Pull request #340: RED-3363: Fixed ignored hints in full analysis

Merge in RED/redaction-service from RED-3363 to release/2.52.x

* commit '0cb127eccbf496bcbbb17aa8b4de51c13aa9d3ea':
  RED-3363: Fixed ignored hints in full analysis

bamboo-specs/src/main/java/buildjob/PlanSpec.java

@@ -93,6 +93,11 @@ public class PlanSpec {
                                                 .description("Resultparser")
                                                 .resultDirectories("**/test-reports/*.xml, **/target/surefire-reports/*.xml, **/target/failsafe-reports/*.xml")
                                                 .enabled(true),
+                                        new ScriptTask()
+                                                .description("Sonar")
+                                                .location(Location.FILE)
+                                                .fileFromPath("bamboo-specs/src/main/resources/scripts/sonar-java.sh")
+                                                .argument(SERVICE_NAME),
                                         new InjectVariablesTask()
                                                 .description("Inject git Tag")
                                                 .path("git.tag")

bamboo-specs/src/main/resources/scripts/sonar-java.sh

@@ -0,0 +1,42 @@
+#!/bin/bash
+set -e
+
+SERVICE_NAME=$1
+
+echo "dependency-check:aggregate"
+${bamboo_capability_system_builder_mvn3_Maven_3}/bin/mvn \
+    --no-transfer-progress \
+    -f ${bamboo_build_working_directory}/$SERVICE_NAME-v1/pom.xml \
+    org.owasp:dependency-check-maven:aggregate
+
+if [[ -z "${bamboo_repository_pr_key}" ]]
+then
+    echo "Sonar Scan for branch: ${bamboo_planRepository_1_branch}"
+    ${bamboo_capability_system_builder_mvn3_Maven_3}/bin/mvn \
+            --no-transfer-progress \
+            -f ${bamboo_build_working_directory}/$SERVICE_NAME-v1/pom.xml \
+            sonar:sonar \
+            -Dsonar.projectKey=RED_$SERVICE_NAME \
+            -Dsonar.host.url=https://sonarqube.iqser.com \
+            -Dsonar.login=${bamboo_sonarqube_api_token_secret} \
+            -Dsonar.branch.name=${bamboo_planRepository_1_branch} \
+            -Dsonar.dependencyCheck.jsonReportPath=target/dependency-check-report.json \
+            -Dsonar.dependencyCheck.xmlReportPath=target/dependency-check-report.xml \
+            -Dsonar.dependencyCheck.htmlReportPath=target/dependency-check-report.html
+
+else
+    echo "Sonar Scan for PR with key1: ${bamboo_repository_pr_key}"
+    ${bamboo_capability_system_builder_mvn3_Maven_3}/bin/mvn \
+            --no-transfer-progress \
+            -f ${bamboo_build_working_directory}/$SERVICE_NAME-v1/pom.xml \
+            sonar:sonar \
+            -Dsonar.projectKey=RED_$SERVICE_NAME \
+            -Dsonar.host.url=https://sonarqube.iqser.com \
+            -Dsonar.login=${bamboo_sonarqube_api_token_secret} \
+            -Dsonar.pullrequest.key=${bamboo_repository_pr_key} \
+            -Dsonar.pullrequest.branch=${bamboo_repository_pr_sourceBranch} \
+            -Dsonar.pullrequest.base=${bamboo_repository_pr_targetBranch} \
+            -Dsonar.dependencyCheck.jsonReportPath=target/dependency-check-report.json \
+            -Dsonar.dependencyCheck.xmlReportPath=target/dependency-check-report.xml \
+            -Dsonar.dependencyCheck.htmlReportPath=target/dependency-check-report.html
+fi

redaction-service-image-v1/pom.xml

@@ -6,6 +6,7 @@
         <groupId>com.iqser.red</groupId>
         <artifactId>platform-docker-dependency</artifactId>
         <version>1.0.0</version>
+        <relativePath />
     </parent>
     <modelVersion>4.0.0</modelVersion>
 

redaction-service-image-v1/src/main/docker/Dockerfile

@@ -13,6 +13,7 @@ RUN apt-get update \
     wget cabextract xfonts-utils fonts-liberation \
  && rm -rf /var/lib/apt/lists/*
 
-RUN curl http://ftp.br.debian.org/debian/pool/contrib/m/msttcorefonts/ttf-mscorefonts-installer_3.8_all.deb -o /tmp/ttf-mscorefonts-installer_3.8_all.deb \
+RUN curl http://ftp.debian.org/debian/pool/contrib/m/msttcorefonts/ttf-mscorefonts-installer_3.8_all.deb -o /tmp/ttf-mscorefonts-installer_3.8_all.deb \
  && dpkg -i /tmp/ttf-mscorefonts-installer_3.8_all.deb \
  && rm /tmp/ttf-mscorefonts-installer_3.8_all.deb \
+

redaction-service-v1/pom.xml

@@ -5,7 +5,8 @@
     <parent>
         <artifactId>platform-dependency</artifactId>
         <groupId>com.iqser.red</groupId>
-        <version>1.1.3</version>
+        <version>1.1.3.3</version>
+        <relativePath />
     </parent>
     <modelVersion>4.0.0</modelVersion>
 

redaction-service-v1/redaction-service-api-v1/src/main/java/com/iqser/red/service/redaction/v1/model/AnalyzeRequest.java

@@ -7,9 +7,8 @@ import lombok.NoArgsConstructor;
 
 import java.time.OffsetDateTime;
 import java.util.ArrayList;
-import java.util.HashMap;
+import java.util.HashSet;
 import java.util.List;
-import java.util.Map;
 import java.util.Set;
 
 @Data
@@ -24,7 +23,11 @@ public class AnalyzeRequest {
     private boolean reanalyseOnlyIfPossible;
     private ManualRedactions manualRedactions;
     private OffsetDateTime lastProcessed;
-    private Set<Integer> excludedPages;
+
+    @Builder.Default
+    private Set<Integer> excludedPages = new HashSet<>();
+    @Builder.Default
+    private Set<Integer> sectionsToReanalyse = new HashSet<>();
 
     @Builder.Default
     private List<FileAttribute> fileAttributes = new ArrayList<>();

redaction-service-v1/redaction-service-api-v1/src/main/java/com/iqser/red/service/redaction/v1/model/AnalyzeResult.java

@@ -15,10 +15,6 @@ public class AnalyzeResult {
     private String fileId;
     private long duration;
     private int numberOfPages;
-    private boolean hasHints;
-    private boolean hasRequests;
-    private boolean hasRedactions;
-    private boolean hasImages;
     private boolean hasUpdates;
     private long dictionaryVersion;
     private long dossierDictionaryVersion;
@@ -27,6 +23,8 @@ public class AnalyzeResult {
 
     private boolean wasReanalyzed;
 
+    private int analysisVersion;
+
 
 }
 

redaction-service-v1/redaction-service-api-v1/src/main/java/com/iqser/red/service/redaction/v1/model/ManualLegalBasisChange.java

@@ -17,6 +17,8 @@ public class ManualLegalBasisChange {
     private String user;
     private Status status;
     private String legalBasis;
+    private String section;
+    private String value;
 
     private OffsetDateTime requestDate;
     private OffsetDateTime processedDate;

redaction-service-v1/redaction-service-api-v1/src/main/java/com/iqser/red/service/redaction/v1/model/ManualRedactionEntry.java

@@ -23,11 +23,10 @@ public class ManualRedactionEntry {
     private String legalBasis;
     private List<Rectangle> positions = new ArrayList<>();
     private Status status;
-    private boolean addToDictionary;
-
     private String section;
-    private int sectionNumber;
+    private boolean rectangle;
 
+    private boolean addToDictionary;
     private boolean addToDossierDictionary;
 
     private OffsetDateTime requestDate;

redaction-service-v1/redaction-service-api-v1/src/main/java/com/iqser/red/service/redaction/v1/model/RedactionLog.java

@@ -10,6 +10,13 @@ import java.util.List;
 @AllArgsConstructor
 public class RedactionLog {
 
+
+    /**
+     * Version 0 Redaction Logs have manual redactions merged inside them
+     * Version 1 Redaction Logs only contain system ( rule/dictionary ) redactions. Manual Redactions are merged in at runtime.
+     */
+    private long analysisVersion;
+
     private List<RedactionLogEntry> redactionLogEntry;
     private List<LegalBasisMapping> legalBasis;
 

redaction-service-v1/redaction-service-api-v1/src/main/java/com/iqser/red/service/redaction/v1/model/RedactionLogEntry.java

@@ -9,6 +9,8 @@ import lombok.NoArgsConstructor;
 import java.util.ArrayList;
 import java.util.List;
 
+
+
 @Data
 @Builder
 @NoArgsConstructor
@@ -20,6 +22,7 @@ public class RedactionLogEntry {
     private String type;
     private String value;
     private String reason;
+    private boolean rectangle;
     private int matchedRule;
     private String legalBasis;
     private boolean redacted;
@@ -28,12 +31,18 @@ public class RedactionLogEntry {
     private String section;
     private float[] color;
 
+    private boolean hasBeenRecategorized;
+    private boolean hasLegalBasisChanged;
+    private boolean hasBeenForced;
+    private boolean hasBeenRemovedByManualOverride;
+
     @Builder.Default
     private List<Rectangle> positions = new ArrayList<>();
     private int sectionNumber;
     private boolean manual;
     private Status status;
     private ManualRedactionType manualRedactionType;
+    private String manualRedactionUserId;
     private boolean isDictionaryEntry;
 
     private String textBefore;
@@ -46,6 +55,7 @@ public class RedactionLogEntry {
     private int endOffset;
 
     private boolean isImage;
+    private boolean imageHasTransparency;
 
     private boolean isDossierDictionaryEntry;
 

redaction-service-v1/redaction-service-api-v1/src/main/java/com/iqser/red/service/redaction/v1/model/RedactionRequest.java

@@ -1,5 +1,8 @@
 package com.iqser.red.service.redaction.v1.model;
 
+import java.util.HashSet;
+import java.util.Set;
+
 import lombok.AllArgsConstructor;
 import lombok.Builder;
 import lombok.Data;
@@ -15,4 +18,8 @@ public class RedactionRequest {
     private String fileId;
     private String dossierTemplateId;
     private ManualRedactions manualRedactions;
+    @Builder.Default
+    private Set<Integer> excludedPages = new HashSet<>();
+
+    private boolean withSectionDataForManualRedactions;
 }

redaction-service-v1/redaction-service-api-v1/src/main/java/com/iqser/red/service/redaction/v1/model/SectionArea.java

@@ -27,7 +27,11 @@ public class SectionArea {
     private String header;
 
     public boolean contains(Rectangle other) {
-        return page == other.getPage() && this.topLeft.getX() <= other.getTopLeft().getX() && this.topLeft.getX() + this.getWidth() >= other.getTopLeft().getX() + other.getWidth() && this.getTopLeft().getY() <= other.getTopLeft().getY() && this.getTopLeft().getY() + this.getHeight() >= other.getTopLeft().getY() + other.getHeight();
+        return page == other.getPage()
+                && topLeft.getX() <= other.getTopLeft().getX()
+                && topLeft.getX() + getWidth() >= other.getTopLeft().getX() + other.getWidth()
+                && getTopLeft().getY() <= other.getTopLeft().getY()
+                && getTopLeft().getY() + getHeight() >= other.getTopLeft().getY() + other.getHeight();
     }
 
 }

redaction-service-v1/redaction-service-api-v1/src/main/java/com/iqser/red/service/redaction/v1/model/SectionGrid.java

@@ -3,10 +3,9 @@ package com.iqser.red.service.redaction.v1.model;
 import lombok.AllArgsConstructor;
 import lombok.Data;
 import lombok.NoArgsConstructor;
+import lombok.RequiredArgsConstructor;
 
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
+import java.util.*;
 
 @Data
 @AllArgsConstructor
@@ -15,4 +14,16 @@ public class SectionGrid {
 
     private Map<Integer, List<SectionRectangle>> rectanglesPerPage = new HashMap<>();
 
+    private List<SectionGridSection> sections = new ArrayList<>();
+
+    @Data
+    @RequiredArgsConstructor
+    public static class SectionGridSection {
+
+        private final int sectionNumber;
+        private final String headline;
+        private final Set<Integer> pages;
+        private final List<SectionArea> sectionAreas;
+
+    }
 }

redaction-service-v1/redaction-service-api-v1/src/main/java/com/iqser/red/service/redaction/v1/model/SectionRectangle.java

@@ -1,10 +1,6 @@
 package com.iqser.red.service.redaction.v1.model;
 
-import lombok.AllArgsConstructor;
-import lombok.Data;
-import lombok.NoArgsConstructor;
-import lombok.NonNull;
-import lombok.RequiredArgsConstructor;
+import lombok.*;
 
 import java.util.List;
 
@@ -30,4 +26,12 @@ public class SectionRectangle {
     private int numberOfParts;
 
     private List<CellRectangle> tableCells;
+
+    public boolean contains(Rectangle other) {
+        return topLeft.getX() <= other.getTopLeft().getX()
+                && topLeft.getX() + getWidth() >= other.getTopLeft().getX() + other.getWidth()
+                && getTopLeft().getY() <= other.getTopLeft().getY()
+                && getTopLeft().getY() + getHeight() >= other.getTopLeft().getY() + other.getHeight();
+
+    }
 }

redaction-service-v1/redaction-service-api-v1/src/main/java/com/iqser/red/service/redaction/v1/resources/RedactionResource.java

@@ -8,10 +8,6 @@ import org.springframework.web.bind.annotation.RequestBody;
 
 public interface RedactionResource {
 
-    String RULE_SET_PARAMETER_NAME = "dossierTemplateId";
-    String RULE_SET_PATH_VARIABLE = "/{" + RULE_SET_PARAMETER_NAME + "}";
-
-
     @PostMapping(value = "/annotate", produces = MediaType.APPLICATION_JSON_VALUE, consumes = MediaType.APPLICATION_JSON_VALUE)
     AnnotateResponse annotate(@RequestBody AnnotateRequest annotateRequest);
 
@@ -24,13 +20,10 @@ public interface RedactionResource {
     @PostMapping(value = "/debug/htmlTables", produces = MediaType.APPLICATION_JSON_VALUE, consumes = MediaType.APPLICATION_JSON_VALUE)
     RedactionResult htmlTables(@RequestBody RedactionRequest redactionRequest);
 
-    @PostMapping(value = "/rules/update" + RULE_SET_PATH_VARIABLE, consumes = MediaType.APPLICATION_JSON_VALUE)
-    void updateRules(@PathVariable(RULE_SET_PARAMETER_NAME) String dossierTemplateId);
-
     @PostMapping(value = "/rules/test", consumes = MediaType.APPLICATION_JSON_VALUE)
     void testRules(@RequestBody String rules);
 
     @PostMapping(value = "/redaction-log/preview", consumes = MediaType.APPLICATION_JSON_VALUE)
-    RedactionLog getRedactionLogPreview(@RequestBody RedactionRequest redactionRequest);
+    RedactionLog getRedactionLog(@RequestBody RedactionRequest redactionRequest);
 
 }

redaction-service-v1/redaction-service-server-v1/pom.xml

@@ -24,7 +24,7 @@
         <dependency>
             <groupId>com.iqser.red.service</groupId>
             <artifactId>file-management-service-api-v1</artifactId>
-            <version>2.25.0</version>
+            <version>2.80.15</version>
             <exclusions>
                 <exclusion>
                     <groupId>com.iqser.red.service</groupId>

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

@@ -1,5 +1,7 @@
 package com.iqser.red.service.redaction.v1.server.classification.service;
 
+import static java.util.stream.Collectors.toSet;
+
 import com.iqser.red.service.redaction.v1.server.classification.model.FloatFrequencyCounter;
 import com.iqser.red.service.redaction.v1.server.classification.model.Orientation;
 import com.iqser.red.service.redaction.v1.server.classification.model.Page;
@@ -16,6 +18,7 @@ import com.iqser.red.service.redaction.v1.server.tableextraction.model.Table;
 import org.springframework.stereotype.Service;
 
 import java.util.ArrayList;
+import java.util.Comparator;
 import java.util.Iterator;
 import java.util.List;
 
@@ -25,9 +28,12 @@ public class BlockificationService {
 
     static final float THRESHOLD = 1f;
 
+
     public Page blockify(List<TextPositionSequence> textPositions, List<Ruling> horizontalRulingLines,
                          List<Ruling> verticalRulingLines) {
 
+        sortRotatedSequences(textPositions);
+
         List<TextPositionSequence> chunkWords = new ArrayList<>();
         List<AbstractTextContainer> chunkBlockList1 = new ArrayList<>();
 
@@ -50,7 +56,7 @@ public class BlockificationService {
             if (prev != null && (lineSeparation || startFromTop || splitByX || newLineAfterSplit || splittedByRuling)) {
 
                 Orientation prevOrientation = null;
-                if(!chunkBlockList1.isEmpty()) {
+                if (!chunkBlockList1.isEmpty()) {
                     prevOrientation = chunkBlockList1.get(chunkBlockList1.size() - 1).getOrientation();
                 }
 
@@ -62,15 +68,11 @@ public class BlockificationService {
                     wasSplitted = true;
                     cb1.setOrientation(Orientation.LEFT);
                     splitX1 = word.getX1();
-                } else
-
-                if (newLineAfterSplit && !splittedByRuling) {
+                } else if (newLineAfterSplit && !splittedByRuling) {
                     wasSplitted = false;
                     cb1.setOrientation(Orientation.RIGHT);
                     splitX1 = null;
-                } else
-
-                if(prevOrientation != null && prevOrientation.equals(Orientation.RIGHT) && (lineSeparation || !startFromTop || !splitByX || !newLineAfterSplit || !splittedByRuling)){
+                } else if (prevOrientation != null && prevOrientation.equals(Orientation.RIGHT) && (lineSeparation || !startFromTop || !splitByX || !newLineAfterSplit || !splittedByRuling)) {
                     cb1.setOrientation(Orientation.LEFT);
                 }
 
@@ -110,16 +112,18 @@ public class BlockificationService {
         while (itty.hasNext()) {
             TextBlock block = (TextBlock) itty.next();
 
-            if(previousLeft != null && block.getOrientation().equals(Orientation.LEFT)){
-                if (previousLeft.getMinY() > block.getMinY() && block.getMaxY() + block.getMostPopularWordHeight() > previousLeft.getMinY()){
+            if (previousLeft != null && block.getOrientation().equals(Orientation.LEFT)) {
+                if (previousLeft.getMinY() > block.getMinY() && block.getMaxY() + block.getMostPopularWordHeight() > previousLeft
+                        .getMinY()) {
                     previousLeft.add(block);
                     itty.remove();
                     continue;
                 }
             }
 
-            if(previousRight != null && block.getOrientation().equals(Orientation.RIGHT)){
-                if (previousRight.getMinY() > block.getMinY() && block.getMaxY() + block.getMostPopularWordHeight() > previousRight.getMinY()){
+            if (previousRight != null && block.getOrientation().equals(Orientation.RIGHT)) {
+                if (previousRight.getMinY() > block.getMinY() && block.getMaxY() + block.getMostPopularWordHeight() > previousRight
+                        .getMinY()) {
                     previousRight.add(block);
                     itty.remove();
                     continue;
@@ -133,16 +137,16 @@ public class BlockificationService {
             }
         }
 
-
         itty = chunkBlockList1.iterator();
         TextBlock previous = null;
         while (itty.hasNext()) {
             TextBlock block = (TextBlock) itty.next();
 
-            if(previous != null && previous.getOrientation().equals(Orientation.LEFT) && block.getOrientation().equals(Orientation.LEFT) && equalsWithThreshold(block.getMaxY(), previous
-                    .getMaxY())||
-                    previous != null && previous.getOrientation().equals(Orientation.LEFT) && block.getOrientation().equals(Orientation.RIGHT) && equalsWithThreshold(block.getMaxY(), previous
-                    .getMaxY())){
+            if (previous != null && previous.getOrientation().equals(Orientation.LEFT) && block.getOrientation()
+                    .equals(Orientation.LEFT) && equalsWithThreshold(block.getMaxY(), previous.getMaxY()) || previous != null && previous
+                    .getOrientation()
+                    .equals(Orientation.LEFT) && block.getOrientation()
+                    .equals(Orientation.RIGHT) && equalsWithThreshold(block.getMaxY(), previous.getMaxY())) {
                 previous.add(block);
                 itty.remove();
                 continue;
@@ -151,11 +155,12 @@ public class BlockificationService {
             previous = block;
         }
 
-
         return new Page(chunkBlockList1);
     }
 
-    private boolean equalsWithThreshold(float f1, float f2){
+
+    private boolean equalsWithThreshold(float f1, float f2) {
+
         return Math.abs(f1 - f2) < THRESHOLD;
     }
 
@@ -197,6 +202,13 @@ public class BlockificationService {
             textBlock.setHighestFontSize(fontSizeFrequencyCounter.getHighest());
         }
 
+        if (textBlock != null && textBlock.getSequences() != null && textBlock.getSequences()
+                .stream()
+                .map(t -> round(t.getY1(), 3))
+                .collect(toSet())
+                .size() == 1) {
+            textBlock.getSequences().sort(Comparator.comparing(TextPositionSequence::getX1));
+        }
         return textBlock;
     }
 
@@ -291,4 +303,30 @@ public class BlockificationService {
         return new Rectangle(minY, minX, maxX - minX, maxY - minY);
     }
 
+
+    private void sortRotatedSequences(List<TextPositionSequence> sequences) {
+
+        List<TextPositionSequence> rotatedWords = new ArrayList<>();
+        Iterator<TextPositionSequence> itty = sequences.iterator();
+        while (itty.hasNext()) {
+            var pos = itty.next();
+            if (pos.getTextPositions().get(0).getDir() == 270) {
+                rotatedWords.add(pos);
+                itty.remove();
+            }
+        }
+
+        if (!rotatedWords.isEmpty() && !sequences.isEmpty()) {
+            rotatedWords.sort(Comparator.comparing(TextPositionSequence::getX1));
+        }
+        sequences.addAll(rotatedWords);
+    }
+
+
+    private double round(float value, int decimalPoints) {
+
+        var d = Math.pow(10, decimalPoints);
+        return Math.round(value * d) / d;
+    }
+
 }

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

@@ -73,8 +73,10 @@ public class ClassificationService {
             }
         } else if (PositionUtils.isWithinBodyTextFrame(bodyTextFrame, textBlock) && textBlock.getMostPopularWordFontSize() > document
                 .getFontSizeCounter()
-                .getMostPopular() && PositionUtils.getApproxLineCount(textBlock) < 4.9 && textBlock.getMostPopularWordStyle()
-                .equals("bold")) {
+                .getMostPopular() && PositionUtils.getApproxLineCount(textBlock) < 4.9 && (textBlock.getMostPopularWordStyle()
+                .equals("bold") || !document.getFontStyleCounter().getCountPerValue().containsKey("bold") && textBlock.getMostPopularWordFontSize() > document
+                .getFontSizeCounter()
+                .getMostPopular() + 1) && textBlock.getSequences().get(0).getTextPositions().get(0).getFontSizeInPt() >= textBlock.getMostPopularWordFontSize()) {
 
             for (int i = 1; i <= headlineFontSizes.size(); i++) {
                 if (textBlock.getMostPopularWordFontSize() == headlineFontSizes.get(i - 1)) {
@@ -86,7 +88,7 @@ public class ClassificationService {
                 .startsWith("Figure ") && PositionUtils.isWithinBodyTextFrame(bodyTextFrame, textBlock) && textBlock.getMostPopularWordStyle()
                 .equals("bold") && !document.getFontStyleCounter()
                 .getMostPopular()
-                .equals("bold") && PositionUtils.getApproxLineCount(textBlock) < 2.9) {
+                .equals("bold") && PositionUtils.getApproxLineCount(textBlock) < 2.9 && textBlock.getSequences().get(0).getTextPositions().get(0).getFontSizeInPt() >= textBlock.getMostPopularWordFontSize()) {
             textBlock.setClassification("H " + (headlineFontSizes.size() + 1));
             document.setHeadlines(true);
         } else if (PositionUtils.isWithinBodyTextFrame(bodyTextFrame, textBlock) && textBlock.getMostPopularWordFontSize() == document

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

@@ -1,6 +1,7 @@
 package com.iqser.red.service.redaction.v1.server.controller;
 
 import com.iqser.red.commons.spring.ErrorMessage;
+import com.iqser.red.service.redaction.v1.server.exception.RedactionLogNotFoundException;
 import com.iqser.red.service.redaction.v1.server.exception.RulesValidationException;
 import lombok.extern.slf4j.Slf4j;
 import org.springframework.http.HttpStatus;
@@ -17,6 +18,13 @@ public class ControllerAdvice {
 
     /* error handling */
 
+    @ResponseBody
+    @ResponseStatus(value = HttpStatus.NOT_FOUND)
+    @ExceptionHandler(value = RedactionLogNotFoundException.class)
+    public ErrorMessage handleRedactionLogNotFoundException(RedactionLogNotFoundException e) {
+        return new ErrorMessage(OffsetDateTime.now(), e.getMessage());
+    }
+
     @ResponseBody
     @ResponseStatus(value = HttpStatus.INTERNAL_SERVER_ERROR)
     @ExceptionHandler(value = NullPointerException.class)

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

@@ -1,19 +1,16 @@
 package com.iqser.red.service.redaction.v1.server.controller;
 
 import com.iqser.red.service.file.management.v1.api.model.FileType;
-import com.iqser.red.service.redaction.v1.model.AnnotateRequest;
-import com.iqser.red.service.redaction.v1.model.AnnotateResponse;
-import com.iqser.red.service.redaction.v1.model.RedactionLog;
-import com.iqser.red.service.redaction.v1.model.RedactionRequest;
-import com.iqser.red.service.redaction.v1.model.RedactionResult;
+import com.iqser.red.service.redaction.v1.model.*;
 import com.iqser.red.service.redaction.v1.resources.RedactionResource;
 import com.iqser.red.service.redaction.v1.server.classification.model.Document;
 import com.iqser.red.service.redaction.v1.server.classification.model.Page;
 import com.iqser.red.service.redaction.v1.server.exception.RedactionException;
+import com.iqser.red.service.redaction.v1.server.exception.RedactionLogNotFoundException;
 import com.iqser.red.service.redaction.v1.server.redaction.service.AnnotationService;
 import com.iqser.red.service.redaction.v1.server.redaction.service.DictionaryService;
 import com.iqser.red.service.redaction.v1.server.redaction.service.DroolsExecutionService;
-import com.iqser.red.service.redaction.v1.server.redaction.service.RedactionLogCreatorService;
+import com.iqser.red.service.redaction.v1.server.redaction.service.RedactionLogMergeService;
 import com.iqser.red.service.redaction.v1.server.segmentation.PdfSegmentationService;
 import com.iqser.red.service.redaction.v1.server.storage.RedactionStorageService;
 import com.iqser.red.service.redaction.v1.server.tableextraction.model.AbstractTextContainer;
@@ -23,12 +20,12 @@ import lombok.RequiredArgsConstructor;
 import lombok.extern.slf4j.Slf4j;
 import org.apache.pdfbox.io.MemoryUsageSetting;
 import org.apache.pdfbox.pdmodel.PDDocument;
-import org.springframework.web.bind.annotation.PathVariable;
 import org.springframework.web.bind.annotation.RequestBody;
 import org.springframework.web.bind.annotation.RestController;
 
 import java.io.ByteArrayOutputStream;
 import java.io.IOException;
+import java.util.stream.Collectors;
 
