Pull request #55 : RED-413: Added user to manual redactions, approved flag to Status.APPROVED

Merge in RED/redaction-service from RED-413 to master * commit '638c4f9c65d35406bba1fd33e20c3bae8a6e6a13': RED-413: Added user to manual redactions, approved flag to Status.APPROVED
RED-413: Added user to manual redactions, approved flag to Status.APPROVED
2020-10-12 12:32:30 +02:00 · 2020-10-12 12:21:18 +02:00 · 2020-10-09 12:17:38 +02:00 · 2020-10-09 12:06:19 +02:00 · 2020-10-08 12:05:42 +02:00 · 2020-10-08 11:51:35 +02:00
26 changed files with 470 additions and 163 deletions
@@ -22,7 +22,7 @@
    </modules>

    <properties>
-        <pdfbox.version>2.0.16</pdfbox.version>
+        <pdfbox.version>2.0.21</pdfbox.version>
    </properties>


@@ -0,0 +1,21 @@
+package com.iqser.red.service.redaction.v1.model;
+
+import java.time.OffsetDateTime;
+
+import lombok.AllArgsConstructor;
+import lombok.Builder;
+import lombok.Data;
+import lombok.NoArgsConstructor;
+
+@Data
+@Builder
+@AllArgsConstructor
+@NoArgsConstructor
+public class Comment {
+
+    private String id;
+    private OffsetDateTime date;
+    private String text;
+    private String user;
+
+}
@@ -0,0 +1,25 @@
+package com.iqser.red.service.redaction.v1.model;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import lombok.AllArgsConstructor;
+import lombok.Builder;
+import lombok.Data;
+import lombok.NoArgsConstructor;
+
+@Data
+@Builder
+@AllArgsConstructor
+@NoArgsConstructor
+public class IdRemoval {
+
+    private String id;
+    private String user;
+    private Status status;
+    private boolean removeFromDictionary;
+
+    @Builder.Default
+    private List<Comment> comments = new ArrayList<>();
+
+}
@@ -4,18 +4,27 @@ import java.util.ArrayList;
 import java.util.List;

 import lombok.AllArgsConstructor;
+import lombok.Builder;
 import lombok.Data;
 import lombok.NoArgsConstructor;

@Data
+@Builder
@AllArgsConstructor
@NoArgsConstructor
 public class ManualRedactionEntry {

+    private String id;
+    private String user;
    private String type;
    private String value;
    private String reason;
    private List<Rectangle> positions = new ArrayList<>();
+    private Status status;
+    private boolean addToDictionary;
+
+    @Builder.Default
+    private List<Comment> comments = new ArrayList<>();

    private String section;
    private int sectionNumber;
@@ -4,14 +4,19 @@ import java.util.HashSet;
 import java.util.Set;

 import lombok.AllArgsConstructor;
+import lombok.Builder;
 import lombok.Data;
 import lombok.NoArgsConstructor;

@Data
+@Builder
@AllArgsConstructor
@NoArgsConstructor
 public class ManualRedactions {

-    private Set<String> idsToRemove = new HashSet<>();
+    @Builder.Default
+    private Set<IdRemoval> idsToRemove = new HashSet<>();
+
+    @Builder.Default
    private Set<ManualRedactionEntry> entriesToAdd = new HashSet<>();
 }
@@ -27,5 +27,6 @@ public class RedactionLogEntry {
    private List<Rectangle> positions = new ArrayList<>();
    private int sectionNumber;
    private boolean manual;
+    private Status status;

 }
@@ -0,0 +1,5 @@
+package com.iqser.red.service.redaction.v1.model;
+
+public enum Status {
+    REQUESTED, APPROVED, DECLINED
+}
@@ -11,25 +11,6 @@

