Pull request #126: First steps for incremental analysis

Merge in RED/redaction-service from incrementAnalysis to master

* commit '511092b9e76d58af33dfff90c1133b92e850d47c':
  First steps for incremental analysis

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

@@ -0,0 +1,15 @@
+package com.iqser.red.service.redaction.v1.model;
+
+import lombok.AllArgsConstructor;
+import lombok.Builder;
+import lombok.Data;
+import lombok.NoArgsConstructor;
+
+@Data
+@Builder
+@NoArgsConstructor
+@AllArgsConstructor
+public class ReanalyzeResult {
+
+    private RedactionLog redactionLog;
+}

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

@@ -0,0 +1,22 @@
+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
+@NoArgsConstructor
+@AllArgsConstructor
+public class RenalyzeRequest {
+
+    private byte[] document;
+    private String ruleSetId;
+    private ManualRedactions manualRedactions;
+    private Text text;
+    private RedactionLog redactionLog;
+    private OffsetDateTime lastProcessed;
+}

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

@@ -26,4 +26,8 @@ public class SectionArea {
 
     private String header;
 
+    public boolean contains(Rectangle other) {
+        return page == other.getPage() && this.topLeft.getX() <= other.getTopLeft().getX() && this.topLeft.getX() + this.getWidth() >= other.getTopLeft().getX() + other.getWidth() && this.getTopLeft().getY() <= other.getTopLeft().getY()  && this.getTopLeft().getY() + this.getHeight() >= other.getTopLeft().getY() + other.getHeight();
+    }
+
 }

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

@@ -4,8 +4,11 @@ import com.iqser.red.service.redaction.v1.model.AnalyzeRequest;
 import com.iqser.red.service.redaction.v1.model.AnalyzeResult;
 import com.iqser.red.service.redaction.v1.model.AnnotateRequest;
 import com.iqser.red.service.redaction.v1.model.AnnotateResponse;
+import com.iqser.red.service.redaction.v1.model.ReanalyzeResult;
 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.RenalyzeRequest;
+
 import org.springframework.http.MediaType;
 import org.springframework.web.bind.annotation.PathVariable;
 import org.springframework.web.bind.annotation.PostMapping;
@@ -21,6 +24,9 @@ public interface RedactionResource {
     @PostMapping(value = "/analyze", produces = MediaType.APPLICATION_JSON_VALUE, consumes = MediaType.APPLICATION_JSON_VALUE)
     AnalyzeResult analyze(@RequestBody AnalyzeRequest analyzeRequest);
 
+    @PostMapping(value = "/reanalyze", produces = MediaType.APPLICATION_JSON_VALUE, consumes = MediaType.APPLICATION_JSON_VALUE)
+    ReanalyzeResult reanalyze(@RequestBody RenalyzeRequest renalyzeRequest);
+
     @PostMapping(value = "/annotate", produces = MediaType.APPLICATION_JSON_VALUE, consumes = MediaType.APPLICATION_JSON_VALUE)
     AnnotateResponse annotate(@RequestBody AnnotateRequest annotateRequest);
 

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

@@ -20,7 +20,7 @@
         <dependency>
             <groupId>com.iqser.red.service</groupId>
             <artifactId>configuration-service-api-v1</artifactId>
-            <version>2.0.0</version>
+            <version>2.2.9</version>
         </dependency>
         <dependency>
             <groupId>org.drools</groupId>

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

@@ -4,10 +4,12 @@ import com.iqser.red.service.redaction.v1.model.AnalyzeRequest;
 import com.iqser.red.service.redaction.v1.model.AnalyzeResult;
 import com.iqser.red.service.redaction.v1.model.AnnotateRequest;
 import com.iqser.red.service.redaction.v1.model.AnnotateResponse;
+import com.iqser.red.service.redaction.v1.model.ReanalyzeResult;
 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.model.RenalyzeRequest;
 import com.iqser.red.service.redaction.v1.model.SectionGrid;
 import com.iqser.red.service.redaction.v1.model.Text;
 import com.iqser.red.service.redaction.v1.resources.RedactionResource;
@@ -18,13 +20,16 @@ import com.iqser.red.service.redaction.v1.server.redaction.service.AnnotationSer
 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.redaction.service.ReanalyzeService;
 import com.iqser.red.service.redaction.v1.server.redaction.service.RedactionLogCreatorService;
 import com.iqser.red.service.redaction.v1.server.segmentation.PdfSegmentationService;
 import com.iqser.red.service.redaction.v1.server.tableextraction.model.AbstractTextContainer;
 import com.iqser.red.service.redaction.v1.server.tableextraction.model.Table;
 import com.iqser.red.service.redaction.v1.server.visualization.service.PdfVisualisationService;
+
 import lombok.RequiredArgsConstructor;
 import lombok.extern.slf4j.Slf4j;
+
 import org.apache.pdfbox.pdmodel.PDDocument;
 import org.springframework.web.bind.annotation.PathVariable;
 import org.springframework.web.bind.annotation.RequestBody;
@@ -47,6 +52,7 @@ public class RedactionController implements RedactionResource {
     private final DroolsExecutionService droolsExecutionService;
     private final DictionaryService dictionaryService;
     private final AnnotationService annotationService;
+    private final ReanalyzeService reanalyzeService;
 
 
     @Override
@@ -68,7 +74,7 @@ public class RedactionController implements RedactionResource {
             return AnalyzeResult.builder()
                     .sectionGrid(classifiedDoc.getSectionGrid())
                     .redactionLog(new RedactionLog(classifiedDoc.getRedactionLogEntities(), classifiedDoc.getDictionaryVersion(), classifiedDoc
-                    .getRulesVersion(), analyzeRequest.getRuleSetId()))
+                            .getRulesVersion(), analyzeRequest.getRuleSetId()))
                     .numberOfPages(classifiedDoc.getPages().size())
                     .text(new Text(classifiedDoc.getSectionText()))
                     .build();
@@ -80,6 +86,12 @@ public class RedactionController implements RedactionResource {
     }
 
 
+    public ReanalyzeResult reanalyze(@RequestBody RenalyzeRequest renalyzeRequest) {
+
+        return reanalyzeService.reanalyze(renalyzeRequest);
+    }
+
+
     public AnnotateResponse annotate(@RequestBody AnnotateRequest annotateRequest) {
 
         try (PDDocument pdDocument = PDDocument.load(new ByteArrayInputStream(annotateRequest.getDocument()))) {