 @Slf4j
 @RestController
@@ -41,7 +38,7 @@ public class RedactionController implements RedactionResource {
     private final AnnotationService annotationService;
     private final PdfSegmentationService pdfSegmentationService;
     private final RedactionStorageService redactionStorageService;
-    private final RedactionLogCreatorService redactionLogCreatorService;
+    private final RedactionLogMergeService redactionLogMergeService;
 
     public AnnotateResponse annotate(@RequestBody AnnotateRequest annotateRequest) {
 
@@ -143,14 +140,6 @@ public class RedactionController implements RedactionResource {
 
     }
 
-
-    @Override
-    public void updateRules(@PathVariable(RULE_SET_PARAMETER_NAME) String dossierTemplateId) {
-
-        droolsExecutionService.updateRules(dossierTemplateId);
-    }
-
-
     @Override
     public void testRules(@RequestBody String rules) {
 
@@ -158,15 +147,46 @@ public class RedactionController implements RedactionResource {
     }
 
     @Override
-    public RedactionLog getRedactionLogPreview(RedactionRequest redactionRequest) {
+    public RedactionLog getRedactionLog(@RequestBody RedactionRequest redactionRequest) {
 
         log.info("Requested preview for: {}", redactionRequest);
         dictionaryService.updateDictionary(redactionRequest.getDossierTemplateId(), redactionRequest.getDossierId());
 
+        SectionGrid sectionGrid = null;
         var redactionLog = redactionStorageService.getRedactionLog(redactionRequest.getDossierId(), redactionRequest.getFileId());
-        return redactionLogCreatorService.getRedactionLogPreview(redactionLog, redactionRequest.getDossierTemplateId(), redactionRequest.getManualRedactions());
-    }
 
+        if (redactionLog == null) {
+            throw new RedactionLogNotFoundException();
+        }
+
+
+        if (redactionRequest.isWithSectionDataForManualRedactions()) {
+            sectionGrid = redactionStorageService.getSectionGrid(redactionRequest.getDossierId(), redactionRequest.getFileId());
+            if (sectionGrid.getSections().isEmpty()) {
+
+                log.info("SectionGrid does not have headlines set. Computing headlines now!");
+                var text = redactionStorageService.getText(redactionRequest.getDossierId(), redactionRequest.getFileId());
+
+                // enhance section grid with headline data
+                for (var sectionText : text.getSectionTexts()) {
+                    sectionGrid.getSections().add(new SectionGrid.SectionGridSection(sectionText.getSectionNumber(),
+                            sectionText.getHeadline(),
+                            sectionText.getSectionAreas().stream().map(SectionArea::getPage).collect(Collectors.toSet()),
+                            sectionText.getSectionAreas()));
+                }
+                redactionStorageService.storeObject(redactionRequest.getDossierId(), redactionRequest.getFileId(), FileType.SECTION_GRID, sectionGrid);
+            }
+        }
+
+
+        log.info("Loaded redaction log with computationalVersion: {}", redactionLog.getAnalysisVersion());
+        if (redactionLog.getAnalysisVersion() == 0) {
+            // old redaction logs are returned directly
+            return redactionLog;
+        } else {
+            return redactionLogMergeService.mergeRedactionLogData(redactionLog, sectionGrid, redactionRequest.getDossierTemplateId(), redactionRequest.getManualRedactions(), redactionRequest.getExcludedPages());
+        }
+    }
 
     private RedactionResult convert(PDDocument document, int numberOfPages) throws IOException {
 

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

@@ -0,0 +1,9 @@
+package com.iqser.red.service.redaction.v1.server.exception;
+
+public class RedactionLogNotFoundException extends RuntimeException {
+
+    public RedactionLogNotFoundException() {
+        super("RedactionLog not found!");
+    }
+
+}

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

@@ -1,16 +1,33 @@
 package com.iqser.red.service.redaction.v1.server.parsing;
 
-import com.iqser.red.service.redaction.v1.server.parsing.model.TextPositionSequence;
-import com.iqser.red.service.redaction.v1.server.redaction.model.PdfImage;
-import com.iqser.red.service.redaction.v1.server.tableextraction.model.Ruling;
-import lombok.Getter;
-import lombok.Setter;
-import lombok.extern.slf4j.Slf4j;
+import java.awt.geom.Point2D;
+import java.awt.geom.Rectangle2D;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;
+
 import org.apache.commons.lang3.reflect.FieldUtils;
 import org.apache.pdfbox.contentstream.operator.Operator;
 import org.apache.pdfbox.contentstream.operator.OperatorName;
-import org.apache.pdfbox.contentstream.operator.color.*;
-import org.apache.pdfbox.contentstream.operator.state.*;
+import org.apache.pdfbox.contentstream.operator.color.SetNonStrokingColor;
+import org.apache.pdfbox.contentstream.operator.color.SetNonStrokingColorN;
+import org.apache.pdfbox.contentstream.operator.color.SetNonStrokingColorSpace;
+import org.apache.pdfbox.contentstream.operator.color.SetNonStrokingDeviceCMYKColor;
+import org.apache.pdfbox.contentstream.operator.color.SetNonStrokingDeviceGrayColor;
+import org.apache.pdfbox.contentstream.operator.color.SetNonStrokingDeviceRGBColor;
+import org.apache.pdfbox.contentstream.operator.color.SetStrokingColor;
+import org.apache.pdfbox.contentstream.operator.color.SetStrokingColorN;
+import org.apache.pdfbox.contentstream.operator.color.SetStrokingColorSpace;
+import org.apache.pdfbox.contentstream.operator.color.SetStrokingDeviceCMYKColor;
+import org.apache.pdfbox.contentstream.operator.color.SetStrokingDeviceGrayColor;
+import org.apache.pdfbox.contentstream.operator.color.SetStrokingDeviceRGBColor;
+import org.apache.pdfbox.contentstream.operator.state.SetFlatness;
+import org.apache.pdfbox.contentstream.operator.state.SetLineCapStyle;
+import org.apache.pdfbox.contentstream.operator.state.SetLineDashPattern;
+import org.apache.pdfbox.contentstream.operator.state.SetLineJoinStyle;
+import org.apache.pdfbox.contentstream.operator.state.SetLineMiterLimit;
+import org.apache.pdfbox.contentstream.operator.state.SetLineWidth;
+import org.apache.pdfbox.contentstream.operator.state.SetRenderingIntent;
 import org.apache.pdfbox.contentstream.operator.text.SetFontAndSize;
 import org.apache.pdfbox.cos.COSBase;
 import org.apache.pdfbox.cos.COSName;
@@ -23,12 +40,14 @@ import org.apache.pdfbox.text.PDFTextStripper;
 import org.apache.pdfbox.text.TextPosition;
 import org.apache.pdfbox.util.Matrix;
 
-import java.awt.geom.AffineTransform;
-import java.awt.geom.Point2D;
-import java.awt.geom.Rectangle2D;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.List;
+import com.iqser.red.service.redaction.v1.server.parsing.model.RedTextPosition;
+import com.iqser.red.service.redaction.v1.server.parsing.model.TextPositionSequence;
+import com.iqser.red.service.redaction.v1.server.redaction.model.PdfImage;
+import com.iqser.red.service.redaction.v1.server.tableextraction.model.Ruling;
+
+import lombok.Getter;
+import lombok.Setter;
+import lombok.extern.slf4j.Slf4j;
 
 @Slf4j
 public class PDFLinesTextStripper extends PDFTextStripper {
@@ -189,17 +208,19 @@ public class PDFLinesTextStripper extends PDFTextStripper {
             COSName objectName = (COSName) arguments.get(0);
             PDXObject xobject = getResources().getXObject(objectName);
             if (xobject instanceof PDImageXObject) {
-                PDImageXObject image = (PDImageXObject)xobject;
-
+                PDImageXObject image = (PDImageXObject) xobject;
                 Matrix ctmNew = getGraphicsState().getCurrentTransformationMatrix();
 
-                Rectangle2D rect = new Rectangle2D.Float(ctmNew.getTranslateX(), ctmNew.getTranslateY(), ctmNew.getScaleX(), ctmNew.getScaleY());
+                Rectangle2D rect = new Rectangle2D.Float(ctmNew.getTranslateX(), ctmNew.getTranslateY(), ctmNew.getScaleX(), ctmNew
+                        .getScaleY());
 
                 // Memory Hack - sofReference kills me
                 FieldUtils.writeField(image, "cachedImageSubsampling", -1, true);
 
                 if (rect.getHeight() > 2 && rect.getWidth() > 2) {
-                    this.images.add(new PdfImage(image.getImage(), rect, pageNumber));
+                    this.images.add(new PdfImage(image.getImage(), rect, pageNumber, image.getImage()
+                            .getColorModel()
+                            .hasAlpha()));
                 }
             }
         } catch (Exception e) {
@@ -208,8 +229,6 @@ public class PDFLinesTextStripper extends PDFTextStripper {
     }
 
 
-
-
     private float floatValue(COSBase value) {
 
         if (value instanceof COSNumber) {
@@ -248,8 +267,16 @@ public class PDFLinesTextStripper extends PDFTextStripper {
     public void writeString(String text, List<TextPosition> textPositions) throws IOException {
 
         int startIndex = 0;
+        RedTextPosition previous = null;
+
         for (int i = 0; i <= textPositions.size() - 1; i++) {
 
+            if (!textPositionSequences.isEmpty()) {
+                previous = textPositionSequences.get(textPositionSequences.size() - 1)
+                        .getTextPositions()
+                        .get(textPositionSequences.get(textPositionSequences.size() - 1).getTextPositions().size() - 1);
+            }
+
             int charWidth = (int) textPositions.get(i).getWidthDirAdj();
             if (charWidth < minCharWidth) {
                 minCharWidth = charWidth;
@@ -268,42 +295,54 @@ public class PDFLinesTextStripper extends PDFTextStripper {
 
             if (i == 0 && (textPositions.get(i).getUnicode().equals(" ") || textPositions.get(i)
                     .getUnicode()
-                    .equals("\u00A0"))) {
+                    .equals("\u00A0") || textPositions.get(i)
+                    .getUnicode()
+                    .equals("\t"))) {
                 startIndex++;
                 continue;
             }
 
             // Strange but sometimes this is happening, for example: Metolachlor2.pdf
-            if (i > 0 && textPositions.get(i).getX() < textPositions.get(i - 1).getX()) {
+            if (i > 0 && textPositions.get(i).getXDirAdj() < textPositions.get(i - 1).getXDirAdj()) {
                 List<TextPosition> sublist = textPositions.subList(startIndex, i);
                 if (!(sublist.isEmpty() || sublist.size() == 1 && (sublist.get(0)
                         .getUnicode()
-                        .equals(" ") || sublist.get(0).getUnicode().equals("\u00A0")))) {
+                        .equals(" ") || sublist.get(0).getUnicode().equals("\u00A0") || sublist.get(0).getUnicode().equals("\t")))) {
                     textPositionSequences.add(new TextPositionSequence(sublist, pageNumber));
                 }
                 startIndex = i;
             }
 
-
-            if (textPositions.get(i).getRotation() == 0 && i > 0 && textPositions.get(i).getX() > textPositions.get(i - 1).getEndX() + 1) {
+            if (textPositions.get(i).getRotation() == 0 && i > 0 && textPositions.get(i)
+                    .getX() > textPositions.get(i - 1).getEndX() + 1) {
                 List<TextPosition> sublist = textPositions.subList(startIndex, i);
                 if (!(sublist.isEmpty() || sublist.size() == 1 && (sublist.get(0)
                         .getUnicode()
-                        .equals(" ") || sublist.get(0).getUnicode().equals("\u00A0")))) {
+                        .equals(" ") || sublist.get(0).getUnicode().equals("\u00A0") || sublist.get(0).getUnicode().equals("\t")))) {
                     textPositionSequences.add(new TextPositionSequence(sublist, pageNumber));
                 }
                 startIndex = i;
             }
 
-
             if (i > 0 && (textPositions.get(i).getUnicode().equals(" ") || textPositions.get(i)
                     .getUnicode()
-                    .equals("\u00A0")) && i <= textPositions.size() - 2) {
+                    .equals("\u00A0") || textPositions.get(i)
+                    .getUnicode()
+                    .equals("\t")) && i <= textPositions.size() - 2) {
                 List<TextPosition> sublist = textPositions.subList(startIndex, i);
                 if (!(sublist.isEmpty() || sublist.size() == 1 && (sublist.get(0)
                         .getUnicode()
-                        .equals(" ") || sublist.get(0).getUnicode().equals("\u00A0")))) {
-                    textPositionSequences.add(new TextPositionSequence(sublist, pageNumber));
+                        .equals(" ") || sublist.get(0).getUnicode().equals("\u00A0") || sublist.get(0).getUnicode().equals("\t")))) {
+
+                    // Remove false sequence ends (whitespaces)
+                    if (previous != null && sublist.get(0).getYDirAdj() == previous.getYDirAdj() && sublist.get(0)
+                            .getXDirAdj() - (previous.getXDirAdj() + previous.getWidthDirAdj()) < 0.01) {
+                        for (TextPosition t : sublist) {
+                            textPositionSequences.get(textPositionSequences.size() - 1).add(t);
+                        }
+                    } else {
+                        textPositionSequences.add(new TextPositionSequence(sublist, pageNumber));
+                    }
                 }
                 startIndex = i + 1;
             }
@@ -312,13 +351,23 @@ public class PDFLinesTextStripper extends PDFTextStripper {
         List<TextPosition> sublist = textPositions.subList(startIndex, textPositions.size());
         if (!sublist.isEmpty() && (sublist.get(sublist.size() - 1)
                 .getUnicode()
-                .equals(" ") || sublist.get(sublist.size() - 1).getUnicode().equals("\u00A0"))) {
+                .equals(" ") || sublist.get(sublist.size() - 1).getUnicode().equals("\u00A0") || sublist.get(sublist.size() - 1).getUnicode().equals("\t"))) {
             sublist = sublist.subList(0, sublist.size() - 1);
         }
+
         if (!(sublist.isEmpty() || sublist.size() == 1 && (sublist.get(0).getUnicode().equals(" ") || sublist.get(0)
                 .getUnicode()
-                .equals("\u00A0")))) {
-            textPositionSequences.add(new TextPositionSequence(sublist, pageNumber));
+                .equals("\u00A0") || sublist.get(0)
+                .getUnicode()
+                .equals("\t")))) {
+            if (previous != null && sublist.get(0).getYDirAdj() == previous.getYDirAdj() && sublist.get(0)
+                    .getXDirAdj() - (previous.getXDirAdj() + previous.getWidthDirAdj()) < 0.01) {
+                for (TextPosition t : sublist) {
+                    textPositionSequences.get(textPositionSequences.size() - 1).add(t);
+                }
+            } else {
+                textPositionSequences.add(new TextPositionSequence(sublist, pageNumber));
+            }
         }
         super.writeString(text);
     }

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

@@ -21,6 +21,8 @@ public class RedTextPosition {
     private float YDirAdj;
     private float width;
     private float heightDir;
+    private float widthDirAdj;
+    private float dir;
 
     // not used in reanalysis
     @JsonIgnore

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

@@ -1,5 +1,7 @@
 package com.iqser.red.service.redaction.v1.server.parsing.model;
 
+import static java.util.stream.Collectors.toSet;
+
 import com.fasterxml.jackson.annotation.JsonIgnore;
 import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
 import com.iqser.red.service.redaction.v1.model.Point;
@@ -136,6 +138,13 @@ public class TextPositionSequence implements CharSequence {
     }
 
 
+    @JsonIgnore
+    public float getRotationAdjustedX() {
+
+        return textPositions.get(0).getXDirAdj();
+    }
+
+
     @JsonIgnore
     public float getY1() {
 
@@ -233,7 +242,7 @@ public class TextPositionSequence implements CharSequence {
         float posYInit;
         float posYEnd;
 
-        if (textPositions.get(0).getRotation() == 90) {
+        if (textPositions.get(0).getRotation() == 90 && textPositions.get(0).getDir() != 0.0f) {
             posXEnd = textPositions.get(0).getYDirAdj() + 2;
             posYInit = getY1();
             posYEnd = textPositions.get(textPositions.size() - 1).getXDirAdj() - height + 4;
@@ -244,9 +253,31 @@ public class TextPositionSequence implements CharSequence {
             posXInit = textPositions.get(0).getPageWidth() - textPositions.get(0).getYDirAdj() - 2;
             posXEnd = textPositions.get(0).getPageWidth() - textPositions.get(textPositions.size() - 1)
                     .getYDirAdj() + height;
-        } else {
+        } else if(textPositions.get(0).getRotation() == 0 && textPositions.get(0).getDir() == 270f) {
+            posYInit = textPositions.get(0).getPageHeight() - getX1();
+            posYEnd = textPositions.get(0).getPageHeight() - getX2() - textPositions.get(0)
+                    .getWidthDirAdj() - textPositions.get(textPositions.size() - 1).getWidthDirAdj() - 3;
+            posXInit = textPositions.get(0).getPageWidth() - textPositions.get(0).getYDirAdj() - 2;
+            posXEnd = textPositions.get(0).getPageWidth() - textPositions.get(textPositions.size() - 1)
+                    .getYDirAdj() + height;
+        } else if(textPositions.get(0).getRotation() == 90 && textPositions.get(0).getDir() == 0.0f){
+            posXInit =  textPositions.get(textPositions.size() - 1)
+                    .getXDirAdj() + textPositions.get(textPositions.size() - 1).getHeightDir();
+            posXEnd = textPositions.get(0).getXDirAdj();
+            posYInit = textPositions.get(0).getPageHeight() - textPositions.get(0).getYDirAdj() - 2;
+            posYEnd = textPositions.get(0).getPageHeight() - textPositions.get(textPositions.size() - 1)
+                    .getYDirAdj() + 2;
+        } else if(textPositions.get(0).getRotation() == 0 && textPositions.get(0).getDir() == 90f){
+            posYInit =  getX1();
+            posYEnd =   getX2() + textPositions.get(0)
+                    .getWidthDirAdj() - textPositions.get(textPositions.size() - 1).getWidthDirAdj() - 3;
+            posXInit =  textPositions.get(0).getYDirAdj() + 2;
+            posXEnd =  textPositions.get(textPositions.size() - 1)
+                    .getYDirAdj() - height;
+        }
+        else {
             posXEnd = textPositions.get(textPositions.size() - 1)
-                    .getXDirAdj() + textPositions.get(textPositions.size() - 1).getWidth() + 1;
+                    .getXDirAdj() + textPositions.get(textPositions.size() - 1).getWidthDirAdj() + 1;
             posYInit = textPositions.get(0).getPageHeight() - textPositions.get(0).getYDirAdj() - 2;
             posYEnd = textPositions.get(0).getPageHeight() - textPositions.get(textPositions.size() - 1)
                     .getYDirAdj() + 2;

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

@@ -39,6 +39,8 @@ public class Entity implements ReasonHolder {
 
     private boolean isDossierDictionaryEntry;
 
+    private boolean ignored;
+
 
     public Entity(String word, String type, boolean redaction, String redactionReason, List<EntityPositionSequence> positionSequences, String headline, int matchedRule, int sectionNumber, String legalBasis, boolean isDictionaryEntry, String textBefore, String textAfter, Integer start, Integer end, boolean isDossierDictionaryEntry) {
 

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

@@ -20,5 +20,7 @@ public class Image implements ReasonHolder {
     private int sectionNumber;
     private String section;
     private int page;
+    private boolean ignored;
+    private boolean hasTransparency;
 
 }

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

@@ -18,14 +18,16 @@ public class PdfImage {
     private RedRectangle2D position;
     private ImageType imageType;
     private boolean isAppendedToParagraph;
+    private boolean hasTransparency;
 
     @NonNull
     private int page;
 
-    public PdfImage(BufferedImage image, Rectangle2D position, int page) {
+    public PdfImage(BufferedImage image, Rectangle2D position, int page, boolean hasTransparency) {
         this.image = image;
         this.position = new RedRectangle2D(position.getX(), position.getY(), position.getWidth(), position.getHeight());
         this.page = page;
+        this.hasTransparency = hasTransparency;
     }
 
 }

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

@@ -1,13 +1,6 @@
 package com.iqser.red.service.redaction.v1.server.redaction.model;
 
-import com.iqser.red.service.redaction.v1.model.FileAttribute;
-import com.iqser.red.service.redaction.v1.server.classification.model.TextBlock;
-import com.iqser.red.service.redaction.v1.server.redaction.utils.EntitySearchUtils;
-import com.iqser.red.service.redaction.v1.server.redaction.utils.Patterns;
-import lombok.Builder;
-import lombok.Data;
-import lombok.extern.slf4j.Slf4j;
-import org.apache.commons.lang3.StringUtils;
+import static com.iqser.red.service.redaction.v1.server.redaction.model.Dictionary.RECOMMENDATION_PREFIX;
 
 import java.util.ArrayList;
 import java.util.Collection;
@@ -20,7 +13,16 @@ import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 import java.util.stream.Collectors;
 
-import static com.iqser.red.service.redaction.v1.server.redaction.model.Dictionary.RECOMMENDATION_PREFIX;
+import org.apache.commons.lang3.StringUtils;
+
+import com.iqser.red.service.redaction.v1.model.FileAttribute;
+import com.iqser.red.service.redaction.v1.server.classification.model.TextBlock;
+import com.iqser.red.service.redaction.v1.server.redaction.utils.EntitySearchUtils;
+import com.iqser.red.service.redaction.v1.server.redaction.utils.Patterns;
+
+import lombok.Builder;
+import lombok.Data;
+import lombok.extern.slf4j.Slf4j;
 
 @Data
 @Slf4j
@@ -59,16 +61,57 @@ public class Section {
     private List<FileAttribute> fileAttributes = new ArrayList<>();
 
 
-    public boolean fileAttributeByIdEquals(String id, String value){
-        return fileAttributes != null && fileAttributes.stream().filter(attribute -> id.equals(attribute.getId()) && value.equals(attribute.getValue())).findFirst().isPresent();
+    public boolean fileAttributeByIdEquals(String id, String value) {
+
+        return fileAttributes != null && fileAttributes.stream()
+                .filter(attribute -> id.equals(attribute.getId()) && value.equals(attribute.getValue()))
+                .findFirst()
+                .isPresent();
     }
 
-    public boolean fileAttributeByPlaceholderEquals(String placeholder, String value){
-        return fileAttributes != null && fileAttributes.stream().filter(attribute -> placeholder.equals(attribute.getPlaceholder()) && value.equals(attribute.getValue())).findFirst().isPresent();
+
+    public boolean fileAttributeByPlaceholderEquals(String placeholder, String value) {
+
+        return fileAttributes != null && fileAttributes.stream()
+                .filter(attribute -> placeholder.equals(attribute.getPlaceholder()) && value.equals(attribute.getValue()))
+                .findFirst()
+                .isPresent();
     }
 
-    public boolean fileAttributeByLabelEquals(String label, String value){
-        return fileAttributes != null && fileAttributes.stream().filter(attribute -> label.equals(attribute.getLabel()) && value.equals(attribute.getValue())).findFirst().isPresent();
+
+    public boolean fileAttributeByLabelEquals(String label, String value) {
+
+        return fileAttributes != null && fileAttributes.stream()
+                .filter(attribute -> label.equals(attribute.getLabel()) && value.equals(attribute.getValue()))
+                .findFirst()
+                .isPresent();
+    }
+
+
+    public boolean fileAttributeByIdEqualsIgnoreCase(String id, String value) {
+
+        return fileAttributes != null && fileAttributes.stream()
+                .filter(attribute -> id.equals(attribute.getId()) && value.equalsIgnoreCase(attribute.getValue()))
+                .findFirst()
+                .isPresent();
+    }
+
+
+    public boolean fileAttributeByPlaceholderEqualsIgnoreCase(String placeholder, String value) {
+
+        return fileAttributes != null && fileAttributes.stream()
+                .filter(attribute -> placeholder.equals(attribute.getPlaceholder()) && value.equalsIgnoreCase(attribute.getValue()))
+                .findFirst()
+                .isPresent();
+    }
+
+
+    public boolean fileAttributeByLabelEqualsIgnoreCase(String label, String value) {
+
+        return fileAttributes != null && fileAttributes.stream()
+                .filter(attribute -> label.equals(attribute.getLabel()) && value.equalsIgnoreCase(attribute.getValue()))
+                .findFirst()
+                .isPresent();
     }
 
 
@@ -91,13 +134,13 @@ public class Section {
 
     public boolean matchesType(String type) {
 
-        return entities.stream().anyMatch(entity -> entity.getType().equals(type));
+        return entities.stream().anyMatch(entity -> !entity.isIgnored() && entity.getType().equals(type));
     }
 
 
     public boolean matchesImageType(String type) {
 
-        return images.stream().anyMatch(image -> image.getType().equals(type));
+        return images.stream().anyMatch(image -> !image.isIgnored() &&  image.getType().equals(type));
     }
 
 
@@ -109,6 +152,18 @@ public class Section {
 
     public void expandByRegEx(String type, String pattern, boolean patternCaseInsensitive, int group) {
 
+        expandByRegEx(type, pattern, patternCaseInsensitive, group, null);
+    }
+
+
+    public void expandByRegEx(String type, String pattern, boolean patternCaseInsensitive, int group,
+                              String withoutPattern) {
+
+        Pattern compiledWithoutPattern = null;
+        if (withoutPattern != null) {
+            compiledWithoutPattern = Patterns.getCompiledPattern(withoutPattern, patternCaseInsensitive);
+        }
+
         Pattern compiledPattern = Patterns.getCompiledPattern(pattern, patternCaseInsensitive);
 
         Set<Entity> expanded = new HashSet<>();
@@ -118,14 +173,21 @@ public class Section {
                 continue;
             }
 
+            if (withoutPattern != null) {
+                Matcher matcherWithout = compiledWithoutPattern.matcher(entity.getWord());
+                if (matcherWithout.find()) {
+                    continue;
+                }
+            }
+
             Matcher matcher = compiledPattern.matcher(entity.getTextAfter());
 
             while (matcher.find()) {
                 String match = matcher.group(group);
-                if (StringUtils.isNotBlank(match)) {
-                    expanded.addAll(findEntities(entity.getWord() + match, type, false, entity.isRedaction(), entity.getMatchedRule(), entity
-                            .getRedactionReason(), entity.getLegalBasis()));
 
+                if (StringUtils.isNotBlank(match)) {
+                    Set<Entity> expandedEntities = findEntities(entity.getWord() + match, type, false, entity.isRedaction(), entity.getMatchedRule(), entity.getRedactionReason(), entity.getLegalBasis());
+                    expanded.addAll(EntitySearchUtils.findNonOverlappingMatchEntities(entities, expandedEntities));
                 }
             }
         }
@@ -191,6 +253,12 @@ public class Section {
     }
 
 
+    public void ignore(String type) {
+
+        entities.removeIf(entity -> entity.getType().equals(type));
+    }
+
+
     public void expandToHintAnnotationByRegEx(String type, String pattern, boolean patternCaseInsensitive, int group,
                                               String asType) {
 

