService {
     }
 
     public void buildVisibilityContext(List<Rule> sources) {
-        this.visibilityContext = new VisibilityContext();
+        VisibilityContext visibilityContext = new VisibilityContext();
-        this.visibilityContext.buildVisibilityContext(sources);
+        visibilityContext.buildVisibilityContext(sources);
-        this.visibilityContext.getVisibilityRules().forEach(item-> this.evaluateVisibility(item));
+        visibilityContext.getVisibilityRules().forEach(this::evaluateVisibility);
     }
 
     private void evaluateVisibility(VisibilityRule rule) {
         List<VisibilityRuleSource> sources = rule.getVisibilityRuleSources();
-        for(int i = 0; i < sources.size(); i++){
+        for(VisibilityRuleSource source: sources){
-            if (properties.containsKey(sources.get(i).getVisibilityRuleSourceId()) && (isContained(properties.get(sources.get(i).getVisibilityRuleSourceId()), sources.get(i).getVisibilityRuleSourceValue()) || properties.get(sources.get(i).getVisibilityRuleSourceId()).equals(sources.get(i).getVisibilityRuleSourceValue()))) {
+            if (properties.containsKey(source.getVisibilityRuleSourceId())
+                    && isContained(properties.get(source.getVisibilityRuleSourceId()), source.getVisibilityRuleSourceValue())) {
                 this.elementVisibility.put(rule.getVisibilityRuleTargetId(), true);
             } else {
-                if (this.elementVisibility.containsKey(rule.getVisibilityRuleTargetId())) {
+                this.elementVisibility.put(rule.getVisibilityRuleTargetId(),
-                    this.elementVisibility.put(rule.getVisibilityRuleTargetId(), this.elementVisibility.get(rule.getVisibilityRuleTargetId()) || false);
+                        this.elementVisibility.getOrDefault(rule.getVisibilityRuleTargetId(), false));
-                } else {
-                    this.elementVisibility.put(rule.getVisibilityRuleTargetId(), false);
-                }
             }
         }
     }
@@ -56,7 +50,8 @@ public class VisibilityRuleServiceImpl implements VisibilityRuleService {
     private Boolean isContained(Object values, String source) {
         if (values instanceof List) {
             return ((Collection<?>) values).contains(source);
+        } else {
+            return values.equals(source);
         }
-        return false;
     }
 }

dmp-backend/web/src/main/java/eu/eudat/logic/services/utilities/UtilitiesService.java

@@ -11,7 +11,5 @@ public interface UtilitiesService {
 
     MailService getMailService();
 
-    VisibilityRuleService getVisibilityRuleService();
-
     ConfirmationEmailService getConfirmationEmailService();
 }

dmp-backend/web/src/main/java/eu/eudat/logic/services/utilities/UtilitiesServiceImpl.java

@@ -1,6 +1,7 @@
 package eu.eudat.logic.services.utilities;
 
 import eu.eudat.logic.services.forms.VisibilityRuleService;
+import eu.eudat.logic.services.forms.VisibilityRuleServiceImpl;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Service;
 
@@ -12,22 +13,15 @@ public class UtilitiesServiceImpl implements UtilitiesService {
 
     private InvitationService invitationService;
     private MailService mailService;
-    private VisibilityRuleService visibilityRuleService;
     private ConfirmationEmailService confirmationEmailService;
 
     @Autowired
-    public UtilitiesServiceImpl(InvitationService invitationService, MailService mailService, VisibilityRuleService visibilityRuleService, ConfirmationEmailService confirmationEmailService) {
+    public UtilitiesServiceImpl(InvitationService invitationService, MailService mailService, ConfirmationEmailService confirmationEmailService) {
         this.invitationService = invitationService;
         this.mailService = mailService;
-        this.visibilityRuleService = visibilityRuleService;
         this.confirmationEmailService = confirmationEmailService;
     }
 
-    @Override
-    public VisibilityRuleService getVisibilityRuleService() {
-        return visibilityRuleService;
-    }
-
     @Override
     public ConfirmationEmailService getConfirmationEmailService() {
         return confirmationEmailService;

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

@@ -27,7 +27,9 @@ import java.io.IOException;
 import java.math.BigInteger;
 import java.text.SimpleDateFormat;
 import java.time.Instant;
+import java.time.LocalDate;
 import java.time.ZoneId;
+import java.time.ZoneOffset;
 import java.time.format.DateTimeFormatter;
 import java.time.format.DateTimeParseException;
 import java.time.temporal.TemporalAccessor;
@@ -397,7 +399,7 @@ public class WordBuilder {
                     try {
                         instant = Instant.parse((String) field.getValue());
                     } catch (DateTimeParseException ex) {
-                        instant = Instant.from(DateTimeFormatter.ofPattern("yyyy-MM-dd").withZone(ZoneId.systemDefault()).parse((String) field.getValue()));
+                        instant = LocalDate.parse((String) field.getValue()).atStartOfDay().toInstant(ZoneOffset.UTC);
                     }
                     return field.getValue() != null ? DateTimeFormatter.ofPattern("yyyy-MM-dd").withZone(ZoneId.systemDefault()).format(instant) : "";
                 }

dmp-frontend/src/app/library/rich-text-editor/rich-text-editor.component.scss

@@ -9,6 +9,7 @@
 //}
 
 .editor-wrapper {
+	position: relative;
 	border: 1px solid transparent !important;
 	border-radius: 5px;
 }
@@ -40,6 +41,14 @@
 	border: 1px solid #f44336 !important;
 }
 
+.clear {
+	position: absolute;
+	right: 5px;
+	bottom: 5px;
+	transform: translate(-50%, -50%);
+	cursor: pointer;
+}
+
 .full-width {
 	width: 100%;
 }

dmp-frontend/src/app/library/rich-text-editor/rich-text-editor.component.ts

@@ -1,5 +1,6 @@
 import {Component, Input} from "@angular/core";
 import {AngularEditorConfig} from "@kolkov/angular-editor";
+import {FormControl} from "@angular/forms";
 
 @Component({
 	selector: 'rich-text-editor-component',
@@ -7,6 +8,7 @@ import {AngularEditorConfig} from "@kolkov/angular-editor";
 		<div class="editor-wrapper" [class]="wrapperClasses" [formGroup]="parentFormGroup">
 			<angular-editor class="full-width editor" [id]="id" [config]="editorConfig" [formControlName]="controlName"
 							placeholder="{{(placeholder? (placeholder | translate) : '') + (required ? ' *': '')}}"></angular-editor>
+			<mat-icon *ngIf="formInput.value" (click)="formInput.patchValue('')" class="clear">close</mat-icon>
 		</div>
 	`,
 	styleUrls: ['./rich-text-editor.component.scss']
@@ -53,6 +55,7 @@ export class RichTextEditorComponent {
 		]
 	};
 
-	constructor() {
+	get formInput(): FormControl {
+		return this.parentFormGroup.get(this.controlName);
 	}
 }