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

@@ -0,0 +1,83 @@
+package com.iqser.red.service.redaction.v1.server.parsing;
+
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;
+
+import org.apache.pdfbox.text.PDFTextStripperByArea;
+import org.apache.pdfbox.text.TextPosition;
+
+import com.iqser.red.service.redaction.v1.server.parsing.model.TextPositionSequence;
+
+import lombok.Getter;
+import lombok.Setter;
+
+public class PDFAreaTextStripper extends PDFTextStripperByArea {
+
+    @Getter
+    private List<TextPositionSequence> textPositionSequences = new ArrayList<>();
+
+    @Setter
+    private int pageNumber;
+
+    public PDFAreaTextStripper() throws IOException {
+
+    }
+
+    @Override
+    public void writeString(String text, List<TextPosition> textPositions) throws IOException {
+
+        int startIndex = 0;
+        for (int i = 0; i <= textPositions.size() - 1; i++) {
+
+            if (i == 0 && (textPositions.get(i).getUnicode().equals(" ") || textPositions.get(i)
+                    .getUnicode()
+                    .equals("\u00A0"))) {
+                startIndex++;
+                continue;
+            }
+
+            // Strange but sometimes this is happening, for example: Metolachlor2.pdf
+            if (i > 0 && textPositions.get(i).getX() < textPositions.get(i - 1).getX()) {
+                List<TextPosition> sublist = textPositions.subList(startIndex, i);
+                if (!(sublist.isEmpty() || sublist.size() == 1 && (sublist.get(0)
+                        .getUnicode()
+                        .equals(" ") || sublist.get(0).getUnicode().equals("\u00A0")))) {
+                    textPositionSequences.add(new TextPositionSequence(sublist, pageNumber));
+                }
+                startIndex = i;
+            }
+
+            if (i > 0 && (textPositions.get(i).getUnicode().equals(" ") || textPositions.get(i)
+                    .getUnicode()
+                    .equals("\u00A0")) && i <= textPositions.size() - 2) {
+                List<TextPosition> sublist = textPositions.subList(startIndex, i);
+                if (!(sublist.isEmpty() || sublist.size() == 1 && (sublist.get(0)
+                        .getUnicode()
+                        .equals(" ") || sublist.get(0).getUnicode().equals("\u00A0")))) {
+                    textPositionSequences.add(new TextPositionSequence(sublist, pageNumber));
+                }
+                startIndex = i + 1;
+            }
+        }
+
+        List<TextPosition> sublist = textPositions.subList(startIndex, textPositions.size());
+        if (!sublist.isEmpty() && (sublist.get(sublist.size() - 1)
+                .getUnicode()
+                .equals(" ") || sublist.get(sublist.size() - 1).getUnicode().equals("\u00A0"))) {
+            sublist = sublist.subList(0, sublist.size() - 1);
+        }
+        if (!(sublist.isEmpty() || sublist.size() == 1 && (sublist.get(0).getUnicode().equals(" ") || sublist.get(0)
+                .getUnicode()
+                .equals("\u00A0")))) {
+            textPositionSequences.add(new TextPositionSequence(sublist, pageNumber));
+        }
+        super.writeString(text);
+    }
+
+
+    public void clearPositions(){
+        textPositionSequences = new ArrayList<>();
+    }
+
+}

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

@@ -0,0 +1,15 @@
+package com.iqser.red.service.redaction.v1.server.redaction.model;
+
+import java.util.Set;
+
+import lombok.AllArgsConstructor;
+import lombok.Data;
+
+@Data
+@AllArgsConstructor
+public class DictionaryIncrement {
+
+    private Set<String> values;
+    private long dictionaryVersion;
+
+}

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

@@ -3,6 +3,9 @@ package com.iqser.red.service.redaction.v1.server.redaction.model;
 
 import java.io.Serializable;
 import java.util.Set;
+import java.util.stream.Collectors;
+
+import com.iqser.red.service.configuration.v1.api.model.DictionaryEntry;
 
 import lombok.AllArgsConstructor;
 import lombok.Data;
@@ -17,11 +20,12 @@ public class DictionaryModel implements Serializable {
     private boolean caseInsensitive;
     private boolean hint;
     private boolean recommendation;
-    private Set<String> entries;
+    private Set<DictionaryEntry> entries;
     private Set<String> localEntries;
 
     public Set<String> getValues(boolean local){
-        return local ? localEntries : entries;
+        return local ? localEntries : entries.stream().filter(e -> !e.isDeleted()).map(e-> e.getValue()).collect(Collectors
+                .toSet());
     }
 
 }

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

@@ -0,0 +1,34 @@
+package com.iqser.red.service.redaction.v1.server.redaction.model;
+
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import com.iqser.red.service.redaction.v1.server.classification.model.TextBlock;
+
+import lombok.Data;
+import lombok.NoArgsConstructor;
+
+@Data
+@NoArgsConstructor
+public class ReanalysisSection {
+
+    private int sectionNumber;
+    private String headline;
+    private List<TextBlock> textBlocks;
+    private Map<String, CellValue> tabularData = new HashMap<>();
+    private List<Integer> cellStarts;
+
+
+    public SearchableText getSearchableText() {
+
+        SearchableText searchableText = new SearchableText();
+        textBlocks.forEach(block -> {
+            if (block instanceof TextBlock) {
+                searchableText.addAll(block.getSequences());
+            }
+        });
+        return searchableText;
+    }
+
+}

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

@@ -1,42 +1,45 @@
 package com.iqser.red.service.redaction.v1.server.redaction.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;
-import com.iqser.red.service.redaction.v1.server.redaction.model.Dictionary;
-import com.iqser.red.service.redaction.v1.server.redaction.model.DictionaryModel;
-import com.iqser.red.service.redaction.v1.server.redaction.model.DictionaryRepresentation;
-import feign.FeignException;
-import lombok.RequiredArgsConstructor;
-import lombok.extern.slf4j.Slf4j;
-import org.apache.commons.collections4.CollectionUtils;
-import org.apache.commons.lang3.SerializationUtils;
-import org.springframework.stereotype.Service;
-
 import java.awt.Color;
 import java.util.ArrayList;
 import java.util.Comparator;
 import java.util.HashMap;
 import java.util.HashSet;
 import java.util.List;
+import java.util.Locale;
 import java.util.Map;
 import java.util.Set;
 import java.util.stream.Collectors;
 
+import org.apache.commons.collections4.CollectionUtils;
+import org.apache.commons.lang3.SerializationUtils;
+import org.springframework.stereotype.Service;
+
+import com.iqser.red.service.configuration.v1.api.model.Colors;
+import com.iqser.red.service.configuration.v1.api.model.DictionaryEntry;
+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;
+import com.iqser.red.service.redaction.v1.server.redaction.model.Dictionary;
+import com.iqser.red.service.redaction.v1.server.redaction.model.DictionaryIncrement;
+import com.iqser.red.service.redaction.v1.server.redaction.model.DictionaryModel;
+import com.iqser.red.service.redaction.v1.server.redaction.model.DictionaryRepresentation;
+
+import feign.FeignException;
+import lombok.RequiredArgsConstructor;
+import lombok.extern.slf4j.Slf4j;
+
 @Slf4j
 @Service
 @RequiredArgsConstructor
 public class DictionaryService {
 
-
     private final DictionaryClient dictionaryClient;
 
-
     private Map<String, DictionaryRepresentation> dictionariesByRuleSets = new HashMap<>();
 
 
-    public void updateDictionary(String ruleSetId) {
+    public long updateDictionary(String ruleSetId) {
 
         long version = dictionaryClient.getVersion(ruleSetId);
 
@@ -45,6 +48,26 @@ public class DictionaryService {
         if (foundDictionary == null || version > foundDictionary.getDictionaryVersion()) {
             updateDictionaryEntry(ruleSetId, version);
         }
+
+        return version;
+    }
+
+
+    public DictionaryIncrement getDictionaryIncrements(String ruleSetId, long fromVersion) {
+
+        long version = updateDictionary(ruleSetId);
+
+        Set<String> newValues = new HashSet<>();
+        List<DictionaryModel> dictionaryModels = dictionariesByRuleSets.get(ruleSetId).getDictionary();
+        dictionaryModels.forEach(dictionaryModel -> {
+            dictionaryModel.getEntries().forEach(dictionaryEntry -> {
+                if (dictionaryEntry.getVersion() > fromVersion) {
+                    newValues.add(dictionaryEntry.getValue());
+                }
+            });
+        });
+
+        return new DictionaryIncrement(newValues, version);
     }
 
 
@@ -63,7 +86,6 @@ public class DictionaryService {
                         .sorted(Comparator.comparingInt(DictionaryModel::getRank).reversed())
                         .collect(Collectors.toList());
 
-
                 dictionary.forEach(dm -> dictionaryRepresentation.getLocalAccessMap().put(dm.getType(), dm));
 
                 Colors colors = dictionaryClient.getColors(ruleSetId);
@@ -86,6 +108,7 @@ public class DictionaryService {
 
 
     public void updateExternalDictionary(Dictionary dictionary, String ruleSetId) {
+
         dictionary.getDictionaryModels().forEach(dm -> {
             if (dm.isRecommendation() && !dm.getLocalEntries().isEmpty()) {
                 dictionaryClient.addEntries(dm.getType(), ruleSetId, new ArrayList<>(dm.getLocalEntries()), false);
@@ -98,17 +121,15 @@ public class DictionaryService {
     }
 