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

@@ -5,35 +5,20 @@ import com.iqser.red.service.redaction.v1.model.RedactionChangeLog;
 import com.iqser.red.service.redaction.v1.model.RedactionLog;
 import com.iqser.red.service.redaction.v1.model.RedactionLogEntry;
 
+import com.iqser.red.service.redaction.v1.server.settings.RedactionServiceSettings;
+import lombok.NoArgsConstructor;
+import lombok.RequiredArgsConstructor;
 import org.springframework.stereotype.Service;
 
 @Service
+@RequiredArgsConstructor
 public class AnalyzeResponseService {
 
+    private final RedactionServiceSettings redactionServiceSettings;
+
     public AnalyzeResult createAnalyzeResponse(String dossierId, String fileId, long duration, int pageCount,
                                                RedactionLog redactionLog, RedactionChangeLog redactionChangeLog) {
 
-        boolean hasHints = redactionLog.getRedactionLogEntry()
-                .stream()
-                .filter(entry -> !entry.isExcluded())
-                .anyMatch(entry -> entry.isHint() && !entry.getType().equals("false_positive"));
-
-        boolean hasRequests = redactionLog.getRedactionLogEntry()
-                .stream()
-                .filter(entry -> !entry.isExcluded())
-                .anyMatch(entry -> entry.isManual() && entry.getStatus()
-                        .equals(com.iqser.red.service.redaction.v1.model.Status.REQUESTED));
-
-        boolean hasRedactions = redactionLog.getRedactionLogEntry()
-                .stream()
-                .filter(entry -> !entry.isExcluded())
-                .anyMatch(entry -> entry.isRedacted() && !entry.isManual() || entry.isManual() && entry.getStatus()
-                        .equals(com.iqser.red.service.redaction.v1.model.Status.APPROVED));
-
-        boolean hasImages = redactionLog.getRedactionLogEntry()
-                .stream()
-                .filter(entry -> !entry.isExcluded())
-                .anyMatch(entry -> entry.isHint() && entry.getType().equals("image") || entry.isImage());
 
         boolean hasUpdates = redactionChangeLog != null && redactionChangeLog.getRedactionLogEntry() != null && !redactionChangeLog
                 .getRedactionLogEntry()
@@ -46,11 +31,8 @@ public class AnalyzeResponseService {
                 .fileId(fileId)
                 .duration(duration)
                 .numberOfPages(pageCount)
-                .hasHints(hasHints)
-                .hasRedactions(hasRedactions)
-                .hasRequests(hasRequests)
-                .hasImages(hasImages)
                 .hasUpdates(hasUpdates)
+                .analysisVersion(redactionServiceSettings.getAnalysisVersion())
                 .rulesVersion(redactionLog.getRulesVersion())
                 .dictionaryVersion(redactionLog.getDictionaryVersion())
                 .legalBasisVersion(redactionLog.getLegalBasisVersion())

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

@@ -212,13 +212,13 @@ public class DictionaryService {
             dossierDictionaryVersion = dossierRepresentation.getDictionaryVersion();
         }
 
-        return new Dictionary(copy, DictionaryVersion.builder().dossierTemplateVersion(dossierTemplateRepresentation.getDictionaryVersion()).dossierVersion(dossierDictionaryVersion).build());
+        return new Dictionary(copy.stream().sorted(Comparator.comparingInt(DictionaryModel::getRank).reversed()).collect(Collectors.toList()), DictionaryVersion.builder().dossierTemplateVersion(dossierTemplateRepresentation.getDictionaryVersion()).dossierVersion(dossierDictionaryVersion).build());
     }
 
 
     public float[] getRequestRemoveColor(String dossierTemplateId) {
 
-        return dictionariesByDossierTemplate.get(dossierTemplateId).getRequestAddColor();
+        return dictionariesByDossierTemplate.get(dossierTemplateId).getRequestRemoveColor();
     }
 
 

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

@@ -63,7 +63,7 @@ public class DroolsExecutionService {
             rulesVersion = -1L;
         }
 
-        if (version > rulesVersion.longValue()) {
+        if (version > rulesVersion) {
             rulesVersionPerDossierTemplateId.put(dossierTemplateId, version);
             return createOrUpdateKieContainer(dossierTemplateId);
         }
@@ -128,7 +128,7 @@ public class DroolsExecutionService {
         if (rulesVersion == null) {
             return -1;
         }
-        return rulesVersion.longValue();
+        return rulesVersion;
     }
 
 }

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

@@ -1,13 +1,6 @@
 package com.iqser.red.service.redaction.v1.server.redaction.service;
 
-import com.iqser.red.service.redaction.v1.model.FileAttribute;
-import com.iqser.red.service.redaction.v1.model.ManualImageRecategorization;
-import com.iqser.red.service.redaction.v1.model.ManualRedactionEntry;
-import com.iqser.red.service.redaction.v1.model.ManualRedactions;
-import com.iqser.red.service.redaction.v1.model.Point;
-import com.iqser.red.service.redaction.v1.model.Rectangle;
-import com.iqser.red.service.redaction.v1.model.SectionArea;
-import com.iqser.red.service.redaction.v1.model.Status;
+import com.iqser.red.service.redaction.v1.model.*;
 import com.iqser.red.service.redaction.v1.server.classification.model.*;
 import com.iqser.red.service.redaction.v1.server.redaction.model.Dictionary;
 import com.iqser.red.service.redaction.v1.server.redaction.model.*;
@@ -15,10 +8,8 @@ import com.iqser.red.service.redaction.v1.server.redaction.utils.EntitySearchUti
 import com.iqser.red.service.redaction.v1.server.redaction.utils.IdBuilder;
 import com.iqser.red.service.redaction.v1.server.tableextraction.model.Cell;
 import com.iqser.red.service.redaction.v1.server.tableextraction.model.Table;
-
 import lombok.RequiredArgsConstructor;
 import lombok.extern.slf4j.Slf4j;
-
 import org.apache.commons.collections4.CollectionUtils;
 import org.apache.commons.lang3.StringUtils;
 import org.kie.api.runtime.KieContainer;
@@ -52,35 +43,13 @@ public class EntityRedactionService {
 
         if (dictionary.hasLocalEntries()) {
 
-            Map<Integer, Set<Entity>> hintsPerSectionNumber = new HashMap<>();
-            documentEntities.stream().forEach(entity -> {
-                if (dictionary.isHint(entity.getType()) && entity.isDictionaryEntry()) {
-                    hintsPerSectionNumber.computeIfAbsent(entity.getSectionNumber(), (x) -> new HashSet<>())
-                            .add(entity);
-                }
-            });
-
+            Map<Integer, Set<Entity>> hintsPerSectionNumber = getHintsPerSection(documentEntities, dictionary);
             Set<Entity> foundByLocal = findEntities(classifiedDoc, container, manualRedactions, dictionary, true, hintsPerSectionNumber, fileAttributes);
             EntitySearchUtils.addEntitiesWithHigherRank(documentEntities, foundByLocal, dictionary);
             EntitySearchUtils.removeEntitiesContainedInLarger(documentEntities);
         }
 
-        for (Entity entity : documentEntities) {
-            Map<Integer, List<EntityPositionSequence>> sequenceOnPage = new HashMap<>();
-            for (EntityPositionSequence entityPositionSequence : entity.getPositionSequences()) {
-                sequenceOnPage.computeIfAbsent(entityPositionSequence.getPageNumber(), (x) -> new ArrayList<>())
-                        .add(entityPositionSequence);
-            }
-
-            for (Map.Entry<Integer, List<EntityPositionSequence>> entry : sequenceOnPage.entrySet()) {
-                classifiedDoc.getEntities()
-                        .computeIfAbsent(entry.getKey(), (x) -> new ArrayList<>())
-                        .add(new Entity(entity.getWord(), entity.getType(), entity.isRedaction(), entity.getRedactionReason(), entry
-                                .getValue(), entity.getHeadline(), entity.getMatchedRule(), entity.getSectionNumber(), entity
-                                .getLegalBasis(), entity.isDictionaryEntry(), entity.getTextBefore(), entity.getTextAfter(), entity
-                                .getStart(), entity.getEnd(), entity.isDossierDictionaryEntry()));
-            }
-        }
+        classifiedDoc.setEntities(convertToEnititesPerPage(documentEntities));
 
         dictionaryService.updateExternalDictionary(dictionary, dossierTemplateId);
 
@@ -89,6 +58,39 @@ public class EntityRedactionService {
     }
 
 
+    public Map<Integer, List<Entity>> convertToEnititesPerPage(Set<Entity> entities){
+        Map<Integer, List<Entity>> entitiesPerPage = new HashMap<>();
+        for (Entity entity : entities) {
+            Map<Integer, List<EntityPositionSequence>> sequenceOnPage = new HashMap<>();
+            for (EntityPositionSequence entityPositionSequence : entity.getPositionSequences()) {
+                sequenceOnPage.computeIfAbsent(entityPositionSequence.getPageNumber(), (x) -> new ArrayList<>())
+                        .add(entityPositionSequence);
+            }
+
+            for (Map.Entry<Integer, List<EntityPositionSequence>> entry : sequenceOnPage.entrySet()) {
+                entitiesPerPage
+                        .computeIfAbsent(entry.getKey(), (x) -> new ArrayList<>())
+                        .add(new Entity(entity.getWord(), entity.getType(), entity.isRedaction(), entity.getRedactionReason(), entry
+                                .getValue(), entity.getHeadline(), entity.getMatchedRule(), entity.getSectionNumber(), entity
+                                .getLegalBasis(), entity.isDictionaryEntry(), entity.getTextBefore(), entity.getTextAfter(), entity
+                                .getStart(), entity.getEnd(), entity.isDossierDictionaryEntry()));
+            }
+        }
+        return entitiesPerPage;
+    }
+
+
+    public Map<Integer, Set<Entity>> getHintsPerSection(Set<Entity> entities, Dictionary dictionary){
+        Map<Integer, Set<Entity>> hintsPerSectionNumber = new HashMap<>();
+        entities.stream().forEach(entity -> {
+            if (dictionary.isHint(entity.getType()) && entity.isDictionaryEntry()) {
+                hintsPerSectionNumber.computeIfAbsent(entity.getSectionNumber(), (x) -> new HashSet<>())
+                        .add(entity);
+            }
+        });
+        return hintsPerSectionNumber;
+    }
+
     private Set<Entity> findEntities(Document classifiedDoc, KieContainer kieContainer,
                                      ManualRedactions manualRedactions, Dictionary dictionary, boolean local,
                                      Map<Integer, Set<Entity>> hintsPerSectionNumber,
@@ -103,9 +105,9 @@ public class EntityRedactionService {
             List<Table> tables = paragraph.getTables();
             for (Table table : tables) {
                 if (table.getColCount() == 2) {
-                    sectionSearchableTextPairs.addAll(processTableAsOneText(classifiedDoc, table, manualRedactions, sectionNumber, dictionary, local, hintsPerSectionNumber, fileAttributes));
+                    sectionSearchableTextPairs.addAll(processTableAsOneText(classifiedDoc, table, sectionNumber, dictionary, local, hintsPerSectionNumber, fileAttributes, manualRedactions));
                 } else {
-                    sectionSearchableTextPairs.addAll(processTablePerRow(classifiedDoc, table, manualRedactions, sectionNumber, dictionary, local, hintsPerSectionNumber, fileAttributes));
+                    sectionSearchableTextPairs.addAll(processTablePerRow(classifiedDoc, table, sectionNumber, dictionary, local, hintsPerSectionNumber, fileAttributes, manualRedactions));
                 }
                 sectionNumber.incrementAndGet();
             }
@@ -132,48 +134,51 @@ public class EntityRedactionService {
         }
 
         sectionSearchableTextPairs.forEach(sectionSearchableTextPair -> {
-            Section analysedRowSection = droolsExecutionService.executeRules(kieContainer, sectionSearchableTextPair.getSection());
-            documentEntities.addAll(analysedRowSection.getEntities());
+            Section analysedSection = droolsExecutionService.executeRules(kieContainer, sectionSearchableTextPair.getSection());
+            documentEntities.addAll(analysedSection.getEntities());
 
-            for (Image image : analysedRowSection.getImages()) {
+            for (Image image : analysedSection.getImages()) {
                 classifiedDoc.getImages().computeIfAbsent(image.getPage(), (a) -> new HashSet<>()).add(image);
             }
 
-            analysedRowSection.getLocalDictionaryAdds().keySet().forEach(key -> {
-                if (dictionary.isRecommendation(key)) {
-                    analysedRowSection.getLocalDictionaryAdds().get(key).forEach(value -> {
-                        if (!dictionary.containsValue(key, value)) {
-                            dictionary.getLocalAccessMap().get(key).getLocalEntries().add(value);
-                        }
-                    });
-                } else {
-                    analysedRowSection.getLocalDictionaryAdds().get(key).forEach(value -> {
-
-                        if (dictionary.getLocalAccessMap().get(key) == null) {
-                            log.warn("Dictionary {} is null", key);
-                        }
-
-                        if (dictionary.getLocalAccessMap().get(key).getLocalEntries() == null) {
-                            log.warn("Dictionary {} localEntries is null", key);
-                        }
-
-                        dictionary.getLocalAccessMap().get(key).getLocalEntries().add(value);
-                    });
-                }
-            });
-
+            addLocalValuesToDictionary(analysedSection, dictionary);
         });
 
         return documentEntities;
     }
 
 
+    public void addLocalValuesToDictionary(Section analysedSection, Dictionary dictionary){
+        analysedSection.getLocalDictionaryAdds().keySet().forEach(key -> {
+            if (dictionary.isRecommendation(key)) {
+                analysedSection.getLocalDictionaryAdds().get(key).forEach(value -> {
+                    if (!dictionary.containsValue(key, value)) {
+                        dictionary.getLocalAccessMap().get(key).getLocalEntries().add(value);
+                    }
+                });
+            } else {
+                analysedSection.getLocalDictionaryAdds().get(key).forEach(value -> {
+
+                    if (dictionary.getLocalAccessMap().get(key) == null) {
+                        log.warn("Dictionary {} is null", key);
+                    }
+
+                    if (dictionary.getLocalAccessMap().get(key).getLocalEntries() == null) {
+                        log.warn("Dictionary {} localEntries is null", key);
+                    }
+
+                    dictionary.getLocalAccessMap().get(key).getLocalEntries().add(value);
+                });
+            }
+        });
+    }
+
+
     private List<SectionSearchableTextPair> processTablePerRow(Document classifiedDoc, Table table,
-                                                               ManualRedactions manualRedactions,
                                                                AtomicInteger sectionNumber, Dictionary dictionary,
                                                                boolean local,
                                                                Map<Integer, Set<Entity>> hintsPerSectionNumber,
-                                                               List<FileAttribute> fileAttributes) {
+                                                               List<FileAttribute> fileAttributes, ManualRedactions manualRedactions) {
 
         List<SectionSearchableTextPair> sectionSearchableTextPairs = new ArrayList<>();
 
@@ -198,7 +203,6 @@ public class EntityRedactionService {
                 sectionText.getSectionAreas().add(sectionArea);
                 sectionText.getTextBlocks().addAll(cell.getTextBlocks());
 
-                addSectionToManualRedactions(cell.getTextBlocks(), manualRedactions, table.getHeadline(), sectionNumber.intValue());
                 int cellStart = start;
 
                 if (!cell.isHeaderCell()) {
@@ -225,6 +229,31 @@ public class EntityRedactionService {
             Set<Entity> rowEntities = findEntities(searchableRow, table.getHeadline(), sectionNumber.intValue(), dictionary, local);
             surroundingWordsService.addSurroundingText(rowEntities, searchableRow, dictionary, cellStarts);
 
+            if (!local && manualRedactions != null) {
+
+
+                var approvedForceRedactions = manualRedactions.getForceRedacts().stream()
+                        .filter(fr -> fr.getStatus() == Status.APPROVED)
+                        .filter(fr -> fr.getRequestDate() != null)
+                        .collect(Collectors.toList());
+                // only approved id removals, that haven't been forced back afterwards
+                var idsToRemove = manualRedactions.getIdsToRemove().stream()
+                        .filter(idr -> idr.getStatus() == Status.APPROVED)
+                        .filter(idr -> idr.getRequestDate() != null)
+                        .filter(idr -> approvedForceRedactions.stream().noneMatch(forceRedact -> forceRedact.getRequestDate().isAfter(idr.getRequestDate())))
+                        .map(IdRemoval::getId).collect(Collectors.toSet());
+
+                log.info("Removed Ids: {}", idsToRemove);
+
+                rowEntities.forEach(entity ->
+                        entity.getPositionSequences().forEach(ps -> {
+                            if (idsToRemove.contains(ps.getId())) {
+                                entity.setIgnored(true);
+                            }
+                        }));
+
+            }
+
             sectionSearchableTextPairs.add(new SectionSearchableTextPair(Section.builder()
                     .isLocal(local)
                     .dictionaryTypes(dictionary.getTypes())
@@ -259,11 +288,10 @@ public class EntityRedactionService {
 
 
     private List<SectionSearchableTextPair> processTableAsOneText(Document classifiedDoc, Table table,
-                                                                  ManualRedactions manualRedactions,
                                                                   AtomicInteger sectionNumber, Dictionary dictionary,
                                                                   boolean local,
                                                                   Map<Integer, Set<Entity>> hintsPerSectionNumber,
-                                                                  List<FileAttribute> fileAttributes) {
+                                                                  List<FileAttribute> fileAttributes, ManualRedactions manualRedactions) {
 
         List<SectionSearchableTextPair> sectionSearchableTextPairs = new ArrayList<>();
         SearchableText entireTableText = new SearchableText();
@@ -288,13 +316,37 @@ public class EntityRedactionService {
                 for (TextBlock textBlock : cell.getTextBlocks()) {
                     entireTableText.addAll(textBlock.getSequences());
                 }
-                addSectionToManualRedactions(cell.getTextBlocks(), manualRedactions, table.getHeadline(), sectionNumber.intValue());
             }
         }
 
         Set<Entity> rowEntities = findEntities(entireTableText, table.getHeadline(), sectionNumber.intValue(), dictionary, local);
         surroundingWordsService.addSurroundingText(rowEntities, entireTableText, dictionary);
 
+        if (!local && manualRedactions != null) {
+
+
+            var approvedForceRedactions = manualRedactions.getForceRedacts().stream()
+                    .filter(fr -> fr.getStatus() == Status.APPROVED)
+                    .filter(fr -> fr.getRequestDate() != null)
+                    .collect(Collectors.toList());
+            // only approved id removals, that haven't been forced back afterwards
+            var idsToRemove = manualRedactions.getIdsToRemove().stream()
+                    .filter(idr -> idr.getStatus() == Status.APPROVED)
+                    .filter(idr -> idr.getRequestDate() != null)
+                    .filter(idr -> approvedForceRedactions.stream().noneMatch(forceRedact -> forceRedact.getRequestDate().isAfter(idr.getRequestDate())))
+                    .map(IdRemoval::getId).collect(Collectors.toSet());
+
+            log.info("Removed Ids: {}", idsToRemove);
+
+            rowEntities.forEach(entity ->
+                    entity.getPositionSequences().forEach(ps -> {
+                        if (idsToRemove.contains(ps.getId())) {
+                            entity.setIgnored(true);
+                        }
+                    }));
+
+        }
+
         sectionSearchableTextPairs.add(new SectionSearchableTextPair(Section.builder()
                 .isLocal(local)
                 .dictionaryTypes(dictionary.getTypes())
@@ -348,10 +400,34 @@ public class EntityRedactionService {
             classifiedDoc.getSectionText().add(sectionText);
         }
 
-        addSectionToManualRedactions(paragraphTextBlocks, manualRedactions, headline, sectionNumber.intValue());
         Set<Entity> entities = findEntities(searchableText, headline, sectionNumber.intValue(), dictionary, local);
         surroundingWordsService.addSurroundingText(entities, searchableText, dictionary);
 
+        if (!local && manualRedactions != null) {
+
+
+            var approvedForceRedactions = manualRedactions.getForceRedacts().stream()
+                    .filter(fr -> fr.getStatus() == Status.APPROVED)
+                    .filter(fr -> fr.getRequestDate() != null)
+                    .collect(Collectors.toList());
+            // only approved id removals, that haven't been forced back afterwards
+            var idsToRemove = manualRedactions.getIdsToRemove().stream()
+                    .filter(idr -> idr.getStatus() == Status.APPROVED)
+                    .filter(idr -> idr.getRequestDate() != null)
+                    .filter(idr -> approvedForceRedactions.stream().noneMatch(forceRedact -> forceRedact.getRequestDate().isAfter(idr.getRequestDate())))
+                    .map(IdRemoval::getId).collect(Collectors.toSet());
+
+            log.info("Removed Ids: {}", idsToRemove);
+
+            entities.forEach(entity ->
+                    entity.getPositionSequences().forEach(ps -> {
+                        if (idsToRemove.contains(ps.getId())) {
+                            entity.setIgnored(true);
+                        }
+                    }));
+
+        }
+
         return new SectionSearchableTextPair(Section.builder()
                 .isLocal(local)
                 .dictionaryTypes(dictionary.getTypes())
@@ -396,26 +472,6 @@ public class EntityRedactionService {
     }
 
 
-    private void addSectionToManualRedactions(List<TextBlock> textBlocks, ManualRedactions manualRedactions,
-                                              String section, int sectionNumber) {
-
-        if (manualRedactions == null || manualRedactions.getEntriesToAdd().isEmpty()) {
-            return;
-        }
-
-        for (TextBlock textBlock : textBlocks) {
-            for (ManualRedactionEntry manualRedactionEntry : manualRedactions.getEntriesToAdd()) {
-                for (Rectangle rectangle : manualRedactionEntry.getPositions()) {
-                    if (textBlock.contains(rectangle)) {
-                        manualRedactionEntry.setSection(section);
-                        manualRedactionEntry.setSectionNumber(sectionNumber);
-                    }
-                }
-            }
-        }
-    }
-
-
     private Image convertAndRecategorize(PdfImage pdfImage, int sectionNumber, String headline, ManualRedactions manualRedactions) {
 
         Image image = Image.builder()
@@ -426,6 +482,7 @@ public class EntityRedactionService {
                 .sectionNumber(sectionNumber)
                 .section(headline)
                 .page(pdfImage.getPage())
+                .hasTransparency(pdfImage.isHasTransparency())
                 .build();
 
         String imageId = IdBuilder.buildId(image.getPosition(), image.getPage());

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

@@ -1,55 +1,29 @@
 package com.iqser.red.service.redaction.v1.server.redaction.service;
 
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-import java.util.stream.Collectors;
-import java.util.stream.Stream;
-
-import org.kie.api.runtime.KieContainer;
-import org.springframework.stereotype.Service;
-import org.springframework.web.bind.annotation.RequestBody;
-
 import com.iqser.red.service.file.management.v1.api.model.FileType;
-import com.iqser.red.service.redaction.v1.model.AnalyzeRequest;
-import com.iqser.red.service.redaction.v1.model.AnalyzeResult;
-import com.iqser.red.service.redaction.v1.model.Comment;
-import com.iqser.red.service.redaction.v1.model.IdRemoval;
-import com.iqser.red.service.redaction.v1.model.ManualForceRedact;
-import com.iqser.red.service.redaction.v1.model.ManualImageRecategorization;
-import com.iqser.red.service.redaction.v1.model.ManualLegalBasisChange;
-import com.iqser.red.service.redaction.v1.model.ManualRedactionEntry;
-import com.iqser.red.service.redaction.v1.model.ManualRedactions;
-import com.iqser.red.service.redaction.v1.model.Rectangle;
-import com.iqser.red.service.redaction.v1.model.RedactionLog;
-import com.iqser.red.service.redaction.v1.model.RedactionLogEntry;
-import com.iqser.red.service.redaction.v1.model.SectionArea;
-import com.iqser.red.service.redaction.v1.model.Status;
+import com.iqser.red.service.redaction.v1.model.*;
 import com.iqser.red.service.redaction.v1.server.classification.model.Document;
 import com.iqser.red.service.redaction.v1.server.classification.model.SectionText;
 import com.iqser.red.service.redaction.v1.server.classification.model.Text;
 import com.iqser.red.service.redaction.v1.server.client.LegalBasisClient;
 import com.iqser.red.service.redaction.v1.server.exception.RedactionException;
 import com.iqser.red.service.redaction.v1.server.redaction.model.Dictionary;
-import com.iqser.red.service.redaction.v1.server.redaction.model.DictionaryIncrement;
-import com.iqser.red.service.redaction.v1.server.redaction.model.DictionaryVersion;
-import com.iqser.red.service.redaction.v1.server.redaction.model.Entity;
-import com.iqser.red.service.redaction.v1.server.redaction.model.EntityPositionSequence;
-import com.iqser.red.service.redaction.v1.server.redaction.model.Image;
-import com.iqser.red.service.redaction.v1.server.redaction.model.RedRectangle2D;
-import com.iqser.red.service.redaction.v1.server.redaction.model.Section;
-import com.iqser.red.service.redaction.v1.server.redaction.model.SectionSearchableTextPair;
+import com.iqser.red.service.redaction.v1.server.redaction.model.*;
 import com.iqser.red.service.redaction.v1.server.redaction.utils.EntitySearchUtils;
 import com.iqser.red.service.redaction.v1.server.redaction.utils.IdBuilder;
 import com.iqser.red.service.redaction.v1.server.segmentation.PdfSegmentationService;
+import com.iqser.red.service.redaction.v1.server.settings.RedactionServiceSettings;
 import com.iqser.red.service.redaction.v1.server.storage.RedactionStorageService;
-
 import lombok.RequiredArgsConstructor;
 import lombok.SneakyThrows;
 import lombok.extern.slf4j.Slf4j;
+import org.kie.api.runtime.KieContainer;
+import org.springframework.stereotype.Service;
+import org.springframework.web.bind.annotation.RequestBody;
+
+import java.util.*;
+import java.util.stream.Collectors;
+import java.util.stream.Stream;
 
 @Slf4j
 @Service
@@ -66,6 +40,7 @@ public class ReanalyzeService {
     private final RedactionChangeLogService redactionChangeLogService;
     private final AnalyzeResponseService analyzeResponseService;
     private final LegalBasisClient legalBasisClient;
+    private final RedactionServiceSettings redactionServiceSettings;
 
 
     public AnalyzeResult analyze(AnalyzeRequest analyzeRequest) {
@@ -87,13 +62,12 @@ public class ReanalyzeService {
 
         entityRedactionService.processDocument(classifiedDoc, analyzeRequest.getDossierTemplateId(), analyzeRequest.getManualRedactions(), analyzeRequest
                 .getDossierId(), analyzeRequest.getFileAttributes());
-        redactionLogCreatorService.createRedactionLog(classifiedDoc, pageCount, analyzeRequest.getManualRedactions(), analyzeRequest
-                .getDossierTemplateId());
+        redactionLogCreatorService.createRedactionLog(classifiedDoc, pageCount, analyzeRequest.getDossierTemplateId());
 
         log.info("Redaction analysis successful...");
 
         var legalBasis = legalBasisClient.getLegalBasisMapping(analyzeRequest.getDossierTemplateId());
-        var redactionLog = new RedactionLog(classifiedDoc.getRedactionLogEntities(), legalBasis, classifiedDoc.getDictionaryVersion()
+        var redactionLog = new RedactionLog(redactionServiceSettings.getAnalysisVersion(), classifiedDoc.getRedactionLogEntities(), legalBasis, classifiedDoc.getDictionaryVersion()
                 .getDossierTemplateVersion(), classifiedDoc.getDictionaryVersion()
                 .getDossierVersion(), classifiedDoc.getRulesVersion(), legalBasisClient.getVersion(analyzeRequest.getDossierTemplateId()));
 
