Pull request #49: RED-373: Fixed multiline annotations view in pdftron

Merge in RED/redaction-service from RED-373-2 to master

* commit 'a4e012762e1adda234decc1137f221cfd70498d3':
  RED-373: Fixed multiline annotations view in pdftron

bamboo-specs/pom.xml

@@ -5,7 +5,7 @@
   <parent>
     <groupId>com.atlassian.bamboo</groupId>
     <artifactId>bamboo-specs-parent</artifactId>
-    <version>7.0.4</version>
+    <version>7.1.2</version>
     <relativePath/>
   </parent>
 
@@ -34,4 +34,4 @@
 
   <!-- run 'mvn test' to perform offline validation of the plan -->
   <!-- run 'mvn -Ppublish-specs' to upload the plan to your Bamboo server -->
-</project>
+</project>

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

@@ -1,4 +1,4 @@
-FROM gin5/platform-base:5.2.0
+FROM red/base-image:1.0.0
 
 ARG PLATFORM_JAR
 
@@ -6,4 +6,4 @@ ENV PLATFORM_JAR ${PLATFORM_JAR}
 
 ENV USES_ELASTICSEARCH false
 
-COPY ["${PLATFORM_JAR}", "/"]
+COPY ["${PLATFORM_JAR}", "/"]

redaction-service-v1/pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <artifactId>platform-dependency</artifactId>
         <groupId>com.iqser.red</groupId>
-        <version>1.0.1</version>
+        <version>1.0.2</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
 
@@ -22,7 +22,7 @@
     </modules>
 
     <properties>
-        <pdfbox.version>2.0.16</pdfbox.version>
+        <pdfbox.version>2.0.21</pdfbox.version>
     </properties>
 
 
@@ -32,21 +32,21 @@
             <dependency>
                 <groupId>com.iqser.red</groupId>
                 <artifactId>platform-commons-dependency</artifactId>
-                <version>1.0.0</version>
+                <version>1.1.0</version>
                 <scope>import</scope>
                 <type>pom</type>
             </dependency>
 
-                <dependency>
-                    <groupId>org.apache.pdfbox</groupId>
-                    <artifactId>pdfbox</artifactId>
-                    <version>${pdfbox.version}</version>
-                </dependency>
-                <dependency>
-                    <groupId>org.apache.pdfbox</groupId>
-                    <artifactId>pdfbox-tools</artifactId>
-                    <version>${pdfbox.version}</version>
-                </dependency>
+            <dependency>
+                <groupId>org.apache.pdfbox</groupId>
+                <artifactId>pdfbox</artifactId>
+                <version>${pdfbox.version}</version>
+            </dependency>
+            <dependency>
+                <groupId>org.apache.pdfbox</groupId>
+                <artifactId>pdfbox-tools</artifactId>
+                <version>${pdfbox.version}</version>
+            </dependency>
 
         </dependencies>
 

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

@@ -0,0 +1,23 @@
+package com.iqser.red.service.redaction.v1.model;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import lombok.AllArgsConstructor;
+import lombok.Data;
+import lombok.NoArgsConstructor;
+
+@Data
+@AllArgsConstructor
+@NoArgsConstructor
+public class ManualRedactionEntry {
+
+    private String type;
+    private String value;
+    private String reason;
+    private List<Rectangle> positions = new ArrayList<>();
+
+    private String section;
+    private int sectionNumber;
+
+}

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

@@ -0,0 +1,17 @@
+package com.iqser.red.service.redaction.v1.model;
+
+import java.util.HashSet;
+import java.util.Set;
+
+import lombok.AllArgsConstructor;
+import lombok.Data;
+import lombok.NoArgsConstructor;
+
+@Data
+@AllArgsConstructor
+@NoArgsConstructor
+public class ManualRedactions {
+
+    private Set<String> idsToRemove = new HashSet<>();
+    private Set<ManualRedactionEntry> entriesToAdd = new HashSet<>();
+}

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

@@ -11,6 +11,19 @@ import lombok.NoArgsConstructor;
 @NoArgsConstructor
 public class RedactionLog {
 
+    public RedactionLog(List<RedactionLogEntry> redactionLogEntry, long dictionaryVersion, long rulesVersion) {
+
+        this.redactionLogEntry = redactionLogEntry;
+        this.dictionaryVersion = dictionaryVersion;
+        this.rulesVersion = rulesVersion;
+    }
+
     private List<RedactionLogEntry> redactionLogEntry;
 
+    private long dictionaryVersion = -1;
+
+    private long rulesVersion = -1;
+
+    private String filename;
+
 }

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

@@ -3,9 +3,15 @@ package com.iqser.red.service.redaction.v1.model;
 import java.util.ArrayList;
 import java.util.List;
 
+import lombok.AllArgsConstructor;
+import lombok.Builder;
 import lombok.Data;
+import lombok.NoArgsConstructor;
 
 @Data
+@Builder
+@NoArgsConstructor
+@AllArgsConstructor
 public class RedactionLogEntry {
 
     private String id;
@@ -16,6 +22,10 @@ public class RedactionLogEntry {
     private boolean isHint;
     private String section;
     private float[] color;
+
+    @Builder.Default
     private List<Rectangle> positions = new ArrayList<>();
+    private int sectionNumber;
+    private boolean manual;
 
 }

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

@@ -13,4 +13,5 @@ public class RedactionRequest {
 
     private byte[] document;
     private boolean flatRedaction;
+    private ManualRedactions manualRedactions;
 }

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

@@ -11,25 +11,6 @@
 
     <artifactId>redaction-service-server-v1</artifactId>
 
-    <properties>
-        <pdfbox.version>2.0.20</pdfbox.version>
-    </properties>
-
-    <dependencyManagement>
-        <dependencies>
-            <dependency>
-                <groupId>org.apache.pdfbox</groupId>
-                <artifactId>pdfbox</artifactId>
-                <version>${pdfbox.version}</version>
-            </dependency>
-            <dependency>
-                <groupId>org.apache.pdfbox</groupId>
-                <artifactId>pdfbox-tools</artifactId>
-                <version>${pdfbox.version}</version>
-            </dependency>
-        </dependencies>
-    </dependencyManagement>
-
     <dependencies>
         <dependency>
             <groupId>com.iqser.red.service</groupId>
@@ -56,17 +37,22 @@
             <artifactId>jts-core</artifactId>
             <version>1.16.1</version>
         </dependency>
+        <dependency>
+            <groupId>com.google.guava</groupId>
+            <artifactId>guava</artifactId>
+            <version>29.0-jre</version>
+        </dependency>
         <!-- commons -->
         <dependency>
-            <groupId>com.iqser.gin4.commons</groupId>
+            <groupId>com.iqser.red.commons</groupId>
             <artifactId>spring-commons</artifactId>
         </dependency>
         <dependency>
-            <groupId>com.iqser.gin4.commons</groupId>
+            <groupId>com.iqser.red.commons</groupId>
             <artifactId>logging-commons</artifactId>
         </dependency>
         <dependency>
-            <groupId>com.iqser.gin4.commons</groupId>
+            <groupId>com.iqser.red.commons</groupId>
             <artifactId>metric-commons</artifactId>
         </dependency>
         <!-- other external -->
@@ -99,7 +85,7 @@
             <scope>test</scope>
         </dependency>
         <dependency>
-            <groupId>com.iqser.gin4.commons</groupId>
+            <groupId>com.iqser.red.commons</groupId>
             <artifactId>test-commons</artifactId>
             <scope>test</scope>
         </dependency>

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

@@ -20,7 +20,7 @@ import org.springframework.cloud.openfeign.EnableFeignClients;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Import;
 
-import com.iqser.gin4.commons.spring.DefaultWebMvcConfiguration;
+import com.iqser.red.commons.spring.DefaultWebMvcConfiguration;
 import com.iqser.red.service.configuration.v1.api.model.RulesResponse;
 import com.iqser.red.service.redaction.v1.server.client.RulesClient;
 import com.iqser.red.service.redaction.v1.server.exception.RulesValidationException;

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

@@ -4,7 +4,6 @@ import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
-import java.util.Set;
 
 import com.iqser.red.service.redaction.v1.model.RedactionLogEntry;
 import com.iqser.red.service.redaction.v1.server.redaction.model.Entity;
@@ -18,7 +17,7 @@ public class Document {
 
     private List<Page> pages = new ArrayList<>();
     private List<Paragraph> paragraphs = new ArrayList<>();
-    private Map<Integer, Set<Entity>> entities = new HashMap<>();
+    private Map<Integer, List<Entity>> entities = new HashMap<>();
     private FloatFrequencyCounter textHeightCounter = new FloatFrequencyCounter();
     private FloatFrequencyCounter fontSizeCounter= new FloatFrequencyCounter();
     private StringFrequencyCounter fontCounter= new StringFrequencyCounter();

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

@@ -10,7 +10,6 @@ import com.iqser.red.service.redaction.v1.server.tableextraction.model.Table;
 import lombok.Data;
 import lombok.NoArgsConstructor;
 
-
 @Data
 @NoArgsConstructor
 public class Paragraph {
@@ -18,10 +17,12 @@ public class Paragraph {
     private List<AbstractTextContainer> pageBlocks = new ArrayList<>();
     private String headline;
 
-    public SearchableText getSearchableText(){
+
+    public SearchableText getSearchableText() {
+
         SearchableText searchableText = new SearchableText();
         pageBlocks.forEach(block -> {
-            if(block instanceof TextBlock){
+            if (block instanceof TextBlock) {
                 searchableText.addAll(((TextBlock) block).getSequences());
             }
         });
@@ -29,14 +30,27 @@ public class Paragraph {
     }
 
 
-    public List<Table> getTables(){
+    public List<Table> getTables() {
+
         List<Table> tables = new ArrayList<>();
         pageBlocks.forEach(block -> {
-            if(block instanceof Table){
+            if (block instanceof Table) {
                 tables.add((Table) block);
             }
         });
         return tables;
     }
 
-}
+
+    public List<TextBlock> getTextBlocks() {
+
+        List<TextBlock> textBlocks = new ArrayList<>();
+        pageBlocks.forEach(block -> {
+            if (block instanceof TextBlock) {
+                textBlocks.add((TextBlock) block);
+            }
+        });
+        return textBlocks;
+    }
+
+}

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

@@ -5,43 +5,45 @@ import java.util.Map;
 
 import lombok.Getter;
 
-/**
- *
- */
 public class StringFrequencyCounter {
 
     @Getter
-    Map<String, Integer> countPerValue = new HashMap<>();
+    private final Map<String, Integer> countPerValue = new HashMap<>();
 
-    public void add(String value){
-        if(!countPerValue.containsKey(value)){
+
+    public void add(String value) {
+
+        if (!countPerValue.containsKey(value)) {
             countPerValue.put(value, 1);
         } else {
             countPerValue.put(value, countPerValue.get(value) + 1);
         }
     }
 
-    public void addAll(Map<String, Integer> otherCounter){
-        for(Map.Entry<String, Integer> entry: otherCounter.entrySet()){
-            if(countPerValue.containsKey(entry.getKey())){
-                countPerValue.put(entry.getKey(), countPerValue.get(entry.getKey())+ entry.getValue());
+
+    public void addAll(Map<String, Integer> otherCounter) {
+
+        for (Map.Entry<String, Integer> entry : otherCounter.entrySet()) {
+            if (countPerValue.containsKey(entry.getKey())) {
+                countPerValue.put(entry.getKey(), countPerValue.get(entry.getKey()) + entry.getValue());
             } else {
                 countPerValue.put(entry.getKey(), entry.getValue());
             }
         }
     }
 
-    public String getMostPopular(){
+
+    public String getMostPopular() {
+
         Map.Entry<String, Integer> mostPopular = null;
-        for(Map.Entry<String, Integer> entry: countPerValue.entrySet()){
-            if(mostPopular == null){
+        for (Map.Entry<String, Integer> entry : countPerValue.entrySet()) {
+            if (mostPopular == null) {
                 mostPopular = entry;
-            } else if(entry.getValue() > mostPopular.getValue()){
+            } else if (entry.getValue() > mostPopular.getValue()) {
                 mostPopular = entry;
             }
         }
         return mostPopular != null ? mostPopular.getKey() : null;
     }
 
-
-}
+}

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

@@ -29,20 +29,16 @@ public class BlockificationService {
         float minX = 1000, maxX = 0, minY = 1000, maxY = 0;
         TextPositionSequence prev = null;
 
-
         for (TextPositionSequence word : textPositions) {
 
             boolean lineSeparation = minY - word.getY2() > word.getHeight() * 1.25;
             boolean startFromTop = word.getY1() > maxY + word.getHeight();
 
-            if (prev != null &&
-                    (lineSeparation
-                            || startFromTop
-                            || word.getRotation() == 0 && isSplittedByRuling(maxX, minY, word.getX1(), word.getY1(), verticalRulingLines)
-                            || word.getRotation() == 0 && isSplittedByRuling(minX, minY, word.getX1(), word.getY2(), horizontalRulingLines)
-                            || word.getRotation() == 90 && isSplittedByRuling(maxX, minY, word.getX1(), word.getY1(), horizontalRulingLines)
-                            || word.getRotation() == 90 && isSplittedByRuling(minX, minY, word.getX1(), word.getY2(), verticalRulingLines)
-                    )) {
+            if (prev != null && (lineSeparation || startFromTop || word.getRotation() == 0 && isSplittedByRuling(maxX, minY, word
+                    .getX1(), word.getY1(), verticalRulingLines) || word.getRotation() == 0 && isSplittedByRuling(minX, minY, word
+                    .getX1(), word.getY2(), horizontalRulingLines) || word.getRotation() == 90 && isSplittedByRuling(maxX, minY, word
+                    .getX1(), word.getY1(), horizontalRulingLines) || word.getRotation() == 90 && isSplittedByRuling(minX, minY, word
+                    .getX1(), word.getY2(), verticalRulingLines))) {
 
                 TextBlock cb1 = buildTextBlock(chunkWords);
                 chunkBlockList1.add(cb1);
@@ -100,11 +96,12 @@ public class BlockificationService {
             styleFrequencyCounter.add(wordBlock.getFontStyle());
 
             if (textBlock == null) {
-                textBlock = new TextBlock(wordBlock.getX1(), wordBlock.getX2(), wordBlock.getY1(), wordBlock.getY2(), wordBlockList, wordBlock.getRotation());
+                textBlock = new TextBlock(wordBlock.getX1(), wordBlock.getX2(), wordBlock.getY1(), wordBlock.getY2(), wordBlockList, wordBlock
+                        .getRotation());
             } else {
                 TextBlock spatialEntity = textBlock.union(wordBlock);
-                textBlock.resize(spatialEntity.getMinX(), spatialEntity.getMinY(),
-                        spatialEntity.getWidth(), spatialEntity.getHeight());
+                textBlock.resize(spatialEntity.getMinX(), spatialEntity.getMinY(), spatialEntity.getWidth(), spatialEntity
+                        .getHeight());
             }
         }
 
@@ -122,6 +119,7 @@ public class BlockificationService {
 
 
     private boolean isSplittedByRuling(float previousX2, float previousY1, float currentX1, float currentY1, List<Ruling> rulingLines) {
+
         for (Ruling ruling : rulingLines) {
             if (ruling.intersectsLine(previousX2, previousY1, currentX1, currentY1)) {
                 return true;
@@ -133,7 +131,6 @@ public class BlockificationService {
 
     public Rectangle calculateBodyTextFrame(List<Page> pages, FloatFrequencyCounter documentFontSizeCounter, boolean landscape) {
 
-
         float minX = 10000;
         float maxX = -100;
         float minY = 10000;
@@ -147,7 +144,6 @@ public class BlockificationService {
 
             for (AbstractTextContainer container : page.getTextBlocks()) {
 
-
                 if (container instanceof TextBlock) {
                     TextBlock textBlock = (TextBlock) container;
                     if (textBlock.getMostPopularWordFont() == null || textBlock.getMostPopularWordStyle() == null) {
@@ -179,16 +175,15 @@ public class BlockificationService {
                     }
                 }
 
-
                 if (container instanceof Table) {
                     Table table = (Table) container;
                     for (List<Cell> row : table.getRows()) {
-                        for (Cell column : row) {
+                        for (Cell cell : row) {
 
-                            if (column == null || column.getTextBlocks() == null) {
+                            if (cell == null || cell.getTextBlocks() == null) {
                                 continue;
                             }
-                            for (TextBlock textBlock : column.getTextBlocks()) {
+                            for (TextBlock textBlock : cell.getTextBlocks()) {
                                 if (textBlock.getMinX() < minX) {
                                     minX = textBlock.getMinX();
                                 }
@@ -211,5 +206,4 @@ public class BlockificationService {
         return new Rectangle(minY, minX, maxX - minX, maxY - minY);
     }
 
-
 }

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

@@ -84,7 +84,7 @@ public class ClassificationService {
         }
         else if (PositionUtils.isWithinBodyTextFrame(bodyTextFrame, textBlock) && textBlock.getMostPopularWordFontSize() == document.getFontSizeCounter().getMostPopular() && textBlock.getMostPopularWordStyle().equals("italic") && !document.getFontStyleCounter().getMostPopular().equals("italic") && PositionUtils.getApproxLineCount(textBlock) < 2.9) {
             textBlock.setClassification("TextBlock Italic");
-        } else if (PositionUtils.isWithinBodyTextFrame(bodyTextFrame, textBlock) && textBlock.getSequences().size() > 3){
+        } else if (PositionUtils.isWithinBodyTextFrame(bodyTextFrame, textBlock)){
             textBlock.setClassification("TextBlock Unknown");
         }
     }

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

@@ -2,13 +2,13 @@ package com.iqser.red.service.redaction.v1.server.controller;
 
 import java.time.OffsetDateTime;
 
+import com.iqser.red.commons.spring.ErrorMessage;
 import org.springframework.http.HttpStatus;
 import org.springframework.web.bind.annotation.ExceptionHandler;
 import org.springframework.web.bind.annotation.ResponseBody;
 import org.springframework.web.bind.annotation.ResponseStatus;
 import org.springframework.web.bind.annotation.RestControllerAdvice;
 
-import com.iqser.gin4.commons.api.errorhandling.ErrorMessage;
 import com.iqser.red.service.redaction.v1.server.exception.RulesValidationException;
 
 import lombok.extern.slf4j.Slf4j;

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

@@ -3,18 +3,21 @@ package com.iqser.red.service.redaction.v1.server.controller;
 import java.io.ByteArrayInputStream;
 import java.io.ByteArrayOutputStream;
 import java.io.IOException;
+import java.util.List;
 
 import org.apache.pdfbox.pdmodel.PDDocument;
 import org.springframework.web.bind.annotation.RequestBody;
 import org.springframework.web.bind.annotation.RestController;
 
 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.RedactionRequest;
 import com.iqser.red.service.redaction.v1.model.RedactionResult;
 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.redaction.service.DictionaryService;
 import com.iqser.red.service.redaction.v1.server.redaction.service.DroolsExecutionService;
 import com.iqser.red.service.redaction.v1.server.redaction.service.EntityRedactionService;
 import com.iqser.red.service.redaction.v1.server.segmentation.PdfSegmentationService;
@@ -36,6 +39,7 @@ public class RedactionController implements RedactionResource {
     private final EntityRedactionService entityRedactionService;
     private final PdfFlattenService pdfFlattenService;
     private final DroolsExecutionService droolsExecutionService;
+    private final DictionaryService dictionaryService;
 
     @Override
     public RedactionResult redact(@RequestBody RedactionRequest redactionRequest) {
@@ -44,15 +48,15 @@ public class RedactionController implements RedactionResource {
             pdDocument.setAllSecurityToBeRemoved(true);
 
             Document classifiedDoc = pdfSegmentationService.parseDocument(pdDocument);
-            entityRedactionService.processDocument(classifiedDoc);
-            annotationHighlightService.highlight(pdDocument, classifiedDoc, redactionRequest.isFlatRedaction());
+            entityRedactionService.processDocument(classifiedDoc, redactionRequest.getManualRedactions());
+            annotationHighlightService.highlight(pdDocument, classifiedDoc, redactionRequest.isFlatRedaction(), redactionRequest.getManualRedactions());
 
             if (redactionRequest.isFlatRedaction()) {
                 PDDocument flatDocument = pdfFlattenService.flattenPDF(pdDocument);
-                return convert(flatDocument, classifiedDoc.getPages().size(), new RedactionLog(classifiedDoc.getRedactionLogEntities()));
+                return convert(flatDocument, classifiedDoc.getPages().size(), classifiedDoc.getRedactionLogEntities());
             }
 
-            return convert(pdDocument, classifiedDoc.getPages().size(), new RedactionLog(classifiedDoc.getRedactionLogEntities()));
+            return convert(pdDocument, classifiedDoc.getPages().size(), classifiedDoc.getRedactionLogEntities());
 
         } catch (IOException e) {
             throw new RedactionException(e);
@@ -130,14 +134,14 @@ public class RedactionController implements RedactionResource {
         return convert(document, numberOfPages, null);
     }
 
-    private RedactionResult convert(PDDocument document, int numberOfPages, RedactionLog redactionLog) throws IOException {
+    private RedactionResult convert(PDDocument document, int numberOfPages, List<RedactionLogEntry> redactionLogEntities) throws IOException {
 
         try (ByteArrayOutputStream byteArrayOutputStream = new ByteArrayOutputStream()) {
             document.save(byteArrayOutputStream);
             return RedactionResult.builder()
                     .document(byteArrayOutputStream.toByteArray())
                     .numberOfPages(numberOfPages)
-                    .redactionLog(redactionLog)
+                    .redactionLog(new RedactionLog(redactionLogEntities,  dictionaryService.getDictionaryVersion(), droolsExecutionService.getRulesVersion()))
                     .build();
         }
 

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

@@ -44,10 +44,10 @@ import lombok.extern.slf4j.Slf4j;
 public class PDFLinesTextStripper extends PDFTextStripper {
 
     @Getter
-    private float minCharWidth = Float.MAX_VALUE;
+    private int maxCharWidths;
 
     @Getter
-    private float minCharHeight = Float.MAX_VALUE;
+    private int maxCharHeight;
 
     @Getter
     private final List<TextPositionSequence> textPositionSequences = new ArrayList<>();
@@ -201,8 +201,16 @@ public class PDFLinesTextStripper extends PDFTextStripper {
 
         int startIndex = 0;
         for (int i = 0; i <= textPositions.size() - 1; i++) {
-            minCharWidth = Math.min(minCharWidth, textPositions.get(i).getWidthDirAdj());
-            minCharHeight = Math.min(minCharHeight, textPositions.get(i).getHeightDir());
+
+            int charHeight = (int) textPositions.get(i).getHeightDir();
+            if(charHeight > maxCharHeight){
+                maxCharHeight = charHeight;
+            }
+
+            int charWidth = (int) textPositions.get(i).getWidthDirAdj();
+            if(charWidth > maxCharWidths){
+                maxCharWidths = charWidth;
+            }
 
             if (i == 0 && textPositions.get(i).getUnicode().equals(" ")) {
                 startIndex++;
@@ -241,8 +249,8 @@ public class PDFLinesTextStripper extends PDFTextStripper {
     @Override
     public String getText(PDDocument doc) throws IOException {
 
