RED-88: Enabled manual redaction

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

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

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

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

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

@@ -3,9 +3,11 @@ package com.iqser.red.service.redaction.v1.model;
 import java.util.ArrayList;
 import java.util.List;
 
+import lombok.Builder;
 import lombok.Data;
 
 @Data
+@Builder
 public class RedactionLogEntry {
 
     private String id;
@@ -16,7 +18,10 @@ public class RedactionLogEntry {
     private boolean isHint;
     private String section;
     private float[] color;
+
+    @Builder.Default
     private List<Rectangle> positions = new ArrayList<>();
     private int sectionNumber;
+    private boolean manual;
 
 }

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

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

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

@@ -56,6 +56,11 @@
             <artifactId>jts-core</artifactId>
             <version>1.16.1</version>
         </dependency>
+        <dependency>
+            <groupId>com.google.guava</groupId>
+            <artifactId>guava</artifactId>
+            <version>29.0-jre</version>
+        </dependency>
         <!-- commons -->
         <dependency>
             <groupId>com.iqser.gin4.commons</groupId>

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

@@ -41,4 +41,16 @@ public class Paragraph {
         return tables;
     }
 
+
+    public List<TextBlock> getTextBlocks() {
+
+        List<TextBlock> textBlocks = new ArrayList<>();
+        pageBlocks.forEach(block -> {
+            if (block instanceof TextBlock) {
+                textBlocks.add((TextBlock) block);
+            }
+        });
+        return textBlocks;
+    }
+
 }

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

@@ -44,8 +44,8 @@ public class RedactionController implements RedactionResource {
             pdDocument.setAllSecurityToBeRemoved(true);
 
             Document classifiedDoc = pdfSegmentationService.parseDocument(pdDocument);
-            entityRedactionService.processDocument(classifiedDoc);
+            entityRedactionService.processDocument(classifiedDoc, redactionRequest.getManualRedactions());
-            annotationHighlightService.highlight(pdDocument, classifiedDoc, redactionRequest.isFlatRedaction());
+            annotationHighlightService.highlight(pdDocument, classifiedDoc, redactionRequest.isFlatRedaction(), redactionRequest.getManualRedactions());
 
             if (redactionRequest.isFlatRedaction()) {
                 PDDocument flatDocument = pdfFlattenService.flattenPDF(pdDocument);

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

@@ -5,6 +5,9 @@ import java.util.List;
 
 import org.apache.pdfbox.text.TextPosition;
 
+import com.iqser.red.service.redaction.v1.model.Point;
+import com.iqser.red.service.redaction.v1.model.Rectangle;
+
 import lombok.Data;
 import lombok.Getter;
 import lombok.RequiredArgsConstructor;
@@ -22,36 +25,48 @@ public class TextPositionSequence implements CharSequence {
 
     private final int page;
 
-    public TextPositionSequence(List<TextPosition> textPositions, int page){
+
+    public TextPositionSequence(List<TextPosition> textPositions, int page) {
+
         this.textPositions = textPositions;
         this.page = page;
     }
 
+
     @Override
     public int length() {
+
         return textPositions.size();
     }
 
+
     @Override
     public char charAt(int index) {
+
         TextPosition textPosition = textPositionAt(index);
         String text = textPosition.getUnicode();
         return text.charAt(0);
     }
 
+
     public char charAt(int index, boolean caseInSensitive) {
+
         TextPosition textPosition = textPositionAt(index);
         String text = textPosition.getUnicode();
         return caseInSensitive ? text.toLowerCase().charAt(0) : text.charAt(0);
     }
 
+
     @Override
     public TextPositionSequence subSequence(int start, int end) {
+
         return new TextPositionSequence(textPositions.subList(start, end), page);
     }
 
+
     @Override
     public String toString() {
+
         StringBuilder builder = new StringBuilder(length());
         for (int i = 0; i < length(); i++) {
             builder.append(charAt(i));
@@ -59,15 +74,21 @@ public class TextPositionSequence implements CharSequence {
         return builder.toString();
     }
 
+
     public TextPosition textPositionAt(int index) {
+
         return textPositions.get(index);
     }
 
+
     public void add(TextPosition textPosition) {
+
         this.textPositions.add(textPosition);
     }
 