@@ -108,6 +82,15 @@ public class ReanalyzeService {
         redactionStorageService.storeObject(analyzeRequest.getDossierId(), analyzeRequest.getFileId(), FileType.REDACTION_LOG, redactionLog);
         redactionStorageService.storeObject(analyzeRequest.getDossierId(), analyzeRequest.getFileId(), FileType.TEXT, new Text(pageCount, classifiedDoc
                 .getSectionText()));
+
+        // enhance section grid with headline data
+        classifiedDoc.getSectionText().forEach(sectionText -> {
+            classifiedDoc
+                    .getSectionGrid().getSections().add(new SectionGrid.SectionGridSection(sectionText.getSectionNumber(),
+                            sectionText.getHeadline(),
+                            sectionText.getSectionAreas().stream().map(SectionArea::getPage).collect(Collectors.toSet()),
+                            sectionText.getSectionAreas()));
+        });
         redactionStorageService.storeObject(analyzeRequest.getDossierId(), analyzeRequest.getFileId(), FileType.SECTION_GRID, classifiedDoc
                 .getSectionGrid());
 
@@ -132,20 +115,66 @@ public class ReanalyzeService {
         DictionaryIncrement dictionaryIncrement = dictionaryService.getDictionaryIncrements(analyzeRequest.getDossierTemplateId(), new DictionaryVersion(redactionLog
                 .getDictionaryVersion(), redactionLog.getDossierDictionaryVersion()), analyzeRequest.getDossierId());
 
-        Set<String> manualForceAndRemoveIds = getForceAndRemoveIds(analyzeRequest.getManualRedactions());
-        Map<String, List<Comment>> comments = null;
-        Set<ManualRedactionEntry> manualAdds = null;
+        Set<Integer> sectionsToReanalyse = !analyzeRequest.getSectionsToReanalyse().isEmpty() ? analyzeRequest.getSectionsToReanalyse() :
+                findSectionsToReanalyse(dictionaryIncrement, redactionLog, text, analyzeRequest);
 
-        if (analyzeRequest.getManualRedactions() != null) {
-            // TODO comments will be removed from redactionLog, so we ignore this first.
-            comments = analyzeRequest.getManualRedactions().getComments();
-            manualAdds = analyzeRequest.getManualRedactions().getEntriesToAdd();
+        if (sectionsToReanalyse.isEmpty()) {
+            return finalizeAnalysis(analyzeRequest, startTime, redactionLog, text, dictionaryIncrement);
         }
 
+        List<SectionText> reanalysisSections = text.getSectionTexts()
+                .stream()
+                .filter(sectionText -> sectionsToReanalyse.contains(sectionText.getSectionNumber()))
+                .collect(Collectors.toList());
+
+        KieContainer kieContainer = droolsExecutionService.updateRules(analyzeRequest.getDossierTemplateId());
+
+        Dictionary dictionary = dictionaryService.getDeepCopyDictionary(analyzeRequest.getDossierTemplateId(), analyzeRequest
+                .getDossierId());
+
+        Map<Integer, Set<Image>> imagesPerPage = new HashMap<>();
+        Set<Entity> entities = findEntities(reanalysisSections, dictionary, kieContainer, analyzeRequest, false, null, imagesPerPage);
+
+        if (dictionary.hasLocalEntries()) {
+            Map<Integer, Set<Entity>> hintsPerSectionNumber = entityRedactionService.getHintsPerSection(entities, dictionary);
+            Set<Entity> foundByLocal = findEntities(reanalysisSections, dictionary, kieContainer, analyzeRequest, true, hintsPerSectionNumber, imagesPerPage);
+            EntitySearchUtils.addEntitiesWithHigherRank(entities, foundByLocal, dictionary);
+            EntitySearchUtils.removeEntitiesContainedInLarger(entities);
+        }
+
+        Map<Integer, List<Entity>> entitiesPerPage = entityRedactionService.convertToEnititesPerPage(entities);
+
+        List<RedactionLogEntry> newRedactionLogEntries = new ArrayList<>();
+        for (int page = 1; page <= text.getNumberOfPages(); page++) {
+            if (entitiesPerPage.get(page) != null) {
+                newRedactionLogEntries.addAll(redactionLogCreatorService.addEntries(entitiesPerPage, page, analyzeRequest
+                        .getDossierTemplateId()));
+            }
+
+            if (imagesPerPage.get(page) != null) {
+                newRedactionLogEntries.addAll(redactionLogCreatorService.addImageEntries(imagesPerPage, page, analyzeRequest
+                        .getDossierTemplateId()));
+            }
+
+        }
+
+        redactionLog.getRedactionLogEntry().removeIf(entry -> sectionsToReanalyse.contains(entry.getSectionNumber()));
+        redactionLog.getRedactionLogEntry().addAll(newRedactionLogEntries);
+        AnalyzeResult analyzeResult = finalizeAnalysis(analyzeRequest, startTime, redactionLog, text, dictionaryIncrement);
+        analyzeResult.setWasReanalyzed(true);
+        return analyzeResult;
+    }
+
+
+    private Set<Integer> findSectionsToReanalyse(DictionaryIncrement dictionaryIncrement, RedactionLog redactionLog,
+                                                 Text text, AnalyzeRequest analyzeRequest) {
+
+        Set<String> relevantManuallyModifiedAnnotationIds = getRelevantManuallyModifiedAnnotationIds(analyzeRequest.getManualRedactions());
+
         Set<Integer> sectionsToReanalyse = new HashSet<>();
         Map<Integer, Set<Image>> imageEntries = new HashMap<>();
         for (RedactionLogEntry entry : redactionLog.getRedactionLogEntry()) {
-            if (entry.isManual() || manualForceAndRemoveIds.contains(entry.getId())) {
+            if (entry.isManual() || relevantManuallyModifiedAnnotationIds.contains(entry.getId())) {
                 sectionsToReanalyse.add(entry.getSectionNumber());
             }
             if (entry.isImage() || entry.getType().equals("image")) {
@@ -159,47 +188,24 @@ public class ReanalyzeService {
                 sectionsToReanalyse.add(sectionText.getSectionNumber());
             }
 
-            if (manualAdds != null) {
-                for (SectionArea sectionArea : sectionText.getSectionAreas()) {
-                    for (ManualRedactionEntry manualAdd : manualAdds) {
-                        for (Rectangle manualPosition : manualAdd.getPositions()) {
-                            if (sectionArea.contains(manualPosition)) {
-                                manualAdd.setSection(sectionText.getHeadline());
-                                manualAdd.setSectionNumber(sectionText.getSectionNumber());
-                            }
-                        }
-                    }
-                }
-            }
         }
 
         log.info("Should reanalyze {} sections for request: {}", sectionsToReanalyse.size(), analyzeRequest);
 
-        if (sectionsToReanalyse.isEmpty() && (manualAdds == null || manualAdds.isEmpty())) {
-            return finalizeAnalysis(analyzeRequest, startTime, redactionLog, text, dictionaryIncrement);
-        }
+        return sectionsToReanalyse;
+    }
 
-        List<SectionText> reanalysisSections = new ArrayList<>();
 
-        for (SectionText sectionText : text.getSectionTexts()) {
-
-            if (sectionsToReanalyse.contains(sectionText.getSectionNumber())) {
-                reanalysisSections.add(sectionText);
-            }
-        }
-
-        //--
-
-        KieContainer kieContainer = droolsExecutionService.updateRules(analyzeRequest.getDossierTemplateId());
-
-        Dictionary dictionary = dictionaryService.getDeepCopyDictionary(analyzeRequest.getDossierTemplateId(), analyzeRequest
-                .getDossierId());
+    private Set<Entity> findEntities(List<SectionText> reanalysisSections, Dictionary dictionary,
+                                     KieContainer kieContainer, AnalyzeRequest analyzeRequest, boolean local,
+                                     Map<Integer, Set<Entity>> hintsPerSectionNumber,
+                                     Map<Integer, Set<Image>> imagesPerPage) {
 
         List<SectionSearchableTextPair> sectionSearchableTextPairs = new ArrayList<>();
         for (SectionText reanalysisSection : reanalysisSections) {
 
             Set<Entity> entities = entityRedactionService.findEntities(reanalysisSection.getSearchableText(), reanalysisSection
-                    .getHeadline(), reanalysisSection.getSectionNumber(), dictionary, false);
+                    .getHeadline(), reanalysisSection.getSectionNumber(), dictionary, local);
             if (reanalysisSection.getCellStarts() != null && !reanalysisSection.getCellStarts().isEmpty()) {
                 surroundingWordsService.addSurroundingText(entities, reanalysisSection.getSearchableText(), dictionary, reanalysisSection
                         .getCellStarts());
@@ -207,24 +213,54 @@ public class ReanalyzeService {
                 surroundingWordsService.addSurroundingText(entities, reanalysisSection.getSearchableText(), dictionary);
             }
 
-            if (reanalysisSection.getImages() != null && !reanalysisSection.getImages()
-                    .isEmpty() && analyzeRequest.getManualRedactions() != null && analyzeRequest.getManualRedactions()
-                    .getImageRecategorizations() != null) {
-                for (Image image : reanalysisSection.getImages()) {
-                    String imageId = IdBuilder.buildId(image.getPosition(), image.getPage());
-                    for(ManualImageRecategorization imageRecategorization: analyzeRequest.getManualRedactions()
-                            .getImageRecategorizations()){
-                        if(imageRecategorization.getStatus().equals(Status.APPROVED) && imageRecategorization.getId().equals(imageId)){
-                            image.setType(imageRecategorization.getType());
+            if (!local && analyzeRequest.getManualRedactions() != null) {
+
+
+                var approvedForceRedactions = analyzeRequest.getManualRedactions().getForceRedacts().stream()
+                        .filter(fr -> fr.getStatus() == Status.APPROVED)
+                        .filter(fr -> fr.getRequestDate() != null)
+                        .collect(Collectors.toList());
+                // only approved id removals, that haven't been forced back afterwards
+                var idsToRemove = analyzeRequest.getManualRedactions().getIdsToRemove().stream()
+                        .filter(idr -> idr.getStatus() == Status.APPROVED)
+                        .filter(idr -> idr.getRequestDate() != null)
+                        .filter(idr -> approvedForceRedactions.stream().noneMatch(forceRedact -> forceRedact.getRequestDate().isAfter(idr.getRequestDate())))
+                        .map(IdRemoval::getId).collect(Collectors.toSet());
+
+                log.info("Removed Ids: {}", idsToRemove);
+
+                if (reanalysisSection.getImages() != null && !reanalysisSection.getImages().isEmpty() && analyzeRequest.getManualRedactions().getImageRecategorizations() != null) {
+                    for (Image image : reanalysisSection.getImages()) {
+                        String imageId = IdBuilder.buildId(image.getPosition(), image.getPage());
+                        for (ManualImageRecategorization imageRecategorization : analyzeRequest.getManualRedactions()
+                                .getImageRecategorizations()) {
+                            if (imageRecategorization.getStatus().equals(Status.APPROVED) && imageRecategorization.getId()
+                                    .equals(imageId)) {
+                                image.setType(imageRecategorization.getType());
+                            }
+                        }
+                        if (idsToRemove.contains(imageId)) {
+                            image.setIgnored(true);
                         }
                     }
                 }
+
+                entities.forEach(entity ->
+                        entity.getPositionSequences().forEach(ps -> {
+                            if (idsToRemove.contains(ps.getId())) {
+                                entity.setIgnored(true);
+                            }
+                        }));
+
             }
 
             sectionSearchableTextPairs.add(new SectionSearchableTextPair(Section.builder()
                     .isLocal(false)
                     .dictionaryTypes(dictionary.getTypes())
-                    .entities(entities)
+                    .entities(hintsPerSectionNumber != null && hintsPerSectionNumber.containsKey(reanalysisSection.getSectionNumber()) ? Stream
+                            .concat(entities.stream(), hintsPerSectionNumber.get(reanalysisSection.getSectionNumber())
+                                    .stream())
+                            .collect(Collectors.toSet()) : entities)
                     .text(reanalysisSection.getSearchableText().getAsStringWithLinebreaks())
                     .searchText(reanalysisSection.getSearchableText().toString())
                     .headline(reanalysisSection.getHeadline())
@@ -238,56 +274,19 @@ public class ReanalyzeService {
         }
 
         Set<Entity> entities = new HashSet<>();
-        Map<Integer, Set<Image>> imagesPerPage = new HashMap<>();
         sectionSearchableTextPairs.forEach(sectionSearchableTextPair -> {
-            Section analysedRowSection = droolsExecutionService.executeRules(kieContainer, sectionSearchableTextPair.getSection());
-            entities.addAll(analysedRowSection.getEntities());
+            Section analysedSection = droolsExecutionService.executeRules(kieContainer, sectionSearchableTextPair.getSection());
+            entities.addAll(analysedSection.getEntities());
             EntitySearchUtils.removeEntitiesContainedInLarger(entities);
 
-            for (Image image : analysedRowSection.getImages()) {
+            for (Image image : analysedSection.getImages()) {
                 imagesPerPage.computeIfAbsent(image.getPage(), (a) -> new HashSet<>()).add(image);
             }
 
+            entityRedactionService.addLocalValuesToDictionary(analysedSection, dictionary);
         });
 
-        Map<Integer, List<Entity>> entitiesPerPage = new HashMap<>();
-        for (Entity entity : entities) {
-            Map<Integer, List<EntityPositionSequence>> sequenceOnPage = new HashMap<>();
-            for (EntityPositionSequence entityPositionSequence : entity.getPositionSequences()) {
-                sequenceOnPage.computeIfAbsent(entityPositionSequence.getPageNumber(), (x) -> new ArrayList<>())
-                        .add(entityPositionSequence);
-            }
-
-            for (Map.Entry<Integer, List<EntityPositionSequence>> entry : sequenceOnPage.entrySet()) {
-                entitiesPerPage.computeIfAbsent(entry.getKey(), (x) -> new ArrayList<>())
-                        .add(new Entity(entity.getWord(), entity.getType(), entity.isRedaction(), entity.getRedactionReason(), entry
-                                .getValue(), entity.getHeadline(), entity.getMatchedRule(), entity.getSectionNumber(), entity
-                                .getLegalBasis(), entity.isDictionaryEntry(), entity.getTextBefore(), entity.getTextAfter(), entity
-                                .getStart(), entity.getEnd(), entity.isDossierDictionaryEntry()));
-            }
-        }
-
-        List<RedactionLogEntry> newRedactionLogEntries = new ArrayList<>();
-        for (int page = 1; page <= text.getNumberOfPages(); page++) {
-            if (entitiesPerPage.get(page) != null) {
-                newRedactionLogEntries.addAll(redactionLogCreatorService.addEntries(entitiesPerPage, analyzeRequest.getManualRedactions(), page, analyzeRequest
-                        .getDossierTemplateId()));
-            }
-
-            if (imagesPerPage.get(page) != null) {
-                newRedactionLogEntries.addAll(redactionLogCreatorService.addImageEntries(imagesPerPage, analyzeRequest.getManualRedactions(), page, analyzeRequest
-                        .getDossierTemplateId()));
-            }
-
-            newRedactionLogEntries.addAll(redactionLogCreatorService.addManualAddEntries(manualAdds, comments, page, analyzeRequest
-                    .getDossierTemplateId()));
-        }
-
-        redactionLog.getRedactionLogEntry().removeIf(entry -> sectionsToReanalyse.contains(entry.getSectionNumber()));
-        redactionLog.getRedactionLogEntry().addAll(newRedactionLogEntries);
-        AnalyzeResult analyzeResult = finalizeAnalysis(analyzeRequest, startTime, redactionLog, text, dictionaryIncrement);
-        analyzeResult.setWasReanalyzed(true);
-        return analyzeResult;
+        return entities;
     }
 
 
@@ -310,19 +309,19 @@ public class ReanalyzeService {
     }
 
 
-    private Set<String> getForceAndRemoveIds(ManualRedactions manualRedactions) {
+    private Set<String> getRelevantManuallyModifiedAnnotationIds(ManualRedactions manualRedactions) {
 
         if (manualRedactions == null) {
             return new HashSet<>();
         }
 
         return Stream.concat(manualRedactions.getManualLegalBasisChanges()
-                .stream()
-                .map(ManualLegalBasisChange::getId), Stream.concat(manualRedactions.getImageRecategorizations()
-                .stream()
-                .map(ManualImageRecategorization::getId), Stream.concat(manualRedactions.getIdsToRemove()
-                .stream()
-                .map(IdRemoval::getId), manualRedactions.getForceRedacts().stream().map(ManualForceRedact::getId))))
+                        .stream()
+                        .map(ManualLegalBasisChange::getId), Stream.concat(manualRedactions.getImageRecategorizations()
+                        .stream()
+                        .map(ManualImageRecategorization::getId), Stream.concat(manualRedactions.getIdsToRemove()
+                        .stream()
+                        .map(IdRemoval::getId), manualRedactions.getForceRedacts().stream().map(ManualForceRedact::getId))))
                 .collect(Collectors.toSet());
     }
 
@@ -338,21 +337,20 @@ public class ReanalyzeService {
                 .sectionNumber(entry.getSectionNumber())
                 .section(entry.getSection())
                 .page(position.getPage())
+                .hasTransparency(entry.isImageHasTransparency())
                 .build();
     }
 
 
     private void excludeExcludedPages(RedactionLog redactionLog, Set<Integer> excludedPages) {
 
-        redactionLog.getRedactionLogEntry().forEach(entry -> {
-            entry.getPositions().forEach(pos -> {
-                if (excludedPages != null && excludedPages.contains(pos.getPage())) {
+        if (excludedPages != null && !excludedPages.isEmpty()) {
+            redactionLog.getRedactionLogEntry().forEach(entry -> entry.getPositions().forEach(pos -> {
+                if (excludedPages.contains(pos.getPage())) {
                     entry.setExcluded(true);
-                } else {
-                    entry.setExcluded(false);
                 }
-            });
-        });
+            }));
+        }
     }
 
 }

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

@@ -1,6 +1,20 @@
 package com.iqser.red.service.redaction.v1.server.redaction.service;
 
-import com.iqser.red.service.redaction.v1.model.*;
+import java.util.ArrayList;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.stream.Collectors;
+
+import org.apache.commons.collections4.CollectionUtils;
+import org.springframework.stereotype.Service;
+
+import com.iqser.red.service.redaction.v1.model.CellRectangle;
+import com.iqser.red.service.redaction.v1.model.Point;
+import com.iqser.red.service.redaction.v1.model.Rectangle;
+import com.iqser.red.service.redaction.v1.model.RedactionLogEntry;
+import com.iqser.red.service.redaction.v1.model.SectionRectangle;
 import com.iqser.red.service.redaction.v1.server.classification.model.Document;
 import com.iqser.red.service.redaction.v1.server.classification.model.Paragraph;
 import com.iqser.red.service.redaction.v1.server.classification.model.TextBlock;
@@ -9,18 +23,12 @@ import com.iqser.red.service.redaction.v1.server.parsing.model.TextPositionSeque
 import com.iqser.red.service.redaction.v1.server.redaction.model.Entity;
 import com.iqser.red.service.redaction.v1.server.redaction.model.EntityPositionSequence;
 import com.iqser.red.service.redaction.v1.server.redaction.model.Image;
-import com.iqser.red.service.redaction.v1.server.redaction.model.ReasonHolder;
 import com.iqser.red.service.redaction.v1.server.redaction.utils.IdBuilder;
 import com.iqser.red.service.redaction.v1.server.tableextraction.model.AbstractTextContainer;
 import com.iqser.red.service.redaction.v1.server.tableextraction.model.Cell;
 import com.iqser.red.service.redaction.v1.server.tableextraction.model.Table;
-import lombok.RequiredArgsConstructor;
-import org.apache.commons.collections4.CollectionUtils;
-import org.springframework.beans.BeanUtils;
-import org.springframework.stereotype.Service;
 
-import java.util.*;
-import java.util.stream.Collectors;
+import lombok.RequiredArgsConstructor;
 
 @Service
 @RequiredArgsConstructor
@@ -29,10 +37,7 @@ public class RedactionLogCreatorService {
     private final DictionaryService dictionaryService;
 
 
-    public void createRedactionLog(Document classifiedDoc, int numberOfPages, ManualRedactions manualRedactions,
-                                   String dossierTemplateId) {
-
-        Set<Integer> manualRedactionPages = getManualRedactionPages(manualRedactions);
+    public void createRedactionLog(Document classifiedDoc, int numberOfPages, String dossierTemplateId) {
 
         for (int page = 1; page <= numberOfPages; page++) {
 
@@ -40,24 +45,19 @@ public class RedactionLogCreatorService {
 
             if (classifiedDoc.getEntities().get(page) != null) {
                 classifiedDoc.getRedactionLogEntities()
-                        .addAll(addEntries(classifiedDoc.getEntities(), manualRedactions, page, dossierTemplateId));
-            }
-
-            if (manualRedactionPages.contains(page)) {
-                classifiedDoc.getRedactionLogEntities()
-                        .addAll(addManualAddEntries(manualRedactions.getEntriesToAdd(), manualRedactions.getComments(), page, dossierTemplateId));
+                        .addAll(addEntries(classifiedDoc.getEntities(), page, dossierTemplateId));
             }
 
             if (classifiedDoc.getImages().get(page) != null && !classifiedDoc.getImages().get(page).isEmpty()) {
                 classifiedDoc.getRedactionLogEntities()
-                        .addAll(addImageEntries(classifiedDoc.getImages(), manualRedactions, page, dossierTemplateId));
+                        .addAll(addImageEntries(classifiedDoc.getImages(), page, dossierTemplateId));
             }
         }
     }
 
 
-    public List<RedactionLogEntry> addImageEntries(Map<Integer, Set<Image>> images, ManualRedactions manualRedactions,
-                                                   int pageNumber, String dossierTemplateId) {
+    public List<RedactionLogEntry> addImageEntries(Map<Integer, Set<Image>> images, int pageNumber,
+                                                   String dossierTemplateId) {
 
         List<RedactionLogEntry> redactionLogEntities = new ArrayList<>();
 
@@ -67,7 +67,7 @@ public class RedactionLogCreatorService {
 
             RedactionLogEntry redactionLogEntry = RedactionLogEntry.builder()
                     .id(id)
-                    .color(getColorForImage(image.getType(), dossierTemplateId, false, image.isRedaction()))
+                    .color(getColor(image.getType(), dossierTemplateId, image.isRedaction()))
                     .isImage(true)
                     .type(image.getType())
                     .redacted(image.isRedaction())
@@ -82,146 +82,20 @@ public class RedactionLogCreatorService {
                             .getX(), (float) image.getPosition().getY()), (float) image.getPosition()
                             .getWidth(), (float) image.getPosition().getHeight(), pageNumber)))
                     .sectionNumber(image.getSectionNumber())
-                    .section(image.getSection())
+                    //.section(image.getSection())
+                    // RED-2622
+                    .section("Image:" + image.getType())
+                    .imageHasTransparency(image.isHasTransparency())
                     .build();
 
-            processImageEntry(manualRedactions, dossierTemplateId, image, redactionLogEntry);
-
             redactionLogEntities.add(redactionLogEntry);
         }
 
         return redactionLogEntities;
     }
 
-    private void processImageEntry(ManualRedactions manualRedactions, String dossierTemplateId, ReasonHolder image, RedactionLogEntry redactionLogEntry) {
-        if (manualRedactions != null && !manualRedactions.getImageRecategorizations().isEmpty()) {
-            for (ManualImageRecategorization recategorization : manualRedactions.getImageRecategorizations()) {
-                if (recategorization.getId().equals(redactionLogEntry.getId())) {
-                    String manualOverrideReason = null;
-                    if (recategorization.getStatus().equals(Status.APPROVED)) {
-                        redactionLogEntry.setStatus(Status.APPROVED);
-                        redactionLogEntry.setType(recategorization.getType());
-                        manualOverrideReason = mergeReasonIfNecessary(image.getRedactionReason(), ", recategorized by manual override");
-                    } else if (recategorization.getStatus().equals(Status.REQUESTED)) {
-                        manualOverrideReason = mergeReasonIfNecessary(image.getRedactionReason(), ", requested to recategorize");
-                        redactionLogEntry.setStatus(Status.REQUESTED);
-                        redactionLogEntry.setColor(getColorForImage(redactionLogEntry.getType(), dossierTemplateId, true, redactionLogEntry.isRedacted()));
-                        redactionLogEntry.setRecategorizationType(recategorization.getType());
-                    } else {
-                        redactionLogEntry.setStatus(Status.DECLINED);
-                    }
 