-        minCharWidth = Float.MAX_VALUE;
-        minCharHeight = Float.MAX_VALUE;
+        maxCharWidths = 0;
+        maxCharWidths = 0;
         textPositionSequences.clear();
         rulings.clear();
         graphicsPath.clear();

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

@@ -17,6 +17,6 @@ public class ParsedElements {
     private boolean landscape;
     private boolean rotated;
 
-    private float minCharWidth;
-    private float minCharHeight;
+    private float maxCharWidth;
+    private float maxCharHeight;
 }

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

@@ -5,10 +5,11 @@ import java.util.List;
 
 import org.apache.pdfbox.text.TextPosition;
 
+import com.iqser.red.service.redaction.v1.model.Point;
+import com.iqser.red.service.redaction.v1.model.Rectangle;
+
 import lombok.Data;
-import lombok.Getter;
 import lombok.RequiredArgsConstructor;
-import lombok.Setter;
 
 @Data
 @RequiredArgsConstructor
@@ -16,42 +17,50 @@ public class TextPositionSequence implements CharSequence {
 
     private List<TextPosition> textPositions = new ArrayList<>();
 
-    @Getter
-    @Setter
-    private float[] annotationColor;
-
     private final int page;
 
-    public TextPositionSequence(List<TextPosition> textPositions, int page){
+
+    public TextPositionSequence(List<TextPosition> textPositions, int page) {
+
         this.textPositions = textPositions;
         this.page = page;
     }
 
+
     @Override
     public int length() {
+
         return textPositions.size();
     }
 
+
     @Override
     public char charAt(int index) {
+
         TextPosition textPosition = textPositionAt(index);
         String text = textPosition.getUnicode();
         return text.charAt(0);
     }
 
+
     public char charAt(int index, boolean caseInSensitive) {
+
         TextPosition textPosition = textPositionAt(index);
         String text = textPosition.getUnicode();
         return caseInSensitive ? text.toLowerCase().charAt(0) : text.charAt(0);
     }
 
+
     @Override
     public TextPositionSequence subSequence(int start, int end) {
+
         return new TextPositionSequence(textPositions.subList(start, end), page);
     }
 
+
     @Override
     public String toString() {
+
         StringBuilder builder = new StringBuilder(length());
         for (int i = 0; i < length(); i++) {
             builder.append(charAt(i));
@@ -59,15 +68,21 @@ public class TextPositionSequence implements CharSequence {
         return builder.toString();
     }
 
+
     public TextPosition textPositionAt(int index) {
+
         return textPositions.get(index);
     }
 
+
     public void add(TextPosition textPosition) {
+
         this.textPositions.add(textPosition);
     }
 
+
     public float getX1() {
+
         if (textPositions.get(0).getRotation() == 90) {
             return textPositions.get(0).getYDirAdj() - getTextHeight();
         } else {
@@ -75,15 +90,20 @@ public class TextPositionSequence implements CharSequence {
         }
     }
 
+
     public float getX2() {
+
         if (textPositions.get(0).getRotation() == 90) {
             return textPositions.get(0).getYDirAdj();
         } else {
-            return textPositions.get(textPositions.size() - 1).getXDirAdj() + textPositions.get(textPositions.size() - 1).getWidth() + 1;
+            return textPositions.get(textPositions.size() - 1)
+                    .getXDirAdj() + textPositions.get(textPositions.size() - 1).getWidth() + 1;
         }
     }
 
+
     public float getY1() {
+
         if (textPositions.get(0).getRotation() == 90) {
             return textPositions.get(0).getXDirAdj();
         } else {
@@ -91,30 +111,46 @@ public class TextPositionSequence implements CharSequence {
         }
     }
 
+
     public float getY2() {
+
         if (textPositions.get(0).getRotation() == 90) {
-            return textPositions.get(textPositions.size() - 1).getXDirAdj() + getTextHeight() -2 ;
+            return textPositions.get(textPositions.size() - 1).getXDirAdj() + getTextHeight() - 2;
         } else {
             return textPositions.get(0).getPageHeight() - textPositions.get(0).getYDirAdj() + getTextHeight();
         }
     }
 
+
     public float getTextHeight() {
+
         return textPositions.get(0).getHeightDir() + 2;
     }
 
+
     public float getHeight() {
+
         return getY2() - getY1();
     }
 
+
     public float getWidth() {
+
         return getX2() - getX1();
     }
 
+
     public String getFont() {
-        return textPositions.get(0).getFont().toString().toLowerCase().replaceAll(",bold", "").replaceAll(",italic", "");
+
+        return textPositions.get(0)
+                .getFont()
+                .toString()
+                .toLowerCase()
+                .replaceAll(",bold", "")
+                .replaceAll(",italic", "");
     }
 
+
     public String getFontStyle() {
 
         String lowercaseFontName = textPositions.get(0).getFont().toString().toLowerCase();
@@ -131,16 +167,48 @@ public class TextPositionSequence implements CharSequence {
 
     }
 
+
     public float getFontSize() {
+
         return textPositions.get(0).getFontSizeInPt();
     }
 
+
     public float getSpaceWidth() {
+
         return textPositions.get(0).getWidthOfSpace();
     }
 
+
     public int getRotation() {
+
         return textPositions.get(0).getRotation();
     }
 
+
+    public Rectangle getRectangle() {
+
+        float height = getTextHeight();
+
+        float posXInit = getX1();
+        float posXEnd;
+        float posYInit;
+        float posYEnd;
+
+        if (textPositions.get(0).getRotation() == 90) {
+            posXEnd = textPositions.get(0).getYDirAdj() + 2;
+            posYInit = getY1();
+            posYEnd = textPositions.get(textPositions.size() - 1).getXDirAdj() - height + 4;
+        } else {
+            posXEnd = textPositions.get(textPositions.size() - 1)
+                    .getXDirAdj() + textPositions.get(textPositions.size() - 1).getWidth() + 1;
+            posYInit = textPositions.get(0).getPageHeight() - textPositions.get(0).getYDirAdj() - 2;
+            posYEnd = textPositions.get(0).getPageHeight() - textPositions.get(textPositions.size() - 1)
+                    .getYDirAdj() + 2;
+        }
+
+        return new Rectangle(new Point(posXInit, posYInit), posXEnd - posXInit, posYEnd - posYInit + height, page);
+    }
+
+
 }

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

@@ -0,0 +1,43 @@
+package com.iqser.red.service.redaction.v1.server.redaction.model;
+
+import com.iqser.red.service.redaction.v1.server.classification.model.TextBlock;
+import com.iqser.red.service.redaction.v1.server.parsing.model.TextPositionSequence;
+import com.iqser.red.service.redaction.v1.server.redaction.utils.TextNormalizationUtilities;
+
+import lombok.RequiredArgsConstructor;
+import lombok.Value;
+
+@Value
+@RequiredArgsConstructor
+public class CellValue {
+
+    TextBlock textBlock;
+
+    int rowSpanStart;
+
+    @Override
+    public String toString() {
+
+        StringBuilder sb = new StringBuilder();
+
+
+            TextPositionSequence previous = null;
+            for (TextPositionSequence word : textBlock.getSequences()) {
+
+                if (previous != null) {
+                    if (Math.abs(previous.getY1() - word.getY1()) > word.getTextHeight()) {
+                        sb.append('\n');
+                    } else {
+                        sb.append(' ');
+                    }
+                }
+                sb.append(word.toString());
+                previous = word;
+            }
+
+        return TextNormalizationUtilities.removeHyphenLineBreaks(sb.toString())
+                .replaceAll("\n", " ")
+                .replaceAll(" {2}", " ");
+    }
+
+}

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

@@ -1,25 +1,37 @@
 package com.iqser.red.service.redaction.v1.server.redaction.model;
 
-
 import java.util.ArrayList;
 import java.util.List;
 
+import com.iqser.red.service.redaction.v1.server.parsing.model.TextPositionSequence;
+
 import lombok.Data;
+import lombok.EqualsAndHashCode;
 
 @Data
+@EqualsAndHashCode(onlyExplicitlyIncluded = true)
 public class Entity {
 
+    @EqualsAndHashCode.Include
     private final String word;
     private final String type;
     private boolean redaction;
     private String redactionReason;
     private List<EntityPositionSequence> positionSequences = new ArrayList<>();
+    private List<TextPositionSequence> targetSequences;
     private Integer start;
     private Integer end;
+
+    @EqualsAndHashCode.Include
     private String headline;
     private int matchedRule;
 
-    public Entity(String word, String type, boolean redaction, String redactionReason, List<EntityPositionSequence> positionSequences, String headline, int matchedRule) {
+    @EqualsAndHashCode.Include
+    private int sectionNumber;
+
+
+    public Entity(String word, String type, boolean redaction, String redactionReason, List<EntityPositionSequence> positionSequences, String headline, int matchedRule, int sectionNumber) {
+
         this.word = word;
         this.type = type;
         this.redaction = redaction;
@@ -27,13 +39,18 @@ public class Entity {
         this.positionSequences = positionSequences;
         this.headline = headline;
         this.matchedRule = matchedRule;
+        this.sectionNumber = sectionNumber;
     }
 
-    public Entity(String word, String type, Integer start, Integer end, String headline) {
+
+    public Entity(String word, String type, Integer start, Integer end, String headline, int sectionNumber) {
+
         this.word = word;
         this.type = type;
         this.start = start;
         this.end = end;
         this.headline = headline;
+        this.sectionNumber = sectionNumber;
     }
+
 }

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

@@ -2,19 +2,23 @@ package com.iqser.red.service.redaction.v1.server.redaction.model;
 
 import java.util.ArrayList;
 import java.util.List;
-import java.util.UUID;
 
 import com.iqser.red.service.redaction.v1.server.parsing.model.TextPositionSequence;
 
+import lombok.AllArgsConstructor;
 import lombok.Data;
+import lombok.EqualsAndHashCode;
 import lombok.RequiredArgsConstructor;
 
-
 @Data
 @RequiredArgsConstructor
+@AllArgsConstructor
+@EqualsAndHashCode
 public class EntityPositionSequence {
 
+    @EqualsAndHashCode.Exclude
     private List<TextPositionSequence> sequences = new ArrayList<>();
     private int pageNumber;
-    private final UUID id;
+    private final String id;
+
 }

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

@@ -1,17 +1,17 @@
 package com.iqser.red.service.redaction.v1.server.redaction.model;
 
 import java.util.ArrayList;
+import java.util.Collections;
 import java.util.List;
-import java.util.UUID;
 import java.util.regex.Pattern;
 
 import com.iqser.red.service.redaction.v1.server.parsing.model.TextPositionSequence;
+import com.iqser.red.service.redaction.v1.server.redaction.utils.IdBuilder;
 import com.iqser.red.service.redaction.v1.server.redaction.utils.TextNormalizationUtilities;
 
-@SuppressWarnings("all")
 public class SearchableText {
 
-    private List<TextPositionSequence> sequences = new ArrayList<>();
+    private final List<TextPositionSequence> sequences = new ArrayList<>();
 
 
     public void add(TextPositionSequence textPositionSequence) {
@@ -28,6 +28,14 @@ public class SearchableText {
 
     public List<EntityPositionSequence> getSequences(String searchString, boolean caseInsensitive) {
 
+        return getSequences(searchString, caseInsensitive, null);
+
+    }
+
+    @SuppressWarnings("checkstyle:ModifiedControlVariable")
+    public List<EntityPositionSequence> getSequences(String searchString, boolean caseInsensitive,
+                                                     List<TextPositionSequence> sequencesSubList) {
+
         String normalizedSearchString;
         if (caseInsensitive) {
             normalizedSearchString = searchString.toLowerCase();
@@ -40,37 +48,50 @@ public class SearchableText {
 
         List<TextPositionSequence> crossSequenceParts = new ArrayList<>();
         List<EntityPositionSequence> finalMatches = new ArrayList<>();
-        for (int i = 0; i < sequences.size(); i++) {
-            TextPositionSequence partMatch = new TextPositionSequence(sequences.get(i).getPage());
-            for (int j = 0; j < sequences.get(i).length(); j++) {
 
-                if (i > 0 && j == 0 && sequences.get(i).charAt(0, caseInsensitive) == ' ' && sequences.get(i - 1)
-                        .charAt(sequences.get(i - 1).length() - 1, caseInsensitive) == ' ' || j > 0 && sequences.get(i)
-                        .charAt(j, caseInsensitive) == ' ' && sequences.get(i).charAt(j - 1, caseInsensitive) == ' ') {
-                    if (j == sequences.get(i).length() - 1 && counter != 0 && !partMatch.getTextPositions().isEmpty()) {
+        List<TextPositionSequence> searchSpace;
+        if (sequencesSubList != null) {
+            int subListIndex = Collections.indexOfSubList(sequences, sequencesSubList);
+            if (subListIndex != -1) {
+                searchSpace = sequences.subList(subListIndex, subListIndex + sequencesSubList.size());
+            } else {
+                searchSpace = sequences;
+            }
+        } else {
+            searchSpace = sequences;
+        }
+
+        for (int i = 0; i < searchSpace.size(); i++) {
+            TextPositionSequence partMatch = new TextPositionSequence(searchSpace.get(i).getPage());
+            for (int j = 0; j < searchSpace.get(i).length(); j++) {
+
+                if (i > 0 && j == 0 && searchSpace.get(i).charAt(0, caseInsensitive) == ' ' && searchSpace.get(i - 1)
+                        .charAt(searchSpace.get(i - 1).length() - 1, caseInsensitive) == ' ' || j > 0 && searchSpace.get(i)
+                        .charAt(j, caseInsensitive) == ' ' && searchSpace.get(i).charAt(j - 1, caseInsensitive) == ' ') {
+                    if (j == searchSpace.get(i).length() - 1 && counter != 0 && !partMatch.getTextPositions().isEmpty()) {
                         crossSequenceParts.add(partMatch);
                     }
                     continue;
                 }
 
-                if (j == 0 && sequences.get(i).charAt(j, caseInsensitive) != ' ' && i != 0 && sequences.get(i - 1)
-                        .charAt(sequences.get(i - 1)
+                if (j == 0 && searchSpace.get(i).charAt(j, caseInsensitive) != ' ' && i != 0 && searchSpace.get(i - 1)
+                        .charAt(searchSpace.get(i - 1)
                                 .length() - 1, caseInsensitive) != ' ' && searchChars[counter] == ' ') {
                     counter++;
                 }
 
-                if (sequences.get(i)
-                        .charAt(j, caseInsensitive) == searchChars[counter] || counter != 0 && sequences.get(i)
+                if (searchSpace.get(i)
+                        .charAt(j, caseInsensitive) == searchChars[counter] || counter != 0 && searchSpace.get(i)
                         .charAt(j, caseInsensitive) == '-') {
 
-                    if (counter != 0 || i == 0 && j == 0 || j != 0 && isSeparator(sequences.get(i)
-                            .charAt(j - 1, caseInsensitive)) || j == 0 && i != 0 && isSeparator(sequences.get(i - 1)
-                            .charAt(sequences.get(i - 1)
-                                    .length() - 1, caseInsensitive)) || j == 0 && i != 0 && sequences.get(i - 1)
-                            .charAt(sequences.get(i - 1).length() - 1, caseInsensitive) != ' ' && sequences.get(i)
+                    if (counter != 0 || i == 0 && j == 0 || j != 0 && isSeparator(searchSpace.get(i)
+                            .charAt(j - 1, caseInsensitive)) || j == 0 && i != 0 && isSeparator(searchSpace.get(i - 1)
+                            .charAt(searchSpace.get(i - 1)
+                                    .length() - 1, caseInsensitive)) || j == 0 && i != 0 && searchSpace.get(i - 1)
+                            .charAt(searchSpace.get(i - 1).length() - 1, caseInsensitive) != ' ' && searchSpace.get(i)
                             .charAt(j, caseInsensitive) != ' ') {
-                        partMatch.add(sequences.get(i).textPositionAt(j));
-                        if (!(j == sequences.get(i).length() - 1 && sequences.get(i)
+                        partMatch.add(searchSpace.get(i).textPositionAt(j));
+                        if (!(j == searchSpace.get(i).length() - 1 && searchSpace.get(i)
                                 .charAt(j, caseInsensitive) == '-' && searchChars[counter] != '-')) {
                             counter++;
                         }
@@ -79,19 +100,19 @@ public class SearchableText {
                     if (counter == searchString.length()) {
                         crossSequenceParts.add(partMatch);
 
-                        if (i == sequences.size() - 1 && j == sequences.get(i).length() - 1 || j != sequences.get(i)
-                                .length() - 1 && isSeparator(sequences.get(i)
-                                .charAt(j + 1, caseInsensitive)) || j == sequences.get(i)
-                                .length() - 1 && isSeparator(sequences.get(i + 1)
-                                .charAt(0, caseInsensitive)) || j == sequences.get(i).length() - 1 && sequences.get(i)
-                                .charAt(j, caseInsensitive) != ' ' && sequences.get(i + 1)
+                        if (i == searchSpace.size() - 1 && j == searchSpace.get(i).length() - 1 || j != searchSpace.get(i)
+                                .length() - 1 && isSeparator(searchSpace.get(i)
+                                .charAt(j + 1, caseInsensitive)) || j == searchSpace.get(i)
+                                .length() - 1 && isSeparator(searchSpace.get(i + 1)
+                                .charAt(0, caseInsensitive)) || j == searchSpace.get(i).length() - 1 && searchSpace.get(i)
+                                .charAt(j, caseInsensitive) != ' ' && searchSpace.get(i + 1)
                                 .charAt(0, caseInsensitive) != ' ') {
                             finalMatches.addAll(buildEntityPositionSequence(crossSequenceParts));
                         }
 
                         counter = 0;
                         crossSequenceParts = new ArrayList<>();
-                        partMatch = new TextPositionSequence(sequences.get(i).getPage());
+                        partMatch = new TextPositionSequence(searchSpace.get(i).getPage());
                     }
                 } else {
                     counter = 0;
@@ -99,24 +120,27 @@ public class SearchableText {
                         j--;
                     }
                     crossSequenceParts = new ArrayList<>();
-                    partMatch = new TextPositionSequence(sequences.get(i).getPage());
+                    partMatch = new TextPositionSequence(searchSpace.get(i).getPage());
                 }
 
-                if (j == sequences.get(i).length() - 1 && counter != 0) {
+                if (j == searchSpace.get(i).length() - 1 && counter != 0) {
                     crossSequenceParts.add(partMatch);
                 }
             }
         }
 
         return finalMatches;
+
     }
 
 
     private List<EntityPositionSequence> buildEntityPositionSequence(List<TextPositionSequence> crossSequenceParts) {
 
-        UUID id = UUID.randomUUID();
+        String plainId = IdBuilder.buildId(crossSequenceParts);
+        String id = plainId;
         List<EntityPositionSequence> result = new ArrayList<>();
         int currentPage = -1;
+        int idDiffentPageSuffix = 1;
         EntityPositionSequence entityPositionSequence = new EntityPositionSequence(id);
         for (TextPositionSequence textPositionSequence : crossSequenceParts) {
             if (currentPage == -1) {
@@ -126,9 +150,13 @@ public class SearchableText {
             } else if (currentPage == textPositionSequence.getPage()) {
                 entityPositionSequence.getSequences().add(textPositionSequence);
             } else {
+                id = plainId + "-" + idDiffentPageSuffix;
+                idDiffentPageSuffix++;
                 result.add(entityPositionSequence);
                 entityPositionSequence = new EntityPositionSequence(id);
                 entityPositionSequence.setPageNumber(textPositionSequence.getPage());
+                entityPositionSequence.getSequences().add(textPositionSequence);
+                currentPage = textPositionSequence.getPage();
             }
         }
         result.add(entityPositionSequence);
@@ -163,7 +191,7 @@ public class SearchableText {
 
         return TextNormalizationUtilities.removeHyphenLineBreaks(sb.toString())
                 .replaceAll("\n", " ")
-                .replaceAll("  ", " ");
+                .replaceAll(" {2}", " ");
     }
 
 
@@ -187,4 +215,4 @@ public class SearchableText {
         return sb.append("\n").toString();
     }
 
-}
+}

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

@@ -3,6 +3,7 @@ package com.iqser.red.service.redaction.v1.server.redaction.model;
 import java.util.ArrayList;
 import java.util.HashSet;
 import java.util.List;
+import java.util.Map;
 import java.util.Set;
 import java.util.regex.Pattern;
 
@@ -10,8 +11,10 @@ import org.apache.commons.lang3.StringUtils;
 
 import lombok.Builder;
 import lombok.Data;
+import lombok.extern.slf4j.Slf4j;
 
 @Data
+@Slf4j
 @Builder
 public class Section {
 
@@ -25,13 +28,34 @@ public class Section {
 
     private String headline;
 
+    private int sectionNumber;
 
-    public boolean contains(String type) {
+    private Map<String, CellValue> tabularData;
+
+
+    public boolean rowEquals(String headerName, String value) {
+
+        String cleanHeaderName = headerName.replaceAll("\n", "").replaceAll(" ", "").replaceAll("-", "");
+
+        return tabularData != null && tabularData.containsKey(cleanHeaderName) && tabularData.get(cleanHeaderName)
+                .getTextBlock()
+                .getText()
+                .equals(value);
+    }
+
+
+    public boolean matchesType(String type) {
 
         return entities.stream().anyMatch(entity -> entity.getType().equals(type));
     }
 
 
+    public boolean headlineContainsWord(String word) {
+
+        return StringUtils.containsIgnoreCase(headline, word);
+    }
+
+
     public void redact(String type, int ruleNumber, String reason) {
 
         entities.forEach(entity -> {
@@ -56,13 +80,29 @@ public class Section {
     }
 
 
+    public void redactIfPrecededBy(String prefix, String type, int ruleNumber, String reason) {
+
+        entities.forEach(entity -> {
+            if (entity.getType().equals(type) && searchText.indexOf(prefix + entity.getWord()) != 1) {
+                entity.setRedaction(true);
+                entity.setMatchedRule(ruleNumber);
+                entity.setRedactionReason(reason);
+            }
+        });
+    }
+
+
     public void redactLineAfter(String start, String asType, int ruleNumber, String reason) {
 
-        String value = StringUtils.substringBetween(text, start, "\n");
+        String[] values = StringUtils.substringsBetween(text, start, "\n");
 