+
     public float getX1() {
+
         if (textPositions.get(0).getRotation() == 90) {
             return textPositions.get(0).getYDirAdj() - getTextHeight();
         } else {
@@ -75,15 +96,20 @@ public class TextPositionSequence implements CharSequence {
         }
     }
 
+
     public float getX2() {
+
         if (textPositions.get(0).getRotation() == 90) {
             return textPositions.get(0).getYDirAdj();
         } else {
-            return textPositions.get(textPositions.size() - 1).getXDirAdj() + textPositions.get(textPositions.size() - 1).getWidth() + 1;
+            return textPositions.get(textPositions.size() - 1)
+                    .getXDirAdj() + textPositions.get(textPositions.size() - 1).getWidth() + 1;
         }
     }
 
+
     public float getY1() {
+
         if (textPositions.get(0).getRotation() == 90) {
             return textPositions.get(0).getXDirAdj();
         } else {
@@ -91,30 +117,46 @@ public class TextPositionSequence implements CharSequence {
         }
     }
 
+
     public float getY2() {
+
         if (textPositions.get(0).getRotation() == 90) {
-            return textPositions.get(textPositions.size() - 1).getXDirAdj() + getTextHeight() -2 ;
+            return textPositions.get(textPositions.size() - 1).getXDirAdj() + getTextHeight() - 2;
         } else {
             return textPositions.get(0).getPageHeight() - textPositions.get(0).getYDirAdj() + getTextHeight();
         }
     }
 
+
     public float getTextHeight() {
+
         return textPositions.get(0).getHeightDir() + 2;
     }
 
+
     public float getHeight() {
+
         return getY2() - getY1();
     }
 
+
     public float getWidth() {
+
         return getX2() - getX1();
     }
 
+
     public String getFont() {
-        return textPositions.get(0).getFont().toString().toLowerCase().replaceAll(",bold", "").replaceAll(",italic", "");
+
+        return textPositions.get(0)
+                .getFont()
+                .toString()
+                .toLowerCase()
+                .replaceAll(",bold", "")
+                .replaceAll(",italic", "");
     }
 
+
     public String getFontStyle() {
 
         String lowercaseFontName = textPositions.get(0).getFont().toString().toLowerCase();
@@ -131,16 +173,51 @@ public class TextPositionSequence implements CharSequence {
 
     }
 
+
     public float getFontSize() {
+
         return textPositions.get(0).getFontSizeInPt();
     }
 
+
     public float getSpaceWidth() {
+
         return textPositions.get(0).getWidthOfSpace();
     }
 
+
     public int getRotation() {
+
         return textPositions.get(0).getRotation();
     }
 
+
+    public Rectangle getRectangle() {
+
+        float height = textPositions.get(0).getHeightDir() + 2;
+
+        float posXInit;
+        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();
+            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;
+            posYEnd = textPositions.get(0).getPageHeight() - textPositions.get(textPositions.size() - 1)
+                    .getYDirAdj() + 2;
+        }
+
+        return new Rectangle(new Point(posXInit, posYInit), posXEnd - posXInit, posYEnd - posYInit + height, page);
+    }
+
 }

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

@@ -2,7 +2,6 @@ package com.iqser.red.service.redaction.v1.server.redaction.model;
 
 import java.util.ArrayList;
 import java.util.List;
-import java.util.UUID;
 
 import com.iqser.red.service.redaction.v1.server.parsing.model.TextPositionSequence;
 
@@ -20,6 +19,6 @@ public class EntityPositionSequence {
     @EqualsAndHashCode.Exclude
     private List<TextPositionSequence> sequences = new ArrayList<>();
     private int pageNumber;
-    private final UUID id;
+    private final String id;
 
 }

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

@@ -2,10 +2,10 @@ package com.iqser.red.service.redaction.v1.server.redaction.model;
 
 import java.util.ArrayList;
 import java.util.List;
-import java.util.UUID;
 import java.util.regex.Pattern;
 
 import com.iqser.red.service.redaction.v1.server.parsing.model.TextPositionSequence;
+import com.iqser.red.service.redaction.v1.server.redaction.utils.IdBuilder;
 import com.iqser.red.service.redaction.v1.server.redaction.utils.TextNormalizationUtilities;
 
 public class SearchableText {
@@ -114,7 +114,7 @@ public class SearchableText {
 
     private List<EntityPositionSequence> buildEntityPositionSequence(List<TextPositionSequence> crossSequenceParts) {
 
