Fixed paragraph recognition

Merge in RED/redaction-service from RED-629 to master

* commit '936683f94dd089d47b267cadb606c42b9e8b5515':
  RED-629: Each annotation is one entry in the RedactionLog

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

@@ -22,7 +22,7 @@
     </modules>
 
     <properties>
-        <pdfbox.version>2.0.16</pdfbox.version>
+        <pdfbox.version>2.0.21</pdfbox.version>
     </properties>
 
 

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

@@ -0,0 +1,21 @@
+package com.iqser.red.service.redaction.v1.model;
+
+import java.time.OffsetDateTime;
+
+import lombok.AllArgsConstructor;
+import lombok.Builder;
+import lombok.Data;
+import lombok.NoArgsConstructor;
+
+@Data
+@Builder
+@AllArgsConstructor
+@NoArgsConstructor
+public class Comment {
+
+    private String id;
+    private OffsetDateTime date;
+    private String text;
+    private String user;
+
+}

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

@@ -0,0 +1,19 @@
+package com.iqser.red.service.redaction.v1.model;
+
+import lombok.AllArgsConstructor;
+import lombok.Builder;
+import lombok.Data;
+import lombok.NoArgsConstructor;
+
+@Data
+@Builder
+@AllArgsConstructor
+@NoArgsConstructor
+public class IdRemoval {
+
+    private String id;
+    private String user;
+    private Status status;
+    private boolean removeFromDictionary;
+
+}

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

@@ -4,18 +4,25 @@ import java.util.ArrayList;
 import java.util.List;
 
 import lombok.AllArgsConstructor;
+import lombok.Builder;
 import lombok.Data;
 import lombok.NoArgsConstructor;
 
 @Data
+@Builder
 @AllArgsConstructor
 @NoArgsConstructor
 public class ManualRedactionEntry {
 
+    private String id;
+    private String user;
     private String type;
     private String value;
     private String reason;
+    private String legalBasis;
     private List<Rectangle> positions = new ArrayList<>();
+    private Status status;
+    private boolean addToDictionary;
 
     private String section;
     private int sectionNumber;

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

@@ -0,0 +1,5 @@
+package com.iqser.red.service.redaction.v1.model;
+
+public enum ManualRedactionType {
+    ADD, REMOVE
+}

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

@@ -1,17 +1,29 @@
 package com.iqser.red.service.redaction.v1.model;
 
+import java.util.HashMap;
 import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
 import java.util.Set;
 
 import lombok.AllArgsConstructor;
+import lombok.Builder;
 import lombok.Data;
 import lombok.NoArgsConstructor;
 
 @Data
+@Builder
 @AllArgsConstructor
 @NoArgsConstructor
 public class ManualRedactions {
 
-    private Set<String> idsToRemove = new HashSet<>();
+    @Builder.Default
+    private Set<IdRemoval> idsToRemove = new HashSet<>();
+
+    @Builder.Default
     private Set<ManualRedactionEntry> entriesToAdd = new HashSet<>();
+
+    @Builder.Default
+    private Map<String, List<Comment>> comments = new HashMap<>();
+
 }

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

@@ -18,6 +18,8 @@ public class RedactionLogEntry {
     private String type;
     private String value;
     private String reason;
+    private int matchedRule;
+    private String legalBasis;
     private boolean redacted;
     private boolean isHint;
     private String section;
@@ -27,5 +29,7 @@ public class RedactionLogEntry {
     private List<Rectangle> positions = new ArrayList<>();
     private int sectionNumber;
     private boolean manual;
+    private Status status;
+    private ManualRedactionType manualRedactionType;
 
 }

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

@@ -0,0 +1,5 @@
+package com.iqser.red.service.redaction.v1.model;
+
+public enum Status {
+    REQUESTED, APPROVED, DECLINED
+}

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>
@@ -39,7 +20,7 @@
         <dependency>
             <groupId>com.iqser.red.service</groupId>
             <artifactId>configuration-service-api-v1</artifactId>
-            <version>1.0.12</version>
+            <version>1.2.0</version>
         </dependency>
         <dependency>
             <groupId>org.drools</groupId>

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

@@ -12,6 +12,7 @@ import org.kie.api.builder.KieModule;
 import org.kie.api.runtime.KieContainer;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.boot.SpringApplication;
+import org.springframework.boot.actuate.autoconfigure.metrics.web.servlet.WebMvcMetricsAutoConfiguration;
 import org.springframework.boot.actuate.autoconfigure.security.servlet.ManagementWebSecurityAutoConfiguration;
 import org.springframework.boot.autoconfigure.SpringBootApplication;
 import org.springframework.boot.autoconfigure.security.servlet.SecurityAutoConfiguration;
@@ -29,7 +30,7 @@ import com.iqser.red.service.redaction.v1.server.settings.RedactionServiceSettin
 @Import({DefaultWebMvcConfiguration.class})
 @EnableFeignClients(basePackageClasses = RulesClient.class)
 @EnableConfigurationProperties(RedactionServiceSettings.class)
-@SpringBootApplication(exclude = {SecurityAutoConfiguration.class, ManagementWebSecurityAutoConfiguration.class})
+@SpringBootApplication(exclude = {SecurityAutoConfiguration.class, ManagementWebSecurityAutoConfiguration.class, WebMvcMetricsAutoConfiguration.class})
 public class Application {
 
     @Autowired

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

@@ -131,7 +131,7 @@ public class TextBlock extends AbstractTextContainer {
         TextPositionSequence previous = null;
         for (TextPositionSequence word : sequences) {
             if (previous != null) {
-                if (Math.abs(previous.getY1() - word.getY1()) > word.getTextHeight()) {
+                if (Math.abs(previous.getRotationAdjustedY() - word.getRotationAdjustedY()) > word.getTextHeight()) {
                     sb.append('\n');
                 } else {
                     sb.append(' ');

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/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) {
@@ -49,10 +53,10 @@ public class RedactionController implements RedactionResource {
 
             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

@@ -9,9 +9,7 @@ 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
@@ -19,10 +17,6 @@ public class TextPositionSequence implements CharSequence {
 
     private List<TextPosition> textPositions = new ArrayList<>();
 
-    @Getter
-    @Setter
-    private float[] annotationColor;
-
     private final int page;
 
 
@@ -107,6 +101,9 @@ public class TextPositionSequence implements CharSequence {
         }
     }
 
+    public float getRotationAdjustedY() {
+        return textPositions.get(0).getY();
+    }
 
     public float getY1() {
 
@@ -194,22 +191,18 @@ public class TextPositionSequence implements CharSequence {
 
     public Rectangle getRectangle() {
 
-        float height = textPositions.get(0).getHeightDir() + 2;
+        float height = getTextHeight();
 
-        float posXInit;
+        float posXInit = getX1();
         float posXEnd;
         float posYInit;
         float posYEnd;
 
         if (textPositions.get(0).getRotation() == 90) {
-
             posXEnd = textPositions.get(0).getYDirAdj() + 2;
-            posXInit = textPositions.get(0).getYDirAdj() - height;
-            posYInit = textPositions.get(0).getXDirAdj();
+            posYInit = getY1();
             posYEnd = textPositions.get(textPositions.size() - 1).getXDirAdj() - height + 4;
         } else {
-
-            posXInit = textPositions.get(0).getXDirAdj();
             posXEnd = textPositions.get(textPositions.size() - 1)
                     .getXDirAdj() + textPositions.get(textPositions.size() - 1).getWidth() + 1;
             posYInit = textPositions.get(0).getPageHeight() - textPositions.get(0).getYDirAdj() - 2;
@@ -220,4 +213,5 @@ public class TextPositionSequence implements CharSequence {
         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 +1,40 @@
+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.Value;
+
+@Value
+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.getRotationAdjustedY() - word.getRotationAdjustedY()) > 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

@@ -17,6 +17,7 @@ public class Entity {
     private final String type;
     private boolean redaction;
     private String redactionReason;
+    private String legalBasis;
     private List<EntityPositionSequence> positionSequences = new ArrayList<>();
     private List<TextPositionSequence> targetSequences;
     private Integer start;
@@ -30,7 +31,7 @@ public class Entity {
     private int sectionNumber;
 
 
-    public Entity(String word, String type, boolean redaction, String redactionReason, List<EntityPositionSequence> positionSequences, String headline, int matchedRule, int sectionNumber) {
+    public Entity(String word, String type, boolean redaction, String redactionReason, List<EntityPositionSequence> positionSequences, String headline, int matchedRule, int sectionNumber, String legalBasis) {
 
         this.word = word;
         this.type = type;
@@ -40,6 +41,7 @@ public class Entity {
         this.headline = headline;
         this.matchedRule = matchedRule;
         this.sectionNumber = sectionNumber;
+        this.legalBasis = legalBasis;
     }
 
 

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

@@ -136,9 +136,11 @@ public class SearchableText {
 
     private List<EntityPositionSequence> buildEntityPositionSequence(List<TextPositionSequence> crossSequenceParts) {
 
-        String id = IdBuilder.buildId(crossSequenceParts);
+        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) {
@@ -148,9 +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);
@@ -173,7 +179,7 @@ public class SearchableText {
         for (TextPositionSequence word : sequences) {
 
             if (previous != null) {
-                if (Math.abs(previous.getY1() - word.getY1()) > word.getTextHeight()) {
+                if (Math.abs(previous.getRotationAdjustedY() - word.getRotationAdjustedY()) > word.getTextHeight()) {
                     sb.append('\n');
                 } else {
                     sb.append(' ');
@@ -197,7 +203,7 @@ public class SearchableText {
         for (TextPositionSequence word : sequences) {
 
             if (previous != null) {
-                if (Math.abs(previous.getY1() - word.getY1()) > word.getTextHeight()) {
+                if (Math.abs(previous.getRotationAdjustedY() - word.getRotationAdjustedY()) > word.getTextHeight()) {
                     sb.append('\n');
                 } else {
                     sb.append(' ');

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

@@ -9,8 +9,6 @@ import java.util.regex.Pattern;
 
 import org.apache.commons.lang3.StringUtils;
 
-import com.iqser.red.service.redaction.v1.server.classification.model.TextBlock;
-
 import lombok.Builder;
 import lombok.Data;
 import lombok.extern.slf4j.Slf4j;
@@ -32,28 +30,21 @@ public class Section {
 
     private int sectionNumber;
 
