DM-285: fix string NPE

redaction-service-v1/redaction-service-server-v1/src/main/java/com/iqser/red/service/redaction/v1/server/model/document/entity/IEntity.java

@@ -35,7 +35,7 @@ public interface IEntity {
 
     default String value() {
 
-        return getManualOverwrite().getValue().orElse(getValue());
+        return getManualOverwrite().getValue().orElse(getValue() == null ? "" : getValue());
     }
 
 

redaction-service-v1/redaction-service-server-v1/src/main/java/com/iqser/red/service/redaction/v1/server/service/DictionarySearchService.java

@@ -43,7 +43,7 @@ public class DictionarySearchService {
         EntityCreationService entityCreationService = new EntityCreationService(entityEnrichmentService);
         searchImplementation.getBoundaries(node.getTextBlock(), node.getTextRange())
                 .stream().filter(boundary -> entityCreationService.isValidEntityTextRange(node.getTextBlock(), boundary))
-                .map(bounds -> entityCreationService.forceByBoundary(bounds, type, entityType, node))
+                .map(bounds -> entityCreationService.forceByTextRange(bounds, type, entityType, node))
                 .peek(entity -> entity.setDictionaryEntry(true))
                 .peek(entity -> entity.setDossierDictionaryEntry(isDossierDictionaryEntry))
                 .forEach(entity -> entity.addEngine(Engine.DICTIONARY));

redaction-service-v1/redaction-service-server-v1/src/main/java/com/iqser/red/service/redaction/v1/server/service/EntityLogCreatorService.java

@@ -118,8 +118,7 @@ public class EntityLogCreatorService {
                 .id(manualEntity.getId())
                 .color(getColor(type, dossierTemplateId, manualEntity.applied()))
                 .reason(manualEntity.buildReasonWithManualChangeDescriptions())
-                .legalBasis(manualEntity.legalBasis())
+                .legalBasis(manualEntity.legalBasis()).value(manualEntity.value())
-                .value(manualEntity.getManualOverwrite().getValue().orElse(manualEntity.getValue()))
                 .type(type)
                 .state(buildEntryState(manualEntity))
                 .entryType(buildEntryType(manualEntity, isHint))
@@ -145,7 +144,7 @@ public class EntityLogCreatorService {
         String imageType = image.getImageType().equals(ImageType.OTHER) ? "image" : image.getImageType().toString().toLowerCase(Locale.ENGLISH);
         boolean isHint = dictionaryService.isHint(imageType, dossierTemplateId);
         return EntityLogEntry.builder()
-                .id(image.getId())
+                .id(image.getId()).value(image.value())
                 .color(getColor(imageType, dossierTemplateId, image.applied()))
                 .type(imageType)
                 .reason(image.buildReasonWithManualChangeDescriptions())

redaction-service-v1/redaction-service-server-v1/src/main/java/com/iqser/red/service/redaction/v1/server/service/document/EntityCreationService.java

@@ -529,7 +529,7 @@ public class EntityCreationService {
     }
 
 
-    public TextEntity forceByBoundary(TextRange textRange, String type, EntityType entityType, SemanticNode node) {
+    public TextEntity forceByTextRange(TextRange textRange, String type, EntityType entityType, SemanticNode node) {
 
         TextRange trimmedTextRange = textRange.trim(node.getTextBlock());
         TextEntity entity = TextEntity.initialEntityNode(trimmedTextRange, type, entityType);
@@ -598,7 +598,7 @@ public class EntityCreationService {
 
     public TextEntity byNerEntity(NerEntities.NerEntity nerEntity, EntityType entityType, SemanticNode semanticNode) {
 
-        var entity = forceByBoundary(nerEntity.textRange(), nerEntity.type(), entityType, semanticNode);
+        var entity = forceByTextRange(nerEntity.textRange(), nerEntity.type(), entityType, semanticNode);
         entity.addEngine(Engine.NER);
         insertToKieSession(entity);
         return entity;
@@ -607,7 +607,7 @@ public class EntityCreationService {
 
     public TextEntity byNerEntity(NerEntities.NerEntity nerEntity, String type, EntityType entityType, SemanticNode semanticNode) {
 