-                    image.setRedactionReason(manualOverrideReason != null ? manualOverrideReason : image.getRedactionReason());
-                    redactionLogEntry.setReason(manualOverrideReason);
-                    redactionLogEntry.setManual(true);
-                    redactionLogEntry.setManualRedactionType(ManualRedactionType.RECATEGORIZE);
-                }
-            }
-        }
-
-        if (manualRedactions != null && !manualRedactions.getIdsToRemove().isEmpty()) {
-            for (IdRemoval manualRemoval : manualRedactions.getIdsToRemove()) {
-                if (manualRemoval.getId().equals(redactionLogEntry.getId())) {
-                    String manualOverrideReason = null;
-                    if (manualRemoval.getStatus().equals(Status.APPROVED)) {
-                        image.setRedaction(false);
-                        redactionLogEntry.setRedacted(false);
-                        redactionLogEntry.setStatus(Status.APPROVED);
-                        manualOverrideReason = mergeReasonIfNecessary(image.getRedactionReason(), ", removed by manual override");
-                        redactionLogEntry.setColor(getColorForImage(redactionLogEntry.getType(), dossierTemplateId, false, redactionLogEntry.isRedacted()));
-                    } else if (manualRemoval.getStatus().equals(Status.REQUESTED)) {
-                        manualOverrideReason = mergeReasonIfNecessary(image.getRedactionReason(), ", requested to remove");
-                        redactionLogEntry.setStatus(Status.REQUESTED);
-                        redactionLogEntry.setColor(getColorForImage(redactionLogEntry.getType(), dossierTemplateId, true, redactionLogEntry.isRedacted()));
-                    } else {
-                        redactionLogEntry.setStatus(Status.DECLINED);
-                    }
-
-                    image.setRedactionReason(manualOverrideReason != null ? manualOverrideReason : image.getRedactionReason());
-                    redactionLogEntry.setReason(manualOverrideReason);
-                    redactionLogEntry.setManual(true);
-                    redactionLogEntry.setManualRedactionType(ManualRedactionType.REMOVE);
-                    redactionLogEntry.setDictionaryEntry(manualRemoval.isRemoveFromDictionary());
-                    redactionLogEntry.setDossierDictionaryEntry(manualRemoval.isRemoveFromDictionary());
-                }
-            }
-        }
-
-        if (manualRedactions != null && !manualRedactions.getForceRedacts().isEmpty()) {
-            for (ManualForceRedact manualForceRedact : manualRedactions.getForceRedacts()) {
-                if (manualForceRedact.getId().equals(redactionLogEntry.getId())) {
-                    String manualOverrideReason = null;
-                    if (manualForceRedact.getStatus().equals(Status.APPROVED)) {
-                        image.setRedaction(true);
-                        redactionLogEntry.setRedacted(true);
-                        redactionLogEntry.setStatus(Status.APPROVED);
-                        redactionLogEntry.setColor(getColorForImage(redactionLogEntry.getType(), dossierTemplateId, false, redactionLogEntry.isRedacted()));
-                        manualOverrideReason = mergeReasonIfNecessary(image.getRedactionReason(), ", forced by manual override");
-                        redactionLogEntry.setLegalBasis(manualForceRedact.getLegalBasis());
-                    } else if (manualForceRedact.getStatus().equals(Status.REQUESTED)) {
-                        manualOverrideReason = mergeReasonIfNecessary(image.getRedactionReason(), ", requested to force redact");
-                        redactionLogEntry.setStatus(Status.REQUESTED);
-                        redactionLogEntry.setColor(getColorForImage(redactionLogEntry.getType(), dossierTemplateId, true, redactionLogEntry.isRedacted()));
-                        redactionLogEntry.setLegalBasis(manualForceRedact.getLegalBasis());
-                    } else {
-                        redactionLogEntry.setStatus(Status.DECLINED);
-                    }
-
-                    image.setRedactionReason(manualOverrideReason != null ? manualOverrideReason : image.getRedactionReason());
-                    redactionLogEntry.setReason(manualOverrideReason);
-                    redactionLogEntry.setManual(true);
-                    redactionLogEntry.setManualRedactionType(ManualRedactionType.FORCE_REDACT);
-                }
-            }
-        }
-
-
-        if (manualRedactions != null && !manualRedactions.getManualLegalBasisChanges().isEmpty()) {
-            for (ManualLegalBasisChange manualLegalBasisChange : manualRedactions.getManualLegalBasisChanges()) {
-                if (manualLegalBasisChange.getId().equals(redactionLogEntry.getId())) {
-                    String manualOverrideReason = null;
-                    if (manualLegalBasisChange.getStatus().equals(Status.APPROVED)) {
-                        redactionLogEntry.setStatus(Status.APPROVED);
-                        manualOverrideReason = mergeReasonIfNecessary(image.getRedactionReason(), ", legal basis was manually changed");
-                        redactionLogEntry.setLegalBasis(manualLegalBasisChange.getLegalBasis());
-                    } else if (manualLegalBasisChange.getStatus().equals(Status.REQUESTED)) {
-                        manualOverrideReason = mergeReasonIfNecessary(image.getRedactionReason(), ", legal basis change requested");
-                        redactionLogEntry.setStatus(Status.REQUESTED);
-                        redactionLogEntry.setColor(getColorForImage(redactionLogEntry.getType(), dossierTemplateId, true, redactionLogEntry.isRedacted()));
-                        redactionLogEntry.setLegalBasisChangeValue(manualLegalBasisChange.getLegalBasis());
-                    } else {
-                        redactionLogEntry.setStatus(Status.DECLINED);
-                    }
-
-                    image.setRedactionReason(manualOverrideReason != null ? manualOverrideReason : image.getRedactionReason());
-                    redactionLogEntry.setReason(manualOverrideReason);
-                    redactionLogEntry.setManual(true);
-                    redactionLogEntry.setManualRedactionType(ManualRedactionType.LEGAL_BASIS_CHANGE);
-                }
-            }
-        }
-    }
-
-
-    private Set<Integer> getManualRedactionPages(ManualRedactions manualRedactions) {
-
-        Set<Integer> manualRedactionPages = new HashSet<>();
-
-        if (manualRedactions == null) {
-            return manualRedactionPages;
-        }
-
-        manualRedactions.getEntriesToAdd().forEach(entry -> {
-            entry.getPositions().forEach(pos -> {
-                manualRedactionPages.add(pos.getPage());
-            });
-        });
-        return manualRedactionPages;
-    }
-
-
-    public List<RedactionLogEntry> addEntries(Map<Integer, List<Entity>> entities, ManualRedactions manualRedactions,
-                                              int page, String dossierTemplateId) {
+    public List<RedactionLogEntry> addEntries(Map<Integer, List<Entity>> entities, int page, String dossierTemplateId) {
 
         List<RedactionLogEntry> redactionLogEntities = new ArrayList<>();
 
@@ -231,7 +105,6 @@ public class RedactionLogCreatorService {
         entityLoop:
         for (Entity entity : entities.get(page)) {
 
-
             for (EntityPositionSequence entityPositionSequence : entity.getPositionSequences()) {
 
                 RedactionLogEntry redactionLogEntry = createRedactionLogEntry(entity, dossierTemplateId);
@@ -244,7 +117,6 @@ public class RedactionLogCreatorService {
                 }
 
                 redactionLogEntry.setId(entityPositionSequence.getId());
-                processRedactionLogEntry(manualRedactions, dossierTemplateId, redactionLogEntry, entity);
 
                 if (CollectionUtils.isNotEmpty(entityPositionSequence.getSequences())) {
                     List<Rectangle> rectanglesPerLine = getRectanglesPerLine(entityPositionSequence.getSequences()
@@ -252,12 +124,10 @@ public class RedactionLogCreatorService {
                             .flatMap(seq -> seq.getTextPositions().stream())
                             .collect(Collectors.toList()), page);
 
-
                     redactionLogEntry.getPositions().addAll(rectanglesPerLine);
 
                 }
 
-
                 // FIXME ids should never be null. Figure out why this happens.
                 if (redactionLogEntry.getId() != null) {
                     redactionLogEntities.add(redactionLogEntry);
@@ -268,112 +138,6 @@ public class RedactionLogCreatorService {
         return redactionLogEntities;
     }
 
-    private void processRedactionLogEntry(ManualRedactions manualRedactions, String dossierTemplateId, RedactionLogEntry redactionLogEntry, ReasonHolder reasonHolder) {
-
-        List<Comment> comments = null;
-
-        if (manualRedactions != null && !manualRedactions.getIdsToRemove().isEmpty()) {
-            for (IdRemoval manualRemoval : manualRedactions.getIdsToRemove()) {
-                if (manualRemoval.getId().equals(redactionLogEntry.getId())) {
-                    comments = manualRedactions.getComments().get(manualRemoval.getId());
-                    String manualOverrideReason = null;
-                    if (manualRemoval.getStatus().equals(Status.APPROVED)) {
-                        reasonHolder.setRedaction(false);
-                        redactionLogEntry.setRedacted(false);
-                        redactionLogEntry.setStatus(Status.APPROVED);
-                        manualOverrideReason = mergeReasonIfNecessary(reasonHolder.getRedactionReason(), ", removed by manual override");
-                        redactionLogEntry.setColor(getColor(redactionLogEntry.getType(), dossierTemplateId, false, redactionLogEntry.isRedacted()));
-                    } else if (manualRemoval.getStatus().equals(Status.REQUESTED)) {
-                        manualOverrideReason = mergeReasonIfNecessary(reasonHolder.getRedactionReason(), ", requested to remove");
-                        redactionLogEntry.setStatus(Status.REQUESTED);
-                        redactionLogEntry.setColor(getColor(redactionLogEntry.getType(), dossierTemplateId, true, redactionLogEntry.isRedacted()));
-                    } else {
-                        redactionLogEntry.setStatus(Status.DECLINED);
-                    }
-
-                    reasonHolder.setRedactionReason(manualOverrideReason != null ? manualOverrideReason : reasonHolder.getRedactionReason());
-                    redactionLogEntry.setReason(manualOverrideReason);
-                    redactionLogEntry.setManual(true);
-                    redactionLogEntry.setManualRedactionType(ManualRedactionType.REMOVE);
-                    redactionLogEntry.setDictionaryEntry(manualRemoval.isRemoveFromDictionary());
-                    redactionLogEntry.setDossierDictionaryEntry(manualRemoval.isRemoveFromDictionary());
-                }
-            }
-        }
-
-        if (manualRedactions != null && !manualRedactions.getForceRedacts().isEmpty()) {
-            for (ManualForceRedact manualForceRedact : manualRedactions.getForceRedacts()) {
-                if (manualForceRedact.getId().equals(redactionLogEntry.getId())) {
-                    String manualOverrideReason = null;
-                    if (manualForceRedact.getStatus().equals(Status.APPROVED)) {
-                        reasonHolder.setRedaction(true);
-                        redactionLogEntry.setRedacted(true);
-                        redactionLogEntry.setStatus(Status.APPROVED);
-                        redactionLogEntry.setColor(getColor(redactionLogEntry.getType(), dossierTemplateId, false, redactionLogEntry.isRedacted()));
-                        manualOverrideReason = mergeReasonIfNecessary(reasonHolder.getRedactionReason(), ", forced by manual override");
-                        redactionLogEntry.setLegalBasis(manualForceRedact.getLegalBasis());
-                    } else if (manualForceRedact.getStatus().equals(Status.REQUESTED)) {
-                        manualOverrideReason = mergeReasonIfNecessary(reasonHolder.getRedactionReason(), ", requested to force redact");
-                        redactionLogEntry.setStatus(Status.REQUESTED);
-                        redactionLogEntry.setColor(getColor(redactionLogEntry.getType(), dossierTemplateId, true, redactionLogEntry.isRedacted()));
-                        redactionLogEntry.setLegalBasis(manualForceRedact.getLegalBasis());
-                    } else {
-                        redactionLogEntry.setStatus(Status.DECLINED);
-                    }
-
-                    reasonHolder.setRedactionReason(manualOverrideReason != null ? manualOverrideReason : reasonHolder.getRedactionReason());
-                    redactionLogEntry.setReason(manualOverrideReason);
-                    redactionLogEntry.setManual(true);
-                    redactionLogEntry.setManualRedactionType(ManualRedactionType.FORCE_REDACT);
-
-                }
-            }
-        }
-
-        if (manualRedactions != null && !manualRedactions.getManualLegalBasisChanges().isEmpty()) {
-            for (ManualLegalBasisChange manualLegalBasisChange : manualRedactions.getManualLegalBasisChanges()) {
-                if (manualLegalBasisChange.getId().equals(redactionLogEntry.getId())) {
-                    String manualOverrideReason = null;
-                    if (manualLegalBasisChange.getStatus().equals(Status.APPROVED)) {
-                        redactionLogEntry.setStatus(Status.APPROVED);
-                        manualOverrideReason = mergeReasonIfNecessary(reasonHolder.getRedactionReason(), ", legal basis was manually changed");
-                        redactionLogEntry.setLegalBasis(manualLegalBasisChange.getLegalBasis());
-                    } else if (manualLegalBasisChange.getStatus().equals(Status.REQUESTED)) {
-                        manualOverrideReason = mergeReasonIfNecessary(reasonHolder.getRedactionReason(), ", legal basis change requested");
-                        redactionLogEntry.setStatus(Status.REQUESTED);
-                        redactionLogEntry.setColor(getColor(redactionLogEntry.getType(), dossierTemplateId, true, redactionLogEntry.isRedacted()));
-                        redactionLogEntry.setLegalBasisChangeValue(manualLegalBasisChange.getLegalBasis());
-                    } else {
-                        redactionLogEntry.setStatus(Status.DECLINED);
-                    }
-
-                    reasonHolder.setRedactionReason(manualOverrideReason != null ? manualOverrideReason : reasonHolder.getRedactionReason());
-                    redactionLogEntry.setReason(manualOverrideReason);
-                    redactionLogEntry.setManual(true);
-                    redactionLogEntry.setManualRedactionType(ManualRedactionType.LEGAL_BASIS_CHANGE);
-                }
-            }
-        }
-
-
-        if (manualRedactions != null) {
-            comments = manualRedactions.getComments().get(redactionLogEntry.getId());
-        }
-
-        redactionLogEntry.setComments(comments);
-    }
-
-    private String mergeReasonIfNecessary(String currentReason, String addition) {
-        if (currentReason != null) {
-            if (!currentReason.contains(addition)) {
-                return currentReason + addition;
-            }
-            return currentReason;
-        } else {
-            return "";
-        }
-    }
-
 
     private List<Rectangle> getRectanglesPerLine(List<RedTextPosition> textPositions, int page) {
 
@@ -381,16 +145,27 @@ public class RedactionLogCreatorService {
         if (textPositions.size() == 1) {
             rectangles.add(TextPositionSequence.fromData(textPositions, page).getRectangle());
         } else {
+            float x = textPositions.get(0).getXDirAdj();
             float y = textPositions.get(0).getYDirAdj();
+            float width = textPositions.get(0).getWidth();
+            float height = textPositions.get(0).getHeightDir();
             int startIndex = 0;
+
             for (int i = 1; i < textPositions.size(); i++) {
+                float xDirAdj = textPositions.get(i).getXDirAdj();
                 float yDirAdj = textPositions.get(i).getYDirAdj();
-                if (yDirAdj != y) {
+                float widthDir = textPositions.get(i).getWidth();
+                float heightDir = textPositions.get(i).getHeightDir();
+
+                if (!(isCharInSameLine(y, yDirAdj, height, heightDir) && isCharClose(x, xDirAdj, width))) {
                     rectangles.add(TextPositionSequence.fromData(textPositions.subList(startIndex, i), page)
                             .getRectangle());
                     y = yDirAdj;
+                    width = widthDir;
+                    height = heightDir;
                     startIndex = i;
                 }
+                x = xDirAdj;
             }
             if (startIndex != textPositions.size()) {
                 rectangles.add(TextPositionSequence.fromData(textPositions.subList(startIndex, textPositions.size()), page)
@@ -402,73 +177,38 @@ public class RedactionLogCreatorService {
     }
 
 
-    public List<RedactionLogEntry> addManualAddEntries(Set<ManualRedactionEntry> manualAdds,
-                                                       Map<String, List<Comment>> comments, int page,
-                                                       String dossierTemplateId) {
+    private boolean isCharClose(float x, float xDirAdj, float width) {
 
-        List<RedactionLogEntry> redactionLogEntities = new ArrayList<>();
-
-        if (manualAdds == null) {
-            return redactionLogEntities;
+        float max = x + (5 * width);
+        if (xDirAdj < max) {
+            return true;
         }
-
-        for (ManualRedactionEntry manualRedactionEntry : manualAdds) {
-
-            String id = manualRedactionEntry.getId();
-
-            RedactionLogEntry redactionLogEntry = createRedactionLogEntry(manualRedactionEntry, id, dossierTemplateId);
-
-            List<Rectangle> rectanglesOnPage = new ArrayList<>();
-            for (Rectangle rectangle : manualRedactionEntry.getPositions()) {
-                if (page == rectangle.getPage()) {
-                    rectanglesOnPage.add(rectangle);
-                    redactionLogEntry.getPositions().add(rectangle);
-                }
-            }
-
-            redactionLogEntry.setComments(comments.get(id));
-            if (!rectanglesOnPage.isEmpty() && !approvedAndShouldBeInDictionary(manualRedactionEntry)) {
-                redactionLogEntities.add(redactionLogEntry);
-            }
-        }
-
-        return redactionLogEntities;
+        return false;
     }
 
 
-    private boolean approvedAndShouldBeInDictionary(ManualRedactionEntry manualRedactionEntry) {
+    private boolean isCharInSameLine(float y, float yCompare, float height, float heightCompare) {
 
-        return manualRedactionEntry.getStatus().equals(Status.APPROVED) && manualRedactionEntry.isAddToDictionary();
-    }
+        float offsetHeight = height / 2;
+        float minHeight = height - offsetHeight;
+        float maxHeight = height + offsetHeight;
 
+        float offsetY = height / 10;
+        float minY = y - offsetY;
+        float maxY = y + offsetY;
 
-    private RedactionLogEntry createRedactionLogEntry(ManualRedactionEntry manualRedactionEntry, String id,
-                                                      String dossierTemplateId) {
+        if (yCompare > minY && yCompare < maxY && heightCompare > minHeight && heightCompare < maxHeight) {
+            return true;
+        }
 
-        return RedactionLogEntry.builder()
-                .id(id)
-                .color(getColorForManualAdd(manualRedactionEntry.getType(), dossierTemplateId, manualRedactionEntry.getStatus()))
-                .reason(manualRedactionEntry.getReason())
-                .legalBasis(manualRedactionEntry.getLegalBasis())
-                .value(manualRedactionEntry.getValue())
-                .type(manualRedactionEntry.getType())
-                .redacted(true)
-                .isHint(false)
-                .section(manualRedactionEntry.getSection())
-                .sectionNumber(manualRedactionEntry.getSectionNumber())
-                .manual(true)
-                .status(manualRedactionEntry.getStatus())
-                .manualRedactionType(ManualRedactionType.ADD)
-                .isDictionaryEntry(false)
-                .isDossierDictionaryEntry(manualRedactionEntry.isAddToDossierDictionary())
-                .build();
+        return false;
     }
 
 
     private RedactionLogEntry createRedactionLogEntry(Entity entity, String dossierTemplateId) {
 
         return RedactionLogEntry.builder()
-                .color(getColor(entity.getType(), dossierTemplateId, false, entity.isRedaction()))
+                .color(getColor(entity.getType(), dossierTemplateId, entity.isRedaction()))
                 .reason(entity.getRedactionReason())
                 .legalBasis(entity.getLegalBasis())
                 .value(entity.getWord())
@@ -489,59 +229,6 @@ public class RedactionLogCreatorService {
     }
 
 
-    private float[] getColor(String type, String dossierTemplateId, boolean requestedToRemove, boolean isRedaction) {
-
-        if (requestedToRemove) {
-            return dictionaryService.getRequestRemoveColor(dossierTemplateId);
-        }
-        if (!isRedaction && !isHint(type, dossierTemplateId)) {
-            return dictionaryService.getNotRedactedColor(dossierTemplateId);
-        }
-        return dictionaryService.getColor(type, dossierTemplateId);
-    }
-
-
-    private float[] getColorForManualAdd(String type, String dossierTemplateId, Status status) {
-
-        if (status.equals(Status.REQUESTED)) {
-            return dictionaryService.getRequestAddColor(dossierTemplateId);
-        } else if (status.equals(Status.DECLINED)) {
-            return dictionaryService.getNotRedactedColor(dossierTemplateId);
-        }
-        return getColor(type, dossierTemplateId);
-    }
-
-
-    private float[] getColor(String type, String dossierTemplateId) {
-
-        return dictionaryService.getColor(type, dossierTemplateId);
-    }
-
-
-    private float[] getColorForImage(String type, String dossierTemplateId, boolean requestedToRemove, boolean isRedaction) {
-
-        if (requestedToRemove) {
-            return dictionaryService.getRequestRemoveColor(dossierTemplateId);
-        }
-        if (!isRedaction && !dictionaryService.isHint(type, dossierTemplateId)) {
-            return dictionaryService.getNotRedactedColor(dossierTemplateId);
-        }
-        return dictionaryService.getColor(type, dossierTemplateId);
-    }
-
-
-    private boolean isHint(String type, String dossierTemplateId) {
-
-        return dictionaryService.isHint(type, dossierTemplateId);
-    }
-
-
-    private boolean isRecommendation(String type, String dossierTemplateId) {
-
-        return dictionaryService.isRecommendation(type, dossierTemplateId);
-    }
-
-
     private void addSectionGrid(Document classifiedDoc, int page) {
 
         for (Paragraph paragraph : classifiedDoc.getParagraphs()) {
@@ -559,8 +246,8 @@ public class RedactionLogCreatorService {
                     classifiedDoc.getSectionGrid()
                             .getRectanglesPerPage()
                             .computeIfAbsent(page, (x) -> new ArrayList<>())
-                            .add(new SectionRectangle(new Point(textBlock.getMinX(), textBlock.getMinY()), textBlock.getWidth(), textBlock
-                                    .getHeight(), i + 1, paragraph.getPageBlocks().size()));
+                            .add(new SectionRectangle(new Point(textBlock.getMinX(), textBlock.getMinY()), textBlock.getWidth(), textBlock.getHeight(), i + 1, paragraph.getPageBlocks()
+                                    .size()));
 
                 } else if (textBlock instanceof Table) {
 
@@ -568,8 +255,7 @@ public class RedactionLogCreatorService {
                     for (List<Cell> row : ((Table) textBlock).getRows()) {
                         for (Cell cell : row) {
                             if (cell != null) {
-                                cellRectangles.add(new CellRectangle(new Point((float) cell.getX(), (float) cell.getY()), (float) cell
-                                        .getWidth(), (float) cell.getHeight()));
+                                cellRectangles.add(new CellRectangle(new Point((float) cell.getX(), (float) cell.getY()), (float) cell.getWidth(), (float) cell.getHeight()));
                             }
                         }
                     }
@@ -577,112 +263,33 @@ public class RedactionLogCreatorService {
                     classifiedDoc.getSectionGrid()
                             .getRectanglesPerPage()
                             .computeIfAbsent(page, (x) -> new ArrayList<>())
-                            .add(new SectionRectangle(new Point(textBlock.getMinX(), textBlock.getMinY()), textBlock.getWidth(), textBlock
-                                    .getHeight(), i + 1, paragraph.getPageBlocks().size(), cellRectangles));
+                            .add(new SectionRectangle(new Point(textBlock.getMinX(), textBlock.getMinY()), textBlock.getWidth(), textBlock.getHeight(), i + 1, paragraph.getPageBlocks()
+                                    .size(), cellRectangles));
 
                 }
             }
         }
     }
 
-    public RedactionLog getRedactionLogPreview(RedactionLog redactionLog, String dossierTemplateId, ManualRedactions manualRedactions) {
 
+    private float[] getColor(String type, String dossierTemplateId, boolean isRedaction) {
 
-        var manualRedactionPages = getManualRedactionPages(manualRedactions);
-
-        // generate all manual entries
-        var manualRedactionLogEntries = new HashMap<String, RedactionLogEntry>();
-        for (var page : manualRedactionPages) {
-
-            var pageEntries = addManualAddEntries(manualRedactions.getEntriesToAdd(), manualRedactions.getComments(), page, dossierTemplateId);
-
-            for (var entry : pageEntries) {
-                manualRedactionLogEntries.put(entry.getId(), entry);
-            }
+        if (!isRedaction && !isHint(type, dossierTemplateId)) {
+            return dictionaryService.getNotRedactedColor(dossierTemplateId);
         }
-
-        for (var manualEntry : manualRedactionLogEntries.values()) {
-            var existingEntry = redactionLog.getRedactionLogEntry().stream().filter(e -> e.getId().equals(manualEntry.getId())).findAny();
-            if (existingEntry.isPresent()) {
-                // if it has already been processed of sorts, update it
-                BeanUtils.copyProperties(manualEntry, existingEntry.get());
-            } else {
-                // not yet in the redaction-log - add it
-                redactionLog.getRedactionLogEntry().add(manualEntry);
-            }
-        }
-
-
-        for (RedactionLogEntry entry : redactionLog.getRedactionLogEntry()) {
-
-            var reasonHolder = new PreviewReasonHolder(entry);
-
-            if (entry.isImage()) {
-                processImageEntry(manualRedactions, dossierTemplateId, reasonHolder, entry);
-            }
-
-            processRedactionLogEntry(manualRedactions, dossierTemplateId, entry, reasonHolder);
-        }
-
-
-        handleAddToDictionary(redactionLog, manualRedactions, dossierTemplateId);
-
-        return redactionLog;
+        return dictionaryService.getColor(type, dossierTemplateId);
     }
 
 
-    private void handleAddToDictionary(RedactionLog redactionLog, ManualRedactions manualRedactions, String dossierTemplateId) {
+    private boolean isHint(String type, String dossierTemplateId) {
 
-        for (var manualRedaction : manualRedactions.getEntriesToAdd()) {
-
-            // not yet processed, and dictionary modifying, show in redaction-log preview
-            if (manualRedaction.getProcessedDate() == null && manualRedaction.isAddToDictionary() || manualRedaction.isAddToDossierDictionary()) {
-                var redactionLogEntry = createRedactionLogEntry(manualRedaction, manualRedaction.getId(), dossierTemplateId);
-                redactionLogEntry.setDictionaryEntry(manualRedaction.isAddToDictionary());
-                redactionLogEntry.setDossierDictionaryEntry(manualRedaction.isAddToDossierDictionary());
-                redactionLogEntry.setPositions(manualRedaction.getPositions());
-
-
-                var found = redactionLog.getRedactionLogEntry().stream().filter(r -> r.getId().equalsIgnoreCase(redactionLogEntry.getId())).findAny();
-                if (found.isPresent()) {
-                    found.get().setDictionaryEntry(manualRedaction.isAddToDictionary());
-                    found.get().setDossierDictionaryEntry(manualRedaction.isAddToDossierDictionary());
-                    found.get().setPositions(manualRedaction.getPositions());
-                } else {
-                    redactionLog.getRedactionLogEntry().add(redactionLogEntry);
-                }
-
-
-            }
-        }
+        return dictionaryService.isHint(type, dossierTemplateId);
     }
 
-    public static class PreviewReasonHolder implements ReasonHolder {
 
-        private final RedactionLogEntry entry;
+    private boolean isRecommendation(String type, String dossierTemplateId) {
 
-        public PreviewReasonHolder(RedactionLogEntry entry) {
-            this.entry = entry;
-        }
-
-        @Override
-        public String getRedactionReason() {
-            return entry.getReason();
-        }
-
-        @Override
-        public void setRedactionReason(String reason) {
-            entry.setReason(reason);
-        }
-
-        @Override
-        public boolean isRedaction() {
-            return entry.isRedacted();
-        }
-
-        @Override
-        public void setRedaction(boolean value) {
-            entry.setRedacted(value);
-        }
+        return dictionaryService.isRecommendation(type, dossierTemplateId);
     }
+
 }