    <artifactId>redaction-service-server-v1</artifactId>

-    <properties>
-        <pdfbox.version>2.0.20</pdfbox.version>
-    </properties>
-
-    <dependencyManagement>
-        <dependencies>
-            <dependency>
-                <groupId>org.apache.pdfbox</groupId>
-                <artifactId>pdfbox</artifactId>
-                <version>${pdfbox.version}</version>
-            </dependency>
-            <dependency>
-                <groupId>org.apache.pdfbox</groupId>
-                <artifactId>pdfbox-tools</artifactId>
-                <version>${pdfbox.version}</version>
-            </dependency>
-        </dependencies>
-    </dependencyManagement>
-
    <dependencies>
        <dependency>
            <groupId>com.iqser.red.service</groupId>
@@ -39,7 +20,7 @@
        <dependency>
            <groupId>com.iqser.red.service</groupId>
            <artifactId>configuration-service-api-v1</artifactId>
-            <version>1.0.12</version>
+            <version>1.1.7</version>
        </dependency>
        <dependency>
            <groupId>org.drools</groupId>
@@ -131,7 +131,7 @@ public class TextBlock extends AbstractTextContainer {
        TextPositionSequence previous = null;
        for (TextPositionSequence word : sequences) {
            if (previous != null) {
-                if (Math.abs(previous.getY1() - word.getY1()) > word.getTextHeight()) {
+                if (Math.abs(previous.getRotationAdjustedY() - word.getRotationAdjustedY()) > word.getTextHeight()) {
                    sb.append('\n');
                } else {
                    sb.append(' ');
@@ -101,6 +101,9 @@ public class TextPositionSequence implements CharSequence {
        }
    }

+    public float getRotationAdjustedY() {
+        return textPositions.get(0).getY();
+    }

    public float getY1() {

@@ -4,36 +4,33 @@ import com.iqser.red.service.redaction.v1.server.classification.model.TextBlock;
 import com.iqser.red.service.redaction.v1.server.parsing.model.TextPositionSequence;
 import com.iqser.red.service.redaction.v1.server.redaction.utils.TextNormalizationUtilities;

-import lombok.RequiredArgsConstructor;
 import lombok.Value;

@Value
-@RequiredArgsConstructor
 public class CellValue {

    TextBlock textBlock;

    int rowSpanStart;

+
    @Override
    public String toString() {

        StringBuilder sb = new StringBuilder();

-
-            TextPositionSequence previous = null;
-            for (TextPositionSequence word : textBlock.getSequences()) {
-
-                if (previous != null) {
-                    if (Math.abs(previous.getY1() - word.getY1()) > word.getTextHeight()) {
-                        sb.append('\n');
-                    } else {
-                        sb.append(' ');
-                    }
+        TextPositionSequence previous = null;
+        for (TextPositionSequence word : textBlock.getSequences()) {
+            if (previous != null) {
+                if (Math.abs(previous.getRotationAdjustedY() - word.getRotationAdjustedY()) > word.getTextHeight()) {
+                    sb.append('\n');
+                } else {
+                    sb.append(' ');
                }
-                sb.append(word.toString());
-                previous = word;
            }
+            sb.append(word.toString());
+            previous = word;
+        }

        return TextNormalizationUtilities.removeHyphenLineBreaks(sb.toString())
                .replaceAll("\n", " ")
@@ -136,9 +136,11 @@ public class SearchableText {

    private List<EntityPositionSequence> buildEntityPositionSequence(List<TextPositionSequence> crossSequenceParts) {

-        String id = IdBuilder.buildId(crossSequenceParts);
+        String plainId = IdBuilder.buildId(crossSequenceParts);
+        String id = plainId;
        List<EntityPositionSequence> result = new ArrayList<>();
        int currentPage = -1;
+        int idDiffentPageSuffix = 1;
        EntityPositionSequence entityPositionSequence = new EntityPositionSequence(id);
        for (TextPositionSequence textPositionSequence : crossSequenceParts) {
            if (currentPage == -1) {
@@ -148,9 +150,13 @@ public class SearchableText {
            } else if (currentPage == textPositionSequence.getPage()) {
                entityPositionSequence.getSequences().add(textPositionSequence);
            } else {
+                id = plainId + "-" + idDiffentPageSuffix;
+                idDiffentPageSuffix++;
                result.add(entityPositionSequence);
                entityPositionSequence = new EntityPositionSequence(id);
                entityPositionSequence.setPageNumber(textPositionSequence.getPage());
+                entityPositionSequence.getSequences().add(textPositionSequence);
+                currentPage = textPositionSequence.getPage();
            }
        }
        result.add(entityPositionSequence);
@@ -173,7 +179,7 @@ public class SearchableText {
        for (TextPositionSequence word : sequences) {

            if (previous != null) {
-                if (Math.abs(previous.getY1() - word.getY1()) > word.getTextHeight()) {
+                if (Math.abs(previous.getRotationAdjustedY() - word.getRotationAdjustedY()) > word.getTextHeight()) {
                    sb.append('\n');
                } else {
                    sb.append(' ');
@@ -197,7 +203,7 @@ public class SearchableText {
        for (TextPositionSequence word : sequences) {

            if (previous != null) {
-                if (Math.abs(previous.getY1() - word.getY1()) > word.getTextHeight()) {
+                if (Math.abs(previous.getRotationAdjustedY() - word.getRotationAdjustedY()) > word.getTextHeight()) {
                    sb.append('\n');
                } else {
                    sb.append(' ');
@@ -44,7 +44,7 @@ public class Section {
    }