-        if (value != null) {
-            Set<Entity> found = findEntity(value.trim(), asType);
-            entities.addAll(found);
+        if (values != null) {
+            for (String value : values) {
+                if (StringUtils.isNotBlank(value)) {
+                    Set<Entity> found = findEntities(value.trim(), asType);
+                    entities.addAll(found);
+                }
+            }
         }
 
         // TODO No need to iterate
@@ -79,11 +119,15 @@ public class Section {
 
     public void redactBetween(String start, String stop, String asType, int ruleNumber, String reason) {
 
-        String value = StringUtils.substringBetween(searchText, start, stop);
+        String[] values = StringUtils.substringsBetween(searchText, start, stop);
 
-        if (value != null) {
-            Set<Entity> found = findEntity(value.trim(), asType);
-            entities.addAll(found);
+        if (values != null) {
+            for (String value : values) {
+                if (StringUtils.isNotBlank(value)) {
+                    Set<Entity> found = findEntities(value.trim(), asType);
+                    entities.addAll(found);
+                }
+            }
         }
 
         // TODO No need to iterate
@@ -97,7 +141,7 @@ public class Section {
     }
 
 
-    private Set<Entity> findEntity(String value, String asType) {
+    private Set<Entity> findEntities(String value, String asType) {
 
         Set<Entity> found = new HashSet<>();
 
@@ -109,13 +153,12 @@ public class Section {
 
             if (startIndex > -1 && (startIndex == 0 || Character.isWhitespace(searchText.charAt(startIndex - 1)) || isSeparator(searchText
                     .charAt(startIndex - 1))) && (stopIndex == searchText.length() || isSeparator(searchText.charAt(stopIndex)))) {
-                found.add(new Entity(searchText.substring(startIndex, stopIndex), asType, startIndex, stopIndex, headline));
+                found.add(new Entity(searchText.substring(startIndex, stopIndex), asType, startIndex, stopIndex,
+                        headline, sectionNumber));
             }
         } while (startIndex > -1);
 
-        removeEntitiesContainedInLarger(found);
-
-        return found;
+        return removeEntitiesContainedInLarger(found);
     }
 
 
@@ -125,7 +168,7 @@ public class Section {
     }
 
 
-    public void removeEntitiesContainedInLarger(Set<Entity> entities) {
+    public Set<Entity> removeEntitiesContainedInLarger(Set<Entity> entities) {
 
         List<Entity> wordsToRemove = new ArrayList<>();
         for (Entity word : entities) {
@@ -137,6 +180,53 @@ public class Section {
             }
         }
         entities.removeAll(wordsToRemove);
+        return entities;
+    }
+
+
+    public void highlightCell(String cellHeader, int ruleNumber, String type) {
+
+        annotateCell(cellHeader, ruleNumber, type, false, null);
+    }
+
+
+    public void redactCell(String cellHeader, int ruleNumber, String type, String reason) {
+
+        annotateCell(cellHeader, ruleNumber, type, true, reason);
+    }
+
+
+    public void redactNotCell(String cellHeader, int ruleNumber, String type, String reason) {
+
+        annotateCell(cellHeader, ruleNumber, type, false, reason);
+    }
+
+
+    private void annotateCell(String cellHeader, int ruleNumber, String type, boolean redact, String reason) {
+
+        String cleanHeaderName = cellHeader.replaceAll("\n", "").replaceAll(" ", "").replaceAll("-", "");
+
+        CellValue value = tabularData.get(cleanHeaderName);
+        if (value == null) {
+            log.warn("Could not find any data for {}.", cellHeader);
+        } else {
+            Entity entity = new Entity(value.toString(), type, value.getRowSpanStart(),
+                    value.getRowSpanStart() + value.toString()
+                    .length(), headline, sectionNumber);
+            entity.setRedaction(redact);
+            entity.setMatchedRule(ruleNumber);
+            entity.setRedactionReason(reason);
+            entity.setTargetSequences(value.getTextBlock()
+                    .getSequences()); // Make sure no other cells with same content are highlighted
+
+            // HashSet keeps the older value, but we want the new only.
+            if (entities.contains(entity)) {
+                entities.remove(entity);
+            }
+            entities.add(entity);
+
+            entities = removeEntitiesContainedInLarger(entities);
+        }
     }
 
 }

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

@@ -27,6 +27,7 @@ public class DictionaryService {
 
     private final DictionaryClient dictionaryClient;
 
+    @Getter
     private long dictionaryVersion = -1;
 
     @Getter
@@ -73,7 +74,7 @@ public class DictionaryService {
                         .filter(TypeResult::isCaseInsensitive)
                         .map(TypeResult::getType)
                         .collect(Collectors.toList());
-                dictionary = entryColors.keySet().stream().collect(Collectors.toMap(type -> type, s -> convertEntries(s)));
+                dictionary = entryColors.keySet().stream().collect(Collectors.toMap(type -> type, this::convertEntries));
                 defaultColor = dictionaryClient.getDefaultColor().getColor();
             }
         } catch (FeignException e) {

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

@@ -18,6 +18,7 @@ import com.iqser.red.service.redaction.v1.server.client.RulesClient;
 import com.iqser.red.service.redaction.v1.server.exception.RulesValidationException;
 import com.iqser.red.service.redaction.v1.server.redaction.model.Section;
 
+import lombok.Getter;
 import lombok.RequiredArgsConstructor;
 
 @Service
@@ -29,6 +30,7 @@ public class DroolsExecutionService {
     @Autowired
     private KieContainer kieContainer;
 
+    @Getter
     private long rulesVersion = -1;
 
     public Section executeRules(Section section) {

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

@@ -1,18 +1,26 @@
 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.regex.Pattern;
 
+import org.apache.commons.collections4.CollectionUtils;
+import org.apache.commons.lang3.StringUtils;
 import org.springframework.stereotype.Service;
 
+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.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;
+import com.iqser.red.service.redaction.v1.server.redaction.model.CellValue;
 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 com.iqser.red.service.redaction.v1.server.redaction.model.Section;
 import com.iqser.red.service.redaction.v1.server.tableextraction.model.Cell;
@@ -28,12 +36,13 @@ public class EntityRedactionService {
     private final DroolsExecutionService droolsExecutionService;
 
 
-    public void processDocument(Document classifiedDoc) {
+    public void processDocument(Document classifiedDoc, ManualRedactions manualRedactions) {
 
         dictionaryService.updateDictionary();
         droolsExecutionService.updateRules();
 
         Set<Entity> documentEntities = new HashSet<>();
+        int sectionNumber = 1;
         for (Paragraph paragraph : classifiedDoc.getParagraphs()) {
 
             SearchableText searchableText = paragraph.getSearchableText();
@@ -41,88 +50,121 @@ public class EntityRedactionService {
             List<Table> tables = paragraph.getTables();
 
             for (Table table : tables) {
+                boolean singleCellTable = table.getRowCount() == 1 && table.getColCount() == 1;
                 for (List<Cell> row : table.getRows()) {
                     SearchableText searchableRow = new SearchableText();
-                    for (Cell column : row) {
-                        if (column == null || column.getTextBlocks() == null) {
+                    Map<String, CellValue> tabularData = new HashMap<>();
+                    int start = 0;
+                    for (Cell cell : row) {
+                        if (!singleCellTable && cell.isHeaderCell() || CollectionUtils.isEmpty(cell.getTextBlocks())) {
                             continue;
                         }
-                        for (TextBlock textBlock : column.getTextBlocks()) {
+                        addSectionToManualRedactions(cell.getTextBlocks(), manualRedactions, table.getHeadline(), sectionNumber);
+                        int cellStart = start;
+                        cell.getHeaderCells().forEach(headerCell -> {
+                            StringBuilder headerBuilder = new StringBuilder();
+                            headerCell.getTextBlocks().forEach(textBlock -> headerBuilder.append(textBlock.getText()));
+                            String headerName = headerBuilder.toString()
+                                    .replaceAll("\n", "")
+                                    .replaceAll(" ", "")
+                                    .replaceAll("-", "");
+                            tabularData.put(headerName, new CellValue(cell.getTextBlocks().get(0), cellStart));
+                        });
+                        start = start + cell.toString().length();
+                        for (TextBlock textBlock : cell.getTextBlocks()) {
                             searchableRow.addAll(textBlock.getSequences());
                         }
                     }
-                    Set<Entity> rowEntities = findEntities(searchableRow, table.getHeadline());
+                    Set<Entity> rowEntities = findEntities(searchableRow, table.getHeadline(), sectionNumber);
 
                     Section analysedRowSection = droolsExecutionService.executeRules(Section.builder()
                             .entities(rowEntities)
                             .text(searchableRow.getAsStringWithLinebreaks())
                             .searchText(searchableRow.toString())
                             .headline(table.getHeadline())
+                            .sectionNumber(sectionNumber)
+                            .tabularData(tabularData)
                             .build());
 
-                    for (Entity entity : analysedRowSection.getEntities()) {
-                        if (dictionaryService.getCaseInsensitiveTypes().contains(entity.getType())) {
-                            entity.setPositionSequences(searchableRow.getSequences(entity.getWord(), true));
-                        } else {
-                            entity.setPositionSequences(searchableRow.getSequences(entity.getWord(), false));
-                        }
-                    }
-                    documentEntities.addAll(analysedRowSection.getEntities());
+                    documentEntities.addAll(clearAndFindPositions(analysedRowSection.getEntities(), searchableRow));
+                    sectionNumber++;
                 }
+                sectionNumber++;
             }
 
-            Set<Entity> entities = findEntities(searchableText, paragraph.getHeadline());
+            addSectionToManualRedactions(paragraph.getTextBlocks(), manualRedactions, paragraph.getHeadline(), sectionNumber);
+            Set<Entity> entities = findEntities(searchableText, paragraph.getHeadline(), sectionNumber);
             Section analysedSection = droolsExecutionService.executeRules(Section.builder()
                     .entities(entities)
                     .text(searchableText.getAsStringWithLinebreaks())
                     .searchText(searchableText.toString())
                     .headline(paragraph.getHeadline())
+                    .sectionNumber(sectionNumber)
                     .build());
 
-            for (Entity entity : analysedSection.getEntities()) {
-                if (dictionaryService.getCaseInsensitiveTypes().contains(entity.getType())) {
-                    entity.setPositionSequences(searchableText.getSequences(entity.getWord(), true));
-                } else {
-                    entity.setPositionSequences(searchableText.getSequences(entity.getWord(), false));
-                }
-            }
-
-            documentEntities.addAll(analysedSection.getEntities());
+            documentEntities.addAll(clearAndFindPositions(analysedSection.getEntities(), searchableText));
+            sectionNumber++;
         }
 
-        documentEntities.forEach(entity -> {
-            entity.getPositionSequences().forEach(sequence -> {
+        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(sequence.getPageNumber(), (x) -> new HashSet<>())
-                        .add(new Entity(entity.getWord(), entity.getType(), entity.isRedaction(), entity.getRedactionReason(), List
-                                .of(sequence), entity.getHeadline(), entity.getMatchedRule()));
-            });
-        });
+                        .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()));
+            }
+        }
+
     }
 
 
-    private Set<Entity> findEntities(SearchableText searchableText, String headline) {
+    private Set<Entity> clearAndFindPositions(Set<Entity> entities, SearchableText text) {
+
+        removeEntitiesContainedInLarger(entities);
+
+        for (Entity entity : entities) {
+            if (dictionaryService.getCaseInsensitiveTypes().contains(entity.getType())) {
+                entity.setPositionSequences(text.getSequences(entity.getWord(), true, entity.getTargetSequences()));
+            } else {
+                entity.setPositionSequences(text.getSequences(entity.getWord(), false, entity.getTargetSequences()));
+            }
+        }
+
+        return entities;
+    }
+
+
+    private Set<Entity> findEntities(SearchableText searchableText, String headline, int sectionNumber) {
+
+        Set<Entity> found = new HashSet<>();
+        if (StringUtils.isEmpty(searchableText.toString())) {
+            return found;
+        }
 
         String inputString = searchableText.toString();
         String lowercaseInputString = inputString.toLowerCase();
-
-        Set<Entity> found = new HashSet<>();
         for (Map.Entry<String, Set<String>> entry : dictionaryService.getDictionary().entrySet()) {
-
             if (dictionaryService.getCaseInsensitiveTypes().contains(entry.getKey())) {
-                found.addAll(find(lowercaseInputString, entry.getValue(), entry.getKey(), headline));
+                found.addAll(find(lowercaseInputString, entry.getValue(), entry.getKey(), headline, sectionNumber));
             } else {
-                found.addAll(find(inputString, entry.getValue(), entry.getKey(), headline));
+                found.addAll(find(inputString, entry.getValue(), entry.getKey(), headline, sectionNumber));
             }
         }
 
         removeEntitiesContainedInLarger(found);
 
         return found;
+
     }
 
 
-    private Set<Entity> find(String inputString, Set<String> values, String type, String headline) {
+    private Set<Entity> find(String inputString, Set<String> values, String type, String headline, int sectionNumber) {
 
         Set<Entity> found = new HashSet<>();
         for (String value : values) {
@@ -134,7 +176,7 @@ public class EntityRedactionService {
 
                 if (startIndex > -1 && (startIndex == 0 || Character.isWhitespace(inputString.charAt(startIndex - 1)) || isSeparator(inputString
                         .charAt(startIndex - 1))) && (stopIndex == inputString.length() || isSeparator(inputString.charAt(stopIndex)))) {
-                    found.add(new Entity(inputString.substring(startIndex, stopIndex), type, startIndex, stopIndex, headline));
+                    found.add(new Entity(inputString.substring(startIndex, stopIndex), type, startIndex, stopIndex, headline, sectionNumber));
                 }
             } while (startIndex > -1);
         }
@@ -162,4 +204,23 @@ public class EntityRedactionService {
         entities.removeAll(wordsToRemove);
     }
 
+
+    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);
+                    }
+                }
+            }
+        }
+    }
+
 }

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

@@ -0,0 +1,32 @@
+package com.iqser.red.service.redaction.v1.server.redaction.utils;
+
+import java.nio.charset.StandardCharsets;
+import java.util.List;
+
+import com.google.common.hash.HashFunction;
+import com.google.common.hash.Hashing;
+import com.iqser.red.service.redaction.v1.model.ManualRedactionEntry;
+import com.iqser.red.service.redaction.v1.server.parsing.model.TextPositionSequence;
+
+import lombok.experimental.UtilityClass;
+
+@UtilityClass
+public class IdBuilder {
+
+    private final HashFunction hashFunction = Hashing.murmur3_128();
+
+    public String buildId(List<TextPositionSequence> crossSequenceParts) {
+
+        StringBuilder sb = new StringBuilder();
+        crossSequenceParts.forEach(sequencePart -> sequencePart.getTextPositions().forEach(textPosition -> {
+            sb.append(textPosition.getTextMatrix());
+        }));
+
+        return hashFunction.hashString(sb.toString(), StandardCharsets.UTF_8).toString();
+    }
+
+
+    public String buildId(ManualRedactionEntry manualRedactionEntry) {
+        return hashFunction.hashString(manualRedactionEntry.toString(), StandardCharsets.UTF_8).toString();
+    }
+}

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

@@ -21,7 +21,6 @@ import com.iqser.red.service.redaction.v1.server.tableextraction.model.AbstractT
 import com.iqser.red.service.redaction.v1.server.tableextraction.model.CleanRulings;
 import com.iqser.red.service.redaction.v1.server.tableextraction.service.RulingCleaningService;
 import com.iqser.red.service.redaction.v1.server.tableextraction.service.TableExtractionService;
-import com.iqser.red.service.redaction.v1.server.tableextraction.utils.Utils;
 
 import lombok.RequiredArgsConstructor;
 import lombok.extern.slf4j.Slf4j;
@@ -29,7 +28,6 @@ import lombok.extern.slf4j.Slf4j;
 @Slf4j
 @Service
 @RequiredArgsConstructor
-@SuppressWarnings("PMD")
 public class PdfSegmentationService {
 
     private final RulingCleaningService rulingCleaningService;
@@ -38,6 +36,7 @@ public class PdfSegmentationService {
     private final ClassificationService classificationService;
     private final SectionsBuilderService sectionsBuilderService;
 
+
     public Document parseDocument(PDDocument pdDocument) throws IOException {
 
         Document document = new Document();
@@ -57,19 +56,21 @@ public class PdfSegmentationService {
             int rotation = pdPage.getRotation();
             boolean isRotated = rotation != 0 && rotation != 360;
 
-            ParsedElements parsedElements = ParsedElements
-                    .builder()
+
+            ParsedElements parsedElements = ParsedElements.builder()
                     .rulings(stripper.getRulings())
                     .sequences(stripper.getTextPositionSequences())
-                    .minCharWidth(Utils.round(stripper.getMinCharWidth(), 2))
-                    .minCharHeight(Utils.round(stripper.getMinCharHeight(), 2))
+                    .maxCharWidth(stripper.getMaxCharWidths())
+                    .maxCharHeight(stripper.getMaxCharWidths())
                     .landscape(isLandscape)
                     .rotated(isRotated)
                     .build();
 
-            CleanRulings cleanRulings = rulingCleaningService.getCleanRulings(parsedElements.getRulings(), parsedElements.getMinCharWidth(), parsedElements.getMinCharHeight());
+            CleanRulings cleanRulings = rulingCleaningService.getCleanRulings(parsedElements.getRulings(), parsedElements
+                    .getMaxCharWidth(), parsedElements.getMaxCharHeight());
 
-            Page page = blockificationService.blockify(parsedElements.getSequences(), cleanRulings.getHorizontal(), cleanRulings.getVertical());
+            Page page = blockificationService.blockify(parsedElements.getSequences(), cleanRulings.getHorizontal(), cleanRulings
+                    .getVertical());
             page.setRotation(rotation);
 
             tableExtractionService.extractTables(cleanRulings, page);
@@ -92,7 +93,10 @@ public class PdfSegmentationService {
 
     }
 
+
+
     private void increaseDocumentStatistics(Page page, Document document) {
+
         if (!page.isLandscape()) {
             document.getFontSizeCounter().addAll(page.getFontSizeCounter().getCountPerValue());
         }
@@ -101,6 +105,7 @@ public class PdfSegmentationService {
         document.getFontStyleCounter().addAll(page.getFontStyleCounter().getCountPerValue());
     }
 
+
     private void buildPageStatistics(Page page) {
 
         // Collect all statistics for the page, except from blocks inside tables, as tables will always be added to BodyTextFrame.

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

@@ -1,9 +1,12 @@
 package com.iqser.red.service.redaction.v1.server.segmentation;
 
 import java.util.ArrayList;
+import java.util.Collections;
 import java.util.Iterator;
 import java.util.List;
+import java.util.stream.Collectors;
 
+import org.apache.commons.collections4.CollectionUtils;
 import org.springframework.stereotype.Service;
 
 import com.iqser.red.service.redaction.v1.server.classification.model.Document;
@@ -11,10 +14,10 @@ import com.iqser.red.service.redaction.v1.server.classification.model.Page;
 import com.iqser.red.service.redaction.v1.server.classification.model.Paragraph;
 import com.iqser.red.service.redaction.v1.server.classification.model.TextBlock;
 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;
 
 @Service
-@SuppressWarnings("all")
 public class SectionsBuilderService {
 
     public void buildSections(Document document) {
@@ -25,6 +28,7 @@ public class SectionsBuilderService {
         AbstractTextContainer prev = null;
 
         String lastHeadline = "";
+        Table previousTable = null;
         for (Page page : document.getPages()) {
             for (AbstractTextContainer current : page.getTextBlocks()) {
 
@@ -36,31 +40,67 @@ public class SectionsBuilderService {
                 current.setPage(page.getPageNumber());
 
                 if (prev != null && current.getClassification().startsWith("H ") || !document.isHeadlines()) {
-
                     Paragraph chunkBlock = buildTextBlock(chunkWords, lastHeadline);
                     chunkBlock.setHeadline(lastHeadline);
-                    lastHeadline = current.getText();
+                    if(document.isHeadlines()) {
+                        lastHeadline = current.getText();
+                    }
                     chunkBlockList.add(chunkBlock);
                     chunkWords = new ArrayList<>();
-
+                    if (CollectionUtils.isNotEmpty(chunkBlock.getTables())) {
+                        previousTable = chunkBlock.getTables().get(chunkBlock.getTables().size() - 1);
+                    }
+                }
+                if (current instanceof Table) {
+                    Table table = (Table) current;
+                    // Distribute header information for subsequent tables
+                    mergeTableMetadata(table, previousTable);
+                    previousTable = table;
                 }
-
                 chunkWords.add(current);
-
                 prev = current;
             }
         }
 
         Paragraph chunkBlock = buildTextBlock(chunkWords, lastHeadline);
-        if (chunkBlock != null) {
-            chunkBlockList.add(chunkBlock);
-            chunkBlock.setHeadline(lastHeadline);
-        }
+        chunkBlock.setHeadline(lastHeadline);
+        chunkBlockList.add(chunkBlock);
 
         document.setParagraphs(chunkBlockList);
     }
 
 
+    private void mergeTableMetadata(Table currentTable, Table previousTable) {
+
+        // Distribute header information for subsequent tables
+        if (previousTable != null && hasInvalidHeaderInformation(currentTable) && hasValidHeaderInformation(previousTable)) {
+            List<Cell> previousTableNonHeaderRow = getRowWithNonHeaderCells(previousTable);
+            List<Cell> tableNonHeaderRow = getRowWithNonHeaderCells(currentTable);
+            // Allow merging of tables if header row is separated from first logical non-header row
+            if (previousTableNonHeaderRow.isEmpty() && previousTable.getRowCount() == 1 && previousTable.getRows()
+                    .get(0)
+                    .size() == tableNonHeaderRow.size()) {
+                previousTableNonHeaderRow = previousTable.getRows().get(0).stream().map(cell -> {
+                    Cell fakeCell = new Cell(cell.getPoints()[0], cell.getPoints()[2]);
+                    fakeCell.setHeaderCells(Collections.singletonList(cell));
+                    return fakeCell;
+                }).collect(Collectors.toList());
+            }
+            if (previousTableNonHeaderRow.size() == tableNonHeaderRow.size()) {
+                for (int i = currentTable.getRowCount() - 1; i >= 0; i--) { // Non header rows are most likely at bottom of table
+                    List<Cell> row = currentTable.getRows().get(i);
+                    if (row.size() == tableNonHeaderRow.size() && row.stream()
+                            .allMatch(cell -> cell.getHeaderCells().isEmpty())) {
+                        for (int j = 0; j < row.size(); j++) {
+                            row.get(j).setHeaderCells(previousTableNonHeaderRow.get(j).getHeaderCells());
+                        }
+                    }
+                }
+            }
+        }
+    }
+
+
     private Paragraph buildTextBlock(List<AbstractTextContainer> wordBlockList, String lastHeadline) {
 