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

@@ -0,0 +1,356 @@
+package com.iqser.red.service.redaction.v1.server.redaction.service;
+
+import com.iqser.red.service.redaction.v1.model.*;
+import lombok.AllArgsConstructor;
+import lombok.Data;
+import lombok.RequiredArgsConstructor;
+import lombok.extern.slf4j.Slf4j;
+import org.springframework.stereotype.Service;
+
+import java.time.OffsetDateTime;
+import java.util.*;
+import java.util.stream.Collectors;
+
+@Slf4j
+@Service
+@RequiredArgsConstructor
+public class RedactionLogMergeService {
+
+    private final DictionaryService dictionaryService;
+    private final SectionTextService sectionTextService;
+
+    public RedactionLog mergeRedactionLogData(RedactionLog redactionLog, SectionGrid sectionGrid, String dossierTemplateId,
+                                              ManualRedactions manualRedactions, Set<Integer> excludedPages) {
+
+        log.info("Merging Redaction log with manual redactions {}", manualRedactions);
+        if (manualRedactions != null) {
+
+            var manualRedactionLogEntries = addManualAddEntries(sectionGrid, manualRedactions.getEntriesToAdd(), manualRedactions.getComments(), dossierTemplateId);
+
+            redactionLog.getRedactionLogEntry().addAll(manualRedactionLogEntries);
+
+            var manualRedactionWrappers = createManualRedactionWrappers(manualRedactions);
+
+            for (RedactionLogEntry entry : redactionLog.getRedactionLogEntry()) {
+
+                processRedactionLogEntry(manualRedactionWrappers.stream()
+                        .filter(mr -> entry.getId().equals(mr.getId()))
+                        .collect(Collectors.toList()), dossierTemplateId, entry);
+
+                entry.setComments(manualRedactions.getComments().get(entry.getId()));
+
+                if (excludedPages != null && !excludedPages.isEmpty()) {
+                    entry.getPositions().forEach(pos -> {
+                        if (excludedPages.contains(pos.getPage())) {
+                            entry.setExcluded(true);
+                        }
+                    });
+                }
+            }
+
+        }
+
+        Set<String> processedIds = new HashSet<>();
+        redactionLog.getRedactionLogEntry().removeIf(entry -> {
+            if(processedIds.contains(entry.getId())){
+                return true;
+            }
+            processedIds.add(entry.getId());
+            return false;
+        });
+        return redactionLog;
+    }
+
+
+    private List<ManualRedactionWrapper> createManualRedactionWrappers(ManualRedactions manualRedactions) {
+
+        List<ManualRedactionWrapper> manualRedactionWrappers = new ArrayList<>();
+
+        manualRedactions.getImageRecategorizations().forEach(item -> {
+            if (item.getSoftDeletedTime() == null) {
+                manualRedactionWrappers.add(new ManualRedactionWrapper(item.getId(), item.getRequestDate(), item));
+            }
+        });
+
+        manualRedactions.getIdsToRemove().forEach(item -> {
+            if (item.getSoftDeletedTime() == null) {
+                manualRedactionWrappers.add(new ManualRedactionWrapper(item.getId(), item.getRequestDate(), item));
+            }
+        });
+
+        manualRedactions.getForceRedacts().forEach(item -> {
+            if (item.getSoftDeletedTime() == null) {
+                manualRedactionWrappers.add(new ManualRedactionWrapper(item.getId(), item.getRequestDate(), item));
+            }
+        });
+
+        manualRedactions.getManualLegalBasisChanges().forEach(item -> {
+            if (item.getSoftDeletedTime() == null) {
+                manualRedactionWrappers.add(new ManualRedactionWrapper(item.getId(), item.getRequestDate(), item));
+            }
+        });
+
+        Collections.sort(manualRedactionWrappers);
+
+        return manualRedactionWrappers;
+    }
+
+
+    private void processRedactionLogEntry(List<ManualRedactionWrapper> manualRedactionWrappers,
+                                          String dossierTemplateId, RedactionLogEntry redactionLogEntry) {
+
+        manualRedactionWrappers.forEach(mrw -> {
+
+            if (mrw.getItem() instanceof ManualImageRecategorization) {
+                var imageRecategorization = (ManualImageRecategorization) mrw.getItem();
+                String manualOverrideReason = null;
+                if (imageRecategorization.getStatus().equals(Status.APPROVED)) {
+                    redactionLogEntry.setStatus(Status.APPROVED);
+                    redactionLogEntry.setType(imageRecategorization.getType());
+                    redactionLogEntry.setHasBeenRecategorized(true);
+
+                    if (dictionaryService.isHint(imageRecategorization.getType(), dossierTemplateId)) {
+                        redactionLogEntry.setRedacted(false);
+                        redactionLogEntry.setHint(true);
+                    } else {
+                        redactionLogEntry.setHint(false);
+                    }
+
+                    redactionLogEntry.setSection("Image:" + redactionLogEntry.getType());
+                    manualOverrideReason = mergeReasonIfNecessary(redactionLogEntry.getReason(), ", recategorized by manual override");
+                } else if (imageRecategorization.getStatus().equals(Status.REQUESTED)) {
+                    manualOverrideReason = mergeReasonIfNecessary(redactionLogEntry.getReason(), ", requested to recategorize");
+                    redactionLogEntry.setStatus(Status.REQUESTED);
+                    redactionLogEntry.setColor(getColor(redactionLogEntry.getType(), dossierTemplateId, false, redactionLogEntry
+                            .isRedacted(), false));
+                    redactionLogEntry.setRecategorizationType(imageRecategorization.getType());
+                } else {
+                    redactionLogEntry.setStatus(Status.DECLINED);
+                }
+
+                redactionLogEntry.setManualRedactionUserId(imageRecategorization.getUser());
+                redactionLogEntry.setReason(manualOverrideReason);
+                redactionLogEntry.setManual(true);
+                redactionLogEntry.setManualRedactionType(ManualRedactionType.RECATEGORIZE);
+            }
+
+            if (mrw.getItem() instanceof IdRemoval) {
+                var manualRemoval = (IdRemoval) mrw.getItem();
+                String manualOverrideReason = null;
+                if (manualRemoval.getStatus().equals(Status.APPROVED)) {
+                    redactionLogEntry.setRedacted(false);
+                    redactionLogEntry.setStatus(Status.APPROVED);
+                    manualOverrideReason = mergeReasonIfNecessary(redactionLogEntry.getReason(), ", removed by manual override");
+                    redactionLogEntry.setColor(getColor(redactionLogEntry.getType(), dossierTemplateId, false, redactionLogEntry
+                            .isRedacted(), true));
+                    redactionLogEntry.setHint(false);
+                    redactionLogEntry.setHasBeenRemovedByManualOverride(true);
+                } else if (manualRemoval.getStatus().equals(Status.REQUESTED)) {
+                    manualOverrideReason = mergeReasonIfNecessary(redactionLogEntry.getReason(), ", requested to remove");
+                    redactionLogEntry.setStatus(Status.REQUESTED);
+                    redactionLogEntry.setColor(getColor(redactionLogEntry.getType(), dossierTemplateId, true, redactionLogEntry
+                            .isRedacted(), false));
+                } else {
+                    redactionLogEntry.setStatus(Status.DECLINED);
+                }
+
+                redactionLogEntry.setReason(manualOverrideReason);
+                redactionLogEntry.setManual(true);
+                redactionLogEntry.setManualRedactionUserId(manualRemoval.getUser());
+                redactionLogEntry.setManualRedactionType(ManualRedactionType.REMOVE);
+                redactionLogEntry.setDictionaryEntry(manualRemoval.isRemoveFromDictionary());
+                redactionLogEntry.setDossierDictionaryEntry(manualRemoval.isRemoveFromDictionary());
+            }
+
+            if (mrw.getItem() instanceof ManualForceRedact) {
+                var manualForceRedact = (ManualForceRedact) mrw.getItem();
+                String manualOverrideReason = null;
+                if (manualForceRedact.getStatus().equals(Status.APPROVED)) {
+
+                    // Forcing a skipped hint should result in a hint
+                    if (dictionaryService.isHint(redactionLogEntry.getType(), dossierTemplateId)) {
+                        redactionLogEntry.setHint(true);
+                    } else {
+                        redactionLogEntry.setRedacted(true);
+                    }
+
+                    redactionLogEntry.setStatus(Status.APPROVED);
+                    redactionLogEntry.setColor(getColor(redactionLogEntry.getType(), dossierTemplateId, false, redactionLogEntry
+                            .isRedacted(), false));
+                    manualOverrideReason = mergeReasonIfNecessary(redactionLogEntry.getReason(), ", forced by manual override");
+                    redactionLogEntry.setLegalBasis(manualForceRedact.getLegalBasis());
+                    redactionLogEntry.setHasBeenForced(true);
+                } else if (manualForceRedact.getStatus().equals(Status.REQUESTED)) {
+                    manualOverrideReason = mergeReasonIfNecessary(redactionLogEntry.getReason(), ", requested to force redact");
+                    redactionLogEntry.setStatus(Status.REQUESTED);
+                    redactionLogEntry.setColor(getColor(redactionLogEntry.getType(), dossierTemplateId, true, redactionLogEntry
+                            .isRedacted(), false));
+                    redactionLogEntry.setLegalBasis(manualForceRedact.getLegalBasis());
+                } else {
+                    redactionLogEntry.setStatus(Status.DECLINED);
+                }
+
+                redactionLogEntry.setManualRedactionUserId(manualForceRedact.getUser());
+                redactionLogEntry.setReason(manualOverrideReason);
+                redactionLogEntry.setManual(true);
+                redactionLogEntry.setManualRedactionType(ManualRedactionType.FORCE_REDACT);
+
+            }
+
+            if (mrw.getItem() instanceof ManualLegalBasisChange) {
+                var manualLegalBasisChange = (ManualLegalBasisChange) mrw.getItem();
+                String manualOverrideReason = null;
+                if (manualLegalBasisChange.getStatus().equals(Status.APPROVED)) {
+                    redactionLogEntry.setStatus(Status.APPROVED);
+                    redactionLogEntry.setRedacted(true);
+                    manualOverrideReason = mergeReasonIfNecessary(redactionLogEntry.getReason(), ", legal basis was manually changed");
+                    redactionLogEntry.setLegalBasis(manualLegalBasisChange.getLegalBasis());
+                    if (manualLegalBasisChange.getSection() != null) {
+                        redactionLogEntry.setSection(manualLegalBasisChange.getSection());
+                    }
+                    if (redactionLogEntry.isRectangle() && manualLegalBasisChange.getValue() != null) {
+                        redactionLogEntry.setValue(manualLegalBasisChange.getValue());
+                    }
+                    redactionLogEntry.setHasLegalBasisChanged(true);
+                } else if (manualLegalBasisChange.getStatus().equals(Status.REQUESTED)) {
+                    manualOverrideReason = mergeReasonIfNecessary(redactionLogEntry.getReason(), ", legal basis change requested");
+                    redactionLogEntry.setStatus(Status.REQUESTED);
+                    redactionLogEntry.setColor(getColor(redactionLogEntry.getType(), dossierTemplateId, true, redactionLogEntry
+                            .isRedacted(), false));
+                    redactionLogEntry.setLegalBasisChangeValue(manualLegalBasisChange.getLegalBasis());
+                } else {
+                    redactionLogEntry.setStatus(Status.DECLINED);
+                }
+
+
+                redactionLogEntry.setManualRedactionUserId(manualLegalBasisChange.getUser());
+                redactionLogEntry.setReason(manualOverrideReason);
+                redactionLogEntry.setManual(true);
+                redactionLogEntry.setManualRedactionType(ManualRedactionType.LEGAL_BASIS_CHANGE);
+            }
+
+        });
+
+    }
+
+
+    private String mergeReasonIfNecessary(String currentReason, String addition) {
+
+        if (currentReason != null) {
+            if (!currentReason.contains(addition)) {
+                return currentReason + addition;
+            }
+            return currentReason;
+        } else {
+            return "";
+        }
+    }
+
+
+    private List<RedactionLogEntry> addManualAddEntries(SectionGrid sectionGrid,
+                                                        Set<ManualRedactionEntry> manualAdds,
+                                                        Map<String, List<Comment>> comments, String dossierTemplateId) {
+
+        List<RedactionLogEntry> redactionLogEntries = new ArrayList<>();
+
+        for (ManualRedactionEntry manualRedactionEntry : manualAdds) {
+
+            if (!approvedAndShouldBeInDictionary(manualRedactionEntry)) {
+
+                RedactionLogEntry redactionLogEntry = createRedactionLogEntry(manualRedactionEntry, manualRedactionEntry
+                        .getId(), dossierTemplateId);
+                redactionLogEntry.setComments(comments.get(manualRedactionEntry.getId()));
+
+                sectionTextService.handleSectionText(sectionGrid, redactionLogEntry);
+
+                redactionLogEntries.add(redactionLogEntry);
+
+            }
+        }
+
+        return redactionLogEntries;
+    }
+
+
+    private boolean approvedAndShouldBeInDictionary(ManualRedactionEntry manualRedactionEntry) {
+
+        return manualRedactionEntry.getStatus()
+                .equals(Status.APPROVED) && (manualRedactionEntry.isAddToDictionary() || manualRedactionEntry.isAddToDossierDictionary());
+    }
+
+
+    private RedactionLogEntry createRedactionLogEntry(ManualRedactionEntry manualRedactionEntry, String id,
+                                                      String dossierTemplateId) {
+
+        return RedactionLogEntry.builder()
+                .id(id)
+                .color(getColorForManualAdd(manualRedactionEntry.getType(), dossierTemplateId, manualRedactionEntry.getStatus()))
+                .reason(manualRedactionEntry.getReason())
+                .isDictionaryEntry(manualRedactionEntry.isAddToDictionary())
+                .isDossierDictionaryEntry(manualRedactionEntry.isAddToDossierDictionary())
+                .legalBasis(manualRedactionEntry.getLegalBasis())
+                .value(manualRedactionEntry.getValue())
+                .section(manualRedactionEntry.getSection())
+                .type(manualRedactionEntry.getType())
+                .rectangle(manualRedactionEntry.isRectangle())
+                .redacted(true)
+                .isHint(false)
+                .sectionNumber(-1)
+                .manual(true)
+                .status(manualRedactionEntry.getStatus())
+                .manualRedactionType(ManualRedactionType.ADD)
+                .positions(manualRedactionEntry.getPositions())
+                .manualRedactionUserId(manualRedactionEntry.getUser())
+                .build();
+    }
+
+
+    private float[] getColor(String type, String dossierTemplateId, boolean requested, boolean isRedaction,
+                             boolean skipped) {
+
+        if (requested) {
+            return dictionaryService.getRequestRemoveColor(dossierTemplateId);
+        }
+        if (skipped || !isRedaction && !dictionaryService.isHint(type, dossierTemplateId)) {
+            return dictionaryService.getNotRedactedColor(dossierTemplateId);
+        }
+        return dictionaryService.getColor(type, dossierTemplateId);
+    }
+
+
+    private float[] getColorForManualAdd(String type, String dossierTemplateId, Status status) {
+
+        if (status.equals(Status.REQUESTED)) {
+            return dictionaryService.getRequestAddColor(dossierTemplateId);
+        } else if (status.equals(Status.DECLINED)) {
+            return dictionaryService.getNotRedactedColor(dossierTemplateId);
+        }
+        return getColor(type, dossierTemplateId);
+    }
+
+
+    private float[] getColor(String type, String dossierTemplateId) {
+
+        return dictionaryService.getColor(type, dossierTemplateId);
+    }
+
+
+    @Data
+    @AllArgsConstructor
+    private static class ManualRedactionWrapper implements Comparable<ManualRedactionWrapper> {
+
+        private String id;
+        private OffsetDateTime date;
+        private Object item;
+
+
+        @Override
+        public int compareTo(ManualRedactionWrapper o) {
+
+            return this.date.compareTo(o.date);
+        }
+
+    }
+
+}
+

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

@@ -0,0 +1,42 @@
+package com.iqser.red.service.redaction.v1.server.redaction.service;
+
+import com.iqser.red.service.redaction.v1.model.RedactionLogEntry;
+import com.iqser.red.service.redaction.v1.model.SectionGrid;
+import lombok.extern.slf4j.Slf4j;
+import org.springframework.stereotype.Service;
+
+@Slf4j
+@Service
+public class SectionTextService {
+
+
+    public void handleSectionText(SectionGrid sectionGrid, RedactionLogEntry redactionLogEntry) {
+
+        log.info("Handling manual redaction match for sections: {} and entry section: {}, positions: {}",
+                sectionGrid != null ? sectionGrid.getSections().size() : "null", redactionLogEntry.getSection(), redactionLogEntry.getPositions());
+
+        if (redactionLogEntry.getSection() != null) {
+            // set by UI
+            return;
+        }
+
+        if (sectionGrid != null) {
+            var firstPosition = !redactionLogEntry.getPositions().isEmpty() ? redactionLogEntry.getPositions().iterator().next() : null;
+
+            if (firstPosition != null) {
+
+                for (var section : sectionGrid.getSections()) {
+                    if (section.getPages().contains(firstPosition.getPage())) {
+                        for (var sectionArea : section.getSectionAreas()) {
+                            if (sectionArea.contains(firstPosition)) {
+                                redactionLogEntry.setSection(section.getHeadline());
+                                redactionLogEntry.setSectionNumber(section.getSectionNumber());
+                                return;
+                            }
+                        }
+                    }
+                }
+            }
+        }
+    }
+}

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

@@ -1,23 +1,30 @@
 package com.iqser.red.service.redaction.v1.server.redaction.utils;
 
+import java.util.ArrayList;
+import java.util.Comparator;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Locale;
+import java.util.Map;
+import java.util.Set;
+import java.util.regex.Pattern;
+import java.util.stream.Collectors;
+
 import com.iqser.red.service.redaction.v1.server.redaction.model.Dictionary;
 import com.iqser.red.service.redaction.v1.server.redaction.model.DictionaryIncrementValue;
 import com.iqser.red.service.redaction.v1.server.redaction.model.Entity;
 import com.iqser.red.service.redaction.v1.server.redaction.model.EntityPositionSequence;
 import com.iqser.red.service.redaction.v1.server.redaction.model.SearchableText;
+
 import lombok.experimental.UtilityClass;
 import lombok.extern.slf4j.Slf4j;
 
-import java.util.*;
-import java.util.regex.Pattern;
-import java.util.stream.Collectors;
-
 @Slf4j
 @UtilityClass
 @SuppressWarnings("PMD")
 public class EntitySearchUtils {
 
-
     public boolean sectionContainsAny(String sectionText, Set<DictionaryIncrementValue> values) {
 
         String inputString = sectionText.toLowerCase(Locale.ROOT);
@@ -38,9 +45,7 @@ public class EntitySearchUtils {
 
                 if (startIndex > -1 && (startIndex == 0 || Character.isWhitespace(inputString.charAt(startIndex - 1)) || isSeparator(inputString
                         .charAt(startIndex - 1))) && (stopIndex == inputString.length() || isSeparator(inputString.charAt(stopIndex)))) {
-                    if (value.isCaseinsensitive() || !value.isCaseinsensitive() && sectionText.substring(startIndex, stopIndex).equals(value.getValue())) {
-                        return true;
-                    }
+                    return true;
                 }
             } while (startIndex > -1);
         }
@@ -98,8 +103,8 @@ public class EntitySearchUtils {
                     .sorted(Comparator.comparing(Entity::getStart))
                     .collect(Collectors.toList());
             Entity firstEntity = orderedEntities.get(0);
-            List<EntityPositionSequence> positionSequences = text.getSequences(firstEntity.getWord().trim(), dictionary.isCaseInsensitiveDictionary(firstEntity
-                    .getType()), firstEntity.getTargetSequences());
+            List<EntityPositionSequence> positionSequences = text.getSequences(firstEntity.getWord()
+                    .trim(), dictionary.isCaseInsensitiveDictionary(firstEntity.getType()), firstEntity.getTargetSequences());
 
             for (int i = 0; i <= orderedEntities.size() - 1; i++) {
                 try {
@@ -133,6 +138,7 @@ public class EntitySearchUtils {
 
 
     public void addEntitiesWithHigherRank(Set<Entity> entities, Set<Entity> found, Dictionary dictionary) {
+
         found.forEach(f -> addEntitiesWithHigherRank(entities, f, dictionary));
     }
 
@@ -148,9 +154,49 @@ public class EntitySearchUtils {
         entities.add(found);
     }
 
+
     public void addEntitiesIgnoreRank(Set<Entity> entities, Set<Entity> found) {
         // HashSet keeps old value but we want the new.
         entities.removeAll(found);
         entities.addAll(found);
+
+        removeEntitiesContainedInLarger(entities);
     }
+
+
+    public Set<Entity> findNonOverlappingMatchEntities(Set<Entity> existingEntities, Set<Entity> foundEntities) {
+
+        Set<Entity> result = new HashSet<>();
+        if (existingEntities != null && foundEntities != null) {
+            for (Entity foundEntity : foundEntities) {
+
+                if (!overlaps(existingEntities, foundEntity)) {
+                    result.add(foundEntity);
+                }
+
+            }
+        }
+        return result;
+    }
+
+
+    private boolean overlaps(Set<Entity> existingEntities, Entity found) {
+
+        for (Entity existing : existingEntities) {
+
+            if(existing.getStart().equals(found.getStart())){
+                continue;
+            }
+
+            for (int i = existing.getStart(); i <= existing.getEnd(); i++) {
+                for (int j = found.getStart(); j <= found.getEnd(); j++) {
+                    if (i == j) {
+                        return true;
+                    }
+                }
+            }
+        }
+        return false;
+    }
+
 }

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

@@ -12,7 +12,7 @@ public class TextNormalizationUtilities {
      * @return Text without line-break hyphenation.
      */
     public static String removeHyphenLineBreaks(String text) {
-        return text.replaceAll("([^\\s\\d\\-]{2,})[\\-\\u00AD]\\R|\n\r(.+ )", "$1$2");
+        return text.replaceAll("([^\\s\\d\\-]{2,})[\\-\\u00AD]\\R", "$1");
     }
 
 }

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

@@ -118,7 +118,7 @@ public class ImageMergeService {
             //set position for merged image with values of image1 and the height of both
             Rectangle2D pos = new Rectangle2D.Float();
             pos.setRect(image1.getPosition().getX(), image2.getPosition().getY(), rotation == 90 ? width + width2: width, rotation == 90 ? height1 : height1 + height2);
-            PdfImage newPdfImage = new PdfImage(mergedImage, pos, image1.getPage());
+            PdfImage newPdfImage = new PdfImage(mergedImage, pos, image1.getPage(), image1.isHasTransparency() || image2.isHasTransparency());
             // Graphics need to be disposed
 
             image1.getImage().flush();

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

@@ -15,4 +15,6 @@ public class RedactionServiceSettings {
 
     private float maxImageCropboxRatio = 0.9f;
 
+    private int analysisVersion = 1;
+
 }

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

@@ -83,7 +83,6 @@ public class RedactionStorageService {
         }
     }
 
-
     @RequiredArgsConstructor
     public enum StorageType {
         PARSED_DOCUMENT(".json");

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

@@ -20,6 +20,8 @@ import com.iqser.red.service.redaction.v1.server.storage.RedactionStorageService
 import com.iqser.red.storage.commons.service.StorageService;
 import lombok.SneakyThrows;
 import org.apache.commons.io.IOUtils;
+import org.apache.commons.lang3.StringUtils;
+import org.assertj.core.util.Sets;
 import org.junit.After;
 import org.junit.Before;
 import org.junit.Ignore;
@@ -84,7 +86,6 @@ public class RedactionIntegrationTest {
 
     private static final String PII = "PII";
 
-
     @Autowired
     private RedactionController redactionController;
 
@@ -127,6 +128,7 @@ public class RedactionIntegrationTest {
     private final Map<String, Integer> rankTypeMap = new HashMap<>();
     private final Colors colors = new Colors();
     private final Map<String, Long> reanlysisVersions = new HashMap<>();
+    private final Set<String> deleted = new HashSet<>();
 
     private final static String TEST_DOSSIER_TEMPLATE_ID = "123";
     private final static String TEST_DOSSIER_ID = "123";
@@ -152,18 +154,20 @@ public class RedactionIntegrationTest {
             return kieServices.newKieContainer(kieModule.getReleaseId());
         }
 
+
         @Bean
         @Primary
         public StorageService inmemoryStorage() {
+
             return new FileSystemBackedStorageService();
         }
 
-
     }
 
 
     @After
     public void cleanupStorage() {
+
         if (this.storageService instanceof FileSystemBackedStorageService) {
             ((FileSystemBackedStorageService) this.storageService).clearStorage();
         }
@@ -179,7 +183,8 @@ public class RedactionIntegrationTest {
         loadDictionaryForTest();
         loadTypeForTest();
         when(dictionaryClient.getVersion(TEST_DOSSIER_TEMPLATE_ID, DictionaryResource.GLOBAL_DOSSIER)).thenReturn(0L);
-        when(dictionaryClient.getAllTypes(TEST_DOSSIER_TEMPLATE_ID, DictionaryResource.GLOBAL_DOSSIER)).thenReturn(TypeResponse.builder()
+        when(dictionaryClient.getAllTypes(TEST_DOSSIER_TEMPLATE_ID, DictionaryResource.GLOBAL_DOSSIER)).thenReturn(TypeResponse
+                .builder()
                 .types(getTypeResponse())
                 .build());
 
@@ -188,7 +193,7 @@ public class RedactionIntegrationTest {
                 .types(List.of(TypeResult.builder()
                         .type(DOSSIER_REDACTIONS)
                         .dossierTemplateId(TEST_DOSSIER_TEMPLATE_ID)
-                        .hexColor( "#ffe187")
+                        .hexColor("#ffe187")
                         .isHint(hintTypeMap.get(DOSSIER_REDACTIONS))
                         .isCaseInsensitive(caseInSensitiveMap.get(DOSSIER_REDACTIONS))
                         .isRecommendation(recommendationTypeMap.get(DOSSIER_REDACTIONS))
@@ -196,26 +201,42 @@ public class RedactionIntegrationTest {
                         .build()))
                 .build());
 