-        UUID id = UUID.randomUUID();
+        String id = IdBuilder.buildId(crossSequenceParts);
         List<EntityPositionSequence> result = new ArrayList<>();
         int currentPage = -1;
         EntityPositionSequence entityPositionSequence = new EntityPositionSequence(id);

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

@@ -12,6 +12,9 @@ import org.apache.commons.collections4.CollectionUtils;
 import org.apache.commons.lang3.StringUtils;
 import org.springframework.stereotype.Service;
 
+import com.iqser.red.service.redaction.v1.model.ManualRedactionEntry;
+import com.iqser.red.service.redaction.v1.model.ManualRedactions;
+import com.iqser.red.service.redaction.v1.model.Rectangle;
 import com.iqser.red.service.redaction.v1.server.classification.model.Document;
 import com.iqser.red.service.redaction.v1.server.classification.model.Paragraph;
 import com.iqser.red.service.redaction.v1.server.classification.model.TextBlock;
@@ -34,7 +37,7 @@ public class EntityRedactionService {
     private final DroolsExecutionService droolsExecutionService;
 
 
-    public void processDocument(Document classifiedDoc) {
+    public void processDocument(Document classifiedDoc, ManualRedactions manualRedactions) {
 
         dictionaryService.updateDictionary();
         droolsExecutionService.updateRules();
@@ -58,6 +61,7 @@ public class EntityRedactionService {
                             continue;
                         }
                         cellValues.add(cell.getTextBlocks().get(0).getText());
+                        addSectionToManualRedactions(cell.getTextBlocks(), manualRedactions, table.getHeadline(), sectionNumber);
                         for (TextBlock textBlock : cell.getTextBlocks()) {
                             searchableRow.addAll(textBlock.getSequences());
                         }
@@ -80,6 +84,7 @@ public class EntityRedactionService {
                 sectionNumber++;
             }
 
+            addSectionToManualRedactions(paragraph.getTextBlocks(), manualRedactions, paragraph.getHeadline(), sectionNumber);
             Set<Entity> entities = findEntities(searchableText, paragraph.getHeadline(), sectionNumber);
             Section analysedSection = droolsExecutionService.executeRules(Section.builder()
                     .entities(entities)
@@ -103,8 +108,7 @@ public class EntityRedactionService {
             for (Map.Entry<Integer, List<EntityPositionSequence>> entry : sequenceOnPage.entrySet()) {
                 classifiedDoc.getEntities()
                         .computeIfAbsent(entry.getKey(), (x) -> new ArrayList<>())
-                        .add(new Entity(entity.getWord(), entity.getType(), entity.isRedaction(),
+                        .add(new Entity(entity.getWord(), entity.getType(), entity.isRedaction(), entity.getRedactionReason(), entry
-                                entity.getRedactionReason(), entry
                                 .getValue(), entity.getHeadline(), entity.getMatchedRule(), entity.getSectionNumber()));
             }
         }
@@ -184,8 +188,7 @@ public class EntityRedactionService {
 
                 if (startIndex > -1 && (startIndex == 0 || Character.isWhitespace(inputString.charAt(startIndex - 1)) || isSeparator(inputString
                         .charAt(startIndex - 1))) && (stopIndex == inputString.length() || isSeparator(inputString.charAt(stopIndex)))) {
-                    found.add(new Entity(inputString.substring(startIndex, stopIndex), type, startIndex, stopIndex,
+                    found.add(new Entity(inputString.substring(startIndex, stopIndex), type, startIndex, stopIndex, headline, sectionNumber));
-                            headline, sectionNumber));
                 }
             } while (startIndex > -1);
         }
@@ -213,4 +216,23 @@ public class EntityRedactionService {
         entities.removeAll(wordsToRemove);
     }
 
+
+    private void addSectionToManualRedactions(List<TextBlock> textBlocks, ManualRedactions manualRedactions, String section, int sectionNumber) {
+
+        if (manualRedactions == null) {
+            return;
+        }
+
+        for (TextBlock textBlock : textBlocks) {
+            for (ManualRedactionEntry manualRedactionEntry : manualRedactions.getEntriesToAdd()) {
+                for (Rectangle rectangle : manualRedactionEntry.getPositions()) {
+                    if (textBlock.contains(rectangle)) {
+                        manualRedactionEntry.setSection(section);
+                        manualRedactionEntry.setSectionNumber(sectionNumber);
+                    }
+                }
+            }
+        }
+    }
+
 }