-    public boolean contains(String type) {
+    public boolean matchesType(String type) {

        return entities.stream().anyMatch(entity -> entity.getType().equals(type));
    }
@@ -80,6 +80,18 @@ public class Section {
    }


+    public void redactIfPrecededBy(String prefix, String type, int ruleNumber, String reason) {
+
+        entities.forEach(entity -> {
+            if (entity.getType().equals(type) && searchText.indexOf(prefix + entity.getWord()) != 1) {
+                entity.setRedaction(true);
+                entity.setMatchedRule(ruleNumber);
+                entity.setRedactionReason(reason);
+            }
+        });
+    }
+
+
    public void redactLineAfter(String start, String asType, int ruleNumber, String reason) {

        String[] values = StringUtils.substringsBetween(text, start, "\n");
@@ -141,7 +153,8 @@ public class Section {

            if (startIndex > -1 && (startIndex == 0 || Character.isWhitespace(searchText.charAt(startIndex - 1)) || isSeparator(searchText
                    .charAt(startIndex - 1))) && (stopIndex == searchText.length() || isSeparator(searchText.charAt(stopIndex)))) {
-                found.add(new Entity(searchText.substring(startIndex, stopIndex), asType, startIndex, stopIndex, headline, sectionNumber));
+                found.add(new Entity(searchText.substring(startIndex, stopIndex), asType, startIndex, stopIndex,
+                        headline, sectionNumber));
            }
        } while (startIndex > -1);

@@ -197,8 +210,13 @@ public class Section {
        if (value == null) {
            log.warn("Could not find any data for {}.", cellHeader);
        } else {
-            Entity entity = new Entity(value.toString(), type, value.getRowSpanStart(), value.getRowSpanStart() + value.toString()
-                    .length(), headline, sectionNumber);
+            String word = value.toString();
+            Entity entity = new Entity(word,
+                                       type,
+                                       value.getRowSpanStart(),
+                                       value.getRowSpanStart() + word.length(),
+                                       headline,
+                                       sectionNumber);
            entity.setRedaction(redact);
            entity.setMatchedRule(ruleNumber);
            entity.setRedactionReason(reason);
@@ -206,9 +224,7 @@ public class Section {
                    .getSequences()); // Make sure no other cells with same content are highlighted

            // HashSet keeps the older value, but we want the new only.
-            if(entities.contains(entity)){
-                entities.remove(entity);
-            }
+            entities.remove(entity);
            entities.add(entity);

            entities = removeEntitiesContainedInLarger(entities);
@@ -1,5 +1,6 @@
 package com.iqser.red.service.redaction.v1.server.redaction.service;

+import java.awt.Color;
 import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.HashSet;
@@ -11,6 +12,7 @@ import java.util.stream.Collectors;
 import org.apache.commons.collections4.CollectionUtils;
 import org.springframework.stereotype.Service;

+import com.iqser.red.service.configuration.v1.api.model.Colors;
 import com.iqser.red.service.configuration.v1.api.model.TypeResponse;
 import com.iqser.red.service.configuration.v1.api.model.TypeResult;
 import com.iqser.red.service.redaction.v1.server.client.DictionaryClient;
@@ -45,6 +47,15 @@ public class DictionaryService {
    @Getter
    private float[] defaultColor;