-    private Map<String, TextBlock> tabularData;
+    private Map<String, CellValue> tabularData;
 
 
-    public boolean isVertebrateStudy() {
-        return tabularData != null
-                && (tabularData.containsKey("Vertebrate study Y/N")
-                && tabularData.get("Vertebrate study Y/N").getText().equals("Y")
-                || tabularData.containsKey("Verte brate study Y/N")
-                && tabularData.get("Verte brate study Y/N").getText().equals("Y"));
+    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 isNotVertebrateStudy() {
-        return tabularData != null
-                && (tabularData.containsKey("Vertebrate study Y/N")
-                && tabularData.get("Vertebrate study Y/N").getText().equals("N")
-                || tabularData.containsKey("Verte brate study Y/N")
-                && tabularData.get("Verte brate study Y/N").getText().equals("N"));
-    }
-
-
-    public boolean contains(String type) {
+    public boolean matchesType(String type) {
 
         return entities.stream().anyMatch(entity -> entity.getType().equals(type));
     }
@@ -65,13 +56,14 @@ public class Section {
     }
 
 
-    public void redact(String type, int ruleNumber, String reason) {
+    public void redact(String type, int ruleNumber, String reason, String legalBasis) {
 
         entities.forEach(entity -> {
             if (entity.getType().equals(type)) {
                 entity.setRedaction(true);
                 entity.setMatchedRule(ruleNumber);
                 entity.setRedactionReason(reason);
+                entity.setLegalBasis(legalBasis);
             }
         });
     }
@@ -89,7 +81,20 @@ public class Section {
     }
 
 
-    public void redactLineAfter(String start, String asType, int ruleNumber, String reason) {
+    public void redactIfPrecededBy(String prefix, String type, int ruleNumber, String reason, String legalBasis) {
+
+        entities.forEach(entity -> {
+            if (entity.getType().equals(type) && searchText.indexOf(prefix + entity.getWord()) != 1) {
+                entity.setRedaction(true);
+                entity.setMatchedRule(ruleNumber);
+                entity.setRedactionReason(reason);
+                entity.setLegalBasis(legalBasis);
+            }
+        });
+    }
+
+
+    public void redactLineAfter(String start, String asType, int ruleNumber, String reason, String legalBasis) {
 
         String[] values = StringUtils.substringsBetween(text, start, "\n");
 
@@ -108,13 +113,14 @@ public class Section {
                 entity.setRedaction(true);
                 entity.setMatchedRule(ruleNumber);
                 entity.setRedactionReason(reason);
+                entity.setLegalBasis(legalBasis);
             }
         });
 
     }
 
 
-    public void redactBetween(String start, String stop, String asType, int ruleNumber, String reason) {
+    public void redactBetween(String start, String stop, String asType, int ruleNumber, String reason, String legalBasis) {
 
         String[] values = StringUtils.substringsBetween(searchText, start, stop);
 
@@ -133,6 +139,7 @@ public class Section {
                 entity.setRedaction(true);
                 entity.setMatchedRule(ruleNumber);
                 entity.setRedactionReason(reason);
+                entity.setLegalBasis(legalBasis);
             }
         });
     }
@@ -148,9 +155,15 @@ public class Section {
             startIndex = searchText.indexOf(value, stopIndex);
             stopIndex = startIndex + value.length();
 
-            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, sectionNumber));
+            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,
+                                     sectionNumber));
             }
         } while (startIndex > -1);
 
@@ -160,7 +173,8 @@ public class Section {
 
     private boolean isSeparator(char c) {
 
-        return Character.isWhitespace(c) || Pattern.matches("\\p{Punct}", String.valueOf(c)) || c == '\"' || c == '‘' || c == '’';
+        return Character.isWhitespace(c) || Pattern.matches("\\p{Punct}",
+                                                            String.valueOf(c)) || c == '\"' || c == '‘' || c == '’';
     }
 
 
@@ -182,18 +196,50 @@ public class Section {
 
     public void highlightCell(String cellHeader, int ruleNumber, String type) {
 
-        TextBlock value = tabularData.get(cellHeader);
+        annotateCell(cellHeader, ruleNumber, type, false, null, null);
+    }
+
+
+    public void redactCell(String cellHeader, int ruleNumber, String type, String reason, String legalBasis) {
+
+        annotateCell(cellHeader, ruleNumber, type, true, reason, legalBasis);
+    }
+
+
+    public void redactNotCell(String cellHeader, int ruleNumber, String type, String reason) {
+
+        annotateCell(cellHeader, ruleNumber, type, false, reason, null);
+    }
+
+
+    private void annotateCell(String cellHeader, int ruleNumber, String type, boolean redact, String reason, String legalBasis) {
+
+        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.getText(), type, 0, value.getText().length(), headline, sectionNumber);
-            entity.setRedaction(false);
+            String word = value.toString();
+            Entity entity = new Entity(word,
+                                       type,
+                                       value.getRowSpanStart(),
+                                       value.getRowSpanStart() + word.length(),
+                                       headline,
+                                       sectionNumber);
+            entity.setRedaction(redact);
             entity.setMatchedRule(ruleNumber);
-            entity.setRedactionReason(cellHeader);
-            entity.setTargetSequences(value.getSequences()); // Make sure no other cells with same content are highlighted
-            entities.add(entity);
-        }
+            entity.setRedactionReason(reason);
+            entity.setTargetSequences(value.getTextBlock()
+                                              .getSequences()); // Make sure no other cells with same content are highlighted
+            entity.setLegalBasis(legalBasis);
 
+            // HashSet keeps the older value, but we want the new only.
+            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

@@ -1,5 +1,6 @@
 package com.iqser.red.service.redaction.v1.server.redaction.service;
 
+import java.awt.Color;
 import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.HashSet;
@@ -11,6 +12,7 @@ import java.util.stream.Collectors;
 import org.apache.commons.collections4.CollectionUtils;
 import org.springframework.stereotype.Service;
 
+import com.iqser.red.service.configuration.v1.api.model.Colors;
 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.server.client.DictionaryClient;
@@ -20,13 +22,14 @@ import lombok.Getter;
 import lombok.RequiredArgsConstructor;
 import lombok.extern.slf4j.Slf4j;
 
+@Slf4j
 @Service
 @RequiredArgsConstructor
-@Slf4j
 public class DictionaryService {
 
     private final DictionaryClient dictionaryClient;
 
+    @Getter
     private long dictionaryVersion = -1;
 
     @Getter
@@ -44,6 +47,15 @@ public class DictionaryService {
     @Getter
     private float[] defaultColor;
 
+    @Getter
+    private float[] requestAddColor;
+
+    @Getter
+    private float[] requestRemoveColor;
+
+    @Getter
+    private float[] notRedactedColor;
+
 
     public void updateDictionary() {
 
@@ -62,7 +74,7 @@ public class DictionaryService {
             if (typeResponse != null && CollectionUtils.isNotEmpty(typeResponse.getTypes())) {
                 entryColors = typeResponse.getTypes()
                         .stream()
-                        .collect(Collectors.toMap(TypeResult::getType, TypeResult::getColor));
+                        .collect(Collectors.toMap(TypeResult::getType, t -> convertColor(t.getHexColor())));
                 hintTypes = typeResponse.getTypes()
                         .stream()
                         .filter(TypeResult::isHint)
@@ -73,8 +85,16 @@ public class DictionaryService {
                         .filter(TypeResult::isCaseInsensitive)
                         .map(TypeResult::getType)
                         .collect(Collectors.toList());
-                dictionary = entryColors.keySet().stream().collect(Collectors.toMap(type -> type, this::convertEntries));
-                defaultColor = dictionaryClient.getDefaultColor().getColor();
+                dictionary = entryColors.keySet()
+                        .stream()
+                        .collect(Collectors.toMap(type -> type, this::convertEntries));
+
+
+                Colors colors = dictionaryClient.getColors();
+                defaultColor = convertColor(colors.getDefaultColor());
+                requestAddColor = convertColor(colors.getRequestAdd());
+                requestRemoveColor = convertColor(colors.getRequestRemove());
+                notRedactedColor = convertColor(colors.getNotRedacted());
             }
         } catch (FeignException e) {
             log.warn("Got some unknown feignException", e);
@@ -84,6 +104,7 @@ public class DictionaryService {
 
 
     private Set<String> convertEntries(String s) {
+
         if (caseInsensitiveTypes.contains(s)) {
             return dictionaryClient.getDictionaryForType(s)
                     .getEntries()
@@ -94,4 +115,11 @@ public class DictionaryService {
         return new HashSet<>(dictionaryClient.getDictionaryForType(s).getEntries());
     }
 
+
+    private float[] convertColor(String hex) {
+
+        Color color = Color.decode(hex);
+        return new float[]{color.getRed() / 255f, color.getGreen() / 255f, color.getBlue() / 255f};
+    }
+
 }

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

@@ -18,6 +18,7 @@ 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;
@@ -26,9 +27,7 @@ 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 EntityRedactionService {
@@ -51,24 +50,30 @@ 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();
-                    Map<String, TextBlock> tabularData = new HashMap<>();
+                    Map<String, CellValue> tabularData = new HashMap<>();
+                    int start = 0;
                     for (Cell cell : row) {
-                        if (cell.isHeaderCell() || CollectionUtils.isEmpty(cell.getTextBlocks())) {
+                        if (!singleCellTable && cell.isHeaderCell() || CollectionUtils.isEmpty(cell.getTextBlocks())) {
                             continue;
                         }
                         addSectionToManualRedactions(cell.getTextBlocks(), manualRedactions, table.getHeadline(), sectionNumber);
+                        int cellStart = start;
                         cell.getHeaderCells().forEach(headerCell -> {
-                            String headerName = headerCell.getTextBlocks().get(0).getText()
-                                    .replaceAll("\n", " ")
-                                    .replaceAll(" ", " ");
-                            tabularData.put(headerName, cell.getTextBlocks().get(0));
+                            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() + 1; // include automatically appended white space
                         for (TextBlock textBlock : cell.getTextBlocks()) {
                             searchableRow.addAll(textBlock.getSequences());
                         }
-
                     }
                     Set<Entity> rowEntities = findEntities(searchableRow, table.getHeadline(), sectionNumber);
 