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

@@ -0,0 +1,31 @@
+package com.iqser.red.service.redaction.v1.server.redaction.utils;
+
+import java.util.List;
+
+import com.google.common.hash.HashFunction;
+import com.google.common.hash.Hashing;
+import com.iqser.red.service.redaction.v1.model.ManualRedactionEntry;
+import com.iqser.red.service.redaction.v1.server.parsing.model.TextPositionSequence;
+
+import lombok.experimental.UtilityClass;
+
+@UtilityClass
+public class IdBuilder {
+
+    private final HashFunction hashFunction = Hashing.murmur3_128();
+
+    public String buildId(List<TextPositionSequence> crossSequenceParts) {
+
+        StringBuilder sb = new StringBuilder();
+        crossSequenceParts.forEach(sequencePart -> sequencePart.getTextPositions().forEach(textPosition -> {
+            sb.append(textPosition.getTextMatrix());
+        }));
+
+        return hashFunction.hashBytes(sb.toString().getBytes()).toString();
+    }
+
+
+    public String buildId(ManualRedactionEntry manualRedactionEntry) {
+        return hashFunction.hashBytes(manualRedactionEntry.toString().getBytes()).toString();
+    }
+}

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

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

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

@@ -16,7 +16,8 @@ import org.apache.pdfbox.pdmodel.interactive.annotation.PDAnnotation;
 import org.apache.pdfbox.pdmodel.interactive.annotation.PDAnnotationTextMarkup;
 import org.springframework.stereotype.Service;
 
-import com.iqser.red.service.redaction.v1.model.Point;
+import com.iqser.red.service.redaction.v1.model.ManualRedactionEntry;
+import com.iqser.red.service.redaction.v1.model.ManualRedactions;
 import com.iqser.red.service.redaction.v1.model.Rectangle;
 import com.iqser.red.service.redaction.v1.model.RedactionLogEntry;
 import com.iqser.red.service.redaction.v1.server.classification.model.Document;
@@ -26,6 +27,7 @@ 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;
@@ -41,139 +43,171 @@ public class AnnotationHighlightService {
     private final DictionaryService dictionaryService;
 
 
-    public void highlight(PDDocument document, Document classifiedDoc, boolean flatRedaction) throws IOException {
+    public void highlight(PDDocument document, Document classifiedDoc, boolean flatRedaction, ManualRedactions manualRedactions) throws IOException {
 
         for (int page = 1; page <= document.getNumberOfPages(); page++) {
 
             PDPage pdPage = document.getPage(page - 1);
 
-            if (!flatRedaction) {
+            drawSectionFrames(document, classifiedDoc, flatRedaction, pdPage, page);
-                PDPageContentStream contentStream = new PDPageContentStream(document, pdPage, PDPageContentStream.AppendMode.APPEND, true);
-
-                for (Paragraph paragraph : classifiedDoc.getParagraphs()) {
-
-                    for (int i = 0; i <= paragraph.getPageBlocks().size() - 1; i++) {
-
-                        AbstractTextContainer textBlock = paragraph.getPageBlocks().get(i);
-
-                        if (textBlock.getPage() != page) {
-                            continue;
-                        }
-                        if (textBlock instanceof TextBlock) {
-                            textBlock.setClassification((i + 1) + "/" + paragraph.getPageBlocks().size());
-                            visualizeTextBlock((TextBlock) textBlock, contentStream);
-                        } else if (textBlock instanceof Table) {
-                            textBlock.setClassification((i + 1) + "/" + paragraph.getPageBlocks().size());
-                            visualizeTable((Table) textBlock, contentStream);
-                        }
-
-                    }
-                }
-
-                contentStream.close();
-            }
 
             if (classifiedDoc.getEntities().get(page) == null) {
                 continue;
             }
 
-            for (Entity entity : classifiedDoc.getEntities().get(page)) {
+            addAnnotations(pdPage, classifiedDoc, flatRedaction, manualRedactions, page);
+            addManualAnnotations(pdPage, classifiedDoc, manualRedactions, page);
+        }
+    }
 