 
-    private Set<String> convertEntries(TypeResult t) {
+    private Set<DictionaryEntry> convertEntries(TypeResult t) {
+
+        Set<DictionaryEntry> entries = new HashSet<>(dictionaryClient.getDictionaryForType(t.getType(), t.getRuleSetId())
+                .getEntries());
 
         if (t.isCaseInsensitive()) {
-            return dictionaryClient.getDictionaryForType(t.getType(), t.getRuleSetId())
+            entries.forEach(entry -> entry.getValue().toLowerCase(Locale.ROOT));
-                    .getEntries()
-                    .stream()
-                    .map(String::toLowerCase)
-                    .collect(Collectors.toSet());
-        } else {
-            return new HashSet<>(dictionaryClient.getDictionaryForType(t.getType(), t.getRuleSetId()).getEntries());
         }
+        return entries;
     }
 
 
@@ -148,6 +169,7 @@ public class DictionaryService {
         return false;
     }
 
+
     public boolean isRecommendation(String type, String ruleSetId) {
 
         DictionaryModel model = dictionariesByRuleSets.get(ruleSetId).getLocalAccessMap().get(type);
@@ -159,6 +181,7 @@ public class DictionaryService {
 
 
     public Dictionary getDeepCopyDictionary(String ruleSetId) {
+
         List<DictionaryModel> copy = new ArrayList<>();
 
         var representation = dictionariesByRuleSets.get(ruleSetId);
@@ -170,15 +193,22 @@ public class DictionaryService {
         return new Dictionary(copy, representation.getDictionaryVersion());
     }
 
+
     public float[] getRequestRemoveColor(String ruleSetId) {
+
         return dictionariesByRuleSets.get(ruleSetId).getRequestAddColor();
     }
 
+
     public float[] getNotRedactedColor(String ruleSetId) {
+
         return dictionariesByRuleSets.get(ruleSetId).getNotRedactedColor();
     }
 
+
     public float[] getRequestAddColor(String ruleSetId) {
+
         return dictionariesByRuleSets.get(ruleSetId).getRequestAddColor();
     }
+
 }

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

@@ -349,7 +349,7 @@ public class EntityRedactionService {
     }
 
 
-    private Set<Entity> findEntities(SearchableText searchableText, String headline, int sectionNumber,
+    public Set<Entity> findEntities(SearchableText searchableText, String headline, int sectionNumber,
                                      Dictionary dictionary, boolean local) {
 
         Set<Entity> found = new HashSet<>();