         Paragraph paragraph = new Paragraph();
@@ -76,19 +116,20 @@ public class SectionsBuilderService {
             AbstractTextContainer container = itty.next();
 
             if (container instanceof Table) {
+                Table table = (Table) container;
                 splitByTable = true;
 
-                if (previous != null && previous instanceof TextBlock && previous.getText().startsWith("Table ")) {
-                    ((Table) container).setHeadline(previous.getText());
+                if (previous != null && previous.getText().startsWith("Table ")) {
+                    table.setHeadline(previous.getText());
                 } else {
-                    ((Table) container).setHeadline("Table in: " + lastHeadline);
+                    table.setHeadline("Table in: " + lastHeadline);
                 }
 
                 if (textBlock != null && !alreadyAdded) {
                     paragraph.getPageBlocks().add(textBlock);
                     alreadyAdded = true;
                 }
-                paragraph.getPageBlocks().add(container);
+                paragraph.getPageBlocks().add(table);
                 continue;
             }
 
@@ -125,4 +166,42 @@ public class SectionsBuilderService {
         return paragraph;
     }
 
-}
+
+    private boolean hasValidHeaderInformation(Table table) {
+
+        return !hasInvalidHeaderInformation(table);
+    }
+
+
+    private boolean hasInvalidHeaderInformation(Table table) {
+
+        return table.getRows().stream()
+                .flatMap(row -> row.stream()
+                        .filter(cell -> CollectionUtils.isNotEmpty(cell.getHeaderCells())))
+                .findAny()
+                .isEmpty();
+
+    }
+
+
+    private List<Cell> getRowWithNonHeaderCells(Table table) {
+
+        for (int i = table.getRowCount() - 1; i >= 0; i--) { // Non header rows are most likely at bottom of table
+            List<Cell> row = table.getRows().get(i);
+            boolean allNonHeader = true;
+            for (Cell cell : row) {
+                if (cell.isHeaderCell()) {
+                    allNonHeader = false;
+                    break;
+                }
+            }
+            if (allNonHeader) {
+                return row;
+            }
+        }
+
+        return Collections.emptyList();
+
+    }
+
+}

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

@@ -1,5 +1,7 @@
 package com.iqser.red.service.redaction.v1.server.tableextraction.model;
 
+import com.iqser.red.service.redaction.v1.model.Rectangle;
+
 import lombok.AllArgsConstructor;
 import lombok.Data;
 import lombok.NoArgsConstructor;
@@ -22,4 +24,8 @@ public abstract class AbstractTextContainer {
         return this.minX <= other.minX && this.maxX >= other.maxX && this.minY >= other.minY && this.maxY <= other.maxY;
     }
 
+    public boolean contains(Rectangle other) {
+        return page == other.getPage() && this.minX <= other.getTopLeft().getX() && this.maxX >= other.getTopLeft().getX() + other.getWidth() && this.minY <= other.getTopLeft().getY()  && this.maxY >= other.getTopLeft().getY() + other.getHeight();
+    }
+
 }

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

@@ -5,6 +5,8 @@ import java.util.ArrayList;
 import java.util.List;
 
 import com.iqser.red.service.redaction.v1.server.classification.model.TextBlock;
+import com.iqser.red.service.redaction.v1.server.parsing.model.TextPositionSequence;
+import com.iqser.red.service.redaction.v1.server.redaction.utils.TextNormalizationUtilities;
 
 import lombok.Data;
 import lombok.EqualsAndHashCode;
@@ -16,11 +18,51 @@ public class Cell extends Rectangle {
 
     private List<TextBlock> textBlocks = new ArrayList<>();
 
+    private List<Cell> headerCells = new ArrayList<>();
+
+    private boolean isHeaderCell;
+
+
     public Cell(Point2D topLeft, Point2D bottomRight) {
-        super((float) topLeft.getY(), (float) topLeft.getX(), (float) (bottomRight.getX() - topLeft.getX()), (float) (bottomRight.getY() - topLeft.getY()));
+
+        super((float) topLeft.getY(), (float) topLeft.getX(), (float) (bottomRight.getX() - topLeft.getX()), (float) (bottomRight
+                .getY() - topLeft.getY()));
     }
 
+
     public void addTextBlock(TextBlock textBlock) {
+
         textBlocks.add(textBlock);
     }
+
+
+    @Override
+    public String toString() {
+
+        StringBuilder sb = new StringBuilder();
+
+        TextPositionSequence previous = null;
+        for (TextBlock textBlock : textBlocks) {
+
+
+            for (TextPositionSequence word : textBlock.getSequences()) {
+
+                if (previous != null) {
+                    if (Math.abs(previous.getY1() - word.getY1()) > word.getTextHeight()) {
+                        sb.append('\n');
+                    } else {
+                        sb.append(' ');
+                    }
+                }
+                sb.append(word.toString());
+                previous = word;
+            }
+        }
+
+        return TextNormalizationUtilities.removeHyphenLineBreaks(sb.toString())
+                .replaceAll("\n", " ")
+                .replaceAll(" {2}", " ");
+    }
+
 }
+

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

@@ -0,0 +1,22 @@
+package com.iqser.red.service.redaction.v1.server.tableextraction.model;
+
+import lombok.RequiredArgsConstructor;
+import lombok.Value;
+
+@Value
+@RequiredArgsConstructor
+public class CellPosition implements Comparable<CellPosition> {
+
+    int row;
+
+    int col;
+
+
+    @Override
+    public int compareTo(CellPosition other) {
+
+        int rowDiff = row - other.row;
+        return rowDiff != 0 ? rowDiff : col - other.col;
+    }
+
+}

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

@@ -8,25 +8,28 @@ import org.locationtech.jts.index.strtree.STRtree;
 
 import com.iqser.red.service.redaction.v1.server.tableextraction.utils.Utils;
 
-
 @SuppressWarnings("all")
 public class RectangleSpatialIndex<T extends Rectangle> {
-    
 
     private final STRtree si = new STRtree();
     private final List<T> rectangles = new ArrayList<>();
 
+
     public void add(T te) {
+
         rectangles.add(te);
         si.insert(new Envelope(te.getLeft(), te.getRight(), te.getBottom(), te.getTop()), te);
     }
-    
-    public List<T> contains(Rectangle r) {
-        List<T> intersection = si.query(new Envelope(r.getLeft(), r.getRight(), r.getTop(), r.getBottom()));
+
+
+    public List<T> contains(Rectangle rectangle) {
+
+        List<T> intersection = si.query(new Envelope(rectangle.getLeft(), rectangle.getRight(), rectangle.getTop(), rectangle
+                .getBottom()));
         List<T> rv = new ArrayList<T>();
 
-        for (T ir: intersection) {
-            if (r.contains(ir)) {
+        for (T ir : intersection) {
+            if (rectangle.contains(ir)) {
                 rv.add(ir);
             }
         }
@@ -34,18 +37,22 @@ public class RectangleSpatialIndex<T extends Rectangle> {
         Utils.sort(rv, Rectangle.ILL_DEFINED_ORDER);
         return rv;
     }
-    
+
+
     public List<T> intersects(Rectangle r) {
+
         List rv = si.query(new Envelope(r.getLeft(), r.getRight(), r.getTop(), r.getBottom()));
         return rv;
     }
-    
+
+
     /**
      * Minimum bounding box of all the Rectangles contained on this RectangleSpatialIndex
-     * 
+     *
      * @return a Rectangle
      */
     public Rectangle getBounds() {
+
         return Rectangle.boundingBoxOf(rectangles);
     }
 

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

@@ -9,31 +9,38 @@ import java.util.List;
 import java.util.Map;
 import java.util.TreeMap;
 
+import org.apache.commons.collections4.CollectionUtils;
+
 import com.iqser.red.service.redaction.v1.server.classification.model.TextBlock;
 import com.iqser.red.service.redaction.v1.server.tableextraction.utils.Utils;
 
 import lombok.Getter;
 import lombok.Setter;
+import lombok.extern.slf4j.Slf4j;
 
-@SuppressWarnings("all")
+@Slf4j
 public class Table extends AbstractTextContainer {
 
     private final TreeMap<CellPosition, Cell> cells = new TreeMap<>();
 
-    private RectangleSpatialIndex<Cell> si = new RectangleSpatialIndex<>();
+    private final RectangleSpatialIndex<Cell> si = new RectangleSpatialIndex<>();
 
     @Getter
     @Setter
     private String headline;
 
-    @Getter
-    private int rowCount = 0;
-    @Getter
-    private int colCount = 0;
+    private int unrotatedRowCount;
 
-    private int rotation = 0;
+    private int unrotatedColCount;
+
+    private int rowCount = -1;
+
+    private int colCount = -1;
+
+    private final int rotation;
+
+    private List<List<Cell>> rows;
 
-    private List<List<Cell>> memoizedRows = null;
 
     public Table(List<Cell> cells, Rectangle area, int rotation) {
 
@@ -47,43 +54,129 @@ public class Table extends AbstractTextContainer {
 
     }
 
+
     public List<List<Cell>> getRows() {
 
-        if (memoizedRows == null) {
-            memoizedRows = computeRows();
+        if (rows == null) {
+            rows = computeRows();
+            computeHeaders();
         }
 
-        return memoizedRows;
+        return rows;
 
     }
 
+
+    public int getRowCount() {
+
+        if (rowCount == -1) {
+            rowCount = getRows().size();
+        }
+        return rowCount;
+    }
+
+
+    public int getColCount() {
+
+        if (colCount == -1) {
+            colCount = getRows().stream().mapToInt(List::size).max().orElse(0);
+        }
+        return colCount;
+
+    }
+
+
+    /**
+     * Detect header cells (either first row or first column):
+     * Column is marked as header if cell text is bold and row cell text is not bold.
+     * Defaults to row.
+     */
+    private void computeHeaders() {
+
+        if (rows == null) {
+            rows = computeRows();
+        }
+        // A bold cell is a header cell as long as every cell to the left/top is bold, too
+        // we move from left to right and top to bottom
+        for (int rowIndex = 0; rowIndex < rows.size(); rowIndex++) {
+            List<Cell> rowCells = rows.get(rowIndex);
+            for (int colIndex = 0; colIndex < rowCells.size(); colIndex++) {
+                Cell cell = rowCells.get(colIndex);
+                List<Cell> cellsToTheLeft = rowCells.subList(0, colIndex);
+                Cell lastHeaderCell = null;
+                for (Cell leftCell : cellsToTheLeft) {
+                    if (leftCell.isHeaderCell()) {
+                        lastHeaderCell = leftCell;
+                    } else {
+                        break;
+                    }
+                }
+                if (lastHeaderCell != null) {
+                    cell.getHeaderCells().add(lastHeaderCell);
+                }
+                List<Cell> cellsToTheTop = new ArrayList<>();
+                for (int i = 0; i < rowIndex; i++) {
+                    try {
+                        cellsToTheTop.add(rows.get(i).get(colIndex));
+                    } catch (IndexOutOfBoundsException e) {
+                        log.debug("No cell {} in row {}, ignoring.", colIndex, rowIndex);
+                    }
+                }
+                for (Cell topCell : cellsToTheTop) {
+                    if (topCell.isHeaderCell()) {
+                        lastHeaderCell = topCell;
+                    } else {
+                        break;
+                    }
+                }
+                if (lastHeaderCell != null) {
+                    cell.getHeaderCells().add(lastHeaderCell);
+                }
+                if (CollectionUtils.isNotEmpty(cell.getTextBlocks()) && cell.getTextBlocks()
+                        .get(0)
+                        .getMostPopularWordStyle()
+                        .equals("bold")) {
+                    cell.setHeaderCell(true);
+                }
+            }
+        }
+
+    }
+
+
     private List<List<Cell>> computeRows() {
 
         List<List<Cell>> rows = new ArrayList<>();
         if (rotation == 90) {
-            for (int i = 0; i < colCount; i++) { // rows
+            for (int i = 0; i < unrotatedColCount; i++) { // rows
                 List<Cell> lastRow = new ArrayList<>();
-                for (int j = rowCount - 1; j >= 0; j--) { // cols
+                for (int j = unrotatedRowCount - 1; j >= 0; j--) { // cols
                     Cell cell = cells.get(new CellPosition(j, i));
-                    lastRow.add(cell);
+                    if (cell != null) {
+                        lastRow.add(cell);
+                    }
                 }
                 rows.add(lastRow);
             }
         } else if (rotation == 270) {
-            for (int i = colCount - 1; i >= 0; i--) { // rows
+            for (int i = unrotatedColCount - 1; i >= 0; i--) { // rows
                 List<Cell> lastRow = new ArrayList<>();
-                for (int j = 0; j < rowCount; j++) { // cols
+                for (int j = 0; j < unrotatedRowCount; j++) { // cols
                     Cell cell = cells.get(new CellPosition(i, j));
-                    lastRow.add(cell);
+                    if (cell != null) {
+                        lastRow.add(cell);
+                    }
                 }
                 rows.add(lastRow);
             }
         } else {
-            for (int i = 0; i < rowCount; i++) {
+            for (int i = 0; i < unrotatedRowCount; i++) {
                 List<Cell> lastRow = new ArrayList<>();
-                for (int j = 0; j < colCount; j++) {
+                for (int j = 0; j < unrotatedColCount; j++) {
                     Cell cell = cells.get(new CellPosition(i, j)); // JAVA_8 use getOrDefault()
-                    lastRow.add(cell);
+                    if (cell != null) {
+                        lastRow.add(cell);
+                    }
                 }
                 rows.add(lastRow);
             }
@@ -93,16 +186,18 @@ public class Table extends AbstractTextContainer {
 
     }
 
-    public void add(Cell chunk, int row, int col) {
 
-        rowCount = Math.max(rowCount, row + 1);
-        colCount = Math.max(colCount, col + 1);
+    private void add(Cell chunk, int row, int col) {
+
+        unrotatedRowCount = Math.max(unrotatedRowCount, row + 1);
+        unrotatedColCount = Math.max(unrotatedColCount, col + 1);
 
         CellPosition cp = new CellPosition(row, col);
         cells.put(cp, chunk);
 
     }
 
+
     private void addCells(List<Cell> cells) {
 
         if (cells.isEmpty()) {
@@ -131,25 +226,21 @@ public class Table extends AbstractTextContainer {
             while (rowCells.hasNext()) {
                 Cell cell = rowCells.next();
                 if (i > 0) {
-                    List<List<Cell>> others = rowsOfCells(
-                            si.contains(
-                                    new Rectangle(cell.getBottom(),
-                                            si.getBounds().getLeft(),
-                                            cell.getLeft() - si.getBounds().getLeft() + 1,
-                                            si.getBounds().getBottom() - cell.getBottom()
-                                    )
-                            ));
+                    Rectangle rectangle = new Rectangle(cell.getBottom(),
+                            si.getBounds().getLeft(),
+                            cell.getLeft() - si.getBounds().getLeft() + 1,
+                            si.getBounds().getBottom() - cell.getBottom());
+                    List<List<Cell>> others = rowsOfCells(si.contains(rectangle));
 
                     for (List<Cell> r : others) {
                         jumpToColumn = Math.max(jumpToColumn, r.size());
                     }
-                }
 
-                while (startColumn != jumpToColumn) {
-                    add(previousNonNullCellForColumnIndex.get(startColumn), i, startColumn);
-                    startColumn++;
+                    while (startColumn != jumpToColumn) {
+                        add(previousNonNullCellForColumnIndex.get(startColumn), i, startColumn);
+                        startColumn++;
+                    }
                 }
-
                 add(cell, i, startColumn);
                 previousNonNullCellForColumnIndex.put(startColumn, cell);
                 startColumn++;
@@ -158,34 +249,24 @@ public class Table extends AbstractTextContainer {
         }
     }
 
-    private static List<List<Cell>> rowsOfCells(List<Cell> cells) {
-        Cell c;
-        float lastTop;
+
+    private List<List<Cell>> rowsOfCells(List<Cell> cells) {
+
         List<List<Cell>> rv = new ArrayList<>();
-        List<Cell> lastRow;
 
         if (cells.isEmpty()) {
             return rv;
         }
+        cells.sort(Comparator.comparingDouble(Rectangle::getLeft));
 
-        Collections.sort(cells, new Comparator<Cell>() {
-            @Override
-            public int compare(Cell arg0, Cell arg1) {
-                return Double.compare(arg0.getLeft(), arg1.getLeft());
-            }
-        });
-
-        Collections.sort(cells, Collections.reverseOrder(new Comparator<Cell>() {
-            @Override
-            public int compare(Cell arg0, Cell arg1) {
-                return Float.compare(Utils.round(arg0.getBottom(), 2), Utils.round(arg1.getBottom(),2));
-            }
-        }));
+        cells.sort(Collections.reverseOrder((arg0, arg1) -> Float.compare(Utils.round(arg0.getBottom(), 2),
+                Utils.round(arg1
+                .getBottom(), 2))));
 
         Iterator<Cell> iter = cells.iterator();
-        c = iter.next();
-        lastTop = c.getBottom();
-        lastRow = new ArrayList<>();
+        Cell c = iter.next();
+        float lastTop = c.getBottom();
+        List<Cell> lastRow = new ArrayList<>();
         lastRow.add(c);
         rv.add(lastRow);
 
@@ -201,6 +282,7 @@ public class Table extends AbstractTextContainer {
         return rv;
     }
 
+
     @Override
     public String getText() {
 
@@ -237,6 +319,7 @@ public class Table extends AbstractTextContainer {
         return sb.toString();
     }
 
+
     public String getTextAsHtml() {
 
         StringBuilder sb = new StringBuilder();
@@ -270,41 +353,4 @@ public class Table extends AbstractTextContainer {
         return sb.toString();
     }
 
-    class CellPosition implements Comparable<CellPosition> {
-
-        CellPosition(int row, int col) {
-            this.row = row;
-            this.col = col;
-        }
-
-        final int row, col;
-
-        @Override
-        public int hashCode() {
-            return row + 101 * col;
-        }
-
-        @Override
-        public boolean equals(Object obj) {
-            if (this == obj) {
-                return true;
-            }
-            if (obj == null) {
-                return false;
-            }
-            if (getClass() != obj.getClass()) {
-                return false;
-            }
-            CellPosition other = (CellPosition) obj;
-            return row == other.row && col == other.col;
-        }
-
-        @Override
-        public int compareTo(CellPosition other) {
-            int rowdiff = row - other.row;
-            return rowdiff != 0 ? rowdiff : col - other.col;
-        }
-
-    }
-
 }

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

@@ -18,9 +18,9 @@ import com.iqser.red.service.redaction.v1.server.tableextraction.utils.Utils;
 @Service
 public class RulingCleaningService {
 
-    public CleanRulings getCleanRulings(List<Ruling> rulings, float minCharWidth, float minCharHeight){
+    public CleanRulings getCleanRulings(List<Ruling> rulings, float maxCharWidth, float maxCharHeight){
         if (!rulings.isEmpty()) {
-            snapPoints(rulings, minCharWidth , minCharHeight);
+            snapPoints(rulings, maxCharWidth , maxCharHeight);
         }
 
         List<Ruling> vrs = new ArrayList<>();

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

@@ -2,7 +2,6 @@ package com.iqser.red.service.redaction.v1.server.tableextraction.service;
 
 import java.awt.geom.Point2D;
 import java.util.ArrayList;
-import java.util.Collections;
 import java.util.Comparator;
 import java.util.HashMap;
 import java.util.HashSet;
@@ -25,26 +24,28 @@ import com.iqser.red.service.redaction.v1.server.tableextraction.model.Table;
 import com.iqser.red.service.redaction.v1.server.tableextraction.utils.Utils;
 
 @Service
-@SuppressWarnings("all")
 public class TableExtractionService {
 
-    public void extractTables(CleanRulings cleanRulings, Page page){
+    public void extractTables(CleanRulings cleanRulings, Page page) {
 
         List<Cell> cells = findCells(cleanRulings.getHorizontal(), cleanRulings.getVertical());
 
-        Iterator<AbstractTextContainer> itty = page.getTextBlocks().iterator();
-        while (itty.hasNext()) {
-            TextBlock textBlock = (TextBlock) itty.next();
+        for (AbstractTextContainer abstractTextContainer : page.getTextBlocks()) {
+            TextBlock textBlock = (TextBlock) abstractTextContainer;
             for (Cell cell : cells) {
-                if (cell.intersects(textBlock.getMinX(), textBlock.getMinY(), textBlock.getWidth(), textBlock.getHeight())) {
+                if (cell.intersects(textBlock.getMinX(), textBlock.getMinY(), textBlock.getWidth(),
+                        textBlock.getHeight())) {
                     cell.addTextBlock(textBlock);
                     break;
                 }
             }
         }
 
-        List<Rectangle> spreadsheetAreas = findSpreadsheetsFromCells(cells)
-                .stream()
+        cells = new ArrayList<>(new HashSet<>(cells));
+        Utils.sort(cells, Rectangle.ILL_DEFINED_ORDER);
+
+
+        List<Rectangle> spreadsheetAreas = findSpreadsheetsFromCells(cells).stream()
                 .filter(r -> r.getWidth() > 0f && r.getHeight() > 0f)
                 .collect(Collectors.toList());
 
@@ -63,9 +64,9 @@ public class TableExtractionService {
         for (Table table : tables) {
             int position = -1;
 
-            itty = page.getTextBlocks().iterator();
+            Iterator<AbstractTextContainer> itty = page.getTextBlocks().iterator();
             while (itty.hasNext()) {
-                AbstractTextContainer textBlock = (AbstractTextContainer) itty.next();
+                AbstractTextContainer textBlock = itty.next();
                 if (table.contains(textBlock)) {
                     if (position == -1) {
                         position = page.getTextBlocks().indexOf(textBlock);
@@ -79,17 +80,18 @@ public class TableExtractionService {
         }
     }
 
+
     public List<Cell> findCells(List<Ruling> horizontalRulingLines, List<Ruling> verticalRulingLines) {
+
         List<Cell> cellsFound = new ArrayList<>();
-        Map<Point2D, Ruling[]> intersectionPoints = Ruling.findIntersections(horizontalRulingLines, verticalRulingLines);
+        Map<Point2D, Ruling[]> intersectionPoints = Ruling.findIntersections(horizontalRulingLines,
+                verticalRulingLines);
         List<Point2D> intersectionPointsList = new ArrayList<>(intersectionPoints.keySet());
-        Collections.sort(intersectionPointsList, POINT_COMPARATOR);
-        boolean doBreak;
+        intersectionPointsList.sort(POINT_COMPARATOR);
 
         for (int i = 0; i < intersectionPointsList.size(); i++) {
             Point2D topLeft = intersectionPointsList.get(i);
             Ruling[] hv = intersectionPoints.get(topLeft);
-            doBreak = false;
 