-                RedactionLogEntry redactionLogEntry = new RedactionLogEntry();
 
-                for (EntityPositionSequence entityPositionSequence : entity.getPositionSequences()) {
+    private void addAnnotations(PDPage pdPage, Document classifiedDoc, boolean flatRedaction, ManualRedactions manualRedactions, int page) throws IOException {
 
-                    if (flatRedaction && !isRedactionType(entity)) {
+        List<PDAnnotation> annotations = pdPage.getAnnotations();
-                        continue;
-                    }
 
-                    for (TextPositionSequence textPositions : entityPositionSequence.getSequences()) {
+        for (Entity entity : classifiedDoc.getEntities().get(page)) {
 
-                        float height = textPositions.getTextPositions().get(0).getHeightDir() + 2;
+            if (flatRedaction && !isRedactionType(entity)) {
-
+                continue;
-                        float posXInit;
-                        float posXEnd;
-                        float posYInit;
-                        float posYEnd;
-
-                        if (textPositions.getTextPositions().get(0).getRotation() == 90) {
-
-                            posXEnd = textPositions.getTextPositions().get(0).getYDirAdj() + 2;
-                            posXInit = textPositions.getTextPositions().get(0).getYDirAdj() - height;
-                            posYInit = textPositions.getTextPositions().get(0).getXDirAdj();
-                            posYEnd = textPositions.getTextPositions()
-                                    .get(textPositions.getTextPositions().size() - 1)
-                                    .getXDirAdj() - height + 4;
-                        } else {
-
-                            posXInit = textPositions.getTextPositions().get(0).getXDirAdj();
-                            posXEnd = textPositions.getTextPositions()
-                                    .get(textPositions.getTextPositions().size() - 1)
-                                    .getXDirAdj() + textPositions.getTextPositions()
-                                    .get(textPositions.getTextPositions().size() - 1)
-                                    .getWidth() + 1;
-                            posYInit = textPositions.getTextPositions()
-                                    .get(0)
-                                    .getPageHeight() - textPositions.getTextPositions().get(0).getYDirAdj() - 2;
-                            posYEnd = textPositions.getTextPositions()
-                                    .get(0)
-                                    .getPageHeight() - textPositions.getTextPositions()
-                                    .get(textPositions.getTextPositions().size() - 1)
-                                    .getYDirAdj() + 2;
-                        }
-
-                        Rectangle textHighlightRectangle = new Rectangle(new Point(posXInit, posYInit), posXEnd - posXInit, posYEnd - posYInit + height, page);
-
-                        List<PDAnnotation> annotations = pdPage.getAnnotations();
-                        PDAnnotationTextMarkup highlight = new PDAnnotationTextMarkup(PDAnnotationTextMarkup.SUB_TYPE_HIGHLIGHT);
-                        highlight.constructAppearances();
-
-                        PDRectangle annotationPosition = new PDRectangle();
-                        annotationPosition.setLowerLeftX(posXInit);
-                        annotationPosition.setLowerLeftY(posYEnd);
-                        annotationPosition.setUpperRightX(posXEnd);
-                        annotationPosition.setUpperRightY(posYEnd + height);
-
-                        highlight.setRectangle(annotationPosition);
-                        if (!flatRedaction && !isHint(entity)) {
-                            highlight.setAnnotationName(entityPositionSequence.getId().toString());
-                            highlight.setTitlePopup(entityPositionSequence.getId().toString());
-                            highlight.setContents("\nRule " + entity.getMatchedRule() + " matched\n\n" + entity.getRedactionReason() + "\n\n" + "In Section : \"" + entity
-                                    .getHeadline() + "\"");
-                        }
-
-                        highlight.setQuadPoints(toQuadPoints(textHighlightRectangle));
-
-                        PDColor color;
-                        if (flatRedaction) {
-                            color = new PDColor(new float[]{0, 0, 0}, PDDeviceRGB.INSTANCE);
-                        } else {
-                            color = new PDColor(getColor(entity), PDDeviceRGB.INSTANCE);
-                        }
-
-                        highlight.setColor(color);
-                        annotations.add(highlight);
-
-                        redactionLogEntry.getPositions().add(textHighlightRectangle);
-
-                    }
-                    redactionLogEntry.setId(entityPositionSequence.getId().toString());
-                }
-                redactionLogEntry.setColor(getColor(entity));
-                redactionLogEntry.setReason(entity.getRedactionReason());
-                redactionLogEntry.setValue(entity.getWord());
-                redactionLogEntry.setType(entity.getType());
-                redactionLogEntry.setRedacted(entity.isRedaction());
-                redactionLogEntry.setSection(entity.getHeadline());
-                redactionLogEntry.setHint(isHint(entity));
-                classifiedDoc.getRedactionLogEntities().add(redactionLogEntry);
-                redactionLogEntry.setSectionNumber(entity.getSectionNumber());
             }
 