@@ -112,7 +117,7 @@ public class EntityRedactionService {
                 classifiedDoc.getEntities()
                         .computeIfAbsent(entry.getKey(), (x) -> new ArrayList<>())
                         .add(new Entity(entity.getWord(), entity.getType(), entity.isRedaction(), entity.getRedactionReason(), entry
-                                .getValue(), entity.getHeadline(), entity.getMatchedRule(), entity.getSectionNumber()));
+                                .getValue(), entity.getHeadline(), entity.getMatchedRule(), entity.getSectionNumber(), entity.getLegalBasis()));
             }
         }
 
@@ -138,17 +143,17 @@ public class EntityRedactionService {
     private Set<Entity> findEntities(SearchableText searchableText, String headline, int sectionNumber) {
 
         Set<Entity> found = new HashSet<>();
-        if (StringUtils.isEmpty(searchableText.toString()) && StringUtils.isEmpty(headline)) {
+        String searchableString = searchableText.toString();
+        if (StringUtils.isEmpty(searchableString)) {
             return found;
         }
 
-        String inputString = searchableText.toString();
-        String lowercaseInputString = inputString.toLowerCase();
+        String lowercaseInputString = searchableString.toLowerCase();
         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, sectionNumber));
             } else {
-                found.addAll(find(inputString, entry.getValue(), entry.getKey(), headline, sectionNumber));
+                found.addAll(find(searchableString, entry.getValue(), entry.getKey(), headline, sectionNumber));
             }
         }
 

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

@@ -5,7 +5,6 @@ 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;
@@ -19,14 +18,9 @@ public class IdBuilder {
 
         StringBuilder sb = new StringBuilder();
         crossSequenceParts.forEach(sequencePart -> sequencePart.getTextPositions().forEach(textPosition -> {
-            sb.append(textPosition.getTextMatrix());
+            sb.append(textPosition.getTextMatrix()).append(sequencePart.getPage());
         }));
 
         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;
@@ -37,6 +36,7 @@ public class PdfSegmentationService {
     private final ClassificationService classificationService;
     private final SectionsBuilderService sectionsBuilderService;
 
+
     public Document parseDocument(PDDocument pdDocument) throws IOException {
 
         Document document = new Document();
@@ -56,19 +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);
@@ -91,7 +93,10 @@ public class PdfSegmentationService {
 
     }
 
+
+
     private void increaseDocumentStatistics(Page page, Document document) {
+
         if (!page.isLandscape()) {
             document.getFontSizeCounter().addAll(page.getFontSizeCounter().getCountPerValue());
         }
@@ -100,6 +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

@@ -4,6 +4,7 @@ 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;
@@ -38,23 +39,30 @@ public class SectionsBuilderService {
 
                 current.setPage(page.getPageNumber());
 
-                if (prev != null && current.getClassification().startsWith("H ") || !document.isHeadlines()) {
-                    Paragraph chunkBlock = buildTextBlock(chunkWords, lastHeadline, previousTable);
+                if (prev != null && current.getClassification().startsWith("H ") && !prev.getClassification().startsWith("H ") || !document.isHeadlines()) {
+                    Paragraph chunkBlock = buildTextBlock(chunkWords, lastHeadline);
                     chunkBlock.setHeadline(lastHeadline);
-                    lastHeadline = current.getText();
-                    if (CollectionUtils.isNotEmpty(chunkBlock.getTables())) {
-                        previousTable = chunkBlock.getTables().get(0);
+                    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, previousTable);
+        Paragraph chunkBlock = buildTextBlock(chunkWords, lastHeadline);
         chunkBlock.setHeadline(lastHeadline);
         chunkBlockList.add(chunkBlock);
 
@@ -62,7 +70,38 @@ public class SectionsBuilderService {
     }
 
 
-    private Paragraph buildTextBlock(List<AbstractTextContainer> wordBlockList, String lastHeadline, Table previousTable) {
+    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();
         TextBlock textBlock = null;
@@ -85,27 +124,6 @@ public class SectionsBuilderService {
                 } else {
                     table.setHeadline("Table in: " + lastHeadline);
                 }
-                // Distribute header information for subsequent tables
-                if (previousTable != null && hasInvalidHeaderInformation(table) && hasValidHeaderInformation(previousTable)) {
-                    List<Cell> previousTableNonHeaderRow = getRowWithNonHeaderCells(previousTable);
-                    List<Cell> tableNonHeaderRow = getRowWithNonHeaderCells(table);
-                    // 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);
-                    }
-                    if (previousTableNonHeaderRow.size() == tableNonHeaderRow.size()) {
-                        for (int i = table.getRows().size() - 1; i >= 0; i--) { // Non header rows are most likely at bottom of table
-                            List<Cell> row = table.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());
-                                }
-                            }
-                        }
-                    }
-                }
 
                 if (textBlock != null && !alreadyAdded) {
                     paragraph.getPageBlocks().add(textBlock);
@@ -168,7 +186,7 @@ public class SectionsBuilderService {
 
     private List<Cell> getRowWithNonHeaderCells(Table table) {
 
-        for (int i = table.getRows().size() - 1; i >= 0; i--) { // Non header rows are most likely at bottom of 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) {

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;
@@ -20,10 +22,10 @@ public class Cell extends Rectangle {
 
     private boolean isHeaderCell;
 
+
     public Cell(Point2D topLeft, Point2D bottomRight) {
 
-        super((float) topLeft.getY(), (float) topLeft.getX(), (float) (bottomRight.getX() - topLeft.getX()),
-                (float) (bottomRight
+        super((float) topLeft.getY(), (float) topLeft.getX(), (float) (bottomRight.getX() - topLeft.getX()), (float) (bottomRight
                 .getY() - topLeft.getY()));
     }
 
@@ -33,4 +35,30 @@ public class Cell extends Rectangle {
         textBlocks.add(textBlock);
     }
 
+
+    @Override
+    public String toString() {
+
+        StringBuilder sb = new StringBuilder();
+
+        for (TextBlock textBlock : textBlocks) {
+            TextPositionSequence previous = null;
+            for (TextPositionSequence word : textBlock.getSequences()) {
+                if (previous != null) {
+                    if (Math.abs(previous.getRotationAdjustedY() - word.getRotationAdjustedY()) > 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/Table.java

@@ -29,11 +29,13 @@ public class Table extends AbstractTextContainer {
     @Setter
     private String headline;
 
-    @Getter
-    private int rowCount;
+    private int unrotatedRowCount;
 
-    @Getter
-    private int colCount;
+    private int unrotatedColCount;
+
+    private int rowCount = -1;
+
+    private int colCount = -1;
 
     private final int rotation;
 
@@ -65,6 +67,25 @@ public class Table extends AbstractTextContainer {
     }
 
 
+    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.
@@ -72,100 +93,54 @@ public class Table extends AbstractTextContainer {
      */
     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
-        cells.forEach((position, cell) -> {
-            List<Cell> cellsToTheLeft = getCellsToTheLeft(position);
-            Cell lastHeaderCell = null;
-            for (Cell leftCell : cellsToTheLeft) {
-                if (CollectionUtils.isNotEmpty(leftCell.getTextBlocks()) && leftCell.getTextBlocks()
+        // 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")) {
-                    lastHeaderCell = leftCell;
-                } else {
-                    break;
+                    cell.setHeaderCell(true);
                 }
             }
-            if (lastHeaderCell != null) {
-                cell.getHeaderCells().add(lastHeaderCell);
-            }
-            lastHeaderCell = null;
-            List<Cell> cellsToTheTop = getCellToTheTop(position);
-            for (Cell topCell : cellsToTheTop) {
-                if (CollectionUtils.isNotEmpty(topCell.getTextBlocks()) && topCell.getTextBlocks()
-                        .get(0)
-                        .getMostPopularWordStyle()
-                        .equals("bold")) {
-                    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<Cell> getCellsToTheLeft(CellPosition cellPosition) {
-
-        List<Cell> result = new ArrayList<>();
-        if (cellPosition.getCol() == 0) {
-            return result;
-        }
-        int row = cellPosition.getRow();
-        for (int i = cellPosition.getCol() - 1; i >= 0; i--) {
-            if (cells.get(new CellPosition(row, i)) != null) {
-                result.add(cells.get(new CellPosition(row, i)));
-            } else {
-                Cell spanningCell = null;
-                while (spanningCell == null && row >= 0) {
-                    row--;
-                    spanningCell = cells.get(new CellPosition(row, i));
-                }
-                if (spanningCell != null) {
-                    result.add(spanningCell);
-                }
-                row = cellPosition.getRow();
-            }
         }
-        Collections.reverse(result);
-        return result;
-    }
 
-
-    private List<Cell> getCellToTheTop(CellPosition cellPosition) {
-
-        List<Cell> result = new ArrayList<>();
-        if (cellPosition.getRow() == 0) {
-            return result;
-        }
-        int col = cellPosition.getCol();
-        for (int i = cellPosition.getRow() - 1; i >= 0; i--) {
-            if (cells.get(new CellPosition(i, col)) != null) {
-                result.add(cells.get(new CellPosition(i, col)));
-            } else {
-                Cell spanningCell = null;
-                while (spanningCell == null && col >= 0) {
-                    col--;
-                    spanningCell = cells.get(new CellPosition(i, col));
-                }
-                if (spanningCell != null) {
-                    result.add(spanningCell);
-                }
-                col = cellPosition.getCol();
-            }
-        }
-        Collections.reverse(result);
-        return result;
     }
 
 
@@ -173,9 +148,9 @@ public class Table extends AbstractTextContainer {
 
         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));
                     if (cell != null) {
                         lastRow.add(cell);
@@ -184,9 +159,9 @@ public class Table extends AbstractTextContainer {
                 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));
                     if (cell != null) {
                         lastRow.add(cell);
@@ -195,9 +170,9 @@ public class Table extends AbstractTextContainer {
                 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()
                     if (cell != null) {
                         lastRow.add(cell);
@@ -214,8 +189,8 @@ public class Table extends AbstractTextContainer {
 
     private void add(Cell chunk, int row, int col) {
 
-        rowCount = Math.max(rowCount, row + 1);
-        colCount = Math.max(colCount, col + 1);
+        unrotatedRowCount = Math.max(unrotatedRowCount, row + 1);
+        unrotatedColCount = Math.max(unrotatedColCount, col + 1);
 