-        when(dictionaryClient.getDictionaryForType(VERTEBRATE, TEST_DOSSIER_TEMPLATE_ID, DictionaryResource.GLOBAL_DOSSIER)).thenReturn(getDictionaryResponse(VERTEBRATE, false));
-        when(dictionaryClient.getDictionaryForType(ADDRESS, TEST_DOSSIER_TEMPLATE_ID, DictionaryResource.GLOBAL_DOSSIER)).thenReturn(getDictionaryResponse(ADDRESS, false));
-        when(dictionaryClient.getDictionaryForType(AUTHOR, TEST_DOSSIER_TEMPLATE_ID, DictionaryResource.GLOBAL_DOSSIER)).thenReturn(getDictionaryResponse(AUTHOR, false));
-        when(dictionaryClient.getDictionaryForType(SPONSOR, TEST_DOSSIER_TEMPLATE_ID, DictionaryResource.GLOBAL_DOSSIER)).thenReturn(getDictionaryResponse(SPONSOR, false));
-        when(dictionaryClient.getDictionaryForType(NO_REDACTION_INDICATOR, TEST_DOSSIER_TEMPLATE_ID, DictionaryResource.GLOBAL_DOSSIER)).thenReturn(getDictionaryResponse(NO_REDACTION_INDICATOR, false));
-        when(dictionaryClient.getDictionaryForType(REDACTION_INDICATOR, TEST_DOSSIER_TEMPLATE_ID, DictionaryResource.GLOBAL_DOSSIER)).thenReturn(getDictionaryResponse(REDACTION_INDICATOR, false));
-        when(dictionaryClient.getDictionaryForType(HINT_ONLY, TEST_DOSSIER_TEMPLATE_ID, DictionaryResource.GLOBAL_DOSSIER)).thenReturn(getDictionaryResponse(HINT_ONLY, false));
-        when(dictionaryClient.getDictionaryForType(MUST_REDACT, TEST_DOSSIER_TEMPLATE_ID, DictionaryResource.GLOBAL_DOSSIER)).thenReturn(getDictionaryResponse(MUST_REDACT, false));
-        when(dictionaryClient.getDictionaryForType(PUBLISHED_INFORMATION, TEST_DOSSIER_TEMPLATE_ID, DictionaryResource.GLOBAL_DOSSIER)).thenReturn(getDictionaryResponse(PUBLISHED_INFORMATION, false));
-        when(dictionaryClient.getDictionaryForType(TEST_METHOD, TEST_DOSSIER_TEMPLATE_ID, DictionaryResource.GLOBAL_DOSSIER)).thenReturn(getDictionaryResponse(TEST_METHOD, false));
+        when(dictionaryClient.getDictionaryForType(VERTEBRATE, TEST_DOSSIER_TEMPLATE_ID, DictionaryResource.GLOBAL_DOSSIER))
+                .thenReturn(getDictionaryResponse(VERTEBRATE, false));
+        when(dictionaryClient.getDictionaryForType(ADDRESS, TEST_DOSSIER_TEMPLATE_ID, DictionaryResource.GLOBAL_DOSSIER))
+                .thenReturn(getDictionaryResponse(ADDRESS, false));
+        when(dictionaryClient.getDictionaryForType(AUTHOR, TEST_DOSSIER_TEMPLATE_ID, DictionaryResource.GLOBAL_DOSSIER))
+                .thenReturn(getDictionaryResponse(AUTHOR, false));
+        when(dictionaryClient.getDictionaryForType(SPONSOR, TEST_DOSSIER_TEMPLATE_ID, DictionaryResource.GLOBAL_DOSSIER))
+                .thenReturn(getDictionaryResponse(SPONSOR, false));
+        when(dictionaryClient.getDictionaryForType(NO_REDACTION_INDICATOR, TEST_DOSSIER_TEMPLATE_ID, DictionaryResource.GLOBAL_DOSSIER))
+                .thenReturn(getDictionaryResponse(NO_REDACTION_INDICATOR, false));
+        when(dictionaryClient.getDictionaryForType(REDACTION_INDICATOR, TEST_DOSSIER_TEMPLATE_ID, DictionaryResource.GLOBAL_DOSSIER))
+                .thenReturn(getDictionaryResponse(REDACTION_INDICATOR, false));
+        when(dictionaryClient.getDictionaryForType(HINT_ONLY, TEST_DOSSIER_TEMPLATE_ID, DictionaryResource.GLOBAL_DOSSIER))
+                .thenReturn(getDictionaryResponse(HINT_ONLY, false));
+        when(dictionaryClient.getDictionaryForType(MUST_REDACT, TEST_DOSSIER_TEMPLATE_ID, DictionaryResource.GLOBAL_DOSSIER))
+                .thenReturn(getDictionaryResponse(MUST_REDACT, false));
+        when(dictionaryClient.getDictionaryForType(PUBLISHED_INFORMATION, TEST_DOSSIER_TEMPLATE_ID, DictionaryResource.GLOBAL_DOSSIER))
+                .thenReturn(getDictionaryResponse(PUBLISHED_INFORMATION, false));
+        when(dictionaryClient.getDictionaryForType(TEST_METHOD, TEST_DOSSIER_TEMPLATE_ID, DictionaryResource.GLOBAL_DOSSIER))
+                .thenReturn(getDictionaryResponse(TEST_METHOD, false));
         when(dictionaryClient.getDictionaryForType(PII, TEST_DOSSIER_TEMPLATE_ID, DictionaryResource.GLOBAL_DOSSIER)).thenReturn(getDictionaryResponse(PII, false));
-        when(dictionaryClient.getDictionaryForType(RECOMMENDATION_AUTHOR, TEST_DOSSIER_TEMPLATE_ID, DictionaryResource.GLOBAL_DOSSIER)).thenReturn(getDictionaryResponse(RECOMMENDATION_AUTHOR, false));
-        when(dictionaryClient.getDictionaryForType(RECOMMENDATION_ADDRESS, TEST_DOSSIER_TEMPLATE_ID, DictionaryResource.GLOBAL_DOSSIER)).thenReturn(getDictionaryResponse(RECOMMENDATION_ADDRESS, false));
-        when(dictionaryClient.getDictionaryForType(FALSE_POSITIVE, TEST_DOSSIER_TEMPLATE_ID, DictionaryResource.GLOBAL_DOSSIER)).thenReturn(getDictionaryResponse(FALSE_POSITIVE, false));
-        when(dictionaryClient.getDictionaryForType(PURITY, TEST_DOSSIER_TEMPLATE_ID, DictionaryResource.GLOBAL_DOSSIER)).thenReturn(getDictionaryResponse(PURITY, false));
+        when(dictionaryClient.getDictionaryForType(RECOMMENDATION_AUTHOR, TEST_DOSSIER_TEMPLATE_ID, DictionaryResource.GLOBAL_DOSSIER))
+                .thenReturn(getDictionaryResponse(RECOMMENDATION_AUTHOR, false));
+        when(dictionaryClient.getDictionaryForType(RECOMMENDATION_ADDRESS, TEST_DOSSIER_TEMPLATE_ID, DictionaryResource.GLOBAL_DOSSIER))
+                .thenReturn(getDictionaryResponse(RECOMMENDATION_ADDRESS, false));
+        when(dictionaryClient.getDictionaryForType(FALSE_POSITIVE, TEST_DOSSIER_TEMPLATE_ID, DictionaryResource.GLOBAL_DOSSIER))
+                .thenReturn(getDictionaryResponse(FALSE_POSITIVE, false));
+        when(dictionaryClient.getDictionaryForType(PURITY, TEST_DOSSIER_TEMPLATE_ID, DictionaryResource.GLOBAL_DOSSIER))
+                .thenReturn(getDictionaryResponse(PURITY, false));
         when(dictionaryClient.getDictionaryForType(IMAGE, TEST_DOSSIER_TEMPLATE_ID, DictionaryResource.GLOBAL_DOSSIER)).thenReturn(getDictionaryResponse(IMAGE, false));
         when(dictionaryClient.getDictionaryForType(OCR, TEST_DOSSIER_TEMPLATE_ID, DictionaryResource.GLOBAL_DOSSIER)).thenReturn(getDictionaryResponse(OCR, false));
         when(dictionaryClient.getDictionaryForType(LOGO, TEST_DOSSIER_TEMPLATE_ID, DictionaryResource.GLOBAL_DOSSIER)).thenReturn(getDictionaryResponse(LOGO, false));
-        when(dictionaryClient.getDictionaryForType(SIGNATURE, TEST_DOSSIER_TEMPLATE_ID, DictionaryResource.GLOBAL_DOSSIER)).thenReturn(getDictionaryResponse(SIGNATURE, false));
-        when(dictionaryClient.getDictionaryForType(FORMULA, TEST_DOSSIER_TEMPLATE_ID, DictionaryResource.GLOBAL_DOSSIER)).thenReturn(getDictionaryResponse(FORMULA, false));
+        when(dictionaryClient.getDictionaryForType(SIGNATURE, TEST_DOSSIER_TEMPLATE_ID, DictionaryResource.GLOBAL_DOSSIER))
+                .thenReturn(getDictionaryResponse(SIGNATURE, false));
+        when(dictionaryClient.getDictionaryForType(FORMULA, TEST_DOSSIER_TEMPLATE_ID, DictionaryResource.GLOBAL_DOSSIER))
+                .thenReturn(getDictionaryResponse(FORMULA, false));
         when(dictionaryClient.getDictionaryForType(DOSSIER_REDACTIONS, TEST_DOSSIER_TEMPLATE_ID, TEST_DOSSIER_ID)).thenReturn(getDictionaryResponse(DOSSIER_REDACTIONS, true));
         when(dictionaryClient.getColors(TEST_DOSSIER_TEMPLATE_ID)).thenReturn(colors);
     }
@@ -477,7 +498,8 @@ public class RedactionIntegrationTest {
 
         return DictionaryResponse.builder()
                 .hexColor(typeColorMap.get(type))
-                .entries(isDossierDictionary ? toDictionaryEntry(dossierDictionary.get(type)) : toDictionaryEntry(dictionary.get(type)))
+                .entries(isDossierDictionary ? toDictionaryEntry(dossierDictionary.get(type)) : toDictionaryEntry(dictionary
+                        .get(type)))
                 .isHint(hintTypeMap.get(type))
                 .isCaseInsensitive(caseInSensitiveMap.get(type))
                 .isRecommendation(recommendationTypeMap.get(type))
@@ -490,7 +512,8 @@ public class RedactionIntegrationTest {
 
         List<DictionaryEntry> dictionaryEntries = new ArrayList<>();
         entries.forEach(entry -> {
-            dictionaryEntries.add(new DictionaryEntry(entry, reanlysisVersions.containsKey(entry) ? reanlysisVersions.get(entry) : 0L, false));
+            dictionaryEntries.add(new DictionaryEntry(entry, reanlysisVersions.containsKey(entry) ? reanlysisVersions.get(entry) : 0L, deleted
+                    .contains(entry) ? true : false));
         });
         return dictionaryEntries;
     }
@@ -498,6 +521,7 @@ public class RedactionIntegrationTest {
 
     @Test
     public void test270Rotated() {
+
         AnalyzeRequest request = prepareStorage("files/Minimal Examples/270Rotated.pdf");
         MemoryStats.printMemoryStats();
         AnalyzeResult result = reanalyzeService.analyze(request);
@@ -508,12 +532,14 @@ public class RedactionIntegrationTest {
     @Test
     @Ignore
     public void testLargeScannedFileOOM() {
+
         AnalyzeRequest request = prepareStorage("scanned/VV-377031.pdf");
         MemoryStats.printMemoryStats();
         AnalyzeResult result = reanalyzeService.analyze(request);
         assertThat(result).isNotNull();
     }
 
+
     @Test
     public void testMergedImages() throws IOException {
 
@@ -543,7 +569,7 @@ public class RedactionIntegrationTest {
                 .fileId(TEST_FILE_ID)
                 .build());
 
-        try (FileOutputStream fileOutputStream = new FileOutputStream("/tmp/Annotated3.pdf")) {
+        try (FileOutputStream fileOutputStream = new FileOutputStream(getTemporaryDirectory() + "/Annotated3.pdf")) {
             fileOutputStream.write(annotateResponse.getDocument());
         }
         long rstart = System.currentTimeMillis();
@@ -552,14 +578,13 @@ public class RedactionIntegrationTest {
         long rend = System.currentTimeMillis();
         System.out.println("reanalysis analysis duration: " + (rend - rstart));
 
-
         long end = System.currentTimeMillis();
 
         System.out.println("duration: " + (end - start));
 
-
     }
 
+
     @Test
     @Ignore
     public void noExceptionShouldBeThrownForAnyFiles() throws IOException {
@@ -627,15 +652,37 @@ public class RedactionIntegrationTest {
     }
 
 
+    @Test
+    public void redactionExpansionOverlap() throws IOException {
+
+        ClassPathResource pdfFileResource = new ClassPathResource("files/Minimal Examples/ExpansionTest.pdf");
+        AnalyzeRequest request = prepareStorage(pdfFileResource.getInputStream());
+
+
+        AnalyzeResult result = reanalyzeService.analyze(request);
+
+        var redactionLog = redactionStorageService.getRedactionLog(TEST_DOSSIER_ID, TEST_FILE_ID);
+
+        var values = redactionLog.getRedactionLogEntry().stream().map(RedactionLogEntry::getValue).collect(Collectors.toList());
+
+        assertThat(values).containsExactlyInAnyOrder("Lastname M.", "Doe", "Doe J.", "M. Mustermann", "Mustermann M.", "F. Lastname");
+    }
+
+
     @Test
     public void redactionTest() throws IOException {
 
         long start = System.currentTimeMillis();
-        ClassPathResource pdfFileResource = new ClassPathResource("files/new/Single Study - Oral (Gavage) Mouse.pdf");
+        ClassPathResource pdfFileResource = new ClassPathResource("files/new/just-a-document-20211215.pdf");
         AnalyzeRequest request = prepareStorage(pdfFileResource.getInputStream());
         request.setExcludedPages(Set.of(1));
 
-        request.setFileAttributes(List.of(FileAttribute.builder().id("fileAttributeId").label("Vertebrate Study").placeholder("{fileattributes.vertebrateStudy}").value("true").build()));
+        request.setFileAttributes(List.of(FileAttribute.builder()
+                .id("fileAttributeId")
+                .label("Vertebrate Study")
+                .placeholder("{fileattributes.vertebrateStudy}")
+                .value("true")
+                .build()));
 
         AnalyzeResult result = reanalyzeService.analyze(request);
 
@@ -652,7 +699,7 @@ public class RedactionIntegrationTest {
 
         System.out.println("first analysis duration: " + (end - start));
 
-        try (FileOutputStream fileOutputStream = new FileOutputStream("/tmp/Test.json")) {
+        try (FileOutputStream fileOutputStream = new FileOutputStream(getTemporaryDirectory() + "/Test.json")) {
             fileOutputStream.write(objectMapper.writeValueAsBytes(redactionStorageService.getText(TEST_DOSSIER_ID, TEST_FILE_ID)));
         }
 
@@ -683,12 +730,18 @@ public class RedactionIntegrationTest {
         dictionary.get(AUTHOR).add("physical");
         reanlysisVersions.put("physical", 2L);
 
-//        dictionary.get(VERTEBRATE).add("s-metolachlor");
-//        reanlysisVersions.put("s-metolachlor", 3L);
+        deleted.add("David Chubb");
+
+        dictionary.get(FALSE_POSITIVE).add("David Chubb");
+        reanlysisVersions.put("David Chubb", 3L);
 
         when(dictionaryClient.getVersion(TEST_DOSSIER_TEMPLATE_ID, DictionaryResource.GLOBAL_DOSSIER)).thenReturn(3L);
 
-        when(dictionaryClient.getDictionaryForType(VERTEBRATE, TEST_DOSSIER_TEMPLATE_ID, DictionaryResource.GLOBAL_DOSSIER)).thenReturn(getDictionaryResponse(VERTEBRATE, false));
+        when(dictionaryClient.getDictionaryForType(VERTEBRATE, TEST_DOSSIER_TEMPLATE_ID, DictionaryResource.GLOBAL_DOSSIER))
+                .thenReturn(getDictionaryResponse(VERTEBRATE, false));
+
+        when(dictionaryClient.getDictionaryForType(FALSE_POSITIVE, TEST_DOSSIER_TEMPLATE_ID, DictionaryResource.GLOBAL_DOSSIER))
+                .thenReturn(getDictionaryResponse(FALSE_POSITIVE, false));
 
         start = System.currentTimeMillis();
 
@@ -702,10 +755,8 @@ public class RedactionIntegrationTest {
 
         request.setManualRedactions(manualRedactions);
 
-
         AnalyzeResult reanalyzeResult = reanalyzeService.reanalyze(request);
 
-
         redactionLog = redactionStorageService.getRedactionLog(TEST_DOSSIER_ID, TEST_FILE_ID);
 
         end = System.currentTimeMillis();
@@ -716,13 +767,85 @@ public class RedactionIntegrationTest {
                 .fileId(TEST_FILE_ID)
                 .build());
 
-        try (FileOutputStream fileOutputStream = new FileOutputStream("/tmp/Annotated.pdf")) {
+        try (FileOutputStream fileOutputStream = new FileOutputStream(getTemporaryDirectory() + "/Annotated.pdf")) {
             fileOutputStream.write(annotateResponse.getDocument());
         }
 
     }
 
 
+    @Test
+    public void testIgnoreHint() {
+
+        System.out.println("testIgnoreHint");
+
+        AnalyzeRequest request = prepareStorage("files/new/test-ignore-hint.pdf");
+        reanalyzeService.analyze(request);
+        var redactionLog = redactionStorageService.getRedactionLog(TEST_DOSSIER_ID, TEST_FILE_ID);
+
+        var manualRedactions = ManualRedactions.builder().idsToRemove(Sets.newLinkedHashSet(
+                IdRemoval.builder()
+                        .id("c630599611e6e3db314518374bcf70f7")
+                        .status(Status.APPROVED)
+                        .user("test")
+                        .removeFromDictionary(false)
+                        .processedDate(OffsetDateTime.now())
+                        .requestDate(OffsetDateTime.now())
+                        .build())).build();
+
+        request.setManualRedactions(manualRedactions);
+        reanalyzeService.reanalyze(request);
+
+
+        var mergedRedactionLog = redactionController.getRedactionLog(RedactionRequest.builder().withSectionDataForManualRedactions(true)
+                .manualRedactions(manualRedactions)
+                .dossierTemplateId(TEST_DOSSIER_TEMPLATE_ID)
+                .dossierId(TEST_DOSSIER_ID)
+                .fileId(TEST_FILE_ID)
+                .build());
+
+        var cbiAddressBeforeHintRemoval = redactionLog.getRedactionLogEntry().stream().filter(re -> re.getType().equalsIgnoreCase("CBI_Address")).findAny().get();
+        assertThat(cbiAddressBeforeHintRemoval.isRedacted()).isFalse();
+
+        var cbiAddressAfterHintRemoval = mergedRedactionLog.getRedactionLogEntry().stream().filter(re -> re.getType().equalsIgnoreCase("CBI_Address")).findAny().get();
+        assertThat(cbiAddressAfterHintRemoval.isRedacted()).isTrue();
+    }
+
+
+
+    @Test
+    public void testIgnoreHintFirstAnalysis() {
+
+        System.out.println("testIgnoreHintFirstAnalysis");
+
+        AnalyzeRequest request = prepareStorage("files/new/test-ignore-hint.pdf");
+
+        var manualRedactions = ManualRedactions.builder().idsToRemove(Sets.newLinkedHashSet(
+                IdRemoval.builder()
+                        .id("c630599611e6e3db314518374bcf70f7")
+                        .status(Status.APPROVED)
+                        .user("test")
+                        .removeFromDictionary(false)
+                        .processedDate(OffsetDateTime.now())
+                        .requestDate(OffsetDateTime.now())
+                        .build())).build();
+
+        request.setManualRedactions(manualRedactions);
+        reanalyzeService.analyze(request);
+
+        var mergedRedactionLog = redactionController.getRedactionLog(RedactionRequest.builder().withSectionDataForManualRedactions(true)
+                .manualRedactions(manualRedactions)
+                .dossierTemplateId(TEST_DOSSIER_TEMPLATE_ID)
+                .dossierId(TEST_DOSSIER_ID)
+                .fileId(TEST_FILE_ID)
+                .build());
+
+        var cbiAddressAfterHintRemoval = mergedRedactionLog.getRedactionLogEntry().stream().filter(re -> re.getType().equalsIgnoreCase("CBI_Address")).findAny().get();
+        assertThat(cbiAddressAfterHintRemoval.isRedacted()).isTrue();
+    }
+
+
+
     @Test
     public void testTableRedaction() throws IOException {
 
@@ -737,7 +860,30 @@ public class RedactionIntegrationTest {
                 .fileId(TEST_FILE_ID)
                 .build());
 
-        try (FileOutputStream fileOutputStream = new FileOutputStream("/tmp/Annotated.pdf")) {
+        try (FileOutputStream fileOutputStream = new FileOutputStream(getTemporaryDirectory() + "/Annotated.pdf")) {
+            fileOutputStream.write(annotateResponse.getDocument());
+        }
+        long end = System.currentTimeMillis();
+
+        System.out.println("duration: " + (end - start));
+        System.out.println("numberOfPages: " + result.getNumberOfPages());
+    }
+
+
+    @Test
+    public void testIgnoreDossierRedactionIfConfidential() throws IOException {
+
+        long start = System.currentTimeMillis();
+
+        AnalyzeRequest request = prepareStorage("files/new/VV-919901.pdf");
+        AnalyzeResult result = reanalyzeService.analyze(request);
+
+        AnnotateResponse annotateResponse = redactionController.annotate(AnnotateRequest.builder()
+                .dossierId(TEST_DOSSIER_ID)
+                .fileId(TEST_FILE_ID)
+                .build());
+
+        try (FileOutputStream fileOutputStream = new FileOutputStream(getTemporaryDirectory() + "/Annotated.pdf")) {
             fileOutputStream.write(annotateResponse.getDocument());
         }
         long end = System.currentTimeMillis();
@@ -775,7 +921,6 @@ public class RedactionIntegrationTest {
                 .status(Status.APPROVED)
                 .build()));
 
-
         manualRedactions.getComments().put("e5be0f1d941bbb92a068e198648d06c4", List.of(comment));
         manualRedactions.getComments().put("0836727c3508a0b2ea271da69c04cc2f", List.of(comment));
         manualRedactions.getComments().put(manualAddId, List.of(comment));
@@ -790,12 +935,10 @@ public class RedactionIntegrationTest {
 
 //        manualRedactions.getEntriesToAdd().add(manualRedactionEntry);
 
-
         AnalyzeRequest request = prepareStorage(pdfFileResource.getInputStream());
         request.setManualRedactions(manualRedactions);
         AnalyzeResult result = reanalyzeService.analyze(request);
 
-
         manualRedactions.getEntriesToAdd().add(manualRedactionEntry);
         manualRedactions.setIdsToRemove(Set.of(IdRemoval.builder()
                 .id("5b940b2cb401ed9f5be6fc24f6e77bcf")
@@ -816,8 +959,7 @@ public class RedactionIntegrationTest {
                 .fileId(TEST_FILE_ID)
                 .build());
 
-
-        try (FileOutputStream fileOutputStream = new FileOutputStream("/tmp/Annotated.pdf")) {
+        try (FileOutputStream fileOutputStream = new FileOutputStream(getTemporaryDirectory() + "/Annotated.pdf")) {
             fileOutputStream.write(annotateResponse.getDocument());
         }
         long end = System.currentTimeMillis();
@@ -833,7 +975,6 @@ public class RedactionIntegrationTest {
         System.out.println("classificationTest");
         ClassPathResource pdfFileResource = new ClassPathResource("files/new/Single Study - Oral (Gavage) Mouse.pdf");
 
-
         AnalyzeRequest request = prepareStorage(pdfFileResource.getInputStream());
 
         RedactionRequest redactionRequest = RedactionRequest.builder()
@@ -844,7 +985,7 @@ public class RedactionIntegrationTest {
 
         RedactionResult result = redactionController.classify(redactionRequest);
 
-        try (FileOutputStream fileOutputStream = new FileOutputStream("/tmp/Classified.pdf")) {
+        try (FileOutputStream fileOutputStream = new FileOutputStream(getTemporaryDirectory() + "/Classified.pdf")) {
             fileOutputStream.write(result.getDocument());
         }
     }
@@ -866,7 +1007,7 @@ public class RedactionIntegrationTest {
 
         RedactionResult result = redactionController.sections(redactionRequest);
 
-        try (FileOutputStream fileOutputStream = new FileOutputStream("/tmp/Sections.pdf")) {
+        try (FileOutputStream fileOutputStream = new FileOutputStream(getTemporaryDirectory() + "/Sections.pdf")) {
             fileOutputStream.write(result.getDocument());
         }
     }
@@ -888,7 +1029,7 @@ public class RedactionIntegrationTest {
 
         RedactionResult result = redactionController.htmlTables(redactionRequest);
 
-        try (FileOutputStream fileOutputStream = new FileOutputStream("/tmp/Tables.html")) {
+        try (FileOutputStream fileOutputStream = new FileOutputStream(getTemporaryDirectory() + "/Tables.html")) {
             fileOutputStream.write(result.getDocument());
         }
     }
@@ -910,7 +1051,7 @@ public class RedactionIntegrationTest {
 
         RedactionResult result = redactionController.htmlTables(redactionRequest);
 
-        try (FileOutputStream fileOutputStream = new FileOutputStream("/tmp/Tables.html")) {
+        try (FileOutputStream fileOutputStream = new FileOutputStream(getTemporaryDirectory() + "/Tables.html")) {
             fileOutputStream.write(result.getDocument());
         }
     }
@@ -934,8 +1075,10 @@ public class RedactionIntegrationTest {
         });
     }
 
+
     @SneakyThrows
     private AnalyzeRequest prepareStorage(String file) {
+
         ClassPathResource pdfFileResource = new ClassPathResource(file);
 
         return prepareStorage(pdfFileResource.getInputStream());
@@ -967,7 +1110,6 @@ public class RedactionIntegrationTest {
         long start = System.currentTimeMillis();
         ClassPathResource pdfFileResource = new ClassPathResource("files/Minimal Examples/sponsor_companies.pdf");
 
-
         AnalyzeRequest request = prepareStorage(pdfFileResource.getInputStream());
 
         AnalyzeResult result = reanalyzeService.analyze(request);
@@ -977,7 +1119,31 @@ public class RedactionIntegrationTest {
                 .fileId(TEST_FILE_ID)
                 .build());
 
-        try (FileOutputStream fileOutputStream = new FileOutputStream("/tmp/Annotated.pdf")) {
+        try (FileOutputStream fileOutputStream = new FileOutputStream(getTemporaryDirectory() + "/Annotated.pdf")) {
+            fileOutputStream.write(annotateResponse.getDocument());
+        }
+        long end = System.currentTimeMillis();
+
+        System.out.println("duration: " + (end - start));
+        System.out.println("numberOfPages: " + result.getNumberOfPages());
+    }
+
+
+    @Test
+    public void testExpandByRegEx() throws IOException {
+
+        System.out.println("expandByRegex");
+        long start = System.currentTimeMillis();
+
+        AnalyzeRequest request = prepareStorage("files/Metolachlor/S-Metolachlor_RAR_02_Volume_2_2018-09-06.pdf");
+        AnalyzeResult result = reanalyzeService.analyze(request);
+
+        AnnotateResponse annotateResponse = redactionController.annotate(AnnotateRequest.builder()
+                .dossierId(TEST_DOSSIER_ID)
+                .fileId(TEST_FILE_ID)
+                .build());
+
+        try (FileOutputStream fileOutputStream = new FileOutputStream(getTemporaryDirectory() + "/Annotated.pdf")) {
             fileOutputStream.write(annotateResponse.getDocument());
         }
         long end = System.currentTimeMillis();
@@ -1005,4 +1171,13 @@ public class RedactionIntegrationTest {
         }
     }
 
+    private static String getTemporaryDirectory() {
+
+//        String tmpdir = System.getProperty("java.io.tmpdir");
+//        if (StringUtils.isNotBlank(tmpdir)) {
+//            return tmpdir;
+//        }
+        return "/tmp";
+    }
+
 }