+            RedactionLogEntry redactionLogEntry = createRedactionLogEntry(entity);
+
+            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);
+                }
+
+                for (TextPositionSequence textPositions : entityPositionSequence.getSequences()) {
+
+                    Rectangle rectangle = textPositions.getRectangle();
+                    redactionLogEntry.getPositions().add(rectangle);
+                    annotations.add(createAnnotation(rectangle, entityPositionSequence.getId(), createAnnotationContent(entity), getColor(entity), !flatRedaction && !isHint(entity)));
+                }
+                redactionLogEntry.setId(entityPositionSequence.getId());
+            }
+            classifiedDoc.getRedactionLogEntities().add(redactionLogEntry);
         }
     }
 
 
+    private void addManualAnnotations(PDPage pdPage, Document classifiedDoc, ManualRedactions manualRedactions, int page) throws IOException {
+
+        if (manualRedactions == null) {
+            return;
+        }
+
+        List<PDAnnotation> annotations = pdPage.getAnnotations();
+
+        for (ManualRedactionEntry manualRedactionEntry : manualRedactions.getEntriesToAdd()) {
+
+            String id = IdBuilder.buildId(manualRedactionEntry);
+
+            RedactionLogEntry redactionLogEntry = createRedactionLogEntry(manualRedactionEntry);
+
+            for (Rectangle rectangle : manualRedactionEntry.getPositions()) {
+
+                if (page != rectangle.getPage()) {
+                    continue;
+                }
+
+                PDAnnotationTextMarkup highlight = createAnnotation(rectangle, id, createAnnotationContent(manualRedactionEntry), getColor(manualRedactionEntry
+                        .getType()), true);
+                annotations.add(highlight);
+
+                redactionLogEntry.getPositions().add(rectangle);
+            }
+            classifiedDoc.getRedactionLogEntities().add(redactionLogEntry);
+        }
+    }
+
+
+    private RedactionLogEntry createRedactionLogEntry(ManualRedactionEntry manualRedactionEntry) {
+
+        return RedactionLogEntry.builder()
+                .color(getColor(manualRedactionEntry.getType()))
+                .reason(manualRedactionEntry.getReason())
+                .value(manualRedactionEntry.getValue())
+                .type(manualRedactionEntry.getType())
+                .redacted(true)
+                .isHint(false)
+                .section(manualRedactionEntry.getSection())
+                .sectionNumber(manualRedactionEntry.getSectionNumber())
+                .manual(true)
+                .build();
+    }
+
+
+    private RedactionLogEntry createRedactionLogEntry(Entity entity) {
+
+        return RedactionLogEntry.builder()
+                .color(getColor(entity))
+                .reason(entity.getRedactionReason())
+                .value(entity.getWord())
+                .type(entity.getType())
+                .redacted(entity.isRedaction())
+                .isHint(isHint(entity))
+                .section(entity.getHeadline())
+                .sectionNumber(entity.getSectionNumber())
+                .build();
+    }
+
+
+    private PDAnnotationTextMarkup createAnnotation(Rectangle rectangle, String id, String content, float[] color, boolean popup) {
+
+        PDAnnotationTextMarkup annotation = new PDAnnotationTextMarkup(PDAnnotationTextMarkup.SUB_TYPE_HIGHLIGHT);
+        annotation.constructAppearances();
+        annotation.setRectangle(toPDRectangle(rectangle));
+        annotation.setQuadPoints(toQuadPoints(rectangle));
+        if (popup) {
+            annotation.setAnnotationName(id);
+            annotation.setTitlePopup(id);
+            annotation.setContents(content);
+        }
+        annotation.setColor(new PDColor(color, PDDeviceRGB.INSTANCE));
+        return annotation;
+    }
+
+
+    private String createAnnotationContent(Entity entity) {
+
+        return new StringBuilder().append("\nRule ")
+                .append(entity.getMatchedRule())
+                .append(" matched")
+                .append("\n\n")
+                .append(entity.getRedactionReason())
+                .append("\n\nIn Section : \"")
+                .append(entity.getHeadline())
+                .append("\"")
+                .toString();
+    }
+
+
+    private String createAnnotationContent(ManualRedactionEntry entry) {
+
+        return new StringBuilder().append("\nManual Redaction")
+                .append("\n\nIn Section : \"")
+                .append(entry.getSection())
+                .append("\"")
+                .toString();
+    }
+
+
+    private PDRectangle toPDRectangle(Rectangle rectangle) {
+
+        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());
+        return annotationPosition;
+    }
+
+
     private float[] toQuadPoints(Rectangle rectangle) {
 