         CellPosition cp = new CellPosition(row, col);
         cells.put(cp, chunk);

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/visualization/service/AnnotationHighlightService.java

@@ -2,7 +2,12 @@ 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.GregorianCalendar;
+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;
@@ -13,13 +18,19 @@ import org.apache.pdfbox.pdmodel.font.PDType1Font;
 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.PDAnnotationText;
 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.Comment;
+import com.iqser.red.service.redaction.v1.model.IdRemoval;
 import com.iqser.red.service.redaction.v1.model.ManualRedactionEntry;
+import com.iqser.red.service.redaction.v1.model.ManualRedactionType;
 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.model.Status;
 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;
@@ -27,15 +38,12 @@ import com.iqser.red.service.redaction.v1.server.parsing.model.TextPositionSeque
 import com.iqser.red.service.redaction.v1.server.redaction.model.Entity;
 import com.iqser.red.service.redaction.v1.server.redaction.model.EntityPositionSequence;
 import com.iqser.red.service.redaction.v1.server.redaction.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 {
@@ -43,7 +51,10 @@ public class AnnotationHighlightService {
     private final DictionaryService dictionaryService;
 
 
-    public void highlight(PDDocument document, Document classifiedDoc, boolean flatRedaction, ManualRedactions manualRedactions) 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++) {
 
@@ -51,51 +62,147 @@ public class AnnotationHighlightService {
 
             drawSectionFrames(document, classifiedDoc, flatRedaction, pdPage, page);
 
-            if (classifiedDoc.getEntities().get(page) == null) {
-                continue;
+            if (classifiedDoc.getEntities().get(page) != null) {
+                addAnnotations(pdPage, classifiedDoc, flatRedaction, manualRedactions, page);
             }
 
-            addAnnotations(pdPage, classifiedDoc, flatRedaction, manualRedactions, page);
-            addManualAnnotations(pdPage, classifiedDoc, manualRedactions, page);
+            if (manualRedactionPages.contains(page)) {
+                addManualAnnotations(pdPage, classifiedDoc, manualRedactions, page);
+            }
         }
     }
 
 
-    private void addAnnotations(PDPage pdPage, Document classifiedDoc, boolean flatRedaction, ManualRedactions manualRedactions, int page) throws IOException {
+    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();
 
+        // Duplicates can exist due table extraction colums over multiple rows.
+        Set<String> processedIds = new HashSet<>();
+
+        entityLoop:
         for (Entity entity : classifiedDoc.getEntities().get(page)) {
 
             if (flatRedaction && !isRedactionType(entity)) {
                 continue;
             }
 
-            RedactionLogEntry redactionLogEntry = createRedactionLogEntry(entity);
+
+            boolean requestedToRemove = false;
+            List<Comment> comments = null;
 
             for (EntityPositionSequence entityPositionSequence : entity.getPositionSequences()) {
 
-                if (manualRedactions != null && manualRedactions.getIdsToRemove()
-                        .contains(entityPositionSequence.getId())) {
-                    entity.setRedaction(false);
-                    entity.setRedactionReason(entity.getRedactionReason() + ", removed by manual override");
-                    redactionLogEntry.setManual(true);
+                RedactionLogEntry redactionLogEntry = createRedactionLogEntry(entity);
+                if (processedIds.contains(entityPositionSequence.getId())) {
+
+                    // TODO refactor this outer loop jump as soon as we have the time.
+                    continue entityLoop;
+                } else {
+                    processedIds.add(entityPositionSequence.getId());
                 }
 
-                for (TextPositionSequence textPositions : entityPositionSequence.getSequences()) {
+                if (manualRedactions != null && !manualRedactions.getIdsToRemove().isEmpty()) {
+                    for (IdRemoval manualRemoval : manualRedactions.getIdsToRemove()) {
+                        if (manualRemoval.getId().equals(entityPositionSequence.getId())) {
+                            comments = manualRedactions.getComments().get(manualRemoval.getId());
+                            String manualOverrideReason = null;
+                            if (manualRemoval.getStatus().equals(Status.APPROVED)) {
+                                entity.setRedaction(false);
+                                redactionLogEntry.setRedacted(false);
+                                redactionLogEntry.setStatus(Status.APPROVED);
+                                manualOverrideReason = entity.getRedactionReason() + ", removed by manual override";
+                            } else if (manualRemoval.getStatus().equals(Status.REQUESTED)) {
+                                requestedToRemove = true;
+                                manualOverrideReason = entity.getRedactionReason() + ", requested to remove";
+                                redactionLogEntry.setStatus(Status.REQUESTED);
+                            } else {
+                                redactionLogEntry.setStatus(Status.DECLINED);
+                            }
+
+                            entity.setRedactionReason(manualOverrideReason != null ? manualOverrideReason : entity.getRedactionReason());
+                            redactionLogEntry.setReason(manualOverrideReason);
+                            redactionLogEntry.setManual(true);
+                            redactionLogEntry.setManualRedactionType(ManualRedactionType.REMOVE);
+                        }
+                    }
 
-                    Rectangle rectangle = textPositions.getRectangle();
-                    redactionLogEntry.getPositions().add(rectangle);
-                    annotations.add(createAnnotation(rectangle, entityPositionSequence.getId(), createAnnotationContent(entity), getColor(entity), !flatRedaction && !isHint(entity)));
                 }
+
+                if (CollectionUtils.isNotEmpty(entityPositionSequence.getSequences())) {
+                    List<Rectangle> rectanglesPerLine = getRectanglesPerLine(entityPositionSequence.getSequences()
+                            .stream()
+                            .flatMap(seq -> seq.getTextPositions().stream())
+                            .collect(Collectors.toList()), page);
+
+                    if (manualRedactions != null) {
+                        comments = manualRedactions.getComments().get(entityPositionSequence.getId());
+                    }
+
+                    redactionLogEntry.getPositions().addAll(rectanglesPerLine);
+
+                    annotations.addAll(createAnnotation(rectanglesPerLine, entityPositionSequence.getId(), createAnnotationContent(entity), getColor(entity, requestedToRemove), comments, !isHint(entity)));
+                }
+
                 redactionLogEntry.setId(entityPositionSequence.getId());
+
+                // FIXME ids should never be null. Figure out why this happens.
+                if (redactionLogEntry.getId() != null) {
+                    classifiedDoc.getRedactionLogEntities().add(redactionLogEntry);
+                }
             }
-            classifiedDoc.getRedactionLogEntities().add(redactionLogEntry);
+
+
         }
+
     }
 
 
-    private void addManualAnnotations(PDPage pdPage, Document classifiedDoc, ManualRedactions manualRedactions, int page) throws IOException {
+    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;
@@ -105,32 +212,40 @@ public class AnnotationHighlightService {
 
         for (ManualRedactionEntry manualRedactionEntry : manualRedactions.getEntriesToAdd()) {
 
-            String id = IdBuilder.buildId(manualRedactionEntry);
+            String id = manualRedactionEntry.getId();
 
-            RedactionLogEntry redactionLogEntry = createRedactionLogEntry(manualRedactionEntry);
+            RedactionLogEntry redactionLogEntry = createRedactionLogEntry(manualRedactionEntry, id);
 
+            List<Rectangle> rectanglesOnPage = new ArrayList<>();
             for (Rectangle rectangle : manualRedactionEntry.getPositions()) {
-
-                if (page != rectangle.getPage()) {
-                    continue;
+                if (page == rectangle.getPage()) {
+                    rectanglesOnPage.add(rectangle);
+                    redactionLogEntry.getPositions().add(rectangle);
                 }
-
-                PDAnnotationTextMarkup highlight = createAnnotation(rectangle, id, createAnnotationContent(manualRedactionEntry), getColor(manualRedactionEntry
-                        .getType()), true);
-                annotations.add(highlight);
-
-                redactionLogEntry.getPositions().add(rectangle);
             }
-            classifiedDoc.getRedactionLogEntities().add(redactionLogEntry);
+
+            if (!rectanglesOnPage.isEmpty() && !approvedAndShouldBeInDictionary(manualRedactionEntry)) {
+                annotations.addAll(createAnnotation(rectanglesOnPage, id, createAnnotationContent(manualRedactionEntry), getColorForManualAdd(manualRedactionEntry
+                        .getType(), manualRedactionEntry.getStatus()), manualRedactions.getComments().get(id), true));
+                classifiedDoc.getRedactionLogEntities().add(redactionLogEntry);
+            }
         }
     }
 
 
-    private RedactionLogEntry createRedactionLogEntry(ManualRedactionEntry manualRedactionEntry) {
+    private boolean approvedAndShouldBeInDictionary(ManualRedactionEntry manualRedactionEntry) {
+
+        return manualRedactionEntry.getStatus().equals(Status.APPROVED) && manualRedactionEntry.isAddToDictionary();
+    }
+
+
+    private RedactionLogEntry createRedactionLogEntry(ManualRedactionEntry manualRedactionEntry, String id) {
 
         return RedactionLogEntry.builder()
+                .id(id)
                 .color(getColor(manualRedactionEntry.getType()))
                 .reason(manualRedactionEntry.getReason())
+                .legalBasis(manualRedactionEntry.getLegalBasis())
                 .value(manualRedactionEntry.getValue())
                 .type(manualRedactionEntry.getType())
                 .redacted(true)
@@ -138,6 +253,8 @@ public class AnnotationHighlightService {
                 .section(manualRedactionEntry.getSection())
                 .sectionNumber(manualRedactionEntry.getSectionNumber())
                 .manual(true)
+                .status(manualRedactionEntry.getStatus())
+                .manualRedactionType(ManualRedactionType.ADD)
                 .build();
     }
 
@@ -145,70 +262,117 @@ public class AnnotationHighlightService {
     private RedactionLogEntry createRedactionLogEntry(Entity entity) {
 
         return RedactionLogEntry.builder()
-                .color(getColor(entity))
+                .color(getColor(entity, false))
                 .reason(entity.getRedactionReason())
+                .legalBasis(entity.getLegalBasis())
                 .value(entity.getWord())
                 .type(entity.getType())
                 .redacted(entity.isRedaction())
                 .isHint(isHint(entity))
                 .section(entity.getHeadline())
                 .sectionNumber(entity.getSectionNumber())
+                .matchedRule(entity.getMatchedRule())
                 .build();
     }
 