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

@@ -0,0 +1,281 @@
+package com.iqser.red.service.redaction.v1.server.redaction.service;
+
+import java.awt.geom.Rectangle2D;
+import java.io.ByteArrayInputStream;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.stream.Collectors;
+import java.util.stream.Stream;
+
+import org.apache.pdfbox.pdmodel.PDDocument;
+import org.apache.pdfbox.pdmodel.PDPage;
+import org.apache.pdfbox.pdmodel.common.PDRectangle;
+import org.kie.api.runtime.KieContainer;
+import org.springframework.stereotype.Service;
+import org.springframework.web.bind.annotation.RequestBody;
+
+import com.iqser.red.service.redaction.v1.model.Comment;
+import com.iqser.red.service.redaction.v1.model.IdRemoval;
+import com.iqser.red.service.redaction.v1.model.ManualForceRedact;
+import com.iqser.red.service.redaction.v1.model.ManualRedactionEntry;
+import com.iqser.red.service.redaction.v1.model.ManualRedactions;
+import com.iqser.red.service.redaction.v1.model.ReanalyzeResult;
+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.RenalyzeRequest;
+import com.iqser.red.service.redaction.v1.model.SectionArea;
+import com.iqser.red.service.redaction.v1.model.SectionText;
+import com.iqser.red.service.redaction.v1.server.classification.model.TextBlock;
+import com.iqser.red.service.redaction.v1.server.exception.RedactionException;
+import com.iqser.red.service.redaction.v1.server.parsing.PDFAreaTextStripper;
+import com.iqser.red.service.redaction.v1.server.parsing.model.TextPositionSequence;
+import com.iqser.red.service.redaction.v1.server.redaction.model.CellValue;
+import com.iqser.red.service.redaction.v1.server.redaction.model.Dictionary;
+import com.iqser.red.service.redaction.v1.server.redaction.model.DictionaryIncrement;
+import com.iqser.red.service.redaction.v1.server.redaction.model.Entity;
+import com.iqser.red.service.redaction.v1.server.redaction.model.EntityPositionSequence;
+import com.iqser.red.service.redaction.v1.server.redaction.model.ReanalysisSection;
+import com.iqser.red.service.redaction.v1.server.redaction.model.Section;
+import com.iqser.red.service.redaction.v1.server.redaction.model.SectionSearchableTextPair;
+import com.iqser.red.service.redaction.v1.server.redaction.utils.EntitySearchUtils;
+import com.iqser.red.service.redaction.v1.server.tableextraction.model.Cell;
+
+import lombok.RequiredArgsConstructor;
+
+@Service
+@RequiredArgsConstructor
+public class ReanalyzeService {
+
+    private final DictionaryService dictionaryService;
+    private final DroolsExecutionService droolsExecutionService;
+    private final SurroundingWordsService surroundingWordsService;
+    private final EntityRedactionService entityRedactionService;
+    private final RedactionLogCreatorService redactionLogCreatorService;
+
+
+    public ReanalyzeResult reanalyze(@RequestBody RenalyzeRequest renalyzeRequest) {
+
+        DictionaryIncrement dictionaryIncrement = dictionaryService.getDictionaryIncrements(renalyzeRequest.getRuleSetId(), renalyzeRequest
+                .getRedactionLog()
+                .getDictionaryVersion());
+
+        Set<String> manualForceAndRemoveIds = getForceAndRemoveIds(renalyzeRequest.getManualRedactions());
+        Map<String, List<Comment>> comments = null;
+        Set<ManualRedactionEntry> manualAdds = null;
+
+        if (renalyzeRequest.getManualRedactions() != null) {
+            // TODO comments will be removed from redactionLog, so we ignore this first.
+            comments = renalyzeRequest.getManualRedactions().getComments();
+            manualAdds = renalyzeRequest.getManualRedactions().getEntriesToAdd();
+        }
+
+        Set<Integer> sectionsToReanaylse = new HashSet<>();
+        for (RedactionLogEntry entry : renalyzeRequest.getRedactionLog().getRedactionLogEntry()) {
+            if (entry.isManual() || manualForceAndRemoveIds.contains(entry.getId())) {
+                sectionsToReanaylse.add(entry.getSectionNumber());
+            }
+        }
+
+        for (SectionText sectionText : renalyzeRequest.getText().getSectionTexts()) {
+            Set<Entity> entities = EntitySearchUtils.find(sectionText.getText(), dictionaryIncrement.getValues(), "find", sectionText
+                    .getHeadline(), sectionText.getSectionNumber(), false);
+            if (!entities.isEmpty()) {
+                sectionsToReanaylse.add(sectionText.getSectionNumber());
+            }
+
+            if (manualAdds != null) {
+                for (SectionArea sectionArea : sectionText.getSectionAreas()) {
+                    for (ManualRedactionEntry manualAdd : manualAdds) {
+                        for (Rectangle manualPosition : manualAdd.getPositions()) {
+                            if (sectionArea.contains(manualPosition)) {
+                                manualAdd.setSection(sectionText.getHeadline());
+                                manualAdd.setSectionNumber(sectionText.getSectionNumber());
+                            }
+                        }
+                    }
+                }
+            }
+        }
+
+        if (sectionsToReanaylse.isEmpty() && (manualAdds == null || manualAdds.isEmpty())) {
+            renalyzeRequest.getRedactionLog().setDictionaryVersion(dictionaryIncrement.getDictionaryVersion());
+            return ReanalyzeResult.builder().redactionLog(renalyzeRequest.getRedactionLog()).build();
+        }
+
+        try (PDDocument pdDocument = PDDocument.load(new ByteArrayInputStream(renalyzeRequest.getDocument()))) {
+
+            List<ReanalysisSection> reanalysisSections = new ArrayList<>();
+            for (SectionText sectionText : renalyzeRequest.getText().getSectionTexts()) {
+
+                if (!sectionsToReanaylse.contains(sectionText.getSectionNumber())) {
+                    continue;
+                }
+
+                ReanalysisSection reanalysisSection = new ReanalysisSection();
+                reanalysisSection.setHeadline(sectionText.getHeadline());
+                reanalysisSection.setSectionNumber(sectionText.getSectionNumber());
+                List<TextBlock> textBlocks = new ArrayList<>();
+
+                Map<Integer, List<SectionArea>> sectionAreasPerPage = new HashMap<>();
+                for (SectionArea sectionArea : sectionText.getSectionAreas()) {
+                    sectionAreasPerPage.computeIfAbsent(sectionArea.getPage(), (x) -> new ArrayList<>())
+                            .add(sectionArea);
+                }
+
+                Map<String, CellValue> tabularData = new HashMap<>();
+                List<Integer> cellStarts = new ArrayList<>();
+                for (Integer page : sectionAreasPerPage.keySet()) {
+                    List<SectionArea> areasOnPage = sectionAreasPerPage.get(page);
+
+                    PDPage pdPage = pdDocument.getPage(page - 1);
+                    PDRectangle cropBox = pdPage.getCropBox();
+                    PDFAreaTextStripper textStripper = new PDFAreaTextStripper();
+                    textStripper.setPageNumber(page);
+
+                    int cellStart = 0;
+                    for (SectionArea sectionArea : areasOnPage) {
+
+                        Rectangle2D rect = null;
+                        if (pdPage.getRotation() == 90) {
+                            rect = new Rectangle2D.Float(sectionArea.getTopLeft().getY(), sectionArea.getTopLeft()
+                                    .getX(), sectionArea.getHeight(), sectionArea.getWidth() + 0.001f);
+                        } else {
+                            rect = new Rectangle2D.Float(sectionArea.getTopLeft().getX(), -sectionArea.getTopLeft()
+                                    .getY() + cropBox.getUpperRightY() - sectionArea.getHeight(), sectionArea.getWidth(), sectionArea
+                                    .getHeight() + 0.001f);
+                        }
+
+                        textStripper.addRegion(String.valueOf(1), rect);
+                        textStripper.extractRegions(pdPage);
+                        textStripper.getTextForRegion(String.valueOf(1));
+                        List<TextPositionSequence> positions = textStripper.getTextPositionSequences();
+
+                        TextBlock textBlock = new TextBlock(sectionArea.getTopLeft().getX(), sectionArea.getTopLeft()
+                                .getX() + sectionArea.getWidth(), sectionArea.getTopLeft()
+                                .getY(), sectionArea.getTopLeft().getY() + sectionArea.getHeight(), positions, 0);
+
+                        if (sectionText.isTable()) {
+                            Cell cell = new Cell();
+                            cell.addTextBlock(textBlock);
+                            tabularData.put(sectionArea.getHeader(), new CellValue(cell.getTextBlocks(), cellStart));
+                            cellStarts.add(cellStart);
+                            cellStart = cellStart + cell.toString().trim().length() + 1;
+                        }
+
+                        textBlocks.add(textBlock);
+                        textStripper.clearPositions();
+                    }
+
+                }
+                reanalysisSection.setTextBlocks(textBlocks);
+                reanalysisSection.setTabularData(tabularData);
+                reanalysisSections.add(reanalysisSection);
+                if (sectionText.isTable()) {
+                    reanalysisSection.setCellStarts(cellStarts);
+                }
+            }
+
+            //--
+
+            KieContainer kieContainer = droolsExecutionService.updateRules(renalyzeRequest.getRuleSetId());
+
+            Dictionary dictionary = dictionaryService.getDeepCopyDictionary(renalyzeRequest.getRuleSetId());
+
+            List<SectionSearchableTextPair> sectionSearchableTextPairs = new ArrayList<>();
+            for (ReanalysisSection reanalysisSection : reanalysisSections) {
+
+                Set<Entity> entities = entityRedactionService.findEntities(reanalysisSection.getSearchableText(), reanalysisSection
+                        .getHeadline(), reanalysisSection.getSectionNumber(), dictionary, false);
+                if (reanalysisSection.getCellStarts() != null) {
+                    surroundingWordsService.addSurroundingText(entities, reanalysisSection.getSearchableText(), dictionary, reanalysisSection
+                            .getCellStarts());
+                } else {
+                    surroundingWordsService.addSurroundingText(entities, reanalysisSection.getSearchableText(), dictionary);
+                }
+
+                sectionSearchableTextPairs.add(new SectionSearchableTextPair(Section.builder()
+                        .isLocal(false)
+                        .dictionaryTypes(dictionary.getTypes())
+                        .entities(entities)
+                        .text(reanalysisSection.getSearchableText().getAsStringWithLinebreaks())
+                        .searchText(reanalysisSection.getSearchableText().toString())
+                        .headline(reanalysisSection.getHeadline())
+                        .sectionNumber(reanalysisSection.getSectionNumber())
+                        .tabularData(reanalysisSection.getTabularData())
+                        .searchableText(reanalysisSection.getSearchableText())
+                        .dictionary(dictionary)
+                        .build(), reanalysisSection.getSearchableText()));
+            }
+
+            Set<Entity> entities = new HashSet<>();
+            sectionSearchableTextPairs.forEach(sectionSearchableTextPair -> {
+                Section analysedRowSection = droolsExecutionService.executeRules(kieContainer, sectionSearchableTextPair
+                        .getSection());
+                entities.addAll(analysedRowSection.getEntities());
+            });
+
+            Map<Integer, List<Entity>> entitiesPerPage = new HashMap<>();
+            for (Entity entity : entities) {
+                Map<Integer, List<EntityPositionSequence>> sequenceOnPage = new HashMap<>();
+                for (EntityPositionSequence entityPositionSequence : entity.getPositionSequences()) {
+                    sequenceOnPage.computeIfAbsent(entityPositionSequence.getPageNumber(), (x) -> new ArrayList<>())
+                            .add(entityPositionSequence);
+                }
+
+                for (Map.Entry<Integer, List<EntityPositionSequence>> entry : sequenceOnPage.entrySet()) {
+                    entitiesPerPage.computeIfAbsent(entry.getKey(), (x) -> new ArrayList<>())
+                            .add(new Entity(entity.getWord(), entity.getType(), entity.isRedaction(), entity.getRedactionReason(), entry
+                                    .getValue(), entity.getHeadline(), entity.getMatchedRule(), entity.getSectionNumber(), entity
+                                    .getLegalBasis(), entity.isDictionaryEntry(), entity.getTextBefore(), entity.getTextAfter(), entity
+                                    .getStart(), entity.getEnd()));
+                }
+            }
+
+            List<RedactionLogEntry> newRedactionLogEntries = new ArrayList<>();
+            for (int page = 1; page <= pdDocument.getNumberOfPages(); page++) {
+                if (entitiesPerPage.get(page) != null) {
+                    newRedactionLogEntries.addAll(redactionLogCreatorService.addEntries(entitiesPerPage, renalyzeRequest
+                            .getManualRedactions(), page, renalyzeRequest.getRuleSetId()));
+                }
+                newRedactionLogEntries.addAll(redactionLogCreatorService.addManualAddEntries(manualAdds, comments, page, renalyzeRequest
+                        .getRuleSetId()));
+            }
+
+            Iterator<RedactionLogEntry> itty = renalyzeRequest.getRedactionLog().getRedactionLogEntry().iterator();
+            while (itty.hasNext()) {
+                RedactionLogEntry entry = itty.next();
+                if (sectionsToReanaylse.contains(entry.getSectionNumber()) || entry.getSectionNumber() == 0) {
+                    itty.remove();
+                }
+            }
+
+            renalyzeRequest.getRedactionLog().getRedactionLogEntry().addAll(newRedactionLogEntries);
+            renalyzeRequest.getRedactionLog().setDictionaryVersion(dictionaryIncrement.getDictionaryVersion());
+
+            return ReanalyzeResult.builder().redactionLog(renalyzeRequest.getRedactionLog()).build();
+
+        } catch (Exception e) {
+            throw new RedactionException(e);
+        }
+
+    }
+
+
+    private Set<String> getForceAndRemoveIds(ManualRedactions manualRedactions) {
+
+        if (manualRedactions == null) {
+            return new HashSet<>();
+        }
+
+        return Stream.concat(manualRedactions.getIdsToRemove()
+                .stream()
+                .map(IdRemoval::getId), manualRedactions.getForceRedacts().stream().map(ManualForceRedact::getId))
+                .collect(Collectors.toSet());
+    }
+
+}