             // CrossingPointsDirectlyBelow( topLeft );
             List<Point2D> xPoints = new ArrayList<>();
@@ -106,10 +108,6 @@ public class TableExtractionService {
             }
             outer:
             for (Point2D xPoint : xPoints) {
-                if (doBreak) {
-                    break;
-                }
-
                 // is there a vertical edge b/w topLeft and xPoint?
                 if (!hv[1].equals(intersectionPoints.get(xPoint)[1])) {
                     continue;
@@ -120,11 +118,9 @@ public class TableExtractionService {
                         continue;
                     }
                     Point2D btmRight = new Point2D.Float((float) yPoint.getX(), (float) xPoint.getY());
-                    if (intersectionPoints.containsKey(btmRight)
-                            && intersectionPoints.get(btmRight)[0].equals(intersectionPoints.get(xPoint)[0])
-                            && intersectionPoints.get(btmRight)[1].equals(intersectionPoints.get(yPoint)[1])) {
+                    if (intersectionPoints.containsKey(btmRight) && intersectionPoints.get(btmRight)[0].equals(intersectionPoints
+                            .get(xPoint)[0]) && intersectionPoints.get(btmRight)[1].equals(intersectionPoints.get(yPoint)[1])) {
                         cellsFound.add(new Cell(topLeft, btmRight));
-                        doBreak = true;
                         break outer;
                     }
                 }
@@ -139,7 +135,7 @@ public class TableExtractionService {
     }
 
 
-    public List<Rectangle> findSpreadsheetsFromCells(List<? extends Rectangle> cells) {
+    private List<Rectangle> findSpreadsheetsFromCells(List<? extends Rectangle> cells) {
         // via: http://stackoverflow.com/questions/13746284/merging-multiple-adjacent-rectangles-into-one-polygon
         List<Rectangle> rectangles = new ArrayList<>();
         Set<Point2D> pointSet = new HashSet<>();
@@ -147,10 +143,6 @@ public class TableExtractionService {
         Map<Point2D, Point2D> edgesV = new HashMap<>();
         int i = 0;
 
-        cells = new ArrayList<>(new HashSet<>(cells));
-
-        Utils.sort(cells, Rectangle.ILL_DEFINED_ORDER);
-
         for (Rectangle cell : cells) {
             for (Point2D pt : cell.getPoints()) {
                 if (pointSet.contains(pt)) { // shared vertex, remove it
@@ -163,10 +155,10 @@ public class TableExtractionService {
 
         // X first sort
         List<Point2D> pointsSortX = new ArrayList<>(pointSet);
-        Collections.sort(pointsSortX, X_FIRST_POINT_COMPARATOR);
+        pointsSortX.sort(X_FIRST_POINT_COMPARATOR);
         // Y first sort
         List<Point2D> pointsSortY = new ArrayList<>(pointSet);
-        Collections.sort(pointsSortY, POINT_COMPARATOR);
+        pointsSortY.sort(POINT_COMPARATOR);
 
         while (i < pointSet.size()) {
             float currY = (float) pointsSortY.get(i).getY();
@@ -203,13 +195,12 @@ public class TableExtractionService {
                     nextVertex = edgesV.get(curr.point);
                     edgesV.remove(curr.point);
                     lastAddedVertex = new PolygonVertex(nextVertex, Direction.VERTICAL);
-                    polygon.add(lastAddedVertex);
                 } else {
                     nextVertex = edgesH.get(curr.point);
                     edgesH.remove(curr.point);
                     lastAddedVertex = new PolygonVertex(nextVertex, Direction.HORIZONTAL);
-                    polygon.add(lastAddedVertex);
                 }
+                polygon.add(lastAddedVertex);
 
                 if (lastAddedVertex.equals(polygon.get(0))) {
                     // closed polygon
@@ -227,10 +218,10 @@ public class TableExtractionService {
 
         // calculate grid-aligned minimum area rectangles for each found polygon
         for (List<PolygonVertex> poly : polygons) {
-            float top = java.lang.Float.MAX_VALUE;
-            float left = java.lang.Float.MAX_VALUE;
-            float bottom = java.lang.Float.MIN_VALUE;
-            float right = java.lang.Float.MIN_VALUE;
+            float top = Float.MAX_VALUE;
+            float left = Float.MAX_VALUE;
+            float bottom = Float.MIN_VALUE;
+            float right = Float.MIN_VALUE;
             for (PolygonVertex pt : poly) {
                 top = (float) Math.min(top, pt.point.getY());
                 left = (float) Math.min(left, pt.point.getX());
@@ -244,69 +235,66 @@ public class TableExtractionService {
     }
 
 
-    private static final Comparator<Point2D> X_FIRST_POINT_COMPARATOR = new Comparator<Point2D>() {
-        @Override
-        public int compare(Point2D arg0, Point2D arg1) {
-            int rv = 0;
-            float arg0X = Utils.round(arg0.getX(), 2);
-            float arg0Y = Utils.round(arg0.getY(), 2);
-            float arg1X = Utils.round(arg1.getX(), 2);
-            float arg1Y = Utils.round(arg1.getY(), 2);
+    private static final Comparator<Point2D> X_FIRST_POINT_COMPARATOR = (arg0, arg1) -> {
 
-            if (arg0X > arg1X) {
-                rv = 1;
-            } else if (arg0X < arg1X) {
-                rv = -1;
-            } else if (arg0Y > arg1Y) {
-                rv = 1;
-            } else if (arg0Y < arg1Y) {
-                rv = -1;
-            }
-            return rv;
+        int rv = 0;
+        float arg0X = Utils.round(arg0.getX(), 2);
+        float arg0Y = Utils.round(arg0.getY(), 2);
+        float arg1X = Utils.round(arg1.getX(), 2);
+        float arg1Y = Utils.round(arg1.getY(), 2);
+
+        if (arg0X > arg1X) {
+            rv = 1;
+        } else if (arg0X < arg1X) {
+            rv = -1;
+        } else if (arg0Y > arg1Y) {
+            rv = 1;
+        } else if (arg0Y < arg1Y) {
+            rv = -1;
         }
+        return rv;
     };
 
+    private static final Comparator<Point2D> POINT_COMPARATOR = (arg0, arg1) -> {
 
-    private static final Comparator<Point2D> POINT_COMPARATOR = new Comparator<Point2D>() {
-        @Override
-        public int compare(Point2D arg0, Point2D arg1) {
-            int rv = 0;
-            float arg0X = Utils.round(arg0.getX(), 2);
-            float arg0Y = Utils.round(arg0.getY(), 2);
-            float arg1X = Utils.round(arg1.getX(), 2);
-            float arg1Y = Utils.round(arg1.getY(), 2);
+        int rv = 0;
+        float arg0X = Utils.round(arg0.getX(), 2);
+        float arg0Y = Utils.round(arg0.getY(), 2);
+        float arg1X = Utils.round(arg1.getX(), 2);
+        float arg1Y = Utils.round(arg1.getY(), 2);
 
-
-            if (arg0Y > arg1Y) {
-                rv = 1;
-            } else if (arg0Y < arg1Y) {
-                rv = -1;
-            } else if (arg0X > arg1X) {
-                rv = 1;
-            } else if (arg0X < arg1X) {
-                rv = -1;
-            }
-            return rv;
+        if (arg0Y > arg1Y) {
+            rv = 1;
+        } else if (arg0Y < arg1Y) {
+            rv = -1;
+        } else if (arg0X > arg1X) {
+            rv = 1;
+        } else if (arg0X < arg1X) {
+            rv = -1;
         }
+        return rv;
     };
 
-
     private enum Direction {
-        HORIZONTAL,
-        VERTICAL
+        HORIZONTAL, VERTICAL
     }
 
     static class PolygonVertex {
+
         Point2D point;
         Direction direction;
 
-        public PolygonVertex(Point2D point, Direction direction) {
+
+        PolygonVertex(Point2D point, Direction direction) {
+
             this.direction = direction;
             this.point = point;
         }
 
+
         @Override
         public boolean equals(Object other) {
+
             if (this == other) {
                 return true;
             }
@@ -316,15 +304,21 @@ public class TableExtractionService {
             return this.point.equals(((PolygonVertex) other).point);
         }
 
+
         @Override
         public int hashCode() {
+
             return this.point.hashCode();
         }
 
+
         @Override
         public String toString() {
-            return String.format("%s[point=%s,direction=%s]", this.getClass().getName(), this.point.toString(), this.direction.toString());
+
+            return String.format("%s[point=%s,direction=%s]", this.getClass()
+                    .getName(), this.point.toString(), this.direction.toString());
         }
+
     }
 
 }

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

@@ -2,7 +2,11 @@ package com.iqser.red.service.redaction.v1.server.visualization.service;
 
 import java.awt.Color;
 import java.io.IOException;
+import java.util.ArrayList;
+import java.util.HashSet;
 import java.util.List;
+import java.util.Set;
+import java.util.stream.Collectors;
 
 import org.apache.commons.collections4.CollectionUtils;
 import org.apache.pdfbox.pdmodel.PDDocument;
@@ -14,9 +18,11 @@ import org.apache.pdfbox.pdmodel.graphics.color.PDColor;
 import org.apache.pdfbox.pdmodel.graphics.color.PDDeviceRGB;
 import org.apache.pdfbox.pdmodel.interactive.annotation.PDAnnotation;
 import org.apache.pdfbox.pdmodel.interactive.annotation.PDAnnotationTextMarkup;
+import org.apache.pdfbox.text.TextPosition;
 import org.springframework.stereotype.Service;
 
-import com.iqser.red.service.redaction.v1.model.Point;
+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.RedactionLogEntry;
 import com.iqser.red.service.redaction.v1.server.classification.model.Document;
@@ -26,14 +32,13 @@ 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.service.DictionaryService;
+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 lombok.extern.slf4j.Slf4j;
 
-@Slf4j
 @Service
 @RequiredArgsConstructor
 public class AnnotationHighlightService {
@@ -41,139 +46,260 @@ public class AnnotationHighlightService {
     private final DictionaryService dictionaryService;
 
 
-    public void highlight(PDDocument document, Document classifiedDoc, boolean flatRedaction) throws IOException {
+    public void highlight(PDDocument document, Document classifiedDoc, boolean flatRedaction,
+                          ManualRedactions manualRedactions) throws IOException {
+
+        Set<Integer> manualRedactionPages = getManualRedactionPages(manualRedactions);
 
         for (int page = 1; page <= document.getNumberOfPages(); page++) {
 
             PDPage pdPage = document.getPage(page - 1);
 
-            if (!flatRedaction) {
-                PDPageContentStream contentStream = new PDPageContentStream(document, pdPage, PDPageContentStream.AppendMode.APPEND, true);
+            drawSectionFrames(document, classifiedDoc, flatRedaction, pdPage, page);
 
-                for (Paragraph paragraph : classifiedDoc.getParagraphs()) {
-
-                    for (int i = 0; i <= paragraph.getPageBlocks().size() - 1; i++) {
-
-                        AbstractTextContainer textBlock = paragraph.getPageBlocks().get(i);
-
-                        if (textBlock.getPage() != page) {
-                            continue;
-                        }
-                        if (textBlock instanceof TextBlock) {
-                            textBlock.setClassification((i + 1) + "/" + paragraph.getPageBlocks().size());
-                            visualizeTextBlock((TextBlock) textBlock, contentStream);
-                        } else if (textBlock instanceof Table) {
-                            textBlock.setClassification((i + 1) + "/" + paragraph.getPageBlocks().size());
-                            visualizeTable((Table) textBlock, contentStream);
-                        }
-
-                    }
-                }
-
-                contentStream.close();
+            if (classifiedDoc.getEntities().get(page) != null) {
+                addAnnotations(pdPage, classifiedDoc, flatRedaction, manualRedactions, page);
             }
 
-            if (classifiedDoc.getEntities().get(page) == null) {
-                continue;
+            if (manualRedactionPages.contains(page)) {
+                addManualAnnotations(pdPage, classifiedDoc, manualRedactions, page);
             }
-
-            for (Entity entity : classifiedDoc.getEntities().get(page)) {
-
-                RedactionLogEntry redactionLogEntry = new RedactionLogEntry();
-
-                for (EntityPositionSequence entityPositionSequence : entity.getPositionSequences()) {
-
-                    if (flatRedaction && !isRedactionType(entity)) {
-                        continue;
-                    }
-
-                    for (TextPositionSequence textPositions : entityPositionSequence.getSequences()) {
-
-                        float height = textPositions.getTextPositions().get(0).getHeightDir() + 2;
-
-                        float posXInit;
-                        float posXEnd;
-                        float posYInit;
-                        float posYEnd;
-
-                        if (textPositions.getTextPositions().get(0).getRotation() == 90) {
-
-                            posXEnd = textPositions.getTextPositions().get(0).getYDirAdj() + 2;
-                            posXInit = textPositions.getTextPositions().get(0).getYDirAdj() - height;
-                            posYInit = textPositions.getTextPositions().get(0).getXDirAdj();
-                            posYEnd = textPositions.getTextPositions()
-                                    .get(textPositions.getTextPositions().size() - 1)
-                                    .getXDirAdj() - height + 4;
-                        } else {
-
-                            posXInit = textPositions.getTextPositions().get(0).getXDirAdj();
-                            posXEnd = textPositions.getTextPositions()
-                                    .get(textPositions.getTextPositions().size() - 1)
-                                    .getXDirAdj() + textPositions.getTextPositions()
-                                    .get(textPositions.getTextPositions().size() - 1)
-                                    .getWidth() + 1;
-                            posYInit = textPositions.getTextPositions()
-                                    .get(0)
-                                    .getPageHeight() - textPositions.getTextPositions().get(0).getYDirAdj() - 2;
-                            posYEnd = textPositions.getTextPositions()
-                                    .get(0)
-                                    .getPageHeight() - textPositions.getTextPositions()
-                                    .get(textPositions.getTextPositions().size() - 1)
-                                    .getYDirAdj() + 2;
-                        }
-
-                        Rectangle textHighlightRectangle = new Rectangle(new Point(posXInit, posYInit), posXEnd - posXInit, posYEnd - posYInit + height, page);
-
-                        List<PDAnnotation> annotations = pdPage.getAnnotations();
-                        PDAnnotationTextMarkup highlight = new PDAnnotationTextMarkup(PDAnnotationTextMarkup.SUB_TYPE_HIGHLIGHT);
-                        highlight.constructAppearances();
-
-                        PDRectangle annotationPosition = new PDRectangle();
-                        annotationPosition.setLowerLeftX(posXInit);
-                        annotationPosition.setLowerLeftY(posYEnd);
-                        annotationPosition.setUpperRightX(posXEnd);
-                        annotationPosition.setUpperRightY(posYEnd + height);
-
-                        highlight.setRectangle(annotationPosition);
-                        if (!flatRedaction && !isHint(entity)) {
-                            highlight.setAnnotationName(entityPositionSequence.getId().toString());
-                            highlight.setTitlePopup(entityPositionSequence.getId().toString());
-                            highlight.setContents("\nRule " + entity.getMatchedRule() + " matched\n\n" + entity.getRedactionReason() + "\n\n" + "In Section : \"" + entity
-                                    .getHeadline() + "\"");
-                        }
-
-                        highlight.setQuadPoints(toQuadPoints(textHighlightRectangle));
-
-                        PDColor color;
-                        if (flatRedaction) {
-                            color = new PDColor(new float[]{0, 0, 0}, PDDeviceRGB.INSTANCE);
-                        } else {
-                            color = new PDColor(getColor(entity), PDDeviceRGB.INSTANCE);
-                        }
-
-                        highlight.setColor(color);
-                        annotations.add(highlight);
-
-                        redactionLogEntry.getPositions().add(textHighlightRectangle);
-
-                    }
-                    redactionLogEntry.setId(entityPositionSequence.getId().toString());
-                }
-                redactionLogEntry.setColor(getColor(entity));
-                redactionLogEntry.setReason(entity.getRedactionReason());
-                redactionLogEntry.setValue(entity.getWord());
-                redactionLogEntry.setType(entity.getType());
-                redactionLogEntry.setRedacted(entity.isRedaction());
-                redactionLogEntry.setSection(entity.getHeadline());
-                redactionLogEntry.setHint(isHint(entity));
-                classifiedDoc.getRedactionLogEntities().add(redactionLogEntry);
-            }
-
         }
     }
 
 
-    private float[] toQuadPoints(Rectangle rectangle) {
+    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;
+    }
+
+
+    private void addAnnotations(PDPage pdPage, Document classifiedDoc, boolean flatRedaction,
+                                ManualRedactions manualRedactions, int page) throws IOException {
+
+        List<PDAnnotation> annotations = pdPage.getAnnotations();
+
+        for (Entity entity : classifiedDoc.getEntities().get(page)) {
+
+            if (flatRedaction && !isRedactionType(entity)) {
+                continue;
+            }
+
+            RedactionLogEntry redactionLogEntry = createRedactionLogEntry(entity);
+
+            for (EntityPositionSequence entityPositionSequence : entity.getPositionSequences()) {
+
+                if (manualRedactions != null && manualRedactions.getIdsToRemove()
+                        .contains(entityPositionSequence.getId())) {
+                    String manualOverrideReason = entity.getRedactionReason() + ", removed by manual override";
+                    entity.setRedaction(false);
+                    entity.setRedactionReason(manualOverrideReason);
+                    redactionLogEntry.setRedacted(false);
+                    redactionLogEntry.setReason(manualOverrideReason);
+                    redactionLogEntry.setManual(true);
+                }
+
+                if (CollectionUtils.isNotEmpty(entityPositionSequence.getSequences())) {
+                    List<Rectangle> rectanglesPerline = getRectanglesPerLine(entityPositionSequence.getSequences()
+                            .stream()
+                            .flatMap(seq -> seq.getTextPositions().stream())
+                            .collect(Collectors.toList()), page);
+
+                    redactionLogEntry.getPositions().addAll(rectanglesPerline);
+                    annotations.add(createAnnotation(rectanglesPerline, entityPositionSequence.getId(), createAnnotationContent(entity), getColor(entity), !flatRedaction && !isHint(entity)));
+                }
+
+                redactionLogEntry.setId(entityPositionSequence.getId());
+            }
+            classifiedDoc.getRedactionLogEntities().add(redactionLogEntry);
+        }
+
+    }
+
+
+    private List<Rectangle> getRectanglesPerLine(List<TextPosition> textPositions, int page) {
+
+        List<Rectangle> rectangles = new ArrayList<>();
+        if (textPositions.size() == 1) {
+            rectangles.add(new TextPositionSequence(textPositions, page).getRectangle());
+        } else {
+            float y = textPositions.get(0).getYDirAdj();
+            int startIndex = 0;
+            for (int i = 1; i < textPositions.size(); i++) {
+                float yDirAdj = textPositions.get(i).getYDirAdj();
+                if (yDirAdj != y) {
+                    rectangles.add(new TextPositionSequence(textPositions.subList(startIndex, i), page).getRectangle());
+                    y = yDirAdj;
+                    startIndex = i;
+                }
+            }
+            if (startIndex != textPositions.size() - 1) {
+                rectangles.add(new TextPositionSequence(textPositions.subList(startIndex, textPositions.size()), page).getRectangle());
+            }
+        }
+
+        return rectangles;
+    }
+
+
+    private void addManualAnnotations(PDPage pdPage, Document classifiedDoc, ManualRedactions manualRedactions,
+                                      int page) throws IOException {
+
+        if (manualRedactions == null) {
+            return;
+        }
+
+        List<PDAnnotation> annotations = pdPage.getAnnotations();
+
+        for (ManualRedactionEntry manualRedactionEntry : manualRedactions.getEntriesToAdd()) {
+
+            String id = IdBuilder.buildId(manualRedactionEntry);
+
+            RedactionLogEntry redactionLogEntry = createRedactionLogEntry(manualRedactionEntry, id);
+
+            boolean foundOnPage = false;
+            for (Rectangle rectangle : manualRedactionEntry.getPositions()) {
+
+                if (page != rectangle.getPage()) {
+                    continue;
+                }
+
+                foundOnPage = true;
+
+                PDAnnotationTextMarkup highlight = createAnnotation(List.of(rectangle), id, createAnnotationContent(manualRedactionEntry), getColor(manualRedactionEntry
+                        .getType()), true);
+                annotations.add(highlight);
+
+                redactionLogEntry.getPositions().add(rectangle);
+            }
+            if (foundOnPage) {
+                classifiedDoc.getRedactionLogEntities().add(redactionLogEntry);
+            }
+        }
+    }
+
+
+    private RedactionLogEntry createRedactionLogEntry(ManualRedactionEntry manualRedactionEntry, String id) {
+
+        return RedactionLogEntry.builder()
+                .id(id)
+                .color(getColor(manualRedactionEntry.getType()))
+                .reason(manualRedactionEntry.getReason())
+                .value(manualRedactionEntry.getValue())
+                .type(manualRedactionEntry.getType())
+                .redacted(true)
+                .isHint(false)
+                .section(manualRedactionEntry.getSection())
+                .sectionNumber(manualRedactionEntry.getSectionNumber())
+                .manual(true)
+                .build();
+    }
+
+
+    private RedactionLogEntry createRedactionLogEntry(Entity entity) {
+
+        return RedactionLogEntry.builder()
+                .color(getColor(entity))
+                .reason(entity.getRedactionReason())
+                .value(entity.getWord())
+                .type(entity.getType())
+                .redacted(entity.isRedaction())
+                .isHint(isHint(entity))
+                .section(entity.getHeadline())
+                .sectionNumber(entity.getSectionNumber())
+                .build();
+    }
+
+
+    private PDAnnotationTextMarkup createAnnotation(List<Rectangle> rectangles, String id, String content,
+                                                    float[] color, boolean popup) {
+
+        PDAnnotationTextMarkup annotation = new PDAnnotationTextMarkup(PDAnnotationTextMarkup.SUB_TYPE_HIGHLIGHT);
+        annotation.constructAppearances();
+        annotation.setRectangle(toPDRectangle(rectangles));
+        annotation.setQuadPoints(toQuadPoints(rectangles));
+        if (popup) {
+            annotation.setAnnotationName(id);
+            annotation.setTitlePopup(id);
+            annotation.setContents(content);
+        }
+        annotation.setColor(new PDColor(color, PDDeviceRGB.INSTANCE));
+        return annotation;
+    }
+
+
+    private String createAnnotationContent(Entity entity) {
+
+        return "\nRule " + entity.getMatchedRule() + " matched" + "\n\n" + entity.getRedactionReason() + "\n\nIn " + "Section : \"" + entity
+                .getHeadline() + "\"";
+    }
+
+
+    private String createAnnotationContent(ManualRedactionEntry entry) {
+
+        return "\nManual Redaction" + "\n\nIn Section : \"" + entry.getSection() + "\"";
+    }
+
+
+    private PDRectangle toPDRectangle(List<Rectangle> rectangles) {
+
+        float lowerLeftX = Float.MAX_VALUE;
+        float upperRightX = 0;
+        float lowerLeftY = 0;
+        float upperRightY = Float.MAX_VALUE;
+
+        for (Rectangle rectangle : rectangles) {
+            if (rectangle.getTopLeft().getX() < lowerLeftX) {
+                lowerLeftX = rectangle.getTopLeft().getX();
+            }
+            if (rectangle.getTopLeft().getX() + rectangle.getWidth() > upperRightX) {
+                upperRightX = rectangle.getTopLeft().getX() + rectangle.getWidth();
+            }
+            if (rectangle.getTopLeft().getY() + rectangle.getHeight() > lowerLeftY) {
+                lowerLeftY = rectangle.getTopLeft().getY() + rectangle.getHeight();
+            }
+            if (rectangle.getTopLeft().getY() < upperRightY) {
+                upperRightY = rectangle.getTopLeft().getY();
+            }
+        }
+
+        PDRectangle annotationPosition = new PDRectangle();
+        annotationPosition.setLowerLeftX(lowerLeftX);
+        annotationPosition.setLowerLeftY(lowerLeftY);
+        annotationPosition.setUpperRightX(upperRightX);
+        annotationPosition.setUpperRightY(upperRightY);
+        return annotationPosition;
+    }
+
+
+    private float[] toQuadPoints(List<Rectangle> rectangles) {
+
+        float[] quadPoints = new float[rectangles.size() * 8];
+        int i = 0;
+
+        for (Rectangle rectangle : rectangles) {
+            float[] quadPoint = toQuadPoint(rectangle);
+            for (int j = 0; j <= 7; j++) {
+                quadPoints[i + j] = quadPoint[j];
+            }
+            i += 8;
+        }
+        return quadPoints;
+    }
+
+
+    private float[] toQuadPoint(Rectangle rectangle) {
 