-        var entity = forceByBoundary(nerEntity.textRange(), type, entityType, semanticNode);
+        var entity = forceByTextRange(nerEntity.textRange(), type, entityType, semanticNode);
         entity.addEngine(Engine.NER);
         insertToKieSession(entity);
         return entity;
@@ -616,8 +616,7 @@ public class EntityCreationService {
 
     public Stream<TextEntity> combineNerEntitiesToCbiAddressDefaults(NerEntities nerEntities, String type, EntityType entityType, SemanticNode semanticNode) {
 
-        return NerEntitiesAdapter.combineNerEntitiesToCbiAddressDefaults(nerEntities)
+        return NerEntitiesAdapter.combineNerEntitiesToCbiAddressDefaults(nerEntities).map(boundary -> forceByTextRange(boundary, type, entityType, semanticNode))
-                .map(boundary -> forceByBoundary(boundary, type, entityType, semanticNode))
                 .peek(entity -> entity.addEngine(Engine.NER))
                 .peek(this::insertToKieSession);
     }

redaction-service-v1/redaction-service-server-v1/src/main/java/com/iqser/red/service/redaction/v1/server/service/document/ManualEntityCreationService.java

@@ -95,7 +95,7 @@ public class ManualEntityCreationService {
      */
     private void createCorrectEntity(ManualEntity manualEntity, SemanticNode node, TextRange closestTextRange) {
 
-        TextEntity correctEntity = entityCreationService.forceByBoundary(closestTextRange, manualEntity.getType(), manualEntity.getEntityType(), node);
+        TextEntity correctEntity = entityCreationService.forceByTextRange(closestTextRange, manualEntity.getType(), manualEntity.getEntityType(), node);
 
         if (manualEntity.isApplied()) {
             correctEntity.apply(manualEntity.getRuleIdentifier(), manualEntity.getReason(), manualEntity.getLegalBasis());
@@ -166,8 +166,7 @@ public class ManualEntityCreationService {
         SearchImplementation searchImplementation = new SearchImplementation(entryValues, true);
 
         return searchImplementation.getBoundaries(node.getTextBlock(), node.getTextRange())
-                .stream()
+                .stream().map(boundary -> entityCreationService.forceByTextRange(boundary, "temp", EntityType.ENTITY, node))
-                .map(boundary -> entityCreationService.forceByBoundary(boundary, "temp", EntityType.ENTITY, node))
                 .collect(groupingBy(entity -> entity.getValue().toLowerCase(Locale.ROOT)));
     }
 

redaction-service-v1/redaction-service-server-v1/src/test/java/com/iqser/red/service/redaction/v1/server/DocumineFloraTest.java

@@ -104,7 +104,7 @@ public class DocumineFloraTest extends AbstractRedactionIntegrationTest {
         // Fix In BodyTextFrameService destroys header detection in files/new/SYNGENTA_EFSA_sanitisation_GFL_v1_moreSections.pdf
         // TODO unify logic
 
-        AnalyzeRequest request = uploadFileToStorage("files/Documine/Flora/ProblemDocs/SOLICITA_VICTRATO-GOLD-II_Item 15_Toxicidade Oral Aguda.pdf");
+        AnalyzeRequest request = uploadFileToStorage("files/Documine/Flora/402Study.pdf");
 
         System.out.println("Start Full integration test");
         analyzeDocumentStructure(LayoutParsingType.DOCUMINE, request);

redaction-service-v1/redaction-service-server-v1/src/test/java/com/iqser/red/service/redaction/v1/server/RedactionIntegrationTest.java