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

@@ -4,6 +4,7 @@ import java.awt.geom.Rectangle2D;
 import java.util.ArrayList;
 import java.util.HashSet;
 import java.util.List;
+import java.util.Map;
 import java.util.Set;
 import java.util.stream.Collectors;
 
@@ -55,11 +56,11 @@ public class RedactionLogCreatorService {
             addSectionGrid(classifiedDoc, page);
 
             if (classifiedDoc.getEntities().get(page) != null) {
-                addEntries(classifiedDoc, manualRedactions, page, ruleSetId);
+                classifiedDoc.getRedactionLogEntities().addAll(addEntries(classifiedDoc.getEntities(), manualRedactions, page, ruleSetId));
             }
 
             if (manualRedactionPages.contains(page)) {
-                addManualEntries(classifiedDoc, manualRedactions, page, ruleSetId);
+                classifiedDoc.getRedactionLogEntities().addAll(addManualAddEntries(manualRedactions.getEntriesToAdd(), manualRedactions.getComments(), page, ruleSetId));
             }
 
             if (!classifiedDoc.getPages().get(page - 1).getImageBounds().isEmpty()) {
@@ -106,13 +107,15 @@ public class RedactionLogCreatorService {
     }
 
 
-    private void addEntries(Document classifiedDoc, ManualRedactions manualRedactions, int page, String ruleSetId) {
+    public List<RedactionLogEntry> addEntries(Map<Integer, List<Entity>> entities, ManualRedactions manualRedactions, int page, String ruleSetId) {
+
+        List<RedactionLogEntry> redactionLogEntities = new ArrayList<>();
 
         // Duplicates can exist due table extraction colums over multiple rows.
         Set<String> processedIds = new HashSet<>();
 
         entityLoop:
-        for (Entity entity : classifiedDoc.getEntities().get(page)) {
+        for (Entity entity : entities.get(page)) {
 
             List<Comment> comments = null;
 
@@ -201,10 +204,12 @@ public class RedactionLogCreatorService {
 
                 // FIXME ids should never be null. Figure out why this happens.
                 if (redactionLogEntry.getId() != null) {
-                    classifiedDoc.getRedactionLogEntities().add(redactionLogEntry);
+                    redactionLogEntities.add(redactionLogEntry);
                 }
             }
         }
+
+        return redactionLogEntities;
     }
 
 
@@ -233,14 +238,16 @@ public class RedactionLogCreatorService {
     }
 
 
-    private void addManualEntries(Document classifiedDoc, ManualRedactions manualRedactions, int page,
+    public List<RedactionLogEntry> addManualAddEntries(Set<ManualRedactionEntry> manualAdds,  Map<String, List<Comment>> comments, int page,
                                   String ruleSetId) {
 
-        if (manualRedactions == null) {
+        List<RedactionLogEntry> redactionLogEntities = new ArrayList<>();
-            return;
+
+        if (manualAdds == null) {
+            return redactionLogEntities;
         }
 
-        for (ManualRedactionEntry manualRedactionEntry : manualRedactions.getEntriesToAdd()) {
+        for (ManualRedactionEntry manualRedactionEntry : manualAdds) {
 
             String id = manualRedactionEntry.getId();
 
@@ -254,11 +261,13 @@ public class RedactionLogCreatorService {
                 }
             }
 
-            redactionLogEntry.setComments(manualRedactions.getComments().get(id));
+            redactionLogEntry.setComments(comments.get(id));
             if (!rectanglesOnPage.isEmpty() && !approvedAndShouldBeInDictionary(manualRedactionEntry)) {
-                classifiedDoc.getRedactionLogEntities().add(redactionLogEntry);
+                redactionLogEntities.add(redactionLogEntry);
             }
         }
+
+        return redactionLogEntities;
     }
 
 

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

@@ -11,10 +11,12 @@ import com.iqser.red.service.redaction.v1.server.redaction.utils.TextNormalizati
 
 import lombok.Data;
 import lombok.EqualsAndHashCode;
+import lombok.NoArgsConstructor;
 
 @SuppressWarnings("serial")
 @Data
 @EqualsAndHashCode(callSuper = true)
+@NoArgsConstructor
 public class Cell extends Rectangle {
 
     private List<TextBlock> textBlocks = new ArrayList<>();

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

@@ -4,8 +4,12 @@ import static org.assertj.core.api.Assertions.assertThat;
 import static org.mockito.Mockito.when;
 import static org.springframework.boot.test.context.SpringBootTest.WebEnvironment.RANDOM_PORT;
 
+import java.awt.Color;
+import java.awt.geom.AffineTransform;
+import java.awt.geom.Rectangle2D;
 import java.io.BufferedReader;
 import java.io.ByteArrayInputStream;
+import java.io.ByteArrayOutputStream;
 import java.io.File;
 import java.io.FileInputStream;
 import java.io.FileOutputStream;
@@ -17,6 +21,7 @@ import java.nio.charset.StandardCharsets;
 import java.time.OffsetDateTime;
 import java.util.ArrayList;
 import java.util.HashMap;
+import java.util.HashSet;
 import java.util.List;
 import java.util.Map;
 import java.util.Set;
@@ -24,7 +29,15 @@ import java.util.UUID;
 import java.util.stream.Collectors;
 
 import org.apache.commons.io.IOUtils;
+import org.apache.pdfbox.pdmodel.PDDocument;
+import org.apache.pdfbox.pdmodel.PDPage;
+import org.apache.pdfbox.pdmodel.PDPageContentStream;
+import org.apache.pdfbox.pdmodel.common.PDRectangle;
+import org.apache.pdfbox.pdmodel.graphics.image.PDImageXObject;
+import org.apache.pdfbox.text.PDFTextStripperByArea;
+import org.apache.pdfbox.util.Matrix;
 import org.junit.Before;
+import org.junit.Ignore;
 import org.junit.Test;
 import org.junit.runner.RunWith;
 import org.kie.api.KieServices;
@@ -32,6 +45,7 @@ import org.kie.api.builder.KieBuilder;
 import org.kie.api.builder.KieFileSystem;
 import org.kie.api.builder.KieModule;
 import org.kie.api.runtime.KieContainer;
+import org.mockito.MockitoAnnotations;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.boot.test.context.SpringBootTest;
 import org.springframework.boot.test.context.TestConfiguration;
@@ -42,6 +56,7 @@ import org.springframework.test.context.junit4.SpringRunner;
 
 import com.fasterxml.jackson.databind.ObjectMapper;
 import com.iqser.red.service.configuration.v1.api.model.Colors;
+import com.iqser.red.service.configuration.v1.api.model.DictionaryEntry;
 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;
@@ -56,17 +71,28 @@ import com.iqser.red.service.redaction.v1.model.ManualForceRedact;
 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.ReanalyzeResult;
 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.RenalyzeRequest;
+import com.iqser.red.service.redaction.v1.model.SectionArea;
 import com.iqser.red.service.redaction.v1.model.SectionText;
 import com.iqser.red.service.redaction.v1.model.Status;
+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.client.DictionaryClient;
 import com.iqser.red.service.redaction.v1.server.client.RulesClient;
 import com.iqser.red.service.redaction.v1.server.controller.RedactionController;
+import com.iqser.red.service.redaction.v1.server.exception.RedactionException;
+import com.iqser.red.service.redaction.v1.server.parsing.PDFAreaTextStripper;
+import com.iqser.red.service.redaction.v1.server.parsing.model.TextPositionSequence;
+import com.iqser.red.service.redaction.v1.server.redaction.model.CellValue;
+import com.iqser.red.service.redaction.v1.server.redaction.model.ReanalysisSection;
 import com.iqser.red.service.redaction.v1.server.redaction.utils.ResourceLoader;
 import com.iqser.red.service.redaction.v1.server.redaction.utils.TextNormalizationUtilities;
+import com.iqser.red.service.redaction.v1.server.tableextraction.model.Cell;
 