+    @Getter
+    private float[] requestAddColor;
+
+    @Getter
+    private float[] requestRemoveColor;
+
+    @Getter
+    private float[] notRedactedColor;
+

    public void updateDictionary() {

@@ -63,7 +74,7 @@ public class DictionaryService {
            if (typeResponse != null && CollectionUtils.isNotEmpty(typeResponse.getTypes())) {
                entryColors = typeResponse.getTypes()
                        .stream()
-                        .collect(Collectors.toMap(TypeResult::getType, TypeResult::getColor));
+                        .collect(Collectors.toMap(TypeResult::getType, t -> convertColor(t.getHexColor())));
                hintTypes = typeResponse.getTypes()
                        .stream()
                        .filter(TypeResult::isHint)
@@ -74,8 +85,16 @@ public class DictionaryService {
                        .filter(TypeResult::isCaseInsensitive)
                        .map(TypeResult::getType)
                        .collect(Collectors.toList());
-                dictionary = entryColors.keySet().stream().collect(Collectors.toMap(type -> type, this::convertEntries));
-                defaultColor = dictionaryClient.getDefaultColor().getColor();
+                dictionary = entryColors.keySet()
+                        .stream()
+                        .collect(Collectors.toMap(type -> type, this::convertEntries));
+
+
+                Colors colors = dictionaryClient.getColors();
+                defaultColor = convertColor(colors.getDefaultColor());
+                requestAddColor = convertColor(colors.getRequestAdd());
+                requestRemoveColor = convertColor(colors.getRequestRemove());
+                notRedactedColor = convertColor(colors.getNotRedacted());
            }
        } catch (FeignException e) {
            log.warn("Got some unknown feignException", e);
@@ -85,6 +104,7 @@ public class DictionaryService {


    private Set<String> convertEntries(String s) {
+
        if (caseInsensitiveTypes.contains(s)) {
            return dictionaryClient.getDictionaryForType(s)
                    .getEntries()
@@ -95,4 +115,11 @@ public class DictionaryService {
        return new HashSet<>(dictionaryClient.getDictionaryForType(s).getEntries());
    }

+
+    private float[] convertColor(String hex) {
+
+        Color color = Color.decode(hex);
+        return new float[]{color.getRed() / 255f, color.getGreen() / 255f, color.getBlue() / 255f};
+    }
+
 }
@@ -70,7 +70,7 @@ public class EntityRedactionService {
                                    .replaceAll("-", "");
                            tabularData.put(headerName, new CellValue(cell.getTextBlocks().get(0), cellStart));
                        });
-                        start = start + cell.toString().length();
+                        start = start + cell.toString().length() + 1; // include automatically appended white space
                        for (TextBlock textBlock : cell.getTextBlocks()) {
                            searchableRow.addAll(textBlock.getSequences());
                        }
@@ -143,17 +143,17 @@ public class EntityRedactionService {
    private Set<Entity> findEntities(SearchableText searchableText, String headline, int sectionNumber) {

        Set<Entity> found = new HashSet<>();
-        if (StringUtils.isEmpty(searchableText.toString())) {
+        String searchableString = searchableText.toString();
+        if (StringUtils.isEmpty(searchableString)) {
            return found;
        }

-        String inputString = searchableText.toString();
-        String lowercaseInputString = inputString.toLowerCase();
+        String lowercaseInputString = searchableString.toLowerCase();
        for (Map.Entry<String, Set<String>> entry : dictionaryService.getDictionary().entrySet()) {
            if (dictionaryService.getCaseInsensitiveTypes().contains(entry.getKey())) {
                found.addAll(find(lowercaseInputString, entry.getValue(), entry.getKey(), headline, sectionNumber));
            } else {
-                found.addAll(find(inputString, entry.getValue(), entry.getKey(), headline, sectionNumber));
+                found.addAll(find(searchableString, entry.getValue(), entry.getKey(), headline, sectionNumber));
            }
        }

@@ -5,7 +5,6 @@ import java.util.List;

 import com.google.common.hash.HashFunction;
 import com.google.common.hash.Hashing;
-import com.iqser.red.service.redaction.v1.model.ManualRedactionEntry;
 import com.iqser.red.service.redaction.v1.server.parsing.model.TextPositionSequence;

 import lombok.experimental.UtilityClass;
@@ -24,9 +23,4 @@ public class IdBuilder {

        return hashFunction.hashString(sb.toString(), StandardCharsets.UTF_8).toString();
    }
-
-
-    public String buildId(ManualRedactionEntry manualRedactionEntry) {
-        return hashFunction.hashString(manualRedactionEntry.toString(), StandardCharsets.UTF_8).toString();
-    }
 }
@@ -41,14 +41,11 @@ public class Cell extends Rectangle {

        StringBuilder sb = new StringBuilder();