 
-    private PDAnnotationTextMarkup createAnnotation(Rectangle rectangle, String id, String content, float[] color, boolean popup) {
+    private List<PDAnnotation> createAnnotation(List<Rectangle> rectangles, String id, String content, float[] color,
+                                                List<Comment> comments, boolean popup) {
+
+        List<PDAnnotation> annotations = new ArrayList<>();
 
         PDAnnotationTextMarkup annotation = new PDAnnotationTextMarkup(PDAnnotationTextMarkup.SUB_TYPE_HIGHLIGHT);
         annotation.constructAppearances();
-        annotation.setRectangle(toPDRectangle(rectangle));
-        annotation.setQuadPoints(toQuadPoints(rectangle));
+        PDRectangle pdRectangle = toPDRectangle(rectangles);
+        annotation.setRectangle(pdRectangle);
+        annotation.setQuadPoints(toQuadPoints(rectangles));
         if (popup) {
-            annotation.setAnnotationName(id);
-            annotation.setTitlePopup(id);
             annotation.setContents(content);
         }
+        annotation.setTitlePopup(id);
+        annotation.setAnnotationName(id);
         annotation.setColor(new PDColor(color, PDDeviceRGB.INSTANCE));
-        return annotation;
+        annotations.add(annotation);
+
+        if (comments != null) {
+            for (Comment comment : comments) {
+                PDAnnotationText txtAnnot = new PDAnnotationText();
+                txtAnnot.setAnnotationName(comment.getId());
+                txtAnnot.setInReplyTo(annotation); // Reference to highlight annotation
+                txtAnnot.setName(PDAnnotationText.NAME_COMMENT);
+                txtAnnot.setCreationDate(GregorianCalendar.from(comment.getDate().toZonedDateTime()));
+                txtAnnot.setTitlePopup(comment.getUser());
+                txtAnnot.setContents(comment.getText());
+                txtAnnot.setRectangle(pdRectangle);
+                annotations.add(txtAnnot);
+            }
+        }
+
+        return annotations;
     }
 
 
     private String createAnnotationContent(Entity entity) {
 
-        return new StringBuilder().append("\nRule ")
-                .append(entity.getMatchedRule())
-                .append(" matched")
-                .append("\n\n")
-                .append(entity.getRedactionReason())
-                .append("\n\nIn Section : \"")
-                .append(entity.getHeadline())
-                .append("\"")
-                .toString();
+        return "\nRule " + entity.getMatchedRule() + " matched\n\n" + entity.getRedactionReason() + "\n\nLegal basis:" + entity
+                .getLegalBasis() + "\n\nIn section: \"" + entity.getHeadline() + "\"";
     }
 
 
     private String createAnnotationContent(ManualRedactionEntry entry) {
 
-        return new StringBuilder().append("\nManual Redaction")
-                .append("\n\nIn Section : \"")
-                .append(entry.getSection())
-                .append("\"")
-                .toString();
+        return "\nManual Redaction\n\nIn Section : \"" + entry.getSection() + "\"";
     }
 
 
-    private PDRectangle toPDRectangle(Rectangle rectangle) {
+    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(rectangle.getTopLeft().getX());
-        annotationPosition.setLowerLeftY(rectangle.getTopLeft().getY() + rectangle.getHeight());
-        annotationPosition.setUpperRightX(rectangle.getTopLeft().getX() + rectangle.getWidth());
-        annotationPosition.setUpperRightY(rectangle.getTopLeft().getY());
+        annotationPosition.setLowerLeftX(lowerLeftX);
+        annotationPosition.setLowerLeftY(lowerLeftY);
+        annotationPosition.setUpperRightX(upperRightX);
+        annotationPosition.setUpperRightY(upperRightY);
         return annotationPosition;
     }
 
 
-    private float[] toQuadPoints(Rectangle rectangle) {
+    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
@@ -224,17 +388,17 @@ public class AnnotationHighlightService {
         if (!entity.isRedaction()) {
             return false;
         }
-        if (isHint(entity)) {
-            return false;
-        }
-        return true;
+        return !isHint(entity);
     }
 
 
-    private float[] getColor(Entity entity) {
+    private float[] getColor(Entity entity, boolean requestedToRemove) {
 
+        if (requestedToRemove) {
+            return dictionaryService.getRequestRemoveColor();
+        }
         if (!entity.isRedaction() && !isHint(entity)) {
-            return new float[]{0.627f, 0.627f, 0.627f};
+            return dictionaryService.getNotRedactedColor();
         }
         if (!dictionaryService.getEntryColors().containsKey(entity.getType())) {
             return dictionaryService.getDefaultColor();
@@ -243,6 +407,17 @@ public class AnnotationHighlightService {
     }
 
 
+    private float[] getColorForManualAdd(String type, Status status) {
+
+        if (status.equals(Status.REQUESTED)) {
+            return dictionaryService.getRequestAddColor();
+        } else if (status.equals(Status.DECLINED)) {
+            return dictionaryService.getNotRedactedColor();
+        }
+        return getColor(type);
+    }
+
+
     private float[] getColor(String type) {
 
         if (!dictionaryService.getEntryColors().containsKey(type)) {
@@ -255,14 +430,12 @@ public class AnnotationHighlightService {
     private boolean isHint(Entity entity) {
 
         List<String> hintTypes = dictionaryService.getHintTypes();
-        if (CollectionUtils.isNotEmpty(hintTypes) && hintTypes.contains(entity.getType())) {
-            return true;
-        }
-        return false;
+        return CollectionUtils.isNotEmpty(hintTypes) && hintTypes.contains(entity.getType());
     }
 
 
-    private void drawSectionFrames(PDDocument document, Document classifiedDoc, boolean flatRedaction, PDPage pdPage, int page) throws IOException {
+    private void drawSectionFrames(PDDocument document, Document classifiedDoc, boolean flatRedaction, PDPage pdPage,
+                                   int page) throws IOException {
 
         if (flatRedaction) {
             return;
@@ -334,4 +507,4 @@ public class AnnotationHighlightService {
         }
     }
 
-}
+}

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

@@ -12,5 +12,6 @@ management:
   endpoint:
     metrics.enabled: ${monitoring.enabled:false}
     prometheus.enabled: ${monitoring.enabled:false}
+    health.enabled: true
   endpoints.web.exposure.include: prometheus, health
   metrics.export.prometheus.enabled: ${monitoring.enabled:false}

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

@@ -2,10 +2,6 @@ spring:
   application:
     name: redaction-service-v1
 
-
-management:
-  endpoints:
-    web:
-      base-path: /
-      path-mapping:
-        health: "health"
+management.endpoints:
+  web.base-path: /
+  enabled-by-default: false

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

@@ -1,5 +1,6 @@
 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;
 
@@ -13,11 +14,13 @@ import java.io.InputStream;
 import java.io.InputStreamReader;
 import java.net.URL;
 import java.nio.charset.StandardCharsets;
+import java.time.OffsetDateTime;
 import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
 import java.util.Set;
+import java.util.UUID;
 import java.util.stream.Collectors;
 
 import org.apache.commons.io.IOUtils;
@@ -37,17 +40,21 @@ 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.Colors;
 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.Comment;
+import com.iqser.red.service.redaction.v1.model.IdRemoval;
 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.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.model.Status;
 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.controller.RedactionController;
@@ -62,6 +69,7 @@ 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";
@@ -77,9 +85,10 @@ public class RedactionIntegrationTest {
     private DictionaryClient dictionaryClient;
 
     private final Map<String, List<String>> dictionary = new HashMap<>();
-    private final Map<String, float[]> typeColorMap = new HashMap<>();
+    private final Map<String, String> typeColorMap = new HashMap<>();
     private final Map<String, Boolean> hintTypeMap = new HashMap<>();
     private final Map<String, Boolean> caseInSensitiveMap = new HashMap<>();
+    private final Colors colors = new Colors();
 
     @TestConfiguration
     public static class RedactionIntegrationTestConfiguration {
@@ -116,11 +125,12 @@ 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}));
+        when(dictionaryClient.getColors()).thenReturn(colors);
     }
 
 
@@ -131,6 +141,11 @@ 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()
@@ -172,17 +187,19 @@ public class RedactionIntegrationTest {
 
     private void loadTypeForTest() {
 
-        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[]{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});
+        typeColorMap.put(VERTEBRATES_CODE, "#00ff00");
+        typeColorMap.put(ADDRESS_CODE, "#00ffff");
+        typeColorMap.put(NAME_CODE, "#ffff00");
+        typeColorMap.put(SPONSOR, "#2c21fc");
+        typeColorMap.put(NO_REDACTION_INDICATOR, "#e600ff");
+        typeColorMap.put(REDACTION_INDICATOR, "#ff7700");
+        typeColorMap.put(HINT_ONLY, "#00fcb1");
+        typeColorMap.put(MUST_REDACT, "#ff0000");
 
         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);
@@ -191,10 +208,16 @@ public class RedactionIntegrationTest {
         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);
+
+        colors.setDefaultColor("#acfc00");
+        colors.setNotRedacted("#cccccc");
+        colors.setRequestAdd("#04b093");
+        colors.setRequestRemove("#04b093");
     }
 