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

@@ -0,0 +1,171 @@
+package com.iqser.red.service.redaction.v1.server.redaction.utils;
+
+import static org.assertj.core.api.Assertions.assertThat;
+
+import java.util.HashSet;
+import java.util.Set;
+
+import org.junit.Test;
+
+import com.iqser.red.service.redaction.v1.server.redaction.model.Entity;
+
+public class EntitySearchUtilsTest {
+
+    /*
+     * Text:     Batman X. Superman Y.
+     * Position: 0123456789
+     *                     0123456789
+     *                               0123456789
+     */
+    @Test
+    public void testNotOverlappingEntitiesExpandedEnd() {
+
+        // Arrange
+        Set<Entity> existingEntities = new HashSet<>();
+        Entity existingEntity1 = new Entity("Batman", "fake type", 0, 5, "fake headline", 0, false, false);
+        Entity existingEntity2 = new Entity("Superman", "fake type", 10, 17, "fake headline", 0, false, false);
+        existingEntities.add(existingEntity1);
+        existingEntities.add(existingEntity2);
+
+        Set<Entity> foundEntities = new HashSet<>();
+        Entity foundEntities1 = new Entity("Batman X.", "fake type", 0, 8, "fake headline", 0, false, false);
+        Entity foundEntities2 = new Entity("Superman Y.", "fake type", 10, 20, "fake headline", 0, false, false);
+        foundEntities.add(foundEntities1);
+        foundEntities.add(foundEntities2);
+
+        // Act
+        Set<Entity> result = EntitySearchUtils.findNonOverlappingMatchEntities(existingEntities, foundEntities);
+
+        // Assert
+        assertThat(result.size()).isEqualTo(2);
+        assertThat(result).contains(foundEntities1);
+        assertThat(result).contains(foundEntities2);
+
+    }
+
+
+    /*
+     * Text:     Batman X. Superman Y.
+     * Position: 0123456789
+     *                     0123456789
+     *                               0123456789
+     */
+    @Test
+    public void testNotOverlappingEntitiesExpandedStartAndEndOverlapping() {
+
+        // Arrange
+        Set<Entity> existingEntities = new HashSet<>();
+        Entity existingEntity1 = new Entity("Batman X.", "fake type", 0, 8, "fake headline", 0, false, false);
+        Entity existingEntity2 = new Entity("Superman", "fake type", 10, 17, "fake headline", 0, false, false);
+        existingEntities.add(existingEntity1);
+        existingEntities.add(existingEntity2);
+
+        Set<Entity> foundEntities = new HashSet<>();
+        Entity foundEntities1 = new Entity("Batman X.", "fake type", 0, 8, "fake headline", 0, false, false);
+        Entity foundEntities2 = new Entity("X. Superman Y.", "fake type", 7, 20, "fake headline", 0, false, false);
+        foundEntities.add(foundEntities1);
+        foundEntities.add(foundEntities2);
+
+        // Act
+        Set<Entity> result = EntitySearchUtils.findNonOverlappingMatchEntities(existingEntities, foundEntities);
+
+        // Assert
+        assertThat(result.size()).isEqualTo(1);
+        assertThat(result).contains(foundEntities1);
+
+    }
+
+
+    /*
+     * Text:     Batman X. Superman Y.
+     * Position: 0123456789
+     *                     0123456789
+     *                               0123456789
+     */
+    @Test
+    public void testNotOverlappingEntitiesExpandedStartAndEnd() {
+
+        // Arrange
+        Set<Entity> existingEntities = new HashSet<>();
+        Entity existingEntity1 = new Entity("Batman X.", "fake type", 0, 8, "fake headline", 0, false, false);
+        Entity existingEntity2 = new Entity("Superman", "fake type", 10, 17, "fake headline", 0, false, false);
+        existingEntities.add(existingEntity1);
+        existingEntities.add(existingEntity2);
+
+        Set<Entity> foundEntities = new HashSet<>();
+        Entity foundEntities1 = new Entity("Batman X.", "fake type", 0, 8, "fake headline", 0, false, false);
+        Entity foundEntities2 = new Entity("X. Superman", "fake type", 7, 17, "fake headline", 0, false, false);
+        foundEntities.add(foundEntities1);
+        foundEntities.add(foundEntities2);
+
+        // Act
+        Set<Entity> result = EntitySearchUtils.findNonOverlappingMatchEntities(existingEntities, foundEntities);
+
+        // Assert
+        assertThat(result.size()).isEqualTo(1);
+        assertThat(result).contains(foundEntities1);
+
+    }
+
+
+    /*
+     * Text:     Batman X. Superman Y.
+     * Position: 0123456789
+     *                     0123456789
+     *                               0123456789
+     */
+    @Test
+    public void testNotOverlappingEntitiesExpandedExistingAndExpandedEnd() {
+
+        // Arrange
+        Set<Entity> existingEntities = new HashSet<>();
+        Entity existingEntity1 = new Entity("X. Superman", "fake type", 7, 17, "fake headline", 0, false, false);
+        Entity existingEntity2 = new Entity("Batman", "fake type", 0, 5, "fake headline", 0, false, false);
+        existingEntities.add(existingEntity1);
+        existingEntities.add(existingEntity2);
+
+        Set<Entity> foundEntities = new HashSet<>();
+        Entity foundEntities1 = new Entity("Batman X.", "fake type", 0, 8, "fake headline", 0, false, false);
+        Entity foundEntities2 = new Entity("Superman", "fake type", 10, 17, "fake headline", 0, false, false);
+        foundEntities.add(foundEntities1);
+        foundEntities.add(foundEntities2);
+
+        // Act
+        Set<Entity> result = EntitySearchUtils.findNonOverlappingMatchEntities(existingEntities, foundEntities);
+
+        // Assert
+        assertThat(result.size()).isEqualTo(0);
+
+    }
+
+    /*
+     * Text:     Batman X. Superman Y.
+     * Position: 0123456789
+     *                     0123456789
+     *                               0123456789
+     */
+    @Test
+    public void testNotOverlappingEntitiesExpandedEndLong() {
+
+        // Arrange
+        Set<Entity> existingEntities = new HashSet<>();
+        Entity existingEntity1 = new Entity("X. Superman", "fake type", 7, 17, "fake headline", 0, false, false);
+        Entity existingEntity2 = new Entity("Batman", "fake type", 0, 5, "fake headline", 0, false, false);
+        existingEntities.add(existingEntity1);
+        existingEntities.add(existingEntity2);
+
+        Set<Entity> foundEntities = new HashSet<>();
+        Entity foundEntities1 = new Entity("Batman X. Superman", "fake type", 0, 17, "fake headline", 0, false, false);
+        Entity foundEntities2 = new Entity("Superman", "fake type", 10, 17, "fake headline", 0, false, false);
+        foundEntities.add(foundEntities1);
+        foundEntities.add(foundEntities2);
+
+        // Act
+        Set<Entity> result = EntitySearchUtils.findNonOverlappingMatchEntities(existingEntities, foundEntities);
+
+        // Assert
+        assertThat(result.size()).isEqualTo(0);
+
+    }
+
+}

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

@@ -0,0 +1,80 @@
+package com.iqser.red.service.redaction.v1.server.redaction.utils;
+
+import com.amazonaws.services.s3.AmazonS3;
+import com.fasterxml.jackson.databind.ObjectMapper;
+import com.iqser.red.service.redaction.v1.model.ManualRedactions;
+import com.iqser.red.service.redaction.v1.model.RedactionLog;
+import com.iqser.red.service.redaction.v1.model.SectionGrid;
+import com.iqser.red.service.redaction.v1.server.Application;
+import com.iqser.red.service.redaction.v1.server.redaction.service.DictionaryService;
+import com.iqser.red.service.redaction.v1.server.redaction.service.RedactionLogMergeService;
+import com.iqser.red.service.redaction.v1.server.redaction.service.SectionTextService;
+import lombok.SneakyThrows;
+import org.apache.commons.compress.utils.Lists;
+import org.assertj.core.util.Sets;
+import org.junit.Test;
+import org.junit.runner.RunWith;
+import org.mockito.Mockito;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.boot.autoconfigure.EnableAutoConfiguration;
+import org.springframework.boot.autoconfigure.amqp.RabbitAutoConfiguration;
+import org.springframework.boot.test.context.SpringBootTest;
+import org.springframework.boot.test.mock.mockito.MockBean;
+import org.springframework.context.annotation.Configuration;
+import org.springframework.context.annotation.Import;
+import org.springframework.core.io.ClassPathResource;
+import org.springframework.test.context.junit4.SpringRunner;
+
+import static org.assertj.core.api.Assertions.assertThat;
+import static org.mockito.Mockito.when;
+
+@RunWith(SpringRunner.class)
+@SpringBootTest(classes = Application.class, webEnvironment = SpringBootTest.WebEnvironment.MOCK)
+@Import(SectionTextServiceTest.TestConfiguration.class)
+public class SectionTextServiceTest {
+
+    @Autowired
+    private ObjectMapper objectMapper;
+
+    @Autowired
+    private SectionTextService service;
+
+    @Autowired
+    private RedactionLogMergeService redactionLogMergeService;
+
+    @MockBean
+    private DictionaryService dictionaryService;
+
+    @MockBean
+    private AmazonS3 amazonS3;
+
+
+    @Configuration
+    @EnableAutoConfiguration(exclude = {RabbitAutoConfiguration.class})
+    public static class TestConfiguration {
+
+    }
+
+
+    @Test
+    @SneakyThrows
+    public void testMerge() {
+
+        when(dictionaryService.getColor(Mockito.anyString(), Mockito.anyString())).thenReturn(new float[]{0, 0, 0});
+
+        ManualRedactions manualRedactions = objectMapper.readValue(new ClassPathResource("contains/manual-redactions.json").getInputStream(), ManualRedactions.class);
+
+        RedactionLog redactionLog = new RedactionLog(1, Lists.newArrayList(), Lists.newArrayList(), 1, 1, 1, 1);
+        SectionGrid sectionGrid = objectMapper.readValue(new ClassPathResource("contains/sections.json").getInputStream(), SectionGrid.class);
+        RedactionLog merged = redactionLogMergeService.mergeRedactionLogData(redactionLog, sectionGrid, "1", manualRedactions, Sets.newHashSet());
+
+        assertThat(merged.getRedactionLogEntry().isEmpty()).isFalse();
+
+        assertThat(merged.getRedactionLogEntry().iterator().next().getSection()).isEqualTo("NOTIFICATION OF AN ACTIVE\n" +
+                "SUBSTANCE UNDER COMMISSION\n" +
+                "REGULATION (EU) 844/2012");
+        assertThat(merged.getRedactionLogEntry().iterator().next().getSectionNumber()).isEqualTo(7);
+    }
+
+
+}

redaction-service-v1/redaction-service-server-v1/src/test/resources/contains/manual-redactions.json

@@ -0,0 +1,54 @@
+{
+  "idsToRemove": [],
+  "entriesToAdd": [
+    {
+      "id": "d5fd9fd9690557703a22d8ab22832c7f",
+      "user": "7adf30b4-a0d8-4abb-adbb-760b1211098f",
+      "type": "manual",
+      "value": "DOCUMENT M-CA, Section 10\nSupplement",
+      "reason": "names and addresses of persons involved in testing on vertebrate animals",
+      "legalBasis": "[Reg (EC) No 1107/2009 Art. 63 (2g)]",
+      "section": null,
+      "positions": [
+        {
+          "topLeft": {
+            "x": 190.92,
+            "y": 376.7999
+          },
+          "width": 227.49368,
+          "height": 14.974969,
+          "page": 1
+        },
+        {
+          "topLeft": {
+            "x": 258.96,
+            "y": 358.31992
+          },
+          "width": 91.47408,
+          "height": 14.974969,
+          "page": 1
+        }
+      ],
+      "status": "APPROVED",
+      "addToDictionary": false,
+      "addToDossierDictionary": false,
+      "requestDate": "2021-11-03T15:01:45Z",
+      "processedDate": "2021-11-03T15:01:45Z",
+      "softDeletedTime": null
+    }
+  ],
+  "forceRedactions": [],
+  "imageRecategorization": [],
+  "legalBasisChanges": [],
+  "comments": {
+    "d5fd9fd9690557703a22d8ab22832c7f": [
+      {
+        "id": "56c1a675-0d64-4190-b76c-6af9d0b361a9",
+        "date": "2021-11-03T15:01:45Z",
+        "text": "test",
+        "user": "7adf30b4-a0d8-4abb-adbb-760b1211098f",
+        "softDeletedTime": null
+      }
+    ]
+  }
+}

redaction-service-v1/redaction-service-server-v1/src/test/resources/contains/sections.json

@@ -0,0 +1,877 @@
+{
+  "rectanglesPerPage": {
+    "1": [
+      {
+        "topLeft": {
+          "x": 251.4,
+          "y": 550.32
+        },
+        "width": 107.763336,
+        "height": 12.02002,
+        "part": 1,
+        "numberOfParts": 1,
+        "tableCells": null
+      },
+      {
+        "topLeft": {
+          "x": 159.24,
+          "y": 280.92004
+        },
+        "width": 291.92004,
+        "height": 212.29996,
+        "part": 1,
+        "numberOfParts": 3,
+        "tableCells": null
+      }
+    ],
+    "2": [
+      {
+        "topLeft": {
+          "x": 70.92,
+          "y": 735.36
+        },
+        "width": 105.64288,
+        "height": 9.02002,
+        "part": 2,
+        "numberOfParts": 3,
+        "tableCells": null
+      },
+      {
+        "topLeft": {
+          "x": 65.56436,
+          "y": 719.9557
+        },
+        "width": 478.4686,
+        "height": -110.91278,
+        "part": 3,
+        "numberOfParts": 3,
+        "tableCells": [
+          {
+            "topLeft": {
+              "x": 65.56436,
+              "y": 684.47955
+            },
+            "width": 83.35573,
+            "height": 35.476135
+          },
+          {
+            "topLeft": {
+              "x": 148.92009,
+              "y": 684.47955
+            },
+            "width": 255.12016,
+            "height": 35.476135
+          },
+          {
+            "topLeft": {
+              "x": 404.04025,
+              "y": 684.47955
+            },
+            "width": 139.9927,
+            "height": 35.476135
+          },
+          {
+            "topLeft": {
+              "x": 65.56436,
+              "y": 659.27954
+            },
+            "width": 83.35573,
+            "height": 25.200012
+          },
+          {
+            "topLeft": {
+              "x": 148.92009,
+              "y": 659.27954
+            },
+            "width": 255.12016,
+            "height": 25.200012
+          },
+          {
+            "topLeft": {
+              "x": 404.04025,
+              "y": 659.27954
+            },
+            "width": 139.9927,
+            "height": 25.200012
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+          {
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+    ],
+    "3": [
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+          "y": 691.2
+        },
+        "width": 468.76624,
+        "height": 53.179993,
+        "part": 1,
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+        "tableCells": null
+      }
+    ],
+    "4": [
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+          "y": 555.48
+        },
+        "width": 461.24002,
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+        "part": 2,
+        "numberOfParts": 3,
+        "tableCells": null
+      },
+      {
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+          "y": 540.55756
+        },
+        "width": 478.58698,
+        "height": -365.55508,
+        "part": 3,
+        "numberOfParts": 3,
+        "tableCells": [
+          {
+            "topLeft": {
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+              "y": 515.4003
+            },
+            "width": 125.808716,
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+              "y": 515.4003
+            },
+            "width": 352.77826,
+            "height": 25.157227
+          },
+          {
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+              "y": 404.75992
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+            "height": 110.64041
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+            "height": 29.400208
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+          {
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+          {
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+            },
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+            "height": 62.519775
+          },
+          {
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+              "y": 218.76001
+            },
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+            "height": 62.519775
+          },
+          {
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+              "y": 175.00247
+            },
+            "width": 125.808716,
+            "height": 43.757538
+          },
+          {
+            "topLeft": {
+              "x": 191.49458,
+              "y": 175.00247
+            },
+            "width": 352.77826,
+            "height": 43.757538
+          }
+        ]
+      }
+    ]
+  },
+  "sections": [
+    {
+      "sectionNumber": 1,
+      "headline": "",
+      "pages": [
+        1
+      ],
+      "sectionAreas": [
+        {
+          "topLeft": {
+            "x": 251.4,
+            "y": 550.32
+          },
+          "width": 107.763336,
+          "height": 12.02002,
+          "page": 1,
+          "header": null
+        }
+      ]
+    },
+    {
+      "sectionNumber": 2,
+      "headline": "Table in: NOTIFICATION OF AN ACTIVE\nSUBSTANCE UNDER COMMISSION\nREGULATION (EU) 844/2012",
+      "pages": [
+        2
+      ],
+      "sectionAreas": [
+        {
+          "topLeft": {
+            "x": 65.56436,
+            "y": 684.47955
+          },
+          "width": 83.35573,
+          "height": 35.476135,
+          "page": 2,
+          "header": null
+        },
+        {
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+            "y": 684.47955
+          },
+          "width": 255.12016,
+          "height": 35.476135,
+          "page": 2,
+          "header": null
+        },
+        {
+          "topLeft": {
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+            "y": 684.47955
+          },
+          "width": 139.9927,
+          "height": 35.476135,
+          "page": 2,
+          "header": null
+        }
+      ]
+    },
+    {
+      "sectionNumber": 3,
+      "headline": "Table in: NOTIFICATION OF AN ACTIVE\nSUBSTANCE UNDER COMMISSION\nREGULATION (EU) 844/2012",
+      "pages": [],
+      "sectionAreas": []
+    },
+    {
+      "sectionNumber": 4,
+      "headline": "Table in: NOTIFICATION OF AN ACTIVE\nSUBSTANCE UNDER COMMISSION\nREGULATION (EU) 844/2012",
+      "pages": [],
+      "sectionAreas": []
+    },
+    {
+      "sectionNumber": 5,
+      "headline": "Table in: NOTIFICATION OF AN ACTIVE\nSUBSTANCE UNDER COMMISSION\nREGULATION (EU) 844/2012",
+      "pages": [
+        2
+      ],
+      "sectionAreas": [
+        {
+          "topLeft": {
+            "x": 65.56436,
+            "y": 609.0429
+          },
+          "width": 83.35573,
+          "height": 25.157837,
+          "page": 2,
+          "header": "Date"
+        }
+      ]
+    },
+    {
+      "sectionNumber": 7,
+      "headline": "NOTIFICATION OF AN ACTIVE\nSUBSTANCE UNDER COMMISSION\nREGULATION (EU) 844/2012",
+      "pages": [
+        1,
+        2
+      ],
+      "sectionAreas": [
+        {
+          "topLeft": {
+            "x": 159.24,
+            "y": 280.92004
+          },
+          "width": 291.92004,
+          "height": 212.29996,
+          "page": 1,
+          "header": null
+        },
+        {
+          "topLeft": {
+            "x": 70.92,
+            "y": 735.36
+          },
+          "width": 105.64288,
+          "height": 9.02002,
+          "page": 2,
+          "header": null
+        }
+      ]
+    },
+    {
+      "sectionNumber": 8,
+      "headline": "Table in: Table of Contents",
+      "pages": [
+        4
+      ],
+      "sectionAreas": [
+        {
+          "topLeft": {
+            "x": 65.68587,
+            "y": 515.4003
+          },
+          "width": 125.808716,
+          "height": 25.157227,
+          "page": 4,
+          "header": null
+        },
+        {
+          "topLeft": {
+            "x": 191.49458,
+            "y": 515.4003
+          },
+          "width": 352.77826,
+          "height": 25.157227,
+          "page": 4,
+          "header": null
+        },
+        {
+          "topLeft": {
+            "x": 65.68587,
+            "y": 404.75992
+          },
+          "width": 125.808716,
+          "height": 110.64041,
+          "page": 4,
+          "header": null
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+        {
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+      ]
+    },
+    {
+      "sectionNumber": 9,
+      "headline": "Table of Contents",
+      "pages": [
+        3,
+        4
+      ],
+      "sectionAreas": [
+        {
+          "topLeft": {
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+            "y": 691.2
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+          },
+          "width": 461.24002,
+          "height": 188.78003,
+          "page": 4,
+          "header": null
+        }
+      ]
+    },
+    {
+      "sectionNumber": 10,
+      "headline": "Header",
+      "pages": [
+        1
+      ],
+      "sectionAreas": [
+        {
+          "topLeft": {
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+            "y": 799.08
+          },
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+          },
+          "width": 5.470215,
+          "height": 6.0200195,
+          "page": 1,
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+      ]
+    },
+    {
+      "sectionNumber": 11,
+      "headline": "Header",
+      "pages": [
+        2
+      ],
+      "sectionAreas": [
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+      "headline": "Header",
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+      ]
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+      "headline": "Header",
+      "pages": [
+        4
+      ],
+      "sectionAreas": [
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+        }
+      ]
+    },
+    {
+      "sectionNumber": 14,
+      "headline": "Footer",
+      "pages": [
+        1
+      ],
+      "sectionAreas": [
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+        }
+      ]
+    },
+    {
+      "sectionNumber": 15,
+      "headline": "Footer",
+      "pages": [
+        2
+      ],
+      "sectionAreas": [
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+          "height": 6.0200005,
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+          "header": null
+        }
+      ]
+    },
+    {
+      "sectionNumber": 16,
+      "headline": "Footer",
+      "pages": [
+        3
+      ],
+      "sectionAreas": [
+        {
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+            "x": 70.92,
+            "y": 37.440002
+          },
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+          "height": 6.0200005,
+          "page": 3,
+          "header": null
+        }
+      ]
+    },
+    {
+      "sectionNumber": 17,
+      "headline": "Footer",
+      "pages": [
+        4
+      ],
+      "sectionAreas": [
+        {
+          "topLeft": {
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+            "y": 37.320007
+          },
+          "width": 93.3805,
+          "height": 6.0360794,
+          "page": 4,
+          "header": null
+        },
+        {
+          "topLeft": {
+            "x": 468.12,
+            "y": 37.320007
+          },
+          "width": 71.984375,
+          "height": 6.0360794,
+          "page": 4,
+          "header": null
+        },
+        {
+          "topLeft": {
+            "x": 71.04,
+            "y": 140.16003
+          },
+          "width": 254.69507,
+          "height": 7.5200043,
+          "page": 4,
+          "header": null
+        },
+        {
+          "topLeft": {
+            "x": 71.04,
+            "y": 115.56
+          },
+          "width": 65.564415,
+          "height": 7.5199966,
+          "page": 4,
+          "header": null
+        },
+        {
+          "topLeft": {
+            "x": 71.04,
+            "y": 90.599976
+          },
+          "width": 424.84805,
+          "height": 7.5199966,
+          "page": 4,
+          "header": null
+        }
+      ]
+    }
+  ]
+}

redaction-service-v1/redaction-service-server-v1/src/test/resources/dictionaries/CBI_address.txt

@@ -1654,3 +1654,12 @@ Zyma SA
 Zyma SA, Nyon, Switzerland
 Mambo-Tox Ltd. Biomedical Sciences Building Bassett Crescent East Southampton SO16 7PX UK
 Syngenta Environmental Sciences Jealott’s Hill International Research Centre Bracknell, Berkshire RG42 6EY UK
+Test Ignored Hint CBI_ADDRESS
+CTL
+CTL - Central Toxicology Laboratory
+CTL/P/3557
+CTL/P/3607
+CTL/P/S 161
+CTL/Pl4333
+CTL/with dictionary entry
+

redaction-service-v1/redaction-service-server-v1/src/test/resources/dictionaries/CBI_author.txt

@@ -1676,7 +1676,6 @@ da Silva Rejane
 Das R
 Das, R.
 Daughtry, CST
-David Chubb
 David Chubb|Lorraine Britton
 David Clarke
 Davies
@@ -8586,4 +8585,9 @@ Zoriki Hosomi R.
 Zoriki Hosomi Rosana
 Zuberer D
 Zubrod J
-Zwicker R.E.
+Zwicker R.E.
+Doe
+M. Mustermann
+F. Lastname
+Mustermann
+Lastname

redaction-service-v1/redaction-service-server-v1/src/test/resources/dictionaries/PII.txt

@@ -0,0 +1,5 @@
+Amendment 1
+Report Number: 33168
+Page
+Report Number: BFI0714
+Tesh Consultants International

redaction-service-v1/redaction-service-server-v1/src/test/resources/dictionaries/dossier_redactions.txt

@@ -1 +1,2 @@
-Difenoconazole
+Difenoconazole
+FENPROPIDIN

redaction-service-v1/redaction-service-server-v1/src/test/resources/dictionaries/false_positive.txt

@@ -235,4 +235,5 @@ N/A
 No details reported
 Not available
 Test facility
-TBD
+TBD
+David Chubb

redaction-service-v1/redaction-service-server-v1/src/test/resources/dictionaries/published_information.txt

@@ -85,3 +85,4 @@ Toxicology and Applied Pharmacology
 Toxicol Sci
 Toxicol Sci.
 Toxicol Sci. 1
+Test Ignored Hint Published Information

redaction-service-v1/redaction-service-server-v1/src/test/resources/drools/allAuthors.drl

@@ -7,12 +7,20 @@ global Section section
 
 // --------------------------------------- CBI rules -------------------------------------------------------------------
 
+//rule "0: Expand CBI Authors with firstname initials"
+//    when
+//        Section(matchesType("CBI_author") || matchesType("recommendation_CBI_author"))
+//    then
+//        section.expandByRegEx("CBI_author", "(,? [A-Z]\\.?( ?[A-Z]\\.?)?( ?[A-Z]\\.?)?\\b\\.?)", false, 1);
+//        section.expandByRegEx("recommendation_CBI_author", "(,? [A-Z]\\.?( ?[A-Z]\\.?)?( ?[A-Z]\\.?)?\\b\\.?)", false, 1);
+//    end
+
 rule "0: Expand CBI Authors with firstname initials"
     when
         Section(matchesType("CBI_author") || matchesType("recommendation_CBI_author"))
     then
-        section.expandByRegEx("CBI_author", "(,? [A-Z]\\.?( ?[A-Z]\\.?)?( ?[A-Z]\\.?)?\\b\\.?)", false, 1);
-        section.expandByRegEx("recommendation_CBI_author", "(,? [A-Z]\\.?( ?[A-Z]\\.?)?( ?[A-Z]\\.?)?\\b\\.?)", false, 1);
+        section.expandByRegEx("CBI_author", "(,? [A-Z]\\.?( ?[A-Z]\\.?)?( ?[A-Z]\\.?)?\\b\\.?)", false, 1, "[^\\s]+");
+        section.expandByRegEx("recommendation_CBI_author", "(,? [A-Z]\\.?( ?[A-Z]\\.?)?( ?[A-Z]\\.?)?\\b\\.?)", false, 1, "[^\\s]+");
     end
 
 

redaction-service-v1/redaction-service-server-v1/src/test/resources/drools/rules.drl

@@ -7,12 +7,20 @@ global Section section
 
 // --------------------------------------- CBI rules -------------------------------------------------------------------
 
+//rule "0: Expand CBI Authors with firstname initials"
+//    when
+//        Section(matchesType("CBI_author") || matchesType("recommendation_CBI_author"))
+//    then
+//        section.expandByRegEx("CBI_author", "(,? [A-Z]\\.?( ?[A-Z]\\.?)?( ?[A-Z]\\.?)?\\b\\.?)", false, 1);
+//        section.expandByRegEx("recommendation_CBI_author", "(,? [A-Z]\\.?( ?[A-Z]\\.?)?( ?[A-Z]\\.?)?\\b\\.?)", false, 1);
+//    end
+
 rule "0: Expand CBI Authors with firstname initials"
     when
         Section(matchesType("CBI_author") || matchesType("recommendation_CBI_author"))
     then
-        section.expandByRegEx("CBI_author", "(,? [A-Z]\\.?( ?[A-Z]\\.?)?( ?[A-Z]\\.?)?\\b\\.?)", false, 1);
-        section.expandByRegEx("recommendation_CBI_author", "(,? [A-Z]\\.?( ?[A-Z]\\.?)?( ?[A-Z]\\.?)?\\b\\.?)", false, 1);
+        section.expandByRegEx("CBI_author", "(,? [A-Z]\\.?( ?[A-Z]\\.?)?( ?[A-Z]\\.?)?\\b\\.?)", false, 1, "[\\s]+");
+        section.expandByRegEx("recommendation_CBI_author", "(,? [A-Z]\\.?( ?[A-Z]\\.?)?( ?[A-Z]\\.?)?\\b\\.?)", false, 1, "[\\s]+");
     end
 
 
@@ -336,4 +344,11 @@ rule "29: Redact Dossier Redactions"
          Section(matchesType("dossier_redactions"))
      then
          section.redact("dossier_redactions", 29, "Dossier Redaction found", "Article 39(1)(2) of Regulation (EC) No 178/2002");
-     end
+     end
+
+rule "30: Ignore dossier_redactions if confidential"
+    when
+        Section(!fileAttributeByLabelEqualsIgnoreCase("Confidentiality","confidential") && matchesType("dossier_redactions"));
+    then
+        section.ignore("dossier_redactions");
+    end