-        TextPositionSequence previous = null;
        for (TextBlock textBlock : textBlocks) {
-
-
+            TextPositionSequence previous = null;
            for (TextPositionSequence word : textBlock.getSequences()) {
-
                if (previous != null) {
-                    if (Math.abs(previous.getY1() - word.getY1()) > word.getTextHeight()) {
+                    if (Math.abs(previous.getRotationAdjustedY() - word.getRotationAdjustedY()) > word.getTextHeight()) {
                        sb.append('\n');
                    } else {
                        sb.append(' ');
@@ -64,5 +61,4 @@ public class Cell extends Rectangle {
                .replaceAll(" {2}", " ");
    }

-}
-
+}
@@ -3,6 +3,7 @@ package com.iqser.red.service.redaction.v1.server.visualization.service;
 import java.awt.Color;
 import java.io.IOException;
 import java.util.ArrayList;
+import java.util.GregorianCalendar;
 import java.util.HashSet;
 import java.util.List;
 import java.util.Set;
@@ -17,14 +18,18 @@ import org.apache.pdfbox.pdmodel.font.PDType1Font;
 import org.apache.pdfbox.pdmodel.graphics.color.PDColor;
 import org.apache.pdfbox.pdmodel.graphics.color.PDDeviceRGB;
 import org.apache.pdfbox.pdmodel.interactive.annotation.PDAnnotation;
+import org.apache.pdfbox.pdmodel.interactive.annotation.PDAnnotationText;
 import org.apache.pdfbox.pdmodel.interactive.annotation.PDAnnotationTextMarkup;
 import org.apache.pdfbox.text.TextPosition;
 import org.springframework.stereotype.Service;

+import com.iqser.red.service.redaction.v1.model.Comment;
+import com.iqser.red.service.redaction.v1.model.IdRemoval;
 import com.iqser.red.service.redaction.v1.model.ManualRedactionEntry;
 import com.iqser.red.service.redaction.v1.model.ManualRedactions;
 import com.iqser.red.service.redaction.v1.model.Rectangle;
 import com.iqser.red.service.redaction.v1.model.RedactionLogEntry;
+import com.iqser.red.service.redaction.v1.model.Status;
 import com.iqser.red.service.redaction.v1.server.classification.model.Document;
 import com.iqser.red.service.redaction.v1.server.classification.model.Paragraph;
 import com.iqser.red.service.redaction.v1.server.classification.model.TextBlock;
@@ -32,7 +37,6 @@ 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;
@@ -97,33 +101,73 @@ public class AnnotationHighlightService {
            }

            RedactionLogEntry redactionLogEntry = createRedactionLogEntry(entity);
-
+            boolean requestedToRemove = false;
+            boolean removeFromDictionary = false;
+            List<Comment> comments = null;
            for (EntityPositionSequence entityPositionSequence : entity.getPositionSequences()) {

-                if (manualRedactions != null && manualRedactions.getIdsToRemove()
-                        .contains(entityPositionSequence.getId())) {
-                    String manualOverrideReason = entity.getRedactionReason() + ", removed by manual override";
-                    entity.setRedaction(false);
-                    entity.setRedactionReason(manualOverrideReason);
-                    redactionLogEntry.setRedacted(false);
-                    redactionLogEntry.setReason(manualOverrideReason);
-                    redactionLogEntry.setManual(true);
+                if (manualRedactions != null && !manualRedactions.getIdsToRemove().isEmpty()) {
+                    for (IdRemoval manualRemoval : manualRedactions.getIdsToRemove()) {
+                        if (manualRemoval.getId().equals(entityPositionSequence.getId())) {
+                            comments = manualRemoval.getComments();
+                            String manualOverrideReason = null;
+                            if (manualRemoval.getStatus().equals(Status.APPROVED)) {
+                                entity.setRedaction(false);
+                                redactionLogEntry.setRedacted(false);
+                                redactionLogEntry.setStatus(Status.APPROVED);
+                                manualOverrideReason = entity.getRedactionReason() + ", removed by manual override";
+                            } else if (manualRemoval.getStatus().equals(Status.REQUESTED)) {
+                                requestedToRemove = true;
+                                manualOverrideReason = entity.getRedactionReason() + ", requested to remove";
+                                if (manualRemoval.isRemoveFromDictionary()) {
+                                    removeFromDictionary = true;
+                                }
+                            }
+
+                            entity.setRedactionReason(manualOverrideReason != null ? manualOverrideReason : entity.getRedactionReason());
+                            redactionLogEntry.setReason(manualOverrideReason);
+                            redactionLogEntry.setManual(true);
+                        }
+                    }
+
                }

