Pull request #228: RED-2276: Fixed sonar bug findings

Merge in RED/redaction-service from RED-2276 to master

* commit '34daa4c22c3b5c8692f2f5f3056a633f9ec09649':
  RED-2276: Fixed sonar bug findings

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

@@ -1,5 +1,7 @@
 package com.iqser.red.service.redaction.v1.server.redaction.model;
 
+import static java.util.stream.Collectors.toSet;
+
 import lombok.Data;
 import lombok.Getter;
 
@@ -8,6 +10,8 @@ import java.util.List;
 import java.util.Map;
 import java.util.Set;
 
+import com.iqser.red.service.persistence.service.v1.api.model.data.configuration.DictionaryEntry;
+
 @Data
 public class Dictionary {
 
@@ -61,11 +65,11 @@ public class Dictionary {
     public boolean containsValue(String type, String value) {
 
         return localAccessMap.containsKey(type) && localAccessMap.get(type)
-                .getEntries()
+                .getEntries().stream().map(DictionaryEntry::getValue).collect(toSet())
                 .contains(value) || localAccessMap.containsKey(type) && localAccessMap.get(type)
                 .getLocalEntries()
                 .contains(value) || localAccessMap.containsKey(RECOMMENDATION_PREFIX + type) && localAccessMap.get(RECOMMENDATION_PREFIX + type)
-                .getEntries()
+                .getEntries().stream().map(DictionaryEntry::getValue).collect(toSet())
                 .contains(value) || localAccessMap.containsKey(RECOMMENDATION_PREFIX + type) && localAccessMap.get(RECOMMENDATION_PREFIX + type)
                 .getLocalEntries()
                 .contains(value);

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

@@ -89,7 +89,7 @@ public class EntityRedactionService {
                     String imageId = IdBuilder.buildId(image.getPosition(), image.getPage());
                     for (ManualImageRecategorization imageRecategorization : analyzeRequest.getManualRedactions()
                             .getImageRecategorization()) {
-                        if (imageRecategorization.getStatus().equals(AnnotationStatus.APPROVED) && imageRecategorization.getId()
+                        if (imageRecategorization.getStatus().equals(AnnotationStatus.APPROVED) && imageRecategorization.getId().getId()
                                 .equals(imageId)) {
                             image.setType(imageRecategorization.getType());
                         }

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

@@ -240,7 +240,7 @@ public class RedactionLogMergeService {
                 RedactionLogEntry redactionLogEntry = createRedactionLogEntry(manualRedactionEntry, manualRedactionEntry
                         .getId().getId(), dossierTemplateId);
                 redactionLogEntry.setPositions(convertPositions(manualRedactionEntry.getPositions()));
-                redactionLogEntry.setComments(comments.get(manualRedactionEntry.getId()));
+                redactionLogEntry.setComments(comments.get(manualRedactionEntry.getId().getId()));
                 redactionLogEntries.add(redactionLogEntry);
             }
         }

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

@@ -140,7 +140,12 @@ public class EntitySearchUtils {
     public void addEntitiesWithHigherRank(Set<Entity> entities, Entity found, Dictionary dictionary) {
 
         if (entities.contains(found)) {
-            Entity existing = entities.stream().filter(entity -> entity.equals(found)).findFirst().get();
+            Optional<Entity> existingOptional = entities.stream().filter(entity -> entity.equals(found)).findFirst();
+            if(!existingOptional.isPresent()){
+                return;
+            }
+            var existing = existingOptional.get();
+
             if (dictionary.getDictionaryRank(existing.getType()) <= dictionary.getDictionaryRank(found.getType())) {
                 entities.remove(found);
                 entities.add(found);
@@ -164,7 +169,11 @@ public class EntitySearchUtils {
 
         for(Entity toAdd: toBeAdded){
             if (existing.contains(toAdd)) {
-                Entity existingEntity = existing.stream().filter(entity -> entity.equals(toAdd)).findFirst().get();
+                Optional<Entity> existingOptional  = existing.stream().filter(entity -> entity.equals(toAdd)).findFirst();
+                if(!existingOptional.isPresent()){
+                    return;
+                }
+                var existingEntity = existingOptional.get();
                 existingEntity.getEngines().addAll(toAdd.getEngines());
             } else {
                 existing.add(toAdd);

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

@@ -60,76 +60,80 @@ public class PdfSegmentationService {
         try {
             //create tempFile
             File tempFile = File.createTempFile("document", ".pdf");
-            IOUtils.copy(documentInputStream, new FileOutputStream(tempFile));
+            try (var fos = new FileOutputStream(tempFile)) {
+                IOUtils.copy(documentInputStream, fos);
 
-            // initialize required variables
+                // initialize required variables
-            Document document = new Document();
+                Document document = new Document();
-            List<Page> pages = new ArrayList<>();
+                List<Page> pages = new ArrayList<>();
 
-            pdDocument = reinitializePDDocument(tempFile, null);
+                pdDocument = reinitializePDDocument(tempFile, null);
-            long pageCount = pdDocument.getNumberOfPages();
+                long pageCount = pdDocument.getNumberOfPages();
 