         // quadPoints is array of x,y coordinates in Z-like order (top-left, top-right, bottom-left,bottom-right)
         // of the area to be highlighted
@@ -189,10 +315,7 @@ public class AnnotationHighlightService {
         if (!entity.isRedaction()) {
             return false;
         }
-        if (isHint(entity)) {
-            return false;
-        }
-        return true;
+        return !isHint(entity);
     }
 
 
@@ -201,40 +324,72 @@ public class AnnotationHighlightService {
         if (!entity.isRedaction() && !isHint(entity)) {
             return new float[]{0.627f, 0.627f, 0.627f};
         }
-
         if (!dictionaryService.getEntryColors().containsKey(entity.getType())) {
             return dictionaryService.getDefaultColor();
         }
-
         return dictionaryService.getEntryColors().get(entity.getType());
     }
 
-    private boolean isHint(Entity entity) {
-        List<String> hintTypes = dictionaryService.getHintTypes();
-        if (CollectionUtils.isNotEmpty(hintTypes) && hintTypes.contains(entity.getType())) {
-            return true;
+
+    private float[] getColor(String type) {
+
+        if (!dictionaryService.getEntryColors().containsKey(type)) {
+            return dictionaryService.getDefaultColor();
         }
-        return false;
+        return dictionaryService.getEntryColors().get(type);
     }
 
+
+    private boolean isHint(Entity entity) {
+
+        List<String> hintTypes = dictionaryService.getHintTypes();
+        return CollectionUtils.isNotEmpty(hintTypes) && hintTypes.contains(entity.getType());
+    }
+
+
+    private void drawSectionFrames(PDDocument document, Document classifiedDoc, boolean flatRedaction, PDPage pdPage,
+                                   int page) throws IOException {
+
+        if (flatRedaction) {
+            return;
+        }
+
+        PDPageContentStream contentStream = new PDPageContentStream(document, pdPage, PDPageContentStream.AppendMode.APPEND, true);
+        for (Paragraph paragraph : classifiedDoc.getParagraphs()) {
+
+            for (int i = 0; i <= paragraph.getPageBlocks().size() - 1; i++) {
+
+                AbstractTextContainer textBlock = paragraph.getPageBlocks().get(i);
+
+                if (textBlock.getPage() != page) {
+                    continue;
+                }
+                if (textBlock instanceof TextBlock) {
+                    textBlock.setClassification((i + 1) + "/" + paragraph.getPageBlocks().size());
+                    visualizeTextBlock((TextBlock) textBlock, contentStream);
+                } else if (textBlock instanceof Table) {
+                    textBlock.setClassification((i + 1) + "/" + paragraph.getPageBlocks().size());
+                    visualizeTable((Table) textBlock, contentStream);
+                }
+            }
+        }
+        contentStream.close();
+    }
+
+
     private void visualizeTextBlock(TextBlock textBlock, PDPageContentStream contentStream) throws IOException {
 
         contentStream.setStrokingColor(Color.LIGHT_GRAY);
         contentStream.setLineWidth(0.5f);
-
         contentStream.addRect(textBlock.getMinX(), textBlock.getMinY(), textBlock.getWidth(), textBlock.getHeight());
         contentStream.stroke();
 
         if (textBlock.getClassification() != null) {
             contentStream.beginText();
-
             contentStream.setNonStrokingColor(Color.DARK_GRAY);
             contentStream.setFont(PDType1Font.TIMES_ROMAN, 8f);
-
             contentStream.newLineAtOffset(textBlock.getMinX(), textBlock.getMaxY());
-
             contentStream.showText(textBlock.getClassification());
-
             contentStream.endText();
         }
     }
@@ -251,26 +406,16 @@ public class AnnotationHighlightService {
                     contentStream.addRect((float) cell.getX(), (float) cell.getY(), (float) cell.getWidth(), (float) cell
                             .getHeight());
                     contentStream.stroke();
-
-//                    contentStream.setStrokingColor(Color.GREEN);
-//                    for (TextBlock textBlock : cell.getTextBlocks()) {
-//                        contentStream.addRect(textBlock.getMinX(), textBlock.getMinY(), textBlock.getWidth(), textBlock.getHeight());
-//                        contentStream.stroke();
-//                    }
                 }
             }
         }
 
         if (table.getClassification() != null) {
             contentStream.beginText();
-
             contentStream.setNonStrokingColor(Color.DARK_GRAY);
             contentStream.setFont(PDType1Font.TIMES_ROMAN, 8f);
-
             contentStream.newLineAtOffset(table.getMinX(), table.getMinY());
-
             contentStream.showText(table.getClassification());
-
             contentStream.endText();
         }
     }

redaction-service-v1/redaction-service-server-v1/src/main/resources/application.yml

@@ -8,12 +8,6 @@ spring:
   profiles:
     active: kubernetes
 
-platform.multi-tenancy:
-  enabled: ${multitenancy.enabled:false}
-  tenantFilter:
-    urlPatterns: /redact
-    urlPatternsToIgnore:
-
 management:
   endpoint:
     metrics.enabled: ${monitoring.enabled:false}

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

@@ -1,10 +1,13 @@
 package com.iqser.red.service.redaction.v1.server;
 
+import static org.assertj.core.api.Assertions.assertThat;
 import static org.mockito.Mockito.when;
 import static org.springframework.boot.test.context.SpringBootTest.WebEnvironment.DEFINED_PORT;
 
 import java.io.BufferedReader;
 import java.io.ByteArrayInputStream;
+import java.io.File;
+import java.io.FileInputStream;
 import java.io.FileOutputStream;
 import java.io.IOException;
 import java.io.InputStream;
@@ -15,11 +18,11 @@ import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
+import java.util.Set;
 import java.util.stream.Collectors;
 
 import org.apache.commons.io.IOUtils;
 import org.junit.Before;
-import org.junit.Ignore;
 import org.junit.Test;
 import org.junit.runner.RunWith;
 import org.kie.api.KieServices;
@@ -40,6 +43,10 @@ import com.iqser.red.service.configuration.v1.api.model.DictionaryResponse;
 import com.iqser.red.service.configuration.v1.api.model.RulesResponse;
 import com.iqser.red.service.configuration.v1.api.model.TypeResponse;
 import com.iqser.red.service.configuration.v1.api.model.TypeResult;
+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.RedactionRequest;
 import com.iqser.red.service.redaction.v1.model.RedactionResult;
 import com.iqser.red.service.redaction.v1.server.client.DictionaryClient;
@@ -48,7 +55,6 @@ import com.iqser.red.service.redaction.v1.server.controller.RedactionController;
 import com.iqser.red.service.redaction.v1.server.redaction.utils.ResourceLoader;
 import com.iqser.red.service.redaction.v1.server.redaction.utils.TextNormalizationUtilities;
 
-@Ignore
 @RunWith(SpringRunner.class)
 @SpringBootTest(webEnvironment = DEFINED_PORT)
 public class RedactionIntegrationTest {
@@ -57,7 +63,11 @@ public class RedactionIntegrationTest {
     private static final String VERTEBRATES_CODE = "vertebrate";
     private static final String ADDRESS_CODE = "address";
     private static final String NAME_CODE = "name";
+    private static final String SPONSOR = "sponsor";
     private static final String NO_REDACTION_INDICATOR = "no_redaction_indicator";
+    private static final String REDACTION_INDICATOR = "redaction_indicator";
+    private static final String HINT_ONLY = "hint_only";
+    private static final String MUST_REDACT = "must_redact";
 
     @Autowired
     private RedactionController redactionController;
@@ -96,7 +106,7 @@ public class RedactionIntegrationTest {
 
 
     @Before
-    public void stubRulesClient() {
+    public void stubClients() {
 
         when(rulesClient.getVersion()).thenReturn(0L);
         when(rulesClient.getRules()).thenReturn(new RulesResponse(RULES));
@@ -108,7 +118,11 @@ public class RedactionIntegrationTest {
         when(dictionaryClient.getDictionaryForType(VERTEBRATES_CODE)).thenReturn(getDictionaryResponse(VERTEBRATES_CODE));
         when(dictionaryClient.getDictionaryForType(ADDRESS_CODE)).thenReturn(getDictionaryResponse(ADDRESS_CODE));
         when(dictionaryClient.getDictionaryForType(NAME_CODE)).thenReturn(getDictionaryResponse(NAME_CODE));
+        when(dictionaryClient.getDictionaryForType(SPONSOR)).thenReturn(getDictionaryResponse(SPONSOR));
         when(dictionaryClient.getDictionaryForType(NO_REDACTION_INDICATOR)).thenReturn(getDictionaryResponse(NO_REDACTION_INDICATOR));
+        when(dictionaryClient.getDictionaryForType(REDACTION_INDICATOR)).thenReturn(getDictionaryResponse(REDACTION_INDICATOR));
+        when(dictionaryClient.getDictionaryForType(HINT_ONLY)).thenReturn(getDictionaryResponse(HINT_ONLY));
+        when(dictionaryClient.getDictionaryForType(MUST_REDACT)).thenReturn(getDictionaryResponse(MUST_REDACT));
         when(dictionaryClient.getDefaultColor()).thenReturn(new DefaultColor(new float[]{1f, 0.502f, 0f}));
     }
 
@@ -120,6 +134,11 @@ public class RedactionIntegrationTest {
                         .stream()
                         .map(this::cleanDictionaryEntry)
                         .collect(Collectors.toSet()));
+        dictionary.computeIfAbsent(SPONSOR, v -> new ArrayList<>())
+                .addAll(ResourceLoader.load("dictionaries/sponsor_companies.txt")
+                        .stream()
+                        .map(this::cleanDictionaryEntry)
+                        .collect(Collectors.toSet()));
         dictionary.computeIfAbsent(VERTEBRATES_CODE, v -> new ArrayList<>())
                 .addAll(ResourceLoader.load("dictionaries/vertebrates.txt")
                         .stream()
@@ -131,7 +150,22 @@ public class RedactionIntegrationTest {
                         .map(this::cleanDictionaryEntry)
                         .collect(Collectors.toSet()));
         dictionary.computeIfAbsent(NO_REDACTION_INDICATOR, v -> new ArrayList<>())
-                .addAll(ResourceLoader.load("dictionaries/NoRedactionIndicator.txt")
+                .addAll(ResourceLoader.load("dictionaries/no_redaction_indicator.txt")
+                        .stream()
+                        .map(this::cleanDictionaryEntry)
+                        .collect(Collectors.toSet()));
+        dictionary.computeIfAbsent(REDACTION_INDICATOR, v -> new ArrayList<>())
+                .addAll(ResourceLoader.load("dictionaries/redaction_indicator.txt")
+                        .stream()
+                        .map(this::cleanDictionaryEntry)
+                        .collect(Collectors.toSet()));
+        dictionary.computeIfAbsent(HINT_ONLY, v -> new ArrayList<>())
+                .addAll(ResourceLoader.load("dictionaries/hint_only.txt")
+                        .stream()
+                        .map(this::cleanDictionaryEntry)
+                        .collect(Collectors.toSet()));
+        dictionary.computeIfAbsent(MUST_REDACT, v -> new ArrayList<>())
+                .addAll(ResourceLoader.load("dictionaries/must_redact.txt")
                         .stream()
                         .map(this::cleanDictionaryEntry)
                         .collect(Collectors.toSet()));
@@ -149,17 +183,29 @@ public class RedactionIntegrationTest {
         typeColorMap.put(VERTEBRATES_CODE, new float[]{0, 1, 0});
         typeColorMap.put(ADDRESS_CODE, new float[]{0, 1, 1});
         typeColorMap.put(NAME_CODE, new float[]{1, 1, 0});
-        typeColorMap.put(NO_REDACTION_INDICATOR, new float[]{1, 0.502f, 0});
+        typeColorMap.put(SPONSOR, new float[]{.5f, .5f, .5f});
+        typeColorMap.put(NO_REDACTION_INDICATOR, new float[]{0.8f, 0, 0.8f});
+        typeColorMap.put(REDACTION_INDICATOR, new float[]{1, 0.502f, 0.1f});
+        typeColorMap.put(HINT_ONLY, new float[]{0.8f, 1, 0.8f});
+        typeColorMap.put(MUST_REDACT, new float[]{1, 0, 0});
 
         hintTypeMap.put(VERTEBRATES_CODE, true);
         hintTypeMap.put(ADDRESS_CODE, false);
         hintTypeMap.put(NAME_CODE, false);
+        hintTypeMap.put(SPONSOR, false);
         hintTypeMap.put(NO_REDACTION_INDICATOR, true);
+        hintTypeMap.put(REDACTION_INDICATOR, true);
+        hintTypeMap.put(HINT_ONLY, true);
+        hintTypeMap.put(MUST_REDACT, true);
 
         caseInSensitiveMap.put(VERTEBRATES_CODE, true);
         caseInSensitiveMap.put(ADDRESS_CODE, false);
         caseInSensitiveMap.put(NAME_CODE, false);
+        caseInSensitiveMap.put(SPONSOR, false);
         caseInSensitiveMap.put(NO_REDACTION_INDICATOR, true);
+        caseInSensitiveMap.put(REDACTION_INDICATOR, true);
+        caseInSensitiveMap.put(HINT_ONLY, true);
+        caseInSensitiveMap.put(MUST_REDACT, true);
     }
 
 
@@ -189,11 +235,52 @@ public class RedactionIntegrationTest {
     }
 
 
+    @Test
+    public void noExceptionShouldBeThrownForAnyFiles() throws IOException {
+
+        System.out.println("noExceptionShouldBeThrownForAnyFiles");
+        ClassLoader loader = getClass().getClassLoader();
+        URL url = loader.getResource("files");
+        File[] files = new File(url.getPath()).listFiles();
+        List<File> input = new ArrayList<>();
+        for (File file : files) {
+            input.addAll(getPathsRecursively(file));
+        }
+        for (File path : input) {
+            RedactionRequest request = RedactionRequest.builder()
+                    .document(IOUtils.toByteArray(new FileInputStream(path)))
+                    .build();
+            System.out.println("Redacting file : " + path.getName());
+            redactionController.redact(request);
+        }
+
+    }
+
+
+    private List<File> getPathsRecursively(File path) {
+
+        List<File> result = new ArrayList<>();
+        if (path == null || path.listFiles() == null) {
+            return result;
+        }
+        for (File f : path.listFiles()) {
+            if (f.isFile()) {
+                result.add(f);
+            } else {
+                result.addAll(getPathsRecursively(f));
+            }
+        }
+        return result;
+
+    }
+
+
     @Test
     public void redactionTest() throws IOException {
 
+        System.out.println("redactionTest");
         long start = System.currentTimeMillis();
-        ClassPathResource pdfFileResource = new ClassPathResource("files/Metolachlor/S-Metolachlor_RAR_01_Volume_1_2018-09-06.pdf");
+        ClassPathResource pdfFileResource = new ClassPathResource("files/Metolachlor/S-Metolachlor_RAR_02_Volume_2_2018-09-06.pdf");
 
         RedactionRequest request = RedactionRequest.builder()
                 .document(IOUtils.toByteArray(pdfFileResource.getInputStream()))
@@ -212,10 +299,70 @@ public class RedactionIntegrationTest {
     }
 
 
+    @Test
+    public void testTableRedaction() throws IOException {
+
+        System.out.println("testTableRedaction");
+        long start = System.currentTimeMillis();
+        ClassPathResource pdfFileResource = new ClassPathResource("files/Metolachlor/S-Metolachlor_RAR_02_Volume_2_2018-09-06.pdf");
+
+        RedactionRequest request = RedactionRequest.builder()
+                .document(IOUtils.toByteArray(pdfFileResource.getInputStream()))
+                .build();
+
+        RedactionResult result = redactionController.redact(request);
+
+        try (FileOutputStream fileOutputStream = new FileOutputStream("/tmp/Redacted.pdf")) {
+            fileOutputStream.write(result.getDocument());
+        }
+        long end = System.currentTimeMillis();
+
+        System.out.println("duration: " + (end - start));
+        System.out.println("numberOfPages: " + result.getNumberOfPages());
+    }
+
+
+    @Test
+    public void testManualRedaction() throws IOException {
+
+        System.out.println("testManualRedaction");
+        long start = System.currentTimeMillis();
+        ClassPathResource pdfFileResource = new ClassPathResource("files/Minimal Examples/Single Table.pdf");
+
+        ManualRedactions manualRedactions = new ManualRedactions();
+        manualRedactions.setIdsToRemove(Set.of("0836727c3508a0b2ea271da69c04cc2f"));
+
+        ManualRedactionEntry manualRedactionEntry = new ManualRedactionEntry();
+        manualRedactionEntry.setType("name");
+        manualRedactionEntry.setValue("O'Loughlin C.K.");
+        manualRedactionEntry.setReason("Manual Redaction");
+        manualRedactionEntry.setPositions(List.of(new Rectangle(new Point(375.61096f, 241.282f), 7.648041f, 43.72262f, 1), new Rectangle(new Point(384.83517f, 241.282f), 7.648041f, 17.043358f, 1)));
+
+        manualRedactions.getEntriesToAdd().add(manualRedactionEntry);
+
+        RedactionRequest request = RedactionRequest.builder()
+                .document(IOUtils.toByteArray(pdfFileResource.getInputStream()))
+                .manualRedactions(manualRedactions)
+                .build();
+
+        RedactionResult result = redactionController.redact(request);
+
+        try (FileOutputStream fileOutputStream = new FileOutputStream("/tmp/Redacted.pdf")) {
+            fileOutputStream.write(result.getDocument());
+        }
+        long end = System.currentTimeMillis();
+
+        System.out.println("duration: " + (end - start));
+        System.out.println("numberOfPages: " + result.getNumberOfPages());
+    }
+
+
     @Test
     public void classificationTest() throws IOException {
 
-        ClassPathResource pdfFileResource = new ClassPathResource("files/Fludioxonil/51 Fludioxonil_RAR_02_Volume_2_2018-02-21.pdf");
+        System.out.println("classificationTest");
+        ClassPathResource pdfFileResource = new ClassPathResource("files/Fludioxonil/51 " +
+                "Fludioxonil_RAR_02_Volume_2_2018-02-21.pdf");
 
         RedactionRequest request = RedactionRequest.builder()
                 .document(IOUtils.toByteArray(pdfFileResource.getInputStream()))
@@ -232,7 +379,9 @@ public class RedactionIntegrationTest {
     @Test
     public void sectionsTest() throws IOException {
 
-        ClassPathResource pdfFileResource = new ClassPathResource("files/Fludioxonil/51 Fludioxonil_RAR_02_Volume_2_2018-02-21.pdf");
+        System.out.println("sectionsTest");
+        ClassPathResource pdfFileResource = new ClassPathResource("files/Fludioxonil/51 " +
+                "Fludioxonil_RAR_02_Volume_2_2018-02-21.pdf");
 
         RedactionRequest request = RedactionRequest.builder()
                 .document(IOUtils.toByteArray(pdfFileResource.getInputStream()))
@@ -249,7 +398,8 @@ public class RedactionIntegrationTest {
     @Test
     public void htmlTablesTest() throws IOException {
 
-        ClassPathResource pdfFileResource = new ClassPathResource("files/Fludioxonil/51 Fludioxonil_RAR_02_Volume_2_2018-02-21.pdf");
+        System.out.println("htmlTablesTest");
+        ClassPathResource pdfFileResource = new ClassPathResource("files/Metolachlor/S-Metolachlor_RAR_02_Volume_2_2018-09-06.pdf");
 
         RedactionRequest request = RedactionRequest.builder()
                 .document(IOUtils.toByteArray(pdfFileResource.getInputStream()))
@@ -266,7 +416,9 @@ public class RedactionIntegrationTest {
     @Test
     public void htmlTableRotationTest() throws IOException {
 
-        ClassPathResource pdfFileResource = new ClassPathResource("files/Metolachlor/S-Metolachlor_RAR_02_Volume_2_2018-09-06.pdf");
+        System.out.println("htmlTableRotationTest");
+        ClassPathResource pdfFileResource = new ClassPathResource("files/Metolachlor/S" +
+                "-Metolachlor_RAR_02_Volume_2_2018-09-06.pdf");
 
         RedactionRequest request = RedactionRequest.builder()
                 .document(IOUtils.toByteArray(pdfFileResource.getInputStream()))
@@ -280,13 +432,57 @@ public class RedactionIntegrationTest {
     }
 