                if (CollectionUtils.isNotEmpty(entityPositionSequence.getSequences())) {
-                    for (Rectangle rectangle : getRectanglesPerLine(entityPositionSequence.getSequences()
+                    List<Rectangle> rectanglesPerline = getRectanglesPerLine(entityPositionSequence.getSequences()
                            .stream()
                            .flatMap(seq -> seq.getTextPositions().stream())
-                            .collect(Collectors.toList()), page)) {
-                        redactionLogEntry.getPositions().add(rectangle);
-                        annotations.add(createAnnotation(rectangle, entityPositionSequence.getId(),
-                                createAnnotationContent(entity), getColor(entity), !flatRedaction && !isHint(entity)));
-                    }
+                            .collect(Collectors.toList()), page);
+
+                    redactionLogEntry.getPositions().addAll(rectanglesPerline);
+                    annotations.addAll(createAnnotation(rectanglesPerline, prefixId(entity, entityPositionSequence.getId(), requestedToRemove, removeFromDictionary), createAnnotationContent(entity), getColor(entity, requestedToRemove), comments, !isHint(entity)));
                }
+
                redactionLogEntry.setId(entityPositionSequence.getId());
            }
            classifiedDoc.getRedactionLogEntities().add(redactionLogEntry);
        }
+
+    }
+
+
+    private String prefixId(Entity entity, String id, boolean requestedToRemove, boolean removeFromDictionary) {
+
+        if (isHint(entity)) {
+            return "hint:" + entity.getType() + ":" + id;
+        }
+
+        if (entity.isRedaction() && requestedToRemove && removeFromDictionary) {
+            return "request:remove:" + entity.getType() + ":" + id;
+        }
+
+        if (entity.isRedaction() && requestedToRemove && !removeFromDictionary) {
+            return "request:remove:only_here:" + id;
+        }
+
+        if (entity.isRedaction()) {
+            return "redaction:" + entity.getType() + ":" + id;
+        }
+        return "ignore:" + entity.getType() + ":" + id;
    }


@@ -163,32 +207,44 @@ public class AnnotationHighlightService {

        for (ManualRedactionEntry manualRedactionEntry : manualRedactions.getEntriesToAdd()) {

-            String id = IdBuilder.buildId(manualRedactionEntry);
+            String id = manualRedactionEntry.getId();

            RedactionLogEntry redactionLogEntry = createRedactionLogEntry(manualRedactionEntry, id);

-            boolean foundOnPage = false;
+            List<Rectangle> rectanglesOnPage = new ArrayList<>();
            for (Rectangle rectangle : manualRedactionEntry.getPositions()) {
-
-                if (page != rectangle.getPage()) {
-                    continue;
+                if (page == rectangle.getPage()) {
+                    rectanglesOnPage.add(rectangle);
+                    redactionLogEntry.getPositions().add(rectangle);
                }
-
-                foundOnPage = true;
-
-                PDAnnotationTextMarkup highlight = createAnnotation(rectangle, id,
-                        createAnnotationContent(manualRedactionEntry), getColor(manualRedactionEntry.getType()), true);
-                annotations.add(highlight);
-
-                redactionLogEntry.getPositions().add(rectangle);
            }
-            if (foundOnPage) {
+
+            if (!rectanglesOnPage.isEmpty()) {
+                annotations.addAll(createAnnotation(rectanglesOnPage, prefixId(manualRedactionEntry, id), createAnnotationContent(manualRedactionEntry), getColorForManualAdd(manualRedactionEntry
+                        .getType(), manualRedactionEntry.getStatus()), manualRedactionEntry.getComments(), true));
                classifiedDoc.getRedactionLogEntities().add(redactionLogEntry);
            }
        }
    }