-            for (int pageNumber = 1; pageNumber <= pageCount; pageNumber++) {
+                for (int pageNumber = 1; pageNumber <= pageCount; pageNumber++) {
 
-                if (pageNumber % MAX_PAGES_BEFORE_GC == 0) {
+                    if (pageNumber % MAX_PAGES_BEFORE_GC == 0) {
-                    pdDocument = reinitializePDDocument(tempFile, pdDocument);
+                        pdDocument = reinitializePDDocument(tempFile, pdDocument);
+                    }
+
+                    PDFLinesTextStripper stripper = new PDFLinesTextStripper();
+                    PDPage pdPage = pdDocument.getPage(pageNumber - 1);
+                    stripper.setPageNumber(pageNumber);
+                    stripper.setStartPage(pageNumber);
+                    stripper.setEndPage(pageNumber);
+                    stripper.setPdpage(pdPage);
+                    stripper.getText(pdDocument);
+
+                    PDRectangle pdr = pdPage.getMediaBox();
+                    boolean isLandscape = pdr.getWidth() > pdr.getHeight();
+
+                    int rotation = pdPage.getRotation();
+                    boolean isRotated = rotation != 0 && rotation != 360;
+
+                    CleanRulings cleanRulings = rulingCleaningService.getCleanRulings(stripper.getRulings(), stripper.getMinCharWidth(), stripper
+                            .getMaxCharHeight());
+
+                    Page page = blockificationService.blockify(stripper.getTextPositionSequences(), cleanRulings.getHorizontal(), cleanRulings
+                            .getVertical());
+
+                    PDRectangle cropbox = pdPage.getCropBox();
+                    float cropboxArea = cropbox.getHeight() * cropbox.getWidth();
+                    page.setCropBoxArea(cropboxArea);
+
+                    page.setRotation(rotation);
+                    page.setLandscape(isLandscape || isRotated);
+                    page.setPageNumber(pageNumber);
+
+                    List<PdfImage> mergedList = imageMergeService.mergeImages(stripper.getImages(), rotation);
+                    page.setImages(mergedList);
+
+                    tableExtractionService.extractTables(cleanRulings, page);
+                    buildPageStatistics(page);
+                    increaseDocumentStatistics(page, document);
+
+                    if (!ignoreImages) {
+                        imageClassificationService.classifyImages(page);
+                    }
+
+                    pages.add(page);
                 }
 
-                PDFLinesTextStripper stripper = new PDFLinesTextStripper();
+                document.setPages(pages);
-                PDPage pdPage = pdDocument.getPage(pageNumber - 1);
-                stripper.setPageNumber(pageNumber);
-                stripper.setStartPage(pageNumber);
-                stripper.setEndPage(pageNumber);
-                stripper.setPdpage(pdPage);
-                stripper.getText(pdDocument);
 
-                PDRectangle pdr = pdPage.getMediaBox();
+                classificationService.classifyDocument(document);
-                boolean isLandscape = pdr.getWidth() > pdr.getHeight();
+                sectionsBuilderService.buildSections(document);
+                sectionsBuilderService.addImagesToSections(document);
 
-                int rotation = pdPage.getRotation();
+                pdDocument = reinitializePDDocument(tempFile, pdDocument);
-                boolean isRotated = rotation != 0 && rotation != 360;
 
-                CleanRulings cleanRulings = rulingCleaningService.getCleanRulings(stripper.getRulings(), stripper.getMinCharWidth(), stripper
+                IOUtils.close(pdDocument);
-                        .getMaxCharHeight());
 
-                Page page = blockificationService.blockify(stripper.getTextPositionSequences(), cleanRulings.getHorizontal(), cleanRulings
+                if(!tempFile.delete()){
-                        .getVertical());
+                    log.warn("Could not delete tmp file");
-
-                PDRectangle cropbox = pdPage.getCropBox();
-                float cropboxArea = cropbox.getHeight() * cropbox.getWidth();
-                page.setCropBoxArea(cropboxArea);
-
-                page.setRotation(rotation);
-                page.setLandscape(isLandscape || isRotated);
-                page.setPageNumber(pageNumber);
-
-                List<PdfImage> mergedList = imageMergeService.mergeImages(stripper.getImages(), rotation);
-                page.setImages(mergedList);
-
-                tableExtractionService.extractTables(cleanRulings, page);
-                buildPageStatistics(page);
-                increaseDocumentStatistics(page, document);
-
-                if (!ignoreImages) {
-                    imageClassificationService.classifyImages(page);
                 }
 
-                pages.add(page);
+                return document;
             }
-
-            document.setPages(pages);
-
-            classificationService.classifyDocument(document);
-            sectionsBuilderService.buildSections(document);
-            sectionsBuilderService.addImagesToSections(document);
-
-            pdDocument = reinitializePDDocument(tempFile, pdDocument);
-
-            IOUtils.close(pdDocument);
-
-            tempFile.delete();
-
-            return document;
         } finally {
             if (pdDocument != null) {
                 pdDocument.close();