 @RunWith(SpringRunner.class)
 @SpringBootTest(webEnvironment = RANDOM_PORT)
@@ -112,6 +138,7 @@ public class RedactionIntegrationTest {
     private final Map<String, Boolean> recommendationTypeMap = new HashMap<>();
     private final Map<String, Integer> rankTypeMap = new HashMap<>();
     private final Colors colors = new Colors();
+    private final Map<String, Long> reanlysisVersions = new HashMap<>();
 
     private final static String TEST_RULESET_ID = "123";
 
@@ -376,7 +403,7 @@ public class RedactionIntegrationTest {
 
         return DictionaryResponse.builder()
                 .hexColor(typeColorMap.get(type))
-                .entries(dictionary.get(type))
+                .entries(toDictionaryEntry(dictionary.get(type)))
                 .isHint(hintTypeMap.get(type))
                 .isCaseInsensitive(caseInSensitiveMap.get(type))
                 .isRecommendation(recommendationTypeMap.get(type))
@@ -385,6 +412,15 @@ public class RedactionIntegrationTest {
     }
 
 
+    private List<DictionaryEntry> toDictionaryEntry(List<String> entries){
+        List<DictionaryEntry> dictionaryEntries = new ArrayList<>();
+        entries.forEach(entry -> {
+            dictionaryEntries.add(new DictionaryEntry(entry, reanlysisVersions.containsKey(entry) ? reanlysisVersions.get(entry) : 0L, false));
+        });
+        return dictionaryEntries;
+    }
+
+
     @Test
     public void noExceptionShouldBeThrownForAnyFiles() throws IOException {
 
@@ -414,6 +450,22 @@ public class RedactionIntegrationTest {
                 assertThat(entry.getValue().size()).isEqualTo(1);
             });
 
+
+            dictionary.get(AUTHOR).add("Drinking water");
+            when(dictionaryClient.getVersion(TEST_RULESET_ID)).thenReturn(1L);
+
+            long rstart = System.currentTimeMillis();
+            ReanalyzeResult reanalyzeResult = redactionController.reanalyze(RenalyzeRequest.builder()
+                    .redactionLog(result.getRedactionLog())
+                    .document(IOUtils.toByteArray(new FileInputStream(path)))
+                    .manualRedactions(null)
+                    .text(result.getText())
+                    .ruleSetId(TEST_RULESET_ID)
+                    .build());
+
+            long rend = System.currentTimeMillis();
+            System.out.println("reanalysis analysis duration: " + (rend - rstart));
+
         }
 
         long end = System.currentTimeMillis();
@@ -455,6 +507,86 @@ public class RedactionIntegrationTest {
 
         AnalyzeResult result = redactionController.analyze(request);
 
+        long end = System.currentTimeMillis();
+
+        System.out.println("first analysis duration: " + (end - start));
+
+        try (FileOutputStream fileOutputStream = new FileOutputStream("/tmp/Test.json")) {
+            fileOutputStream.write(objectMapper.writeValueAsBytes(result.getText()));
+        }
+
+        int correctFound = 0;
+        loop:
+        for (RedactionLogEntry redactionLogEntry : result.getRedactionLog().getRedactionLogEntry()) {
+            for (SectionText sectionText : result.getText().getSectionTexts()) {
+                if (redactionLogEntry.getType().equals("image")) {
+                    correctFound++;
+                    continue loop;
+                }
+                if (redactionLogEntry.getSectionNumber() == sectionText.getSectionNumber()) {
+                    String value = sectionText.getText()
+                            .substring(redactionLogEntry.getStartOffset(), redactionLogEntry.getEndOffset());
+                    if (redactionLogEntry.getValue().equalsIgnoreCase(value)) {
+                        correctFound++;
+                    } else {
+                        throw new RuntimeException("WTF");
+                    }
+                }
+            }
+        }
+        assertThat(correctFound).isEqualTo(result.getRedactionLog().getRedactionLogEntry().size());
+
+
+        dictionary.get(AUTHOR).add("properties");
+        reanlysisVersions.put("properties", 1L);
+
+        dictionary.get(AUTHOR).add("physical");
+        reanlysisVersions.put("physical", 2L);
+
+        when(dictionaryClient.getVersion(TEST_RULESET_ID)).thenReturn(2L);
+        when(dictionaryClient.getDictionaryForType(AUTHOR, TEST_RULESET_ID)).thenReturn(getDictionaryResponse(AUTHOR));
+
+        start = System.currentTimeMillis();
+        ReanalyzeResult reanalyzeResult = redactionController.reanalyze(RenalyzeRequest.builder()
+                .redactionLog(result.getRedactionLog())
+                .document(IOUtils.toByteArray(pdfFileResource.getInputStream()))
+                .manualRedactions(null)
+                .text(result.getText())
+                .ruleSetId(TEST_RULESET_ID)
+                .build());
+
+        end = System.currentTimeMillis();
+        System.out.println("reanalysis analysis duration: " + (end - start));
+
+        AnnotateResponse annotateResponse = redactionController.annotate(AnnotateRequest.builder()
+                .document(IOUtils.toByteArray(pdfFileResource.getInputStream()))
+                .redactionLog(reanalyzeResult.getRedactionLog())
+                .sectionGrid(result.getSectionGrid())
+                .build());
+
+        try (FileOutputStream fileOutputStream = new FileOutputStream("/tmp/Annotated.pdf")) {
+            fileOutputStream.write(annotateResponse.getDocument());
+        }
+
+    }
+
+
+
+    @Test
+    @Ignore
+    public void fillRecanTest() throws IOException {
+
+        System.out.println("redactionTest");
+        long start = System.currentTimeMillis();
+        ClassPathResource pdfFileResource = new ClassPathResource("files/S5.pdf");
+
+        AnalyzeRequest request = AnalyzeRequest.builder()
+                .ruleSetId(TEST_RULESET_ID)
+                .document(IOUtils.toByteArray(pdfFileResource.getInputStream()))
+                .build();
+
+        AnalyzeResult result = redactionController.analyze(request);
+
         AnnotateResponse annotateResponse = redactionController.annotate(AnnotateRequest.builder()
                 .document(IOUtils.toByteArray(pdfFileResource.getInputStream()))
                 .redactionLog(result.getRedactionLog())
@@ -496,9 +628,70 @@ public class RedactionIntegrationTest {
 