 
@@ -204,7 +227,7 @@ public class RedactionIntegrationTest {
                 .stream()
                 .map(typeColor -> TypeResult.builder()
                         .type(typeColor.getKey())
-                        .color(typeColor.getValue())
+                        .hexColor(typeColor.getValue())
                         .isHint(hintTypeMap.get(typeColor.getKey()))
                         .isCaseInsensitive(caseInSensitiveMap.get(typeColor.getKey()))
                         .build())
@@ -216,7 +239,7 @@ public class RedactionIntegrationTest {
     private DictionaryResponse getDictionaryResponse(String type) {
 
         return DictionaryResponse.builder()
-                .color(typeColorMap.get(type))
+                .hexColor(typeColorMap.get(type))
                 .entries(dictionary.get(type))
                 .isHint(hintTypeMap.get(type))
                 .isCaseInsensitive(caseInSensitiveMap.get(type))
@@ -240,7 +263,16 @@ public class RedactionIntegrationTest {
                     .document(IOUtils.toByteArray(new FileInputStream(path)))
                     .build();
             System.out.println("Redacting file : " + path.getName());
-            redactionController.redact(request);
+            RedactionResult result = redactionController.redact(request);
+
+            Map<String, List<RedactionLogEntry>> duplicates = new HashMap<>();
+            result.getRedactionLog().getRedactionLogEntry().forEach(entry -> {
+                duplicates.computeIfAbsent(entry.getId(), v -> new ArrayList<>()).add(entry);
+            });
+
+            duplicates.entrySet().forEach(entry -> {
+                assertThat(entry.getValue().size()).isEqualTo(1);
+            });
         }
 
     }
@@ -269,7 +301,7 @@ public class RedactionIntegrationTest {
 
         System.out.println("redactionTest");
         long start = System.currentTimeMillis();
-        ClassPathResource pdfFileResource = new ClassPathResource("files/Trinexapac/96 Trinexapac-ethyl_RAR_09_Volume_3CA_B-7_2018-02-23.pdf");
+        ClassPathResource pdfFileResource = new ClassPathResource("files/Metolachlor/S-Metolachlor_RAR_01_Volume_1_2018-09-06.pdf");
 
         RedactionRequest request = RedactionRequest.builder()
                 .document(IOUtils.toByteArray(pdfFileResource.getInputStream()))
@@ -319,9 +351,26 @@ public class RedactionIntegrationTest {
         ClassPathResource pdfFileResource = new ClassPathResource("files/Minimal Examples/Single Table.pdf");
 
         ManualRedactions manualRedactions = new ManualRedactions();
-        manualRedactions.setIdsToRemove(Set.of("0836727c3508a0b2ea271da69c04cc2f"));
+
+        String manualAddId = UUID.randomUUID().toString();
+
+        Comment comment = Comment.builder()
+                .date(OffsetDateTime.now())
+                .user("TEST_USER")
+                .text("This is a comment test")
+                .build();
+        manualRedactions.setIdsToRemove(Set.of(IdRemoval.builder()
+                .id("0836727c3508a0b2ea271da69c04cc2f")
+                .status(Status.REQUESTED)
+                .build()));
+
+        manualRedactions.getComments().put("e5be0f1d941bbb92a068e198648d06c4", List.of(comment));
+        manualRedactions.getComments().put("0836727c3508a0b2ea271da69c04cc2f", List.of(comment));
+        manualRedactions.getComments().put(manualAddId, List.of(comment));
 
         ManualRedactionEntry manualRedactionEntry = new ManualRedactionEntry();
+        manualRedactionEntry.setId(manualAddId);
+        manualRedactionEntry.setStatus(Status.REQUESTED);
         manualRedactionEntry.setType("name");
         manualRedactionEntry.setValue("O'Loughlin C.K.");
         manualRedactionEntry.setReason("Manual Redaction");
@@ -350,8 +399,7 @@ public class RedactionIntegrationTest {
     public void classificationTest() throws IOException {
 
         System.out.println("classificationTest");
-        ClassPathResource pdfFileResource = new ClassPathResource("files/Fludioxonil/51 " +
-                "Fludioxonil_RAR_02_Volume_2_2018-02-21.pdf");
+        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()))
@@ -369,8 +417,7 @@ public class RedactionIntegrationTest {
     public void sectionsTest() throws IOException {
 
         System.out.println("sectionsTest");
-        ClassPathResource pdfFileResource = new ClassPathResource("files/Fludioxonil/51 " +
-                "Fludioxonil_RAR_02_Volume_2_2018-02-21.pdf");
+        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()))
@@ -388,8 +435,7 @@ public class RedactionIntegrationTest {
     public void htmlTablesTest() throws IOException {
 
         System.out.println("htmlTablesTest");
-        ClassPathResource pdfFileResource = new ClassPathResource("files/Fludioxonil/51 " +
-                "Fludioxonil_RAR_02_Volume_2_2018-02-21.pdf");
+        ClassPathResource pdfFileResource = new ClassPathResource("files/Minimal Examples/line_breaks.pdf");
 
         RedactionRequest request = RedactionRequest.builder()
                 .document(IOUtils.toByteArray(pdfFileResource.getInputStream()))
@@ -407,8 +453,7 @@ public class RedactionIntegrationTest {
     public void htmlTableRotationTest() throws IOException {
 
         System.out.println("htmlTableRotationTest");
-        ClassPathResource pdfFileResource = new ClassPathResource("files/Metolachlor/S" +
-                "-Metolachlor_RAR_02_Volume_2_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()))
@@ -422,14 +467,56 @@ 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

@@ -35,7 +35,7 @@ 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.Colors;
 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;
@@ -55,8 +55,11 @@ 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 String SPONSOR_CODE = "sponsor";
 
     private static final AtomicLong DICTIONARY_VERSION = new AtomicLong();
+    private static final AtomicLong RULES_VERSION = new AtomicLong();
+
     @MockBean
     private DictionaryClient dictionaryClient;
 
@@ -69,6 +72,9 @@ public class EntityRedactionServiceTest {
     @Autowired
     private PdfSegmentationService pdfSegmentationService;
 
+    @Autowired
+    private DroolsExecutionService droolsExecutionService;
+
     @TestConfiguration
     public static class RedactionIntegrationTestConfiguration {
 
@@ -130,7 +136,35 @@ public class EntityRedactionServiceTest {
             Document classifiedDoc = pdfSegmentationService.parseDocument(pdDocument);
             entityRedactionService.processDocument(classifiedDoc, null);
             assertThat(classifiedDoc.getEntities()).hasSize(1); // one page
-            assertThat(classifiedDoc.getEntities().get(1)).hasSize(5); // 4 out of 5 entities recognized on page 1
+            assertThat(classifiedDoc.getEntities().get(1)).hasSize(7);// 3 author cells, 1 address, 1 Y and 2 N entities
+        }
+    }
+
+
+    @Test
+    public void testNestedRedaction() throws IOException {
+
+        ClassPathResource pdfFileResource = new ClassPathResource("files/Minimal Examples/nested_redaction.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 author cells, 1 address, 1 Y and 2 N entities
         }
     }
 
@@ -185,7 +219,7 @@ public class EntityRedactionServiceTest {
         try (PDDocument pdDocument = PDDocument.load(pdfFileResource.getInputStream())) {
             Document classifiedDoc = pdfSegmentationService.parseDocument(pdDocument);
             entityRedactionService.processDocument(classifiedDoc, null);
-            assertThat(classifiedDoc.getEntities()).hasSize(1); // two pages
+            assertThat(classifiedDoc.getEntities()).hasSize(1); // one page
             assertThat(classifiedDoc.getEntities().get(1).stream()
                     .filter(entity -> entity.getMatchedRule() == 9)
                     .count()).isEqualTo(10);
@@ -193,6 +227,105 @@ public class EntityRedactionServiceTest {
 
     }
 
+
+    @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\", \"Reg" +
+                " (EC) No 1107/2009 Art. 63 (2g)\");\n" +
+                "       section.redactBetween(\"Address:\", \"Contact\", \"address\", 6, \"Applicant information was found\", \"Reg (EC) No 1107/2009 Art. 63 (2g)\");\n" +
+                "       section.redactLineAfter(\"Contact point:\",  \"address\", 6, \"Applicant information was found\", \"Reg (EC) No 1107/2009 Art. 63 (2g)\");\n" +
+                "       section.redactLineAfter(\"Phone:\", \"address\", 6, \"Applicant information was found\", " +
+                "\"Reg (EC) No 1107/2009 Art. 63 (2g)\");\n" +
+                "       section.redactLineAfter(\"Fax:\", \"address\", 6, \"Applicant information was found\", \"Reg " +
+                "(EC) No 1107/2009 Art. 63 (2g)\");\n" +
+                "       section.redactLineAfter(\"Tel.:\", \"address\", 6, \"Applicant information was found\", \"Reg" +
+                " (EC) No 1107/2009 Art. 63 (2g)\");\n" +
+                "       section.redactLineAfter(\"Tel:\", \"address\", 6, \"Applicant information was found\", \"Reg " +
+                "(EC) No 1107/2009 Art. 63 (2g)\");\n" +
+                "       section.redactLineAfter(\"E-mail:\", \"address\", 6, \"Applicant information was found\", " +
+                "\"Reg (EC) No 1107/2009 Art. 63 (2g)\");\n" +
+                "       section.redactLineAfter(\"Email:\", \"address\", 6, \"Applicant information was found\", " +
+                "\"Reg (EC) No 1107/2009 Art. 63 (2g)\");\n" +
+                "       section.redactLineAfter(\"Contact:\", \"address\", 6, \"Applicant information was found\", " +
+                "\"Reg (EC) No 1107/2009 Art. 63 (2g)\");\n" +
+                "       section.redactLineAfter(\"Telephone number:\", \"address\", 6, \"Applicant information was found\", \"Reg (EC) No 1107/2009 Art. 63 (2g)\");\n" +
+                "       section.redactLineAfter(\"Fax number:\", \"address\", 6, \"Applicant information was found\"," +
+                " \"Reg (EC) No 1107/2009 Art. 63 (2g)\");\n" +
+                "       section.redactLineAfter(\"Telephone:\", \"address\", 6, \"Applicant information was found\", " +
+                "\"Reg (EC) No 1107/2009 Art. 63 (2g)\");\n" +
+                "       section.redactBetween(\"No:\", \"Fax\", \"address\", 6, \"Applicant information was found\", " +
+                "\"Reg (EC) No 1107/2009 Art. 63 (2g)\");\n" +
+                "       section.redactBetween(\"Contact:\", \"Tel.:\", \"address\", 6, \"Applicant information was found\", \"Reg (EC) No 1107/2009 Art. 63 (2g)\");\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 testSponsorInCell() 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 \"11: Redact sponsor company\"\n" + "    when\n" + "        " +
+                "Section(searchText.toLowerCase().contains(\"batches produced at\"))\n" + "    then\n" + "        section" +
+                ".redactIfPrecededBy(\"batches produced at\", \"sponsor\", 11, \"Redacted because it represents a " +
+                "sponsor company\", \"Reg (EC) No 1107/2009 Art. 63 (2g)\");\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/batches_new_line.pdf");
+        when(dictionaryClient.getVersion()).thenReturn(DICTIONARY_VERSION.incrementAndGet());
+        DictionaryResponse dictionaryResponse = DictionaryResponse.builder()
+                .entries(new ArrayList<>(ResourceLoader.load("dictionaries/sponsor_companies.txt")))
+                .build();
+        when(dictionaryClient.getDictionaryForType(SPONSOR_CODE)).thenReturn(dictionaryResponse);
+        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() == 11)
+                    .count()).isEqualTo(1);
+        }
+
+    }
+
+
     @Test
     public void headerPropagation() throws IOException {
 