 
+    @Test
+    public void phantomCellsDocumentTest() throws IOException {
+
+        ClassPathResource pdfFileResource = new ClassPathResource("files/Minimal Examples/Phantom Cells.pdf");
+
+        RedactionRequest request = RedactionRequest.builder()
+                .document(IOUtils.toByteArray(pdfFileResource.getInputStream()))
+                .build();
+        request.setFlatRedaction(false);
+
+        RedactionResult result = redactionController.redact(request);
+
+        result.getRedactionLog().getRedactionLogEntry().forEach(entry -> {
+            if (!entry.isHint()) {
+                assertThat(entry.getReason()).isEqualTo("Not redacted because row is not a vertebrate study");
+            }
+        });
+    }
+
+
+    @Test
+    public void sponsorCompanyTest() throws IOException {
+
+        long start = System.currentTimeMillis();
+        ClassPathResource pdfFileResource = new ClassPathResource("files/Minimal Examples/sponsor_companies.pdf");
+
+        RedactionRequest request = RedactionRequest.builder()
+                .document(IOUtils.toByteArray(pdfFileResource.getInputStream()))
+                .build();
+        request.setFlatRedaction(false);
+
+        RedactionResult result = redactionController.redact(request);
+
+        try (FileOutputStream fileOutputStream = new FileOutputStream("/tmp/Redacted.pdf")) {
+            fileOutputStream.write(result.getDocument());
+        }
+        long end = System.currentTimeMillis();
+
+        System.out.println("duration: " + (end - start));
+        System.out.println("numberOfPages: " + result.getNumberOfPages());
+    }
+
+
     private static String loadFromClassPath(String path) {
 
         URL resource = ResourceLoader.class.getClassLoader().getResource(path);
         if (resource == null) {
             throw new IllegalArgumentException("could not load classpath resource: drools/rules.drl");
         }
-        try (BufferedReader br = new BufferedReader(new InputStreamReader(resource.openStream(), StandardCharsets.UTF_8))) {
+        try (BufferedReader br = new BufferedReader(new InputStreamReader(resource.openStream(),
+                StandardCharsets.UTF_8))) {
             StringBuilder sb = new StringBuilder();
             String str;
             while ((str = br.readLine()) != null) {

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

@@ -0,0 +1,382 @@
+package com.iqser.red.service.redaction.v1.server.redaction.service;
+
+import static org.assertj.core.api.Assertions.assertThat;
+import static org.mockito.Mockito.when;
+
+import java.io.BufferedReader;
+import java.io.ByteArrayInputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.net.URL;
+import java.nio.charset.StandardCharsets;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.HashSet;
+import java.util.Set;
+import java.util.concurrent.atomic.AtomicLong;
+
+import org.apache.commons.io.IOUtils;
+import org.apache.pdfbox.pdmodel.PDDocument;
+import org.junit.Before;
+import org.junit.Test;
+import org.junit.runner.RunWith;
+import org.kie.api.KieServices;
+import org.kie.api.builder.KieBuilder;
+import org.kie.api.builder.KieFileSystem;
+import org.kie.api.builder.KieModule;
+import org.kie.api.runtime.KieContainer;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.boot.test.context.SpringBootTest;
+import org.springframework.boot.test.context.TestConfiguration;
+import org.springframework.boot.test.mock.mockito.MockBean;
+import org.springframework.context.annotation.Bean;
+import org.springframework.core.io.ClassPathResource;
+import org.springframework.test.context.junit4.SpringRunner;
+
+import com.iqser.red.service.configuration.v1.api.model.DefaultColor;
+import com.iqser.red.service.configuration.v1.api.model.DictionaryResponse;
+import com.iqser.red.service.configuration.v1.api.model.RulesResponse;
+import com.iqser.red.service.configuration.v1.api.model.TypeResponse;
+import com.iqser.red.service.configuration.v1.api.model.TypeResult;
+import com.iqser.red.service.redaction.v1.model.RedactionRequest;
+import com.iqser.red.service.redaction.v1.server.classification.model.Document;
+import com.iqser.red.service.redaction.v1.server.client.DictionaryClient;
+import com.iqser.red.service.redaction.v1.server.client.RulesClient;
+import com.iqser.red.service.redaction.v1.server.redaction.model.Entity;
+import com.iqser.red.service.redaction.v1.server.redaction.utils.ResourceLoader;
+import com.iqser.red.service.redaction.v1.server.segmentation.PdfSegmentationService;
+
+@SpringBootTest
+@RunWith(SpringRunner.class)
+public class EntityRedactionServiceTest {
+
+    private static final String DEFAULT_RULES = loadFromClassPath("drools/rules.drl");
+    private static final String NAME_CODE = "name";
+    private static final String ADDRESS_CODE = "address";
+
+    private static final AtomicLong DICTIONARY_VERSION = new AtomicLong();
+    private static final AtomicLong RULES_VERSION = new AtomicLong();
+    @MockBean
+    private DictionaryClient dictionaryClient;
+
+    @MockBean
+    private RulesClient rulesClient;
+
+    @Autowired
+    private EntityRedactionService entityRedactionService;
+
+    @Autowired
+    private PdfSegmentationService pdfSegmentationService;
+
+    @Autowired
+    private DroolsExecutionService droolsExecutionService;
+
+    @TestConfiguration
+    public static class RedactionIntegrationTestConfiguration {
+
+        @Bean
+        public KieContainer kieContainer() {
+
+            KieServices kieServices = KieServices.Factory.get();
+
+            KieFileSystem kieFileSystem = kieServices.newKieFileSystem();
+            InputStream input = new ByteArrayInputStream(DEFAULT_RULES.getBytes(StandardCharsets.UTF_8));
+            kieFileSystem.write("src/test/resources/drools/rules.drl", kieServices.getResources()
+                    .newInputStreamResource(input));
+            KieBuilder kieBuilder = kieServices.newKieBuilder(kieFileSystem);
+            kieBuilder.buildAll();
+            KieModule kieModule = kieBuilder.getKieModule();
+
+            return kieServices.newKieContainer(kieModule.getReleaseId());
+        }
+
+    }
+
+
+    @Test
+    public void testNestedEntitiesRemoval() {
+
+        Set<Entity> entities = new HashSet<>();
+        Entity nested = new Entity("nested", "fake type", 10, 16, "fake headline", 0);
+        Entity nesting = new Entity("nesting nested", "fake type", 2, 16, "fake headline", 0);
+        entities.add(nested);
+        entities.add(nesting);
+        entityRedactionService.removeEntitiesContainedInLarger(entities);
+
+        assertThat(entities.size()).isEqualTo(1);
+        assertThat(entities).contains(nesting);
+
+    }
+
+
+    @Test
+    public void testTableRedaction() throws IOException {
+
+        ClassPathResource pdfFileResource = new ClassPathResource("files/Minimal Examples/Single Table.pdf");
+
+        RedactionRequest redactionRequest = RedactionRequest.builder()
+                .document(IOUtils.toByteArray(pdfFileResource.getInputStream()))
+                .build();
+
+        DictionaryResponse dictionaryResponse = DictionaryResponse.builder()
+                .entries(Arrays.asList("Casey, H.W.", "O’Loughlin,  C.K.", "Salamon, C.M.", "Smith, S.H."))
+                .build();
+        when(dictionaryClient.getVersion()).thenReturn(DICTIONARY_VERSION.incrementAndGet());
+        when(dictionaryClient.getDictionaryForType(NAME_CODE)).thenReturn(dictionaryResponse);
+        DictionaryResponse addressResponse = DictionaryResponse.builder()
+                .entries(Collections.singletonList("Toxigenics, Inc., Decatur, IL 62526, USA"))
+                .build();
+        when(dictionaryClient.getDictionaryForType(ADDRESS_CODE)).thenReturn(addressResponse);
+
+        try (PDDocument pdDocument = PDDocument.load(new ByteArrayInputStream(redactionRequest.getDocument()))) {
+            Document classifiedDoc = pdfSegmentationService.parseDocument(pdDocument);
+            entityRedactionService.processDocument(classifiedDoc, null);
+            assertThat(classifiedDoc.getEntities()).hasSize(1); // one page
+            assertThat(classifiedDoc.getEntities().get(1)).hasSize(7);// 3 names, 1 address, 1 Y and 2 N entities
+        }
+    }
+
+
+    @Test
+    public void testTrueNegativesInTable() throws IOException {
+
+        ClassPathResource pdfFileResource = new ClassPathResource("files/Cyprodinil/40 Cyprodinil - EU AIR3 - LCA Section 1" +
+                " Supplement - Identity of the active substance - Reference list.pdf");
+        when(dictionaryClient.getVersion()).thenReturn(DICTIONARY_VERSION.incrementAndGet());
+        DictionaryResponse dictionaryResponse = DictionaryResponse.builder()
+                .entries(new ArrayList<>(ResourceLoader.load("dictionaries/names.txt")))
+                .build();
+        when(dictionaryClient.getDictionaryForType(NAME_CODE)).thenReturn(dictionaryResponse);
+        DictionaryResponse addressResponse = DictionaryResponse.builder()
+                .entries(new ArrayList<>(ResourceLoader.load("dictionaries/addresses.txt")))
+                .build();
+        when(dictionaryClient.getDictionaryForType(ADDRESS_CODE)).thenReturn(addressResponse);
+        try (PDDocument pdDocument = PDDocument.load(pdfFileResource.getInputStream())) {
+            Document classifiedDoc = pdfSegmentationService.parseDocument(pdDocument);
+            entityRedactionService.processDocument(classifiedDoc, null);
+            assertThat(classifiedDoc.getEntities()
+                    .entrySet()
+                    .stream()
+                    .noneMatch(entry -> entry.getValue().stream().anyMatch(e -> e.getMatchedRule() == 9))).isTrue();
+        }
+        pdfFileResource = new ClassPathResource("files/Compounds/27 A8637C - EU AIR3 - MCP Section 1 - Identity of " +
+                "the plant protection product.pdf");
+        try (PDDocument pdDocument = PDDocument.load(pdfFileResource.getInputStream())) {
+            Document classifiedDoc = pdfSegmentationService.parseDocument(pdDocument);
+            entityRedactionService.processDocument(classifiedDoc, null);
+            assertThat(classifiedDoc.getEntities()
+                    .entrySet()
+                    .stream()
+                    .noneMatch(entry -> entry.getValue().stream().anyMatch(e -> e.getMatchedRule() == 9))).isTrue();
+        }
+    }
+
+    @Test
+    public void testFalsePositiveInWrongCell() throws IOException {
+
+        ClassPathResource pdfFileResource = new ClassPathResource("files/Minimal Examples/Row With Ambiguous Redaction.pdf");
+        when(dictionaryClient.getVersion()).thenReturn(DICTIONARY_VERSION.incrementAndGet());
+        DictionaryResponse dictionaryResponse = DictionaryResponse.builder()
+                .entries(new ArrayList<>(ResourceLoader.load("dictionaries/names.txt")))
+                .build();
+        when(dictionaryClient.getDictionaryForType(NAME_CODE)).thenReturn(dictionaryResponse);
+        DictionaryResponse addressResponse = DictionaryResponse.builder()
+                .entries(new ArrayList<>(ResourceLoader.load("dictionaries/addresses.txt")))
+                .build();
+        when(dictionaryClient.getDictionaryForType(ADDRESS_CODE)).thenReturn(addressResponse);
+        try (PDDocument pdDocument = PDDocument.load(pdfFileResource.getInputStream())) {
+            Document classifiedDoc = pdfSegmentationService.parseDocument(pdDocument);
+            entityRedactionService.processDocument(classifiedDoc, null);
+            assertThat(classifiedDoc.getEntities()).hasSize(1); // one page
+            assertThat(classifiedDoc.getEntities().get(1).stream()
+                    .filter(entity -> entity.getMatchedRule() == 9)
+                    .count()).isEqualTo(10);
+        }
+
+    }
+
+
+    @Test
+    public void testApplicantInTableRedaction() throws IOException {
+
+        String tableRules = "package drools\n" +
+                "\n" +
+                "import com.iqser.red.service.redaction.v1.server.redaction.model.Section\n" +
+                "\n" +
+                "global Section section\n" +
+                "rule \"6: Redact contact information if applicant is found\"\n" +
+                "   when\n" +
+                "       eval(section.headlineContainsWord(\"applicant\") || section.getText().contains(\"Applicant\"));\n" +
+                "   then\n" +
+                "       section.redactLineAfter(\"Name:\", \"address\", 6, \"Applicant information was found\");\n" +
+                "       section.redactBetween(\"Address:\", \"Contact\", \"address\", 6, \"Applicant information was found\");\n" +
+                "       section.redactLineAfter(\"Contact point:\",  \"address\", 6, \"Applicant information was found\");\n" +
+                "       section.redactLineAfter(\"Phone:\", \"address\", 6, \"Applicant information was found\");\n" +
+                "       section.redactLineAfter(\"Fax:\", \"address\", 6, \"Applicant information was found\");\n" +
+                "       section.redactLineAfter(\"Tel.:\", \"address\", 6, \"Applicant information was found\");\n" +
+                "       section.redactLineAfter(\"Tel:\", \"address\", 6, \"Applicant information was found\");\n" +
+                "       section.redactLineAfter(\"E-mail:\", \"address\", 6, \"Applicant information was found\");\n" +
+                "       section.redactLineAfter(\"Email:\", \"address\", 6, \"Applicant information was found\");\n" +
+                "       section.redactLineAfter(\"Contact:\", \"address\", 6, \"Applicant information was found\");\n" +
+                "       section.redactLineAfter(\"Telephone number:\", \"address\", 6, \"Applicant information was found\");\n" +
+                "       section.redactLineAfter(\"Fax number:\", \"address\", 6, \"Applicant information was found\");\n" +
+                "       section.redactLineAfter(\"Telephone:\", \"address\", 6, \"Applicant information was found\");\n" +
+                "       section.redactBetween(\"No:\", \"Fax\", \"address\", 6, \"Applicant information was found\");\n" +
+                "       section.redactBetween(\"Contact:\", \"Tel.:\", \"address\", 6, \"Applicant information was found\");\n" +
+                "   end";
+        when(rulesClient.getVersion()).thenReturn(RULES_VERSION.incrementAndGet());
+        when(rulesClient.getRules()).thenReturn(new RulesResponse(tableRules));
+        droolsExecutionService.updateRules();
+
+        ClassPathResource pdfFileResource = new ClassPathResource("files/Minimal Examples/Applicant Producer Table.pdf");
+        when(dictionaryClient.getVersion()).thenReturn(DICTIONARY_VERSION.incrementAndGet());
+        DictionaryResponse dictionaryResponse = DictionaryResponse.builder()
+                .entries(new ArrayList<>(ResourceLoader.load("dictionaries/names.txt")))
+                .build();
+        when(dictionaryClient.getDictionaryForType(NAME_CODE)).thenReturn(dictionaryResponse);
+        DictionaryResponse addressResponse = DictionaryResponse.builder()
+                .entries(new ArrayList<>(ResourceLoader.load("dictionaries/addresses.txt")))
+                .build();
+        when(dictionaryClient.getDictionaryForType(ADDRESS_CODE)).thenReturn(addressResponse);
+        try (PDDocument pdDocument = PDDocument.load(pdfFileResource.getInputStream())) {
+            Document classifiedDoc = pdfSegmentationService.parseDocument(pdDocument);
+            entityRedactionService.processDocument(classifiedDoc, null);
+            assertThat(classifiedDoc.getEntities()).hasSize(1); // one page
+            assertThat(classifiedDoc.getEntities().get(1).stream()
+                    .filter(entity -> entity.getMatchedRule() == 6)
+                    .count()).isEqualTo(18);
+        }
+
+    }
+
+
+    @Test
+    public void headerPropagation() throws IOException {
+
+        ClassPathResource pdfFileResource = new ClassPathResource("files/Minimal Examples/Header Propagation.pdf");
+
+        DictionaryResponse dictionaryResponse = DictionaryResponse.builder()
+                .entries(Arrays.asList("Bissig R.", "Thanei P."))
+                .build();
+
+        when(dictionaryClient.getVersion()).thenReturn(DICTIONARY_VERSION.incrementAndGet());
+        when(dictionaryClient.getDictionaryForType(NAME_CODE)).thenReturn(dictionaryResponse);
+        DictionaryResponse addressResponse = DictionaryResponse.builder()
+                .entries(Collections.singletonList("Novartis Crop Protection AG, Basel, Switzerland"))
+                .build();
+        when(dictionaryClient.getDictionaryForType(ADDRESS_CODE)).thenReturn(addressResponse);
+
+        try (PDDocument pdDocument = PDDocument.load(pdfFileResource.getInputStream())) {
+            Document classifiedDoc = pdfSegmentationService.parseDocument(pdDocument);
+            entityRedactionService.processDocument(classifiedDoc, null);
+            assertThat(classifiedDoc.getEntities()).hasSize(2); // two pages
+            assertThat(classifiedDoc.getEntities().get(1).stream().filter(entity -> entity.getMatchedRule() == 9).count()).isEqualTo(8);
+            assertThat(classifiedDoc.getEntities().get(2).stream().filter(entity -> entity.getMatchedRule() == 9).count()).isEqualTo(4);
+        }
+
+        pdfFileResource = new ClassPathResource("files/Minimal Examples/Header Propagation2.pdf");
+
+        dictionaryResponse = DictionaryResponse.builder()
+                .entries(Arrays.asList("Tribolet, R.", "Muir, G.", "Kühne-Thu, H.", "Close, C."))
+                .build();
+
+        when(dictionaryClient.getVersion()).thenReturn(DICTIONARY_VERSION.incrementAndGet());
+        when(dictionaryClient.getDictionaryForType(NAME_CODE)).thenReturn(dictionaryResponse);
+        addressResponse = DictionaryResponse.builder()
+                .entries(Collections.singletonList("Novartis Crop Protection AG, Basel, Switzerland"))
+                .build();
+        when(dictionaryClient.getDictionaryForType(ADDRESS_CODE)).thenReturn(addressResponse);
+
+        try (PDDocument pdDocument = PDDocument.load(pdfFileResource.getInputStream())) {
+            Document classifiedDoc = pdfSegmentationService.parseDocument(pdDocument);
+            entityRedactionService.processDocument(classifiedDoc, null);
+            assertThat(classifiedDoc.getEntities()).hasSize(1); // one page
+            assertThat(classifiedDoc.getEntities().get(1).stream().filter(entity -> entity.getMatchedRule() == 9).count()).isEqualTo(3);
+            assertThat(classifiedDoc.getEntities().get(1).stream().filter(entity -> entity.getMatchedRule() == 8).count()).isEqualTo(8);
+        }
+    }
+
+
+    @Test
+    public void testNGuideline() throws IOException {
+
+        ClassPathResource pdfFileResource = new ClassPathResource("files/Minimal Examples/Empty Tabular Data.pdf");
+
+        DictionaryResponse dictionaryResponse = DictionaryResponse.builder()
+                .entries(Collections.singletonList("Aldershof S."))
+                .build();
+
+        when(dictionaryClient.getVersion()).thenReturn(DICTIONARY_VERSION.incrementAndGet());
+        when(dictionaryClient.getDictionaryForType(NAME_CODE)).thenReturn(dictionaryResponse);
+        DictionaryResponse addressResponse = DictionaryResponse.builder()
+                .entries(Collections.singletonList("Novartis Crop Protection AG, Basel, Switzerland"))
+                .build();
+        when(dictionaryClient.getDictionaryForType(ADDRESS_CODE)).thenReturn(addressResponse);
+
+        try (PDDocument pdDocument = PDDocument.load(pdfFileResource.getInputStream())) {
+            Document classifiedDoc = pdfSegmentationService.parseDocument(pdDocument);
+            entityRedactionService.processDocument(classifiedDoc, null);
+            assertThat(classifiedDoc.getEntities()).hasSize(1); // one page
+            assertThat(classifiedDoc.getEntities().get(1).stream().filter(entity -> entity.getMatchedRule() == 8).count()).isEqualTo(6);
+        }
+    }
+
+
+    @Before
+    public void stubRedaction() {
+        String tableRules = "package drools\n" +
+                "\n" +
+                "import com.iqser.red.service.redaction.v1.server.redaction.model.Section\n" +
+                "\n" +
+                "global Section section\n" +
+                "rule \"8: Not redacted because Vertebrate Study = N\"\n" +
+                "    when\n" +
+                "        Section(rowEquals(\"Vertebrate study Y/N\", \"N\") || rowEquals(\"Vertebrate study Y/N\", \"No\"))\n" +
+                "    then\n" +
+                "        section.redactNot(\"name\", 8, \"Not redacted because row is not a vertebrate study\");\n" +
+                "        section.redactNot(\"address\", 8, \"Not redacted because row is not a vertebrate study\");\n" +
+                "        section.highlightCell(\"Vertebrate study Y/N\", 8, \"hint_only\");\n" +
+                "    end\n" +
+                "rule \"9: Redact Authors and Addresses in Reference Table, if it is a Vertebrate study\"\n" +
+                "    when\n" +
+                "        Section(rowEquals(\"Vertebrate study Y/N\", \"Y\") || rowEquals(\"Vertebrate study Y/N\", " +
+                "\"Yes\"))\n" +
+                "    then\n" +
+                "        section.redact(\"name\", 9, \"Redacted because row is a vertebrate study\");\n" +
+                "        section.redact(\"address\", 9, \"Redacted because row is a vertebrate study\");\n" +
+                "        section.highlightCell(\"Vertebrate study Y/N\", 9, \"must_redact\");\n" +
+                "    end";
+        when(rulesClient.getVersion()).thenReturn(RULES_VERSION.incrementAndGet());
+        when(rulesClient.getRules()).thenReturn(new RulesResponse(tableRules));
+        TypeResponse typeResponse = TypeResponse.builder()
+                .types(Arrays.asList(
+                        TypeResult.builder().type(NAME_CODE).color(new float[]{1, 1, 0}).build(),
+                        TypeResult.builder().type(ADDRESS_CODE).color(new float[]{0, 1, 1}).build()))
+                .build();
+        when(dictionaryClient.getVersion()).thenReturn(DICTIONARY_VERSION.incrementAndGet());
+        when(dictionaryClient.getAllTypes()).thenReturn(typeResponse);
+        when(dictionaryClient.getDefaultColor()).thenReturn(new DefaultColor());
+    }
+
+
+    private static String loadFromClassPath(String path) {
+
+        URL resource = ResourceLoader.class.getClassLoader().getResource(path);
+        if (resource == null) {
+            throw new IllegalArgumentException("could not load classpath resource: drools/rules.drl");
+        }
+        try (BufferedReader br = new BufferedReader(new InputStreamReader(resource.openStream(), StandardCharsets.UTF_8))) {
+            StringBuilder sb = new StringBuilder();
+            String str;
+            while ((str = br.readLine()) != null) {
+                sb.append(str).append("\n");
+            }
+            return sb.toString();
+        } catch (IOException e) {
+            throw new IllegalArgumentException("could not load classpath resource: " + path, e);
+        }
+    }
+
+}