         System.out.println("duration: " + (end - start));
         System.out.println("numberOfPages: " + result.getNumberOfPages());
+
+        SectionArea sectionArea = result.getText().getSectionTexts().get(3).getSectionAreas().get(5);
+
+        try (PDDocument pdDocument = PDDocument.load(new ByteArrayInputStream(IOUtils.toByteArray(pdfFileResource.getInputStream())))) {
+
+            PDPage docPage = pdDocument.getPage(0);
+
+            PDFTextStripperByArea textStripper = new PDFTextStripperByArea();
+
+            PDRectangle cropBox = docPage.getCropBox();
+            PDRectangle mediaBox = docPage.getMediaBox();
+
+
+//            if (textPositions.get(0).getRotation() == 90) {
+//                posXEnd = textPositions.get(0).getYDirAdj() + 2;
+//                posYInit = getY1();
+//                posYEnd = textPositions.get(textPositions.size() - 1).getXDirAdj() - height + 4;
+//            } else {
+//                posXEnd = textPositions.get(textPositions.size() - 1)
+//                        .getXDirAdj() + textPositions.get(textPositions.size() - 1).getWidth() + 1;
+//                posYInit = textPositions.get(0).getPageHeight() - textPositions.get(0).getYDirAdj() - 2;
+//                posYEnd = textPositions.get(0).getPageHeight() - textPositions.get(textPositions.size() - 1)
+//                        .getYDirAdj() + 2;
+//            }
+
+
+            Rectangle2D rect = new Rectangle2D.Float(sectionArea.getTopLeft()
+                    .getY(), sectionArea.getTopLeft()
+                    .getX() , sectionArea.getHeight(), sectionArea
+                    .getWidth() + 0.001f);
+
+            textStripper.addRegion("region", rect);
+
+
+
+            textStripper.extractRegions(docPage);
+
+            String textForRegion = textStripper.getTextForRegion("region");
+
+            System.out.println(textForRegion);
+
+            // fill a rectangle
+            PDPageContentStream contents = new PDPageContentStream (pdDocument, docPage, PDPageContentStream.AppendMode.APPEND, false, false);
+            contents.setNonStrokingColor (Color.RED);
+            contents.addRect (sectionArea.getTopLeft().getX(), sectionArea.getTopLeft().getY(), sectionArea.getWidth(), sectionArea.getHeight());
+            contents.fill ();
+            contents.close ();
+            try (ByteArrayOutputStream byteArrayOutputStream = new ByteArrayOutputStream()) {
+                pdDocument.save(byteArrayOutputStream);
+                try (FileOutputStream fileOutputStream = new FileOutputStream("/tmp/Annotated2.pdf")) {
+                    fileOutputStream.write(byteArrayOutputStream.toByteArray());
+                }
+            }
+
+        } catch (Exception e) {
+            throw new RedactionException(e);
+        }
+
     }
 
 
+
+
+
     @Test
     public void testTableRedaction() throws IOException {
 
@@ -569,7 +762,7 @@ public class RedactionIntegrationTest {
         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);
+//        manualRedactions.getEntriesToAdd().add(manualRedactionEntry);
 
         AnalyzeRequest request = AnalyzeRequest.builder()
                 .ruleSetId(TEST_RULESET_ID)
@@ -579,9 +772,25 @@ public class RedactionIntegrationTest {
 
         AnalyzeResult result = redactionController.analyze(request);
 
+        manualRedactions.getEntriesToAdd().add(manualRedactionEntry);
+        manualRedactions.setIdsToRemove(Set.of(IdRemoval.builder()
+                .id("5b940b2cb401ed9f5be6fc24f6e77bcf")
+                .status(Status.APPROVED)
+                .build()));
+
+
+        ReanalyzeResult reanalyzeResult = redactionController.reanalyze(RenalyzeRequest.builder()
+                .redactionLog(result.getRedactionLog())
+                .document(IOUtils.toByteArray(pdfFileResource.getInputStream()))
+                .manualRedactions(manualRedactions)
+                .text(result.getText())
+                .ruleSetId(TEST_RULESET_ID)
+                .build());
+
+
         AnnotateResponse annotateResponse = redactionController.annotate(AnnotateRequest.builder()
                 .document(IOUtils.toByteArray(pdfFileResource.getInputStream()))
-                .redactionLog(result.getRedactionLog())
+                .redactionLog(reanalyzeResult.getRedactionLog())
                 .sectionGrid(result.getSectionGrid())
                 .build());
 

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

@@ -1,6 +1,7 @@
 package com.iqser.red.service.redaction.v1.server.redaction.service;
 
 import com.iqser.red.service.configuration.v1.api.model.Colors;
+import com.iqser.red.service.configuration.v1.api.model.DictionaryEntry;
 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;
@@ -129,12 +130,12 @@ public class EntityRedactionServiceTest {
                 .build();
 
         DictionaryResponse dictionaryResponse = DictionaryResponse.builder()
-                .entries(Arrays.asList("Casey, H.W.", "O’Loughlin,  C.K.", "Salamon, C.M.", "Smith, S.H."))
+                .entries(toDictionaryEntry(Arrays.asList("Casey, H.W.", "O’Loughlin,  C.K.", "Salamon, C.M.", "Smith, S.H.")))
                 .build();
         when(dictionaryClient.getVersion(TEST_RULESET_ID)).thenReturn(DICTIONARY_VERSION.incrementAndGet());
         when(dictionaryClient.getDictionaryForType(AUTHOR_CODE, TEST_RULESET_ID)).thenReturn(dictionaryResponse);
         DictionaryResponse addressResponse = DictionaryResponse.builder()
-                .entries(Collections.singletonList("Toxigenics, Inc., Decatur, IL 62526, USA"))
+                .entries(toDictionaryEntry(Collections.singletonList("Toxigenics, Inc., Decatur, IL 62526, USA")))
                 .build();
         when(dictionaryClient.getDictionaryForType(ADDRESS_CODE, TEST_RULESET_ID)).thenReturn(addressResponse);
 
@@ -162,12 +163,12 @@ public class EntityRedactionServiceTest {
                 .build();
 