@@ -214,7 +347,53 @@ public class EntityRedactionServiceTest {
             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);
+            assertThat(classifiedDoc.getEntities().get(2).stream().filter(entity -> entity.getMatchedRule() == 9).count()).isEqualTo(5); // 2 names, 1 address, 2 Y
+        }
+
+        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);
         }
     }
 
@@ -226,24 +405,53 @@ public class EntityRedactionServiceTest {
                 "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.redactNotCell(\"Author(s)\", 8,  \"name\", \"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(isVertebrateStudy())\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 rows is a vertebrate study\");\n" +
+                "        section.redactCell(\"Author(s)\", 9,  \"name\", \"Redacted because row is a vertebrate study\", \"Reg (EC) No 1107/2009 Art. 63 (2g)\");\n" +
+                "        section.redact(\"address\", 9, \"Redacted because row is a vertebrate study\", \"Reg (EC) No" +
+                " 1107/2009 Art. 63 (2g)\");\n" +
                 "        section.highlightCell(\"Vertebrate study Y/N\", 9, \"must_redact\");\n" +
                 "    end";
-        when(rulesClient.getVersion()).thenReturn(1L);
+        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()))
+                        TypeResult.builder().type(NAME_CODE).hexColor("#ffff00").build(),
+                        TypeResult.builder().type(ADDRESS_CODE).hexColor("#ff00ff").build(),
+                        TypeResult.builder().type(SPONSOR_CODE).hexColor("#00ffff").build()))
                 .build();
         when(dictionaryClient.getVersion()).thenReturn(DICTIONARY_VERSION.incrementAndGet());
         when(dictionaryClient.getAllTypes()).thenReturn(typeResponse);
-        when(dictionaryClient.getDefaultColor()).thenReturn(new DefaultColor());
+
+        // Default empty return to prevent NPEs
+        DictionaryResponse dictionaryResponse = DictionaryResponse.builder()
+                .build();
+        when(dictionaryClient.getDictionaryForType(NAME_CODE)).thenReturn(dictionaryResponse);
+        DictionaryResponse addressResponse = DictionaryResponse.builder()
+                .build();
+        when(dictionaryClient.getDictionaryForType(ADDRESS_CODE)).thenReturn(addressResponse);
+        DictionaryResponse sponsorResponse = DictionaryResponse.builder()
+                .build();
+        when(dictionaryClient.getDictionaryForType(SPONSOR_CODE)).thenReturn(sponsorResponse);
+
+        Colors colors = new Colors();
+        colors.setDefaultColor("#acfc00");
+        colors.setNotRedacted("#cccccc");
+        colors.setRequestAdd("#04b093");
+        colors.setRequestRemove("#04b093");
+
+        when(dictionaryClient.getColors()).thenReturn(colors);
     }
 
 

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

@@ -3,6 +3,7 @@ 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;
 
@@ -94,6 +95,46 @@ public class PdfSegmentationServiceTest {
             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()
@@ -105,4 +146,44 @@ public class PdfSegmentationServiceTest {
         }
     }
 
+
+    @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/addresses.txt

@@ -227,6 +227,7 @@ CIBA-GEIGY Limited, Toxicology Services, Short-term Toxicology, 4332 Stein, Swit
 CIBA-GEIGY Ltd. CH-4002 Basle, Switzerland
 CIBA-GEIGY Ltd., Product Safety, Ecotoxicology, CH-4002 Basel, Switzerland
 CIBA-GEIGY Ltd., Switzerland
+CibaGeigy Ltd., CH-4002, Basel, Switzerland
 CIP Chemisches Institut Pforzheim GmbH, Pforzheim, Germany
 CL PHARMA AG
 CL PHARMA AG, Linz, Austria
@@ -1563,4 +1564,36 @@ Zyma SA
 Zyma SA, Nyon, Switzerland
 “Bayer CropScience AG” Monheim
 “Biologische Bundesanstalt (BBA)”, Berlin-Dahlem
-“W. Neudorff GmbH KG”, An der Mühle 3, D- 31860 Emmertal
+“W. Neudorff GmbH KG”, An der Mühle 3, D- 31860 Emmertal
+Syngenta Ltd Jealott’s Hill Int. Research Centre Bracknell, Berkshire, RG42 6EY, United Kingdom
+MITOX Consultants Science Park 408, 1098XH Amsterdam, NL
+Eurofins Agrosciences Services Eco-Chem GmbH, Eutinger Str. 24, 75233 Niefern-Öschelbronn, Germany
+Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), 57392 Schmallenberg, Germany
+Syngenta Crop Protection AGRCC Cytotest Cell Research GmbH, Germany
+BASF SE, Ludwigshafen, Germany
+AGRCC Ltd., Switzerland
+AGWIL Research Lab. Inc., USA
+Charles River Laboratories, UK
+Ciba-Geigy Corporation Environmental Health Centre, Farmington
+Syngenta Crop Protection, Inc., Greensboro, United States
+Experimental Toxicology and Ecology, BASF SE
+Wildlife International, Ltd. 8598 Commerce Drive Easton, MD 21601 USA
+Küberich, Wiesentheid / Geesdorf, Germany
+CiToxLAB Hungary Ltd. H8200 Veszprém, Szabadságpuszta, Hungary
+Forellenzucht Trostadt GbR, Trostadt, Germany
+Osage Catfisheries Inc., Osage Beach, MO, USA
+Fischzucht Rhönforelle, Gersfeld, Germany
+Aquatic Biosystems, Ft. Collins, Colorado, USA
+West Aquarium GmbH, 37431 Bad Lauterberg, Germany
+Aquatic BioSystems, Fort Collins, Colorado, USA
+“U.S. Environmental Research Laboratory”, Duluth, Minnesota, USA
+Continuous laboratory cultures
+Wildlife International, Ltd. 8598 Commerce Drive Easton, MD 21601 USA
+Osage Catfisheries, Inc., Osage Beach, MO, USA
+Osage catfisheries, Osage Beach (MO), USA
+Ciba-Geigy Corporation, Environmental Health Centre, Farmington
+Novartis Crop Protection Inc., Greensboro, United States
+Syngenta, Jealott’s Hill International Research Station, UK
+Hillandale Farms, Kenansville, Florida, USA
+Jealott’s Hill International Research Station, UK
+L & C Dairy, Avon Park, Florida, UK

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

@@ -1,3 +1,2 @@
-Batches Produced at
 CTL
-for determination of residues
+determination of residues

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

@@ -5290,6 +5290,7 @@ Naeb O.
 Nagai K.
 Nagashima Yoshikazu
 Nagata H.|Tanaka T.
+Nagra, B
 Nagra B.S
 Nagra B.|Kingdom N.
 Nagy K
@@ -5640,6 +5641,7 @@ Pedersen Carol
 Pedersen Carol|DuCharme Darlene
 Pedersen C|Ducharme D.
 Pederson C.A.
+Pederson
 Peffer
 Peffer R
 Peffer R.
@@ -6249,6 +6251,7 @@ Roth M.
 Roth Markus
 Roth RN|Heilman RD
 Roth, M.
+Roth
 Rotroff
 Rouaud, J. L.
 Roussel C
@@ -6848,7 +6851,7 @@ Sokolowshi Andrea
 Sokolowski A
 Sokolowski A.
 Sokolowski Andrea
-Sokolowski,
+Sokolowski
 Sole
 Sole C
 Sole, C.
@@ -7248,6 +7251,7 @@ Thanei, P.
 Tharp BE
 Thede B.
 Theophilidis G
+Thevenaz
 Thevenaz P
 Thevenaz P.
 Thevenaz Ph.
@@ -8193,4 +8197,113 @@ Zoriki Hosomi R.
 Zoriki Hosomi Rosana
 Zuberer D
 Zubrod J
-Zwicker R.E.
+Zwicker R.E.
+Ott
+Argus et al
+Mihail
+Clapp
+Murfitt R
+Yang
+Swarbrick
+Hertl
+Breitwieser
+Seville, A
+Trumper, C.
+Gasso-Brown, D.
+Váliczkó, É
+Váliczkó, É.
+Durando, J.
+Tarcai, Z.
+Pooles, A
+Roig, J.
+Schäfers, C.
+Nixon, W.
+Zok, S.
+Durjava M.K. et al
+Jatzek J
+Salinas E
+Sousa J. V
+Caferella, M.A.
+Salina, E.
+Walraven J
+Kaspers et al
+Schneider et al
+Lowrie C
+Macdougall J
+Roberts S
+Madrid, S.O.
+Maynard, M.S.
+Ray, W.
+Ray, W.J.
+Váliczkó É
+Tarcai Z
+Orovecz B
+Kaspers
+Tarcai Z.
+Gizler, A
+Whitlow
+Johnson et al
+Bryden et al
+Váliczkó
+Höger
+Dorgerloh
+Schäfers C
+Caferella M.A
+Salinas, E
+Zok S
+Tummon OJ
+Eckstein CL
+Francis PD
+Ott M
+Richeux F
+Rajsekhar PV
+Webbley
+O’Hagan
+MacDonald
+Jewkes
+Harris
+Tomlinson
+Tomlinson et al
+Nagy
+Török-Bathó
+Hargitai
+Shearer
+Robertson
+Strepka
+Hackford
+Blunt
+Sieber
+Elcombe
+Haines
+Kang
+Sayers
+Harris J
+Baxter A
+Macdonald M
+PetusArpasy M
+TorokBatho M.
+van Ravenzwaa y B
+Cords S
+Dymarkows ka K.
+Bahig M
+Pekari K
+Bercz J
+Russell L
+Kitchen K
+Miyagawa M.
+Sasaki Y
+Yin D
+Huff J
+Blackburn K
+Carlson G
+Pereira M
+Stoner G
+Zelenak V
+Valiczko E
+Tomlinso n J
+Trumper C
+Senciuc M
+Vance C.
+Przeorska J.
+Melville S.
+Wicksted G.