         // quadPoints is array of x,y coordinates in Z-like order (top-left, top-right, bottom-left,bottom-right)
@@ -202,15 +236,24 @@ public class AnnotationHighlightService {
         if (!entity.isRedaction() && !isHint(entity)) {
             return new float[]{0.627f, 0.627f, 0.627f};
         }
-
         if (!dictionaryService.getEntryColors().containsKey(entity.getType())) {
             return dictionaryService.getDefaultColor();
         }
-
         return dictionaryService.getEntryColors().get(entity.getType());
     }
 
+
+    private float[] getColor(String type) {
+
+        if (!dictionaryService.getEntryColors().containsKey(type)) {
+            return dictionaryService.getDefaultColor();
+        }
+        return dictionaryService.getEntryColors().get(type);
+    }
+
+
     private boolean isHint(Entity entity) {
+
         List<String> hintTypes = dictionaryService.getHintTypes();
         if (CollectionUtils.isNotEmpty(hintTypes) && hintTypes.contains(entity.getType())) {
             return true;
@@ -218,24 +261,49 @@ public class AnnotationHighlightService {
         return false;
     }
 
+
+    private void drawSectionFrames(PDDocument document, Document classifiedDoc, boolean flatRedaction, PDPage pdPage, int page) throws IOException {
+
+        if (flatRedaction) {
+            return;
+        }
+
+        PDPageContentStream contentStream = new PDPageContentStream(document, pdPage, PDPageContentStream.AppendMode.APPEND, true);
+        for (Paragraph paragraph : classifiedDoc.getParagraphs()) {
+
+            for (int i = 0; i <= paragraph.getPageBlocks().size() - 1; i++) {
+
+                AbstractTextContainer textBlock = paragraph.getPageBlocks().get(i);
+
+                if (textBlock.getPage() != page) {
+                    continue;
+                }
+                if (textBlock instanceof TextBlock) {
+                    textBlock.setClassification((i + 1) + "/" + paragraph.getPageBlocks().size());
+                    visualizeTextBlock((TextBlock) textBlock, contentStream);
+                } else if (textBlock instanceof Table) {
+                    textBlock.setClassification((i + 1) + "/" + paragraph.getPageBlocks().size());
+                    visualizeTable((Table) textBlock, contentStream);
+                }
+            }
+        }
+        contentStream.close();
+    }
+
+
     private void visualizeTextBlock(TextBlock textBlock, PDPageContentStream contentStream) throws IOException {
 
         contentStream.setStrokingColor(Color.LIGHT_GRAY);
         contentStream.setLineWidth(0.5f);
-
         contentStream.addRect(textBlock.getMinX(), textBlock.getMinY(), textBlock.getWidth(), textBlock.getHeight());
         contentStream.stroke();
 