         DictionaryResponse dictionaryResponse = DictionaryResponse.builder()
-                .entries(Arrays.asList("Casey, H.W.", "O’Loughlin,  C.K.", "Salamon, C.M.", "Smith, S.H."))
+                .entries(toDictionaryEntry(Arrays.asList("Casey, H.W.", "O’Loughlin,  C.K.", "Salamon, C.M.", "Smith, S.H.")))
                 .build();
         when(dictionaryClient.getVersion(TEST_RULESET_ID)).thenReturn(DICTIONARY_VERSION.incrementAndGet());
         when(dictionaryClient.getDictionaryForType(AUTHOR_CODE, TEST_RULESET_ID)).thenReturn(dictionaryResponse);
         DictionaryResponse addressResponse = DictionaryResponse.builder()
-                .entries(Collections.singletonList("Toxigenics, Inc., Decatur, IL 62526, USA"))
+                .entries(toDictionaryEntry(Collections.singletonList("Toxigenics, Inc., Decatur, IL 62526, USA")))
                 .build();
         when(dictionaryClient.getDictionaryForType(ADDRESS_CODE, TEST_RULESET_ID)).thenReturn(addressResponse);
         DictionaryResponse sponsorResponse = DictionaryResponse.builder()
@@ -191,11 +192,11 @@ public class EntityRedactionServiceTest {
                 " Supplement - Identity of the active substance - Reference list.pdf");
         when(dictionaryClient.getVersion(TEST_RULESET_ID)).thenReturn(DICTIONARY_VERSION.incrementAndGet());
         DictionaryResponse dictionaryResponse = DictionaryResponse.builder()
-                .entries(new ArrayList<>(ResourceLoader.load("dictionaries/CBI_author.txt")))
+                .entries(toDictionaryEntry(new ArrayList<>(ResourceLoader.load("dictionaries/CBI_author.txt"))))
                 .build();
         when(dictionaryClient.getDictionaryForType(AUTHOR_CODE, TEST_RULESET_ID)).thenReturn(dictionaryResponse);
         DictionaryResponse addressResponse = DictionaryResponse.builder()
-                .entries(new ArrayList<>(ResourceLoader.load("dictionaries/CBI_address.txt")))
+                .entries(toDictionaryEntry(new ArrayList<>(ResourceLoader.load("dictionaries/CBI_address.txt"))))
                 .build();
         when(dictionaryClient.getDictionaryForType(ADDRESS_CODE, TEST_RULESET_ID)).thenReturn(addressResponse);
         DictionaryResponse sponsorResponse = DictionaryResponse.builder()
@@ -228,15 +229,15 @@ public class EntityRedactionServiceTest {
         ClassPathResource pdfFileResource = new ClassPathResource("files/Minimal Examples/Row With Ambiguous Redaction.pdf");
         when(dictionaryClient.getVersion(TEST_RULESET_ID)).thenReturn(DICTIONARY_VERSION.incrementAndGet());
         DictionaryResponse dictionaryResponse = DictionaryResponse.builder()
-                .entries(new ArrayList<>(ResourceLoader.load("dictionaries/CBI_author.txt")))
+                .entries(toDictionaryEntry(new ArrayList<>(ResourceLoader.load("dictionaries/CBI_author.txt"))))
                 .build();
         when(dictionaryClient.getDictionaryForType(AUTHOR_CODE, TEST_RULESET_ID)).thenReturn(dictionaryResponse);
         DictionaryResponse addressResponse = DictionaryResponse.builder()
-                .entries(new ArrayList<>(ResourceLoader.load("dictionaries/CBI_address.txt")))
+                .entries(toDictionaryEntry(new ArrayList<>(ResourceLoader.load("dictionaries/CBI_address.txt"))))
                 .build();
         when(dictionaryClient.getDictionaryForType(ADDRESS_CODE, TEST_RULESET_ID)).thenReturn(addressResponse);
         DictionaryResponse sponsorResponse = DictionaryResponse.builder()
-                .entries(new ArrayList<>(ResourceLoader.load("dictionaries/CBI_sponsor.txt")))
+                .entries(toDictionaryEntry(new ArrayList<>(ResourceLoader.load("dictionaries/CBI_sponsor.txt"))))
                 .build();
         when(dictionaryClient.getDictionaryForType(SPONSOR_CODE, TEST_RULESET_ID)).thenReturn(sponsorResponse);
         try (PDDocument pdDocument = PDDocument.load(pdfFileResource.getInputStream())) {
@@ -297,11 +298,11 @@ public class EntityRedactionServiceTest {
         ClassPathResource pdfFileResource = new ClassPathResource("files/Minimal Examples/Applicant Producer Table.pdf");
         when(dictionaryClient.getVersion(TEST_RULESET_ID)).thenReturn(DICTIONARY_VERSION.incrementAndGet());
         DictionaryResponse dictionaryResponse = DictionaryResponse.builder()
-                .entries(new ArrayList<>(ResourceLoader.load("dictionaries/CBI_author.txt")))
+                .entries(toDictionaryEntry(new ArrayList<>(ResourceLoader.load("dictionaries/CBI_author.txt"))))
                 .build();
         when(dictionaryClient.getDictionaryForType(AUTHOR_CODE, TEST_RULESET_ID)).thenReturn(dictionaryResponse);
         DictionaryResponse addressResponse = DictionaryResponse.builder()
-                .entries(new ArrayList<>(ResourceLoader.load("dictionaries/CBI_address.txt")))
+                .entries(toDictionaryEntry(new ArrayList<>(ResourceLoader.load("dictionaries/CBI_address.txt"))))
                 .build();
         when(dictionaryClient.getDictionaryForType(ADDRESS_CODE, TEST_RULESET_ID)).thenReturn(addressResponse);
         DictionaryResponse sponsorResponse = DictionaryResponse.builder()
@@ -346,7 +347,7 @@ public class EntityRedactionServiceTest {
                 .build();
         when(dictionaryClient.getDictionaryForType(AUTHOR_CODE, TEST_RULESET_ID)).thenReturn(authorResponse);
         DictionaryResponse dictionaryResponse = DictionaryResponse.builder()
-                .entries(new ArrayList<>(ResourceLoader.load("dictionaries/CBI_sponsor.txt")))
+                .entries(toDictionaryEntry(new ArrayList<>(ResourceLoader.load("dictionaries/CBI_sponsor.txt"))))
                 .build();
         when(dictionaryClient.getDictionaryForType(SPONSOR_CODE, TEST_RULESET_ID)).thenReturn(dictionaryResponse);
         try (PDDocument pdDocument = PDDocument.load(pdfFileResource.getInputStream())) {
@@ -367,13 +368,13 @@ public class EntityRedactionServiceTest {
         ClassPathResource pdfFileResource = new ClassPathResource("files/Minimal Examples/Header Propagation.pdf");
 
         DictionaryResponse dictionaryResponse = DictionaryResponse.builder()
-                .entries(Arrays.asList("Bissig R.", "Thanei P."))
+                .entries(toDictionaryEntry(Arrays.asList("Bissig R.", "Thanei P.")))
                 .build();
 
         when(dictionaryClient.getVersion(TEST_RULESET_ID)).thenReturn(DICTIONARY_VERSION.incrementAndGet());
         when(dictionaryClient.getDictionaryForType(AUTHOR_CODE, TEST_RULESET_ID)).thenReturn(dictionaryResponse);
         DictionaryResponse addressResponse = DictionaryResponse.builder()
-                .entries(Collections.singletonList("Novartis Crop Protection AG, Basel, Switzerland"))
+                .entries(toDictionaryEntry(Collections.singletonList("Novartis Crop Protection AG, Basel, Switzerland")))
                 .build();
         when(dictionaryClient.getDictionaryForType(ADDRESS_CODE, TEST_RULESET_ID)).thenReturn(addressResponse);
 
@@ -392,13 +393,13 @@ public class EntityRedactionServiceTest {
         pdfFileResource = new ClassPathResource("files/Minimal Examples/Header Propagation2.pdf");
 
         dictionaryResponse = DictionaryResponse.builder()
-                .entries(Arrays.asList("Tribolet, R.", "Muir, G.", "Kühne-Thu, H.", "Close, C."))
+                .entries(toDictionaryEntry(Arrays.asList("Tribolet, R.", "Muir, G.", "Kühne-Thu, H.", "Close, C.")))
                 .build();
 
         when(dictionaryClient.getVersion(TEST_RULESET_ID)).thenReturn(DICTIONARY_VERSION.incrementAndGet());
         when(dictionaryClient.getDictionaryForType(AUTHOR_CODE, TEST_RULESET_ID)).thenReturn(dictionaryResponse);
         addressResponse = DictionaryResponse.builder()
-                .entries(Collections.singletonList("Novartis Crop Protection AG, Basel, Switzerland"))
+                .entries(toDictionaryEntry(Collections.singletonList("Novartis Crop Protection AG, Basel, Switzerland")))
                 .build();
         when(dictionaryClient.getDictionaryForType(ADDRESS_CODE, TEST_RULESET_ID)).thenReturn(addressResponse);
 
@@ -419,13 +420,13 @@ public class EntityRedactionServiceTest {
         ClassPathResource pdfFileResource = new ClassPathResource("files/Minimal Examples/Empty Tabular Data.pdf");
 
         DictionaryResponse dictionaryResponse = DictionaryResponse.builder()
-                .entries(Collections.singletonList("Aldershof S."))
+                .entries(toDictionaryEntry(Collections.singletonList("Aldershof S.")))
                 .build();
 
         when(dictionaryClient.getVersion(TEST_RULESET_ID)).thenReturn(DICTIONARY_VERSION.incrementAndGet());
         when(dictionaryClient.getDictionaryForType(AUTHOR_CODE, TEST_RULESET_ID)).thenReturn(dictionaryResponse);
         DictionaryResponse addressResponse = DictionaryResponse.builder()
-                .entries(Collections.singletonList("Novartis Crop Protection AG, Basel, Switzerland"))
+                .entries(toDictionaryEntry(Collections.singletonList("Novartis Crop Protection AG, Basel, Switzerland")))
                 .build();
         when(dictionaryClient.getDictionaryForType(ADDRESS_CODE, TEST_RULESET_ID)).thenReturn(addressResponse);
 
@@ -517,4 +518,12 @@ public class EntityRedactionServiceTest {
         }
     }
 
+    private List<DictionaryEntry> toDictionaryEntry(List<String> entries){
+        List<DictionaryEntry> dictionaryEntries = new ArrayList<>();
+        entries.forEach(entry -> {
+            dictionaryEntries.add(new DictionaryEntry(entry, 1L, false));
+        });
+        return dictionaryEntries;
+    }
+
 }