@@ -4,7 +4,6 @@ import static org.assertj.core.api.Assertions.assertThat;
 import static org.junit.jupiter.api.Assertions.assertEquals;
 import static org.mockito.ArgumentMatchers.anyLong;
 import static org.mockito.ArgumentMatchers.anyString;
-import static org.mockito.Mockito.doThrow;
 import static org.mockito.Mockito.when;
 
 import java.io.FileOutputStream;
@@ -68,7 +67,6 @@ import com.iqser.red.service.redaction.v1.server.model.document.nodes.Section;
 import com.iqser.red.service.redaction.v1.server.redaction.utils.OsUtils;
 import com.iqser.red.service.redaction.v1.server.service.document.DocumentGraphMapper;
 import com.iqser.red.service.redaction.v1.server.storage.RedactionStorageService;
-import com.iqser.red.service.redaction.v1.server.utils.ExceptionProvider;
 import com.iqser.red.storage.commons.StorageAutoConfiguration;
 import com.iqser.red.storage.commons.service.StorageService;
 import com.knecon.fforesight.service.layoutparser.internal.api.queue.LayoutParsingType;
@@ -215,7 +213,7 @@ public class RedactionIntegrationTest extends AbstractRedactionIntegrationTest {
     @Test
     public void titleExtraction() throws IOException {
 
-        AnalyzeRequest request = uploadFileToStorage("files/Metolachlor/S-Metolachlor_RAR_01_Volume_1_2018-09-06.pdf");
+        AnalyzeRequest request = uploadFileToStorage("files/new/crafted document.pdf");
         System.out.println("Start Full integration test");
         analyzeDocumentStructure(LayoutParsingType.REDACT_MANAGER, request);
         System.out.println("Finished structure analysis");
@@ -591,6 +589,11 @@ public class RedactionIntegrationTest extends AbstractRedactionIntegrationTest {
     }
 
 
+    public void testRedactionLogAndEntityLogEquality() {
+
+    }
+
+
     @Test
     public void testRemovePublishedInformations() throws IOException {
 

redaction-service-v1/redaction-service-server-v1/src/test/java/com/iqser/red/service/redaction/v1/server/manualchanges/ManualChangesEnd2EndTest.java

@@ -2,7 +2,6 @@ package com.iqser.red.service.redaction.v1.server.manualchanges;
 
 import static org.junit.jupiter.api.Assertions.assertEquals;
 import static org.junit.jupiter.api.Assertions.assertFalse;
-import static org.mockito.Mockito.doThrow;
 import static org.mockito.Mockito.when;
 import static org.wildfly.common.Assert.assertTrue;
 
@@ -16,6 +15,9 @@ import java.util.Comparator;
 import java.util.List;
 import java.util.Set;
 import java.util.UUID;
+import java.util.function.Function;
+import java.util.stream.Collectors;
+import java.util.stream.Stream;
 