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/drools/rules.drl

@@ -7,16 +7,16 @@ 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");
+		section.redact("name", 1, "Redacted because Section contains Vertebrate", "Reg (EC) No 1107/2009 Art. 63 (2g)");
+		section.redact("address", 1, "Redacted because Section contains Vertebrate", "Reg (EC) No 1107/2009 Art. 63 (2g)");
 	end
 
 
 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");
@@ -25,7 +25,7 @@ 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");
@@ -34,88 +34,102 @@ rule "3: Do not redact Names and Addresses if no redaction Indicator is containe
 
 rule "4: Redact Names and Addresses if no_redaction_indicator and redaction_indicator is contained"
 	when
-		eval(section.contains("vertebrate")==true && section.contains("no_redaction_indicator")==true && section.contains("redaction_indicator")==true);
+		Section(matchesType("vertebrate"), matchesType("no_redaction_indicator"), matchesType("redaction_indicator"))
 	then
-		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");
+		section.redact("name", 4, "Vertebrate was found and no_redaction_indicator and redaction_indicator", "Reg (EC) No 1107/2009 Art. 63 (2g)");
+		section.redact("address", 4, "Vertebrate was found and no_redaction_indicator and redaction_indicator", "Reg (EC) No 1107/2009 Art. 63 (2g)");
 	end
 
 
 rule "5: Do not redact in guideline sections"
 	when
-		eval(section.headlineContainsWord("guideline") || section.headlineContainsWord("Guidance"));
+		Section(headlineContainsWord("guideline") || headlineContainsWord("Guidance"))
 	then
 		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"
+
+rule "6: Redact contact information if applicant is found"
 	when
-		eval(section.headlineContainsWord("applicant") || section.getText().contains("Applicant"));
+		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("Contact:", "address", 6, "Applicant information was found");
-		section.redactLineAfter("Telephone number:", "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.redactBetween("No:", "Fax", "address", 6, "Applicant information was found");
-		section.redactBetween("Contact:", "Tel.:", "address", 6, "Applicant information was found");
+		section.redactLineAfter("Name:", "address", 6, "Applicant information was found", "Reg (EC) No 1107/2009 Art. 63 (2g)");
+		section.redactBetween("Address:", "Contact", "address", 6, "Applicant information was found", "Reg (EC) No 1107/2009 Art. 63 (2g)");
+		section.redactLineAfter("Contact point:",  "address", 6, "Applicant information was found", "Reg (EC) No 1107/2009 Art. 63 (2g)");
+		section.redactLineAfter("Phone:", "address", 6, "Applicant information was found", "Reg (EC) No 1107/2009 Art. 63 (2g)");
+		section.redactLineAfter("Fax:", "address", 6, "Applicant information was found", "Reg (EC) No 1107/2009 Art. 63 (2g)");
+		section.redactLineAfter("Tel.:", "address", 6, "Applicant information was found", "Reg (EC) No 1107/2009 Art. 63 (2g)");
+		section.redactLineAfter("Tel:", "address", 6, "Applicant information was found", "Reg (EC) No 1107/2009 Art. 63 (2g)");
+		section.redactLineAfter("E-mail:", "address", 6, "Applicant information was found", "Reg (EC) No 1107/2009 Art. 63 (2g)");
+		section.redactLineAfter("Email:", "address", 6, "Applicant information was found", "Reg (EC) No 1107/2009 Art. 63 (2g)");
+		section.redactLineAfter("e-mail:", "address", 6, "Applicant information was found", "Reg (EC) No 1107/2009 Art. 63 (2g)");
+		section.redactLineAfter("E-mail address:", "address", 6, "Applicant information was found", "Reg (EC) No 1107/2009 Art. 63 (2g)");
+		section.redactLineAfter("Contact:", "address", 6, "Applicant information was found", "Reg (EC) No 1107/2009 Art. 63 (2g)");
+		section.redactLineAfter("Alternative contact:", "address", 6, "Applicant information was found", "Reg (EC) No 1107/2009 Art. 63 (2g)");
+		section.redactLineAfter("Telephone number:", "address", 6, "Applicant information was found", "Reg (EC) No 1107/2009 Art. 63 (2g)");
+		section.redactLineAfter("Telephone No:", "address", 6, "Applicant information was found", "Reg (EC) No 1107/2009 Art. 63 (2g)");
+		section.redactLineAfter("Fax number:", "address", 6, "Applicant information was found", "Reg (EC) No 1107/2009 Art. 63 (2g)");
+		section.redactLineAfter("Telephone:", "address", 6, "Applicant information was found", "Reg (EC) No 1107/2009 Art. 63 (2g)");
+		section.redactLineAfter("Company:", "address", 6, "Applicant information was found", "Reg (EC) No 1107/2009 Art. 63 (2g)");
+		section.redactBetween("No:", "Fax", "address", 6, "Applicant information was found", "Reg (EC) No 1107/2009 Art. 63 (2g)");
+		section.redactBetween("Contact:", "Tel.:", "address", 6, "Applicant information was found", "Reg (EC) No 1107/2009 Art. 63 (2g)");
 	end
 
-rule "7: Redact contact information, if Producer is found"
+
+rule "7: Redact contact information if Producer is found"
 	when
-		eval(section.getText().toLowerCase().contains("producer of the plant protection") || section.getText().toLowerCase().contains("producer of the active substance") || section.getText().contains("Manufacturer of the active substance") || section.getText().contains("Manufacturer:") || section.getText().contains("Producer or producers of the active substance"));
+		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");
+		section.redactLineAfter("Name:", "address", 7, "Producer was found", "Reg (EC) No 1107/2009 Art. 63 (2g)");
+		section.redactBetween("Address:", "Contact", "address", 7, "Producer was found", "Reg (EC) No 1107/2009 Art. 63 (2g)");
+		section.redactBetween("Contact:", "Phone", "address", 7, "Producer was found", "Reg (EC) No 1107/2009 Art. 63 (2g)");
+		section.redactBetween("Contact:", "Telephone number:", "address", 7, "Producer was found", "Reg (EC) No 1107/2009 Art. 63 (2g)");
+		section.redactBetween("Address:", "Manufacturing", "address", 7, "Producer was found", "Reg (EC) No 1107/2009 Art. 63 (2g)");
+		section.redactLineAfter("Telephone:", "address", 7, "Producer was found", "Reg (EC) No 1107/2009 Art. 63 (2g)");
+		section.redactLineAfter("Phone:", "address", 7, "Producer was found", "Reg (EC) No 1107/2009 Art. 63 (2g)");
+		section.redactLineAfter("Fax:", "address", 7, "Producer was found", "Reg (EC) No 1107/2009 Art. 63 (2g)");
+		section.redactLineAfter("E-mail:", "address", 7, "Producer was found", "Reg (EC) No 1107/2009 Art. 63 (2g)");
+		section.redactLineAfter("Contact:", "address", 7, "Producer was found", "Reg (EC) No 1107/2009 Art. 63 (2g)");
+		section.redactLineAfter("Fax number:", "address", 7, "Producer was found", "Reg (EC) No 1107/2009 Art. 63 (2g)");
+		section.redactLineAfter("Telephone number:", "address", 7, "Producer was found", "Reg (EC) No 1107/2009 Art. 63 (2g)");
+		section.redactLineAfter("Tel:", "address", 7, "Producer was found", "Reg (EC) No 1107/2009 Art. 63 (2g)");
+		section.redactBetween("No:", "Fax", "address", 7, "Producer was found", "Reg (EC) No 1107/2009 Art. 63 (2g)");
 	end
 
 
 rule "8: Not redacted because Vertebrate Study = N"
     when
-        Section(isNotVertebrateStudy())
+        Section(rowEquals("Vertebrate study Y/N", "N") || rowEquals("Vertebrate study Y/N", "No"))
     then
-        section.redactNot("name", 8, "Not redacted because row is not a vertebrate study");
+        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");
-        section.highlightCell("Verte brate study Y/N", 8, "hint_only");
     end
 
 
 rule "9: Redact if must redact entry is found"
 	when
-		eval(section.contains("must_redact")==true);
+		Section(matchesType("must_redact"))
 	then
-		section.redact("name", 9, "must_redact entry was found.");
-		section.redact("address", 9, "must_redact entry was found.");
+		section.redact("name", 9, "must_redact entry was found.", "Reg (EC) No 1107/2009 Art. 63 (2g)");
+		section.redact("address", 9, "must_redact entry was found.", "Reg (EC) No 1107/2009 Art. 63 (2g)");
 	end
 
-rule "10: Redact Authors and Addresses in Reference Table, if it is a Vertebrate study"
+
+rule "10: Redact Authors and Addresses in Reference Table if it is a Vertebrate study"
     when
-        Section(isVertebrateStudy())
+        Section(rowEquals("Vertebrate study Y/N", "Y") || rowEquals("Vertebrate study Y/N", "Yes"))
     then
-        section.redact("name", 10, "Redacted because row is a vertebrate study");
-        section.redact("address", 10, "Redacted because row is a vertebrate study");
+        section.redactCell("Author(s)", 10, "name", "Redacted because row is a vertebrate study", "Reg (EC) No 1107/2009 Art. 63 (2g)");
+        section.redact("address", 10, "Redacted because row is a vertebrate study", "Reg (EC) No 1107/2009 Art. 63 (2g)");
         section.highlightCell("Vertebrate study Y/N", 10, "must_redact");
-        section.highlightCell("Verte brate study Y/N", 10, "must_redact");
+    end
+
+
+rule "11: Redact sponsor company"
+    when
+        Section(searchText.toLowerCase().contains("batches produced at"))
+    then
+        section.redactIfPrecededBy("batches produced at", "sponsor", 11, "Redacted because it represents a sponsor company", "Reg (EC) No 1107/2009 Art. 63 (2g)");
     end