         if (textBlock.getClassification() != null) {
             contentStream.beginText();
-
             contentStream.setNonStrokingColor(Color.DARK_GRAY);
             contentStream.setFont(PDType1Font.TIMES_ROMAN, 8f);
-
             contentStream.newLineAtOffset(textBlock.getMinX(), textBlock.getMaxY());
-
             contentStream.showText(textBlock.getClassification());
-
             contentStream.endText();
         }
     }
@@ -252,26 +320,16 @@ public class AnnotationHighlightService {
                     contentStream.addRect((float) cell.getX(), (float) cell.getY(), (float) cell.getWidth(), (float) cell
                             .getHeight());
                     contentStream.stroke();
-
-//                    contentStream.setStrokingColor(Color.GREEN);
-//                    for (TextBlock textBlock : cell.getTextBlocks()) {
-//                        contentStream.addRect(textBlock.getMinX(), textBlock.getMinY(), textBlock.getWidth(), textBlock.getHeight());
-//                        contentStream.stroke();
-//                    }
                 }
             }
         }
 
         if (table.getClassification() != null) {
             contentStream.beginText();
-
             contentStream.setNonStrokingColor(Color.DARK_GRAY);
             contentStream.setFont(PDType1Font.TIMES_ROMAN, 8f);
-
             contentStream.newLineAtOffset(table.getMinX(), table.getMinY());
-
             contentStream.showText(table.getClassification());
-
             contentStream.endText();
         }
     }

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

@@ -17,6 +17,7 @@ import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
+import java.util.Set;
 import java.util.stream.Collectors;
 
 import org.apache.commons.io.IOUtils;
@@ -41,6 +42,10 @@ import com.iqser.red.service.configuration.v1.api.model.DictionaryResponse;
 import com.iqser.red.service.configuration.v1.api.model.RulesResponse;
 import com.iqser.red.service.configuration.v1.api.model.TypeResponse;
 import com.iqser.red.service.configuration.v1.api.model.TypeResult;
+import com.iqser.red.service.redaction.v1.model.ManualRedactionEntry;
+import com.iqser.red.service.redaction.v1.model.ManualRedactions;
+import com.iqser.red.service.redaction.v1.model.Point;
+import com.iqser.red.service.redaction.v1.model.Rectangle;
 import com.iqser.red.service.redaction.v1.model.RedactionRequest;
 import com.iqser.red.service.redaction.v1.model.RedactionResult;
 import com.iqser.red.service.redaction.v1.server.client.DictionaryClient;
@@ -303,6 +308,40 @@ public class RedactionIntegrationTest {
     }
 
 
+    @Test
+    public void testManualRedaction() throws IOException {
+
+        long start = System.currentTimeMillis();
+        ClassPathResource pdfFileResource = new ClassPathResource("files/Minimal Examples/Single Table.pdf");
+
+        ManualRedactions manualRedactions = new ManualRedactions();
+        manualRedactions.setIdsToRemove(Set.of("0836727c3508a0b2ea271da69c04cc2f"));
+
+        ManualRedactionEntry manualRedactionEntry = new ManualRedactionEntry();
+        manualRedactionEntry.setType("name");
+        manualRedactionEntry.setValue("O'Loughlin C.K.");
+        manualRedactionEntry.setReason("Manual Redaction");
+        manualRedactionEntry.setPositions(List.of(new Rectangle(new Point(375.61096f, 241.282f), 7.648041f, 43.72262f, 1), new Rectangle(new Point(384.83517f, 241.282f), 7.648041f, 17.043358f, 1)));
+
+        manualRedactions.getEntriesToAdd().add(manualRedactionEntry);
+
+        RedactionRequest request = RedactionRequest.builder()
+                .document(IOUtils.toByteArray(pdfFileResource.getInputStream()))
+                .manualRedactions(manualRedactions)
+                .build();
+
+        RedactionResult result = redactionController.redact(request);
+
+        try (FileOutputStream fileOutputStream = new FileOutputStream("/tmp/Redacted.pdf")) {
+            fileOutputStream.write(result.getDocument());
+        }
+        long end = System.currentTimeMillis();
+
+        System.out.println("duration: " + (end - start));
+        System.out.println("numberOfPages: " + result.getNumberOfPages());
+    }
+
+
     @Test
     public void classificationTest() throws IOException {
 

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

@@ -147,7 +147,7 @@ public class EntityRedactionServiceTest {
         when(dictionaryClient.getDefaultColor()).thenReturn(new DefaultColor());
         try (PDDocument pdDocument = PDDocument.load(new ByteArrayInputStream(redactionRequest.getDocument()))) {
             Document classifiedDoc = pdfSegmentationService.parseDocument(pdDocument);
-            entityRedactionService.processDocument(classifiedDoc);
+            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
         }