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

@@ -0,0 +1,189 @@
+package com.iqser.red.service.redaction.v1.server.segmentation;
+
+import static org.assertj.core.api.Assertions.assertThat;
+
+import java.io.IOException;
+import java.util.Collections;
+import java.util.List;
+import java.util.stream.Collectors;
+
+import org.apache.pdfbox.pdmodel.PDDocument;
+import org.junit.Test;
+import org.junit.runner.RunWith;
+import org.kie.api.runtime.KieContainer;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.boot.test.context.SpringBootTest;
+import org.springframework.boot.test.mock.mockito.MockBean;
+import org.springframework.core.io.ClassPathResource;
+import org.springframework.test.context.junit4.SpringRunner;
+
+import com.iqser.red.service.redaction.v1.server.classification.model.Document;
+import com.iqser.red.service.redaction.v1.server.classification.service.BlockificationService;
+import com.iqser.red.service.redaction.v1.server.tableextraction.model.Cell;
+import com.iqser.red.service.redaction.v1.server.tableextraction.model.Table;
+import com.iqser.red.service.redaction.v1.server.tableextraction.service.RulingCleaningService;
+import com.iqser.red.service.redaction.v1.server.tableextraction.service.TableExtractionService;
+
+@SpringBootTest
+@RunWith(SpringRunner.class)
+public class PdfSegmentationServiceTest {
+
+    @Autowired
+    private PdfSegmentationService pdfSegmentationService;
+
+    @Autowired
+    private RulingCleaningService rulingCleaningService;
+
+    @Autowired
+    private TableExtractionService tableExtractionService;
+
+    @Autowired
+    private BlockificationService blockificationService;
+
+    @MockBean
+    private KieContainer kieContainer;
+
+
+    @Test
+    public void testPDFSegmentationWithComplexTable() throws IOException {
+
+        ClassPathResource pdfFileResource = new ClassPathResource("files/Minimal Examples/Spanning Cells.pdf");
+
+        try (PDDocument pdDocument = PDDocument.load(pdfFileResource.getInputStream())) {
+            Document document = pdfSegmentationService.parseDocument(pdDocument);
+            assertThat(document.getParagraphs()
+                    .stream()
+                    .flatMap(paragraph -> paragraph.getTables().stream())
+                    .collect(Collectors.toList())).isNotEmpty();
+            Table table = document.getParagraphs()
+                    .stream()
+                    .flatMap(paragraph -> paragraph.getTables().stream())
+                    .collect(Collectors.toList())
+                    .get(0);
+            assertThat(table.getColCount()).isEqualTo(6);
+            assertThat(table.getRowCount()).isEqualTo(13);
+            assertThat(table.getRows().stream().mapToInt(List::size).sum()).isEqualTo(6 * 13);
+        }
+    }
+
+
+    @Test
+    public void testTableExtraction() throws IOException {
+
+        ClassPathResource pdfFileResource = new ClassPathResource("files/Minimal Examples/Merge Table.pdf");
+
+        try (PDDocument pdDocument = PDDocument.load(pdfFileResource.getInputStream())) {
+            Document document = pdfSegmentationService.parseDocument(pdDocument);
+            assertThat(document.getParagraphs()
+                    .stream()
+                    .flatMap(paragraph -> paragraph.getTables().stream())
+                    .collect(Collectors.toList())).isNotEmpty();
+            Table firstTable = document.getParagraphs()
+                    .stream()
+                    .flatMap(paragraph -> paragraph.getTables().stream())
+                    .collect(Collectors.toList())
+                    .get(0);
+            assertThat(firstTable.getColCount()).isEqualTo(8);
+            assertThat(firstTable.getRowCount()).isEqualTo(1);
+            Table secondTable = document.getParagraphs()
+                    .stream()
+                    .flatMap(paragraph -> paragraph.getTables().stream())
+                    .collect(Collectors.toList())
+                    .get(1);
+            assertThat(secondTable.getColCount()).isEqualTo(8);
+            assertThat(secondTable.getRowCount()).isEqualTo(2);
+            List<List<Cell>> firstTableHeaderCells = firstTable.getRows()
+                    .get(0)
+                    .stream()
+                    .map(Collections::singletonList)
+                    .collect(Collectors.toList());
+            assertThat(secondTable.getRows().stream()
+                    .allMatch(row -> row.stream()
+                            .map(Cell::getHeaderCells)
+                            .collect(Collectors.toList())
+                            .equals(firstTableHeaderCells)))
+                    .isTrue();
+        }
+    }
+
+
+    @Test
+    public void testMultiPageMetadataPropagation() throws IOException {
+
+        ClassPathResource pdfFileResource = new ClassPathResource("files/Minimal Examples/Merge Multi Page Table.pdf");
+
+        try (PDDocument pdDocument = PDDocument.load(pdfFileResource.getInputStream())) {
+            Document document = pdfSegmentationService.parseDocument(pdDocument);
+            assertThat(document.getParagraphs()
+                    .stream()
+                    .flatMap(paragraph -> paragraph.getTables().stream())
+                    .collect(Collectors.toList())).isNotEmpty();
+            Table firstTable = document.getParagraphs()
+                    .stream()
+                    .flatMap(paragraph -> paragraph.getTables().stream())
+                    .collect(Collectors.toList())
+                    .get(0);
+            assertThat(firstTable.getColCount()).isEqualTo(9);
+            assertThat(firstTable.getRowCount()).isEqualTo(5);
+            Table secondTable = document.getParagraphs()
+                    .stream()
+                    .flatMap(paragraph -> paragraph.getTables().stream())
+                    .collect(Collectors.toList())
+                    .get(1);
+            assertThat(secondTable.getColCount()).isEqualTo(9);
+            assertThat(secondTable.getRowCount()).isEqualTo(6);
+            List<List<Cell>> firstTableHeaderCells = firstTable.getRows()
+                    .get(firstTable.getRowCount() - 1)
+                    .stream()
+                    .map(Cell::getHeaderCells)
+                    .collect(Collectors.toList());
+            assertThat(secondTable.getRows().stream()
+                    .allMatch(row -> row.stream()
+                            .map(Cell::getHeaderCells)
+                            .collect(Collectors.toList())
+                            .equals(firstTableHeaderCells)))
+                    .isTrue();
+        }
+    }
+
+
+    @Test
+    public void testHeaderCellsForRotatedTable() throws IOException {
+
+        ClassPathResource pdfFileResource = new ClassPathResource("files/Minimal Examples/Rotated Table Headers.pdf");
+
+        try (PDDocument pdDocument = PDDocument.load(pdfFileResource.getInputStream())) {
+            Document document = pdfSegmentationService.parseDocument(pdDocument);
+            assertThat(document.getParagraphs()
+                    .stream()
+                    .flatMap(paragraph -> paragraph.getTables().stream())
+                    .collect(Collectors.toList())).isNotEmpty();
+            Table firstTable = document.getParagraphs()
+                    .stream()
+                    .flatMap(paragraph -> paragraph.getTables().stream())
+                    .collect(Collectors.toList())
+                    .get(0);
+            assertThat(firstTable.getColCount()).isEqualTo(8);
+            assertThat(firstTable.getRowCount()).isEqualTo(1);
+            Table secondTable = document.getParagraphs()
+                    .stream()
+                    .flatMap(paragraph -> paragraph.getTables().stream())
+                    .collect(Collectors.toList())
+                    .get(1);
+            assertThat(secondTable.getColCount()).isEqualTo(8);
+            assertThat(secondTable.getRowCount()).isEqualTo(6);
+            List<List<Cell>> firstTableHeaderCells = firstTable.getRows()
+                    .get(0)
+                    .stream()
+                    .map(Collections::singletonList)
+                    .collect(Collectors.toList());
+            assertThat(secondTable.getRows().stream()
+                    .allMatch(row -> row.stream()
+                            .map(Cell::getHeaderCells)
+                            .collect(Collectors.toList())
+                            .equals(firstTableHeaderCells)))
+                    .isTrue();
+        }
+    }
+
+}

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

@@ -1 +0,0 @@
-In Vitro

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

@@ -0,0 +1,2 @@
+guideline
+unpublished

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

@@ -0,0 +1,2 @@
+CTL
+determination of residues

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

@@ -0,0 +1,3 @@
+published paper
+in vitro
+in-vitro

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

@@ -0,0 +1,9 @@
+in vivo
+in-vivo
+dermal penetration
+oral toxicity
+oral-toxicity
+acute toxicity
+acute-toxicity
+eco toxicity
+eco-toxicity

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

@@ -0,0 +1,7 @@
+Monthey Syngenta Crop Protection AG, Basel, Switzerland
+Syngenta Crop Protection, Monthey, Switzerland
+Fine Organics Limited, Middlesbrough, United Kingdom
+Syngenta Monthey Switzerland
+Hunan Haili Chemical Industry Co., Ltd., Hunan, China
+Syngenta, Switzerland
+Syngenta Nantong, China

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

@@ -1,48 +1,63 @@
-Vulpes vulpes
+a. sylvaticus
 african clawed frog
 agalychnis callidryas
+albino rat
+american bullfrog tadpole
+american toad
 amphibian
 amphibians
-American bullfrog tadpole
-american toad
 anad platyrhynchos
-Anas platyrhynchos
+anas platyrhynchos
 anuran
 anurans
+apodemus
+apodemus flavicollis
 apodemus syl vaticus
+apodemus sylvaticus
+arvicola terrestris
 avian
+bank vole
 bird
 birds
 bluegill
 bluegill sunfish
 bobwhite
 bobwhite quail
-bullfrog
-Bufo americanus
 brachydanio rerio
+brown hare
+bufo americanus
+bullfrog
 canary
 carassius carassius
 carp
+catesbeiana
 catfish
 cattle
 cattles
 channel catfish
-Chinook
 chicken
-Colinus virginianus
+chinese hamster
+chinese hamsters
+chinook
+coho salmon
 colinus virginianus
-Common carp
+columba palumbus
+columbidae
+common carp
+common vole
 coturnix japonica
-Coturnix japonica
 cow
 cows
-Crucian carp
+crocidura russula
+crucian carp
 cyprinodon variegatus
 cyprinus carpio
 dog
 dogs
 duck
 ducks
+european brown hare
+european rabbit
 fathead minnow
 fish
 fishes
@@ -56,174 +71,121 @@ galaxias truttaceus
 gasterosteus aculeatus
 goat
 goats
+greater white-toothed shrew
 guinea
 guinea pig
 guinea pigs
-Guppy
+guinea-pigs
+guppy
 hamster
 hamsters
 hen
 hens
-Hyla versicolor
+house mouse
+hyla versicolor
 ictalurus melas
 ictalurus punctatus
 japanese quail
 japonica
+kisutch
+lagomorph
 lebistes reticulatus
 leiostomus xanthurus
 leisostomus xanthurus
 lepomis macrochirus
+lepus europaeus
+limnocharis
+limnodynastes
+limnodynastes tasmaniensis
 livestock
 livestocks
+mallard
 mallard duck
 mammal
+mammalian
 mammals
-Mammalian
+marten
+martes
 mice
+microtus
+microtus agrestis
+microtus arvalis
+microtus subterraneus
 midwestern anurans
+minnow
+minnows
 monkey
 mouse
+mus musculus
+myodes glareolus
 northern bobwhite
+o. cuniculus
 o. mykiss
-Oncorhynchus mykiss
-Oncorhynchus
-O. mykiss
+o. tshawytscha
+oncorhynchus
+oncorhynchus mykiss
+oncorhynchus tshawytscha
+oryctolagus cuniculus
 oryzias melastigma
 oryzias melastigma larvae
 p. promelas
 pagrus major
+palumbus
 pig
 pigeon
 pigeons
+pigs
+pimephales promela
 pimephales promelas
-Pseudacris triseriata
 poecilia reticulata
 poultry
+pseudacris
+pseudacris triseriata
 quail
+r. catesbeiana
+rabbit
+rabbits
 rainbow trout
-Rana limnocharis
 rana
-limnocharis
+rana catesbeiana
+rana limnocharis
 rana pipiens
+rat
+rats
 reptile
 reptiles
 ricefish
 ruminant
 ruminants
+salmo gairdneri
+salmon
+serinus canaria
 sheepshead minnow
 sheepshead minnows
-spea multiplicata
-Salmo gairdneri
-salmon
-spotted march frog
-tadpoles
-treefrog
-toad
-terrestrial vertrebrates
-Limnodynastes tasmaniensis
-trout
-Vulpes vulpes
-wistar
-xenopus laevis
-xenpous leavis
-zebra fish
-zebrafish
-Salmo gairdneri
-minnow
-minnows
-Pimephales promela
-Cyprinodon variegatus
-limnodynastes
-Rana catesbeiana
-R. catesbeiana
-coho salmon
-Oncorhynchus tshawytscha
-O. tshawytscha
-tshawytscha
-catesbeiana
-kisutch
-Pseudacris triseriata
-Pseudacris
-triseriata
-Wood pigeon
-Columba palumbus
-palumbus
-Columbidae
 shrew
 shrews
-bank vole
-common vole
+sorex araneus
+spea multiplicata
+spotted march frog
+tadpoles
+terrestrial vertrebrates
+toad
+treefrog
+triseriata
+trout
+tshawytscha
 vole
 voles
-lagomorph
-Wood mouse
-Apodemus sylvaticus
-A. sylvaticus
-Apodemus flavicollis
-Apodemus
-mus musculus
-Microtus arvalis
-Microtus agrestis
-Microtus
-Arvicola terrestris
-Sorex araneus
-Myodes glareolus
-yellow-necked mouse
-house mouse
-Oryctolagus cuniculus
-marten
-martes
+vulpes vulpes
+white rabbits
 white-toothed shrew
-greater white-toothed shrew
-Lepus europaeus
-brown hare
-European brown hare
-European rabbit
-O. cuniculus
-Crocidura russula
-Chinese Hamster
-Rat
-Rats
-Dog
-Chinese hamsters
-Chinese hamster
-Mouse
-Guinea pig
-Wistar rats
-Rabbit
-mammalian
-Japanese quail
-Microtus subterraneus
-Lepomis macrochirus
-P. promelas
-Cyprinus carpio
-Fish
-Ictalurus punctatus
-Carassius carassius
-Lepomis macrochirus
-Poecilia reticulata
-Lebistes reticulatus
-Lepomis macrochirus
-Leiostomus xanthurus
-Pimephales promelas
-Lepomis macrochirus
-Albino rat
-Hen
-Goat
-Livestock
-Guinea Pigs
-Hamster
+wistar
+wistar rats
+wood mice
 wood mouse
-Rabbits
-Mice
-Rainbow trout
-Canary
-Serinus canaria
-Guinea Pig
-Cow
-Pigs
-Poultry
-Guinea-pigs
-White rabbits
-Birds
-Wood mice
+wood pigeon
+xenopus laevis
+xenpous leavis
+yellow-necked mouse
+zebra fish
+zebrafish

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

@@ -7,7 +7,7 @@ global Section section
 
 rule "1: Redacted because Section contains Vertebrate"
 	when
-		eval(section.contains("vertebrate")==true);
+		Section(matchesType("vertebrate"))
 	then
 		section.redact("name", 1, "Redacted because Section contains Vertebrate");
 		section.redact("address", 1, "Redacted because Section contains Vertebrate");
@@ -16,7 +16,7 @@ rule "1: Redacted because Section contains Vertebrate"
 
 rule "2: Not Redacted because Section contains no Vertebrate"
 	when
-		eval(section.contains("vertebrate")==false);
+		Section(matchesType("vertebrate"))
 	then
 		section.redactNot("name", 2, "Not Redacted because Section contains no Vertebrate");
 		section.redactNot("address", 2, "Not Redacted because Section contains no Vertebrate");
@@ -25,34 +25,110 @@ rule "2: Not Redacted because Section contains no Vertebrate"
 
 rule "3: Do not redact Names and Addresses if no redaction Indicator is contained"
 	when
-		eval(section.contains("vertebrate")==true && section.contains("no_redaction_indicator")==true);
+		Section(matchesType("vertebrate"), matchesType("no_redaction_indicator"))
 	then
 		section.redactNot("name", 3, "Vertebrate was found, but also a no redaction indicator");
 		section.redactNot("address", 3, "Vertebrate was found, but also a no redaction indicator");
 	end
 
 
-rule "4: Redact contact information, if applicant is found"
+rule "4: Redact Names and Addresses if no_redaction_indicator and redaction_indicator is contained"
 	when
-		eval(section.getText().toLowerCase().contains("applicant"));
+		Section(matchesType("vertebrate"), matchesType("no_redaction_indicator"), matchesType("redaction_indicator"))
 	then
-		section.redactLineAfter("Name:", "address", 4, "Redacted because of Rule 4");
-		section.redactBetween("Address:", "Contact", "address", 4, "Redacted because of Rule 4");
-		section.redactLineAfter("Contact point:",  "address", 4, "Redacted because of Rule 4");
-		section.redactLineAfter("Phone:", "address", 4, "Redacted because of Rule 4");
-		section.redactLineAfter("Fax:", "address", 4, "Redacted because of Rule 4");
-		section.redactLineAfter("E-mail:", "address", 4, "Redacted because of Rule 4");
+		section.redact("name", 4, "Vertebrate was found and no_redaction_indicator and redaction_indicator");
+		section.redact("address", 4, "Vertebrate was found and no_redaction_indicator and redaction_indicator");
 	end
 
 
-rule "5: Redact contact information, if 'Producer of the plant protection product' is found"
+rule "5: Do not redact in guideline sections"
 	when
-		eval(section.getText().contains("Producer of the plant protection product"));
+		Section(headlineContainsWord("guideline") || headlineContainsWord("Guidance"))
 	then
-		section.redactLineAfter("Name:", "address", 5, "xxxx");
-		section.redactBetween("Address:", "Contact", "address", 5, "xxxx");
-		section.redactBetween("Contact:", "Phone", "address", 5, "xxxx");
-		section.redactLineAfter("Phone:", "address", 5, "xxxx");
-		section.redactLineAfter("Fax:", "address", 5, "xxxx");
-		section.redactLineAfter("E-mail:", "address", 5, "xxxx");
-	end
+		section.redactNot("name", 5, "Section is a guideline section.");
+		section.redactNot("address", 5, "Section is a guideline section.");
+	end
+
+
+rule "6: Redact contact information if applicant is found"
+	when
+		Section(headlineContainsWord("applicant") || text.contains("Applicant") || headlineContainsWord("Primary contact") || headlineContainsWord("Alternative contact"))
+	then
+		section.redactLineAfter("Name:", "address", 6, "Applicant information was found");
+		section.redactBetween("Address:", "Contact", "address", 6, "Applicant information was found");
+		section.redactLineAfter("Contact point:",  "address", 6, "Applicant information was found");
+		section.redactLineAfter("Phone:", "address", 6, "Applicant information was found");
+		section.redactLineAfter("Fax:", "address", 6, "Applicant information was found");
+		section.redactLineAfter("Tel.:", "address", 6, "Applicant information was found");
+		section.redactLineAfter("Tel:", "address", 6, "Applicant information was found");
+		section.redactLineAfter("E-mail:", "address", 6, "Applicant information was found");
+		section.redactLineAfter("Email:", "address", 6, "Applicant information was found");
+		section.redactLineAfter("e-mail:", "address", 6, "Applicant information was found");
+		section.redactLineAfter("E-mail address:", "address", 6, "Applicant information was found");
+		section.redactLineAfter("Contact:", "address", 6, "Applicant information was found");
+		section.redactLineAfter("Alternative contact:", "address", 6, "Applicant information was found");
+		section.redactLineAfter("Telephone number:", "address", 6, "Applicant information was found");
+		section.redactLineAfter("Telephone No:", "address", 6, "Applicant information was found");
+		section.redactLineAfter("Fax number:", "address", 6, "Applicant information was found");
+		section.redactLineAfter("Telephone:", "address", 6, "Applicant information was found");
+		section.redactLineAfter("Company:", "address", 6, "Applicant information was found");
+		section.redactBetween("No:", "Fax", "address", 6, "Applicant information was found");
+		section.redactBetween("Contact:", "Tel.:", "address", 6, "Applicant information was found");
+	end
+
+
+rule "7: Redact contact information if Producer is found"
+	when
+		Section(text.toLowerCase().contains("producer of the plant protection") || text.toLowerCase().contains("producer of the active substance") || text.contains("Manufacturer of the active substance") || text.contains("Manufacturer:") || text.contains("Producer or producers of the active substance"))
+	then
+		section.redactLineAfter("Name:", "address", 7, "Producer was found");
+		section.redactBetween("Address:", "Contact", "address", 7, "Producer was found");
+		section.redactBetween("Contact:", "Phone", "address", 7, "Producer was found");
+		section.redactBetween("Contact:", "Telephone number:", "address", 7, "Producer was found");
+		section.redactBetween("Address:", "Manufacturing", "address", 7, "Producer was found");
+		section.redactLineAfter("Telephone:", "address", 7, "Producer was found");
+		section.redactLineAfter("Phone:", "address", 7, "Producer was found");
+		section.redactLineAfter("Fax:", "address", 7, "Producer was found");
+		section.redactLineAfter("E-mail:", "address", 7, "Producer was found");
+		section.redactLineAfter("Contact:", "address", 7, "Producer was found");
+		section.redactLineAfter("Fax number:", "address", 7, "Producer was found");
+		section.redactLineAfter("Telephone number:", "address", 7, "Producer was found");
+		section.redactLineAfter("Tel:", "address", 7, "Producer was found");
+		section.redactBetween("No:", "Fax", "address", 7, "Producer was found");
+	end
+
+
+rule "8: Not redacted because Vertebrate Study = N"
+    when
+        Section(rowEquals("Vertebrate study Y/N", "N") || rowEquals("Vertebrate study Y/N", "No"))
+    then
+        section.redactNotCell("Author(s)", 8, "name", "Not redacted because row is not a vertebrate study");
+        section.redactNot("address", 8, "Not redacted because row is not a vertebrate study");
+        section.highlightCell("Vertebrate study Y/N", 8, "hint_only");
+    end
+
+
+rule "9: Redact if must redact entry is found"
+	when
+		Section(matchesType("must_redact"))
+	then
+		section.redact("name", 9, "must_redact entry was found.");
+		section.redact("address", 9, "must_redact entry was found.");
+	end
+
+
+rule "10: Redact Authors and Addresses in Reference Table if it is a Vertebrate study"
+    when
+        Section(rowEquals("Vertebrate study Y/N", "Y") || rowEquals("Vertebrate study Y/N", "Yes"))
+    then
+        section.redactCell("Author(s)", 10, "name", "Redacted because row is a vertebrate study");
+        section.redact("address", 10, "Redacted because row is a vertebrate study");
+        section.highlightCell("Vertebrate study Y/N", 10, "must_redact");
+    end
+
+rule "11: Redact sponsor company"
+    when
+        Section(text.toLowerCase().contains("batches produced at"))
+    then
+        section.redactIfPrecededBy("batches produced at", "sponsor", 11, "Redacted because it represents a sponsor company");
+    end