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
@@ -41,8 +43,8 @@ import com.iqser.red.service.persistence.service.v1.api.shared.model.annotations
 import com.iqser.red.service.persistence.service.v1.api.shared.model.annotations.Rectangle;
 import com.iqser.red.service.persistence.service.v1.api.shared.model.annotations.entitymapped.IdRemoval;
 import com.iqser.red.service.persistence.service.v1.api.shared.model.annotations.entitymapped.ManualForceRedaction;
-import com.iqser.red.service.persistence.service.v1.api.shared.model.annotations.entitymapped.ManualRecategorization;
 import com.iqser.red.service.persistence.service.v1.api.shared.model.annotations.entitymapped.ManualLegalBasisChange;
+import com.iqser.red.service.persistence.service.v1.api.shared.model.annotations.entitymapped.ManualRecategorization;
 import com.iqser.red.service.persistence.service.v1.api.shared.model.annotations.entitymapped.ManualRedactionEntry;
 import com.iqser.red.service.persistence.service.v1.api.shared.model.annotations.entitymapped.ManualResizeRedaction;
 import com.iqser.red.service.persistence.service.v1.api.shared.model.common.JSONPrimitive;
@@ -55,14 +57,13 @@ import com.iqser.red.service.redaction.v1.server.Application;
 import com.iqser.red.service.redaction.v1.server.FileSystemBackedStorageService;
 import com.iqser.red.service.redaction.v1.server.annotate.AnnotateRequest;
 import com.iqser.red.service.redaction.v1.server.annotate.AnnotateResponse;
-import com.iqser.red.service.redaction.v1.server.service.document.DocumentGraphMapper;
 import com.iqser.red.service.redaction.v1.server.model.document.entity.EntityType;
 import com.iqser.red.service.redaction.v1.server.model.document.entity.TextEntity;
 import com.iqser.red.service.redaction.v1.server.model.document.nodes.Document;
+import com.iqser.red.service.redaction.v1.server.redaction.utils.OsUtils;
+import com.iqser.red.service.redaction.v1.server.service.document.DocumentGraphMapper;
 import com.iqser.red.service.redaction.v1.server.service.document.EntityCreationService;
 import com.iqser.red.service.redaction.v1.server.service.document.EntityEnrichmentService;
-import com.iqser.red.service.redaction.v1.server.redaction.utils.OsUtils;
-import com.iqser.red.service.redaction.v1.server.utils.ExceptionProvider;
 import com.iqser.red.storage.commons.StorageAutoConfiguration;
 import com.iqser.red.storage.commons.service.StorageService;
 import com.knecon.fforesight.service.layoutparser.internal.api.queue.LayoutParsingType;
@@ -114,7 +115,6 @@ public class ManualChangesEnd2EndTest extends AbstractRedactionIntegrationTest {
         when(rulesClient.getRules(TEST_DOSSIER_TEMPLATE_ID, RuleFileType.ENTITY)).thenReturn(JSONPrimitive.of(RULES));
         when(rulesClient.getVersion(TEST_DOSSIER_TEMPLATE_ID, RuleFileType.COMPONENT)).thenReturn(-1L);
 
-
         loadDictionaryForTest();
         loadTypeForTest();
         loadNerForTest();
@@ -296,6 +296,18 @@ public class ManualChangesEnd2EndTest extends AbstractRedactionIntegrationTest {
                 .findFirst()
                 .get();
 
+        var mouses = redactionLog.getRedactionLogEntry().stream().filter(entry -> entry.getType().equals("vertebrate")).filter(entry -> entry.getValue().equals("Mouse")).toList();
+
+        var recategorizations = mouses.stream()
+                .map(mouse -> ManualRecategorization.builder()
+                        .requestDate(OffsetDateTime.now())
+                        .status(AnnotationStatus.APPROVED)
+                        .type("published_information")
+                        .annotationId(mouse.getId())
+                        .fileId(TEST_FILE_ID)
+                        .build())
+                .toList();
+
         assertEquals("CBI.3.2", asyaLyon.getMatchedRule());
         assertEquals("No vertebrate found", asyaLyon.getReason());
 
@@ -308,7 +320,8 @@ public class ManualChangesEnd2EndTest extends AbstractRedactionIntegrationTest {
                 .build();
 
         request.setManualRedactions(new ManualRedactions());
-        request.getManualRedactions().setRecategorizations(Set.of(recategorization));
+        request.getManualRedactions()
+                .setRecategorizations(Stream.of(Stream.of(recategorization), recategorizations.stream()).flatMap(Function.identity()).collect(Collectors.toSet()));
 
         analyzeService.reanalyze(request);
         RedactionLog redactionLog2 = redactionStorageService.getRedactionLog(TEST_DOSSIER_ID, TEST_FILE_ID);
@@ -324,6 +337,10 @@ public class ManualChangesEnd2EndTest extends AbstractRedactionIntegrationTest {
                 .findFirst()
                 .get();
 
+        for (RedactionLogEntry mouse : mouses) {
+            assertEquals("published_information", redactionLog2.getRedactionLogEntry().stream().filter(entry -> entry.getId().equals(mouse.getId())).findFirst().get().getType());
+        }
+
         assertEquals(1, oxfordUniversityPressRecategorized.getManualChanges().size());
     }