+    private String prefixId(ManualRedactionEntry manualRedactionEntry, String id) {
+
+        if (manualRedactionEntry.getStatus().equals(Status.APPROVED)) {
+            return "redaction:" + manualRedactionEntry.getType() + ":" + id;
+        }
+
+        if(manualRedactionEntry.getStatus().equals(Status.REQUESTED)) {
+            if (manualRedactionEntry.isAddToDictionary()) {
+                return "request:add:" + manualRedactionEntry.getType() + ":" + id;
+            }
+            return "request:add:only_here" + ":" + id;
+        }
+
+        return "ignore:" + manualRedactionEntry.getType() + ":" + id;
+    }
+
+
    private RedactionLogEntry createRedactionLogEntry(ManualRedactionEntry manualRedactionEntry, String id) {

        return RedactionLogEntry.builder()
@@ -202,6 +258,7 @@ public class AnnotationHighlightService {
                .section(manualRedactionEntry.getSection())
                .sectionNumber(manualRedactionEntry.getSectionNumber())
                .manual(true)
+                .status(manualRedactionEntry.getStatus())
                .build();
    }

@@ -209,7 +266,7 @@ public class AnnotationHighlightService {
    private RedactionLogEntry createRedactionLogEntry(Entity entity) {

        return RedactionLogEntry.builder()
-                .color(getColor(entity))
+                .color(getColor(entity, false))
                .reason(entity.getRedactionReason())
                .value(entity.getWord())
                .type(entity.getType())
@@ -221,27 +278,45 @@ public class AnnotationHighlightService {
    }


-    private PDAnnotationTextMarkup createAnnotation(Rectangle rectangle, String id, String content, float[] color,
-                                                    boolean popup) {
+    private List<PDAnnotation> createAnnotation(List<Rectangle> rectangles, String id, String content, float[] color,
+                                                List<Comment> comments, boolean popup) {
+
+        List<PDAnnotation> annotations = new ArrayList<>();

        PDAnnotationTextMarkup annotation = new PDAnnotationTextMarkup(PDAnnotationTextMarkup.SUB_TYPE_HIGHLIGHT);
        annotation.constructAppearances();
-        annotation.setRectangle(toPDRectangle(rectangle));
-        annotation.setQuadPoints(toQuadPoints(rectangle));
+        PDRectangle pdRectangle = toPDRectangle(rectangles);
+        annotation.setRectangle(pdRectangle);
+        annotation.setQuadPoints(toQuadPoints(rectangles));
        if (popup) {
-            annotation.setAnnotationName(id);
-            annotation.setTitlePopup(id);
            annotation.setContents(content);
        }
+        annotation.setTitlePopup(id);
+        annotation.setAnnotationName(id);
        annotation.setColor(new PDColor(color, PDDeviceRGB.INSTANCE));
-        return annotation;
+        annotations.add(annotation);
+
+        if (comments != null) {
+            for (Comment comment : comments) {
+                PDAnnotationText txtAnnot = new PDAnnotationText();
+                txtAnnot.setAnnotationName(comment.getId());
+                txtAnnot.setInReplyTo(annotation); // Reference to highlight annotation
+                txtAnnot.setName(PDAnnotationText.NAME_COMMENT);
+                txtAnnot.setCreationDate(GregorianCalendar.from(comment.getDate().toZonedDateTime()));
+                txtAnnot.setTitlePopup(comment.getUser());
+                txtAnnot.setContents(comment.getText());
+                txtAnnot.setRectangle(pdRectangle);
+                annotations.add(txtAnnot);
+            }
+        }
+
+        return annotations;
    }


    private String createAnnotationContent(Entity entity) {

-        return "\nRule " + entity.getMatchedRule() + " matched" + "\n\n" + entity.getRedactionReason() + "\n\nIn " +
-                "Section : \"" + entity
+        return "\nRule " + entity.getMatchedRule() + " matched" + "\n\n" + entity.getRedactionReason() + "\n\nIn " + "Section : \"" + entity
                .getHeadline() + "\"";
    }

@@ -252,24 +327,59 @@ public class AnnotationHighlightService {
    }


-    private PDRectangle toPDRectangle(Rectangle rectangle) {
+    private PDRectangle toPDRectangle(List<Rectangle> rectangles) {
+
+        float lowerLeftX = Float.MAX_VALUE;
+        float upperRightX = 0;
+        float lowerLeftY = 0;
+        float upperRightY = Float.MAX_VALUE;
+
+        for (Rectangle rectangle : rectangles) {
+            if (rectangle.getTopLeft().getX() < lowerLeftX) {
+                lowerLeftX = rectangle.getTopLeft().getX();
+            }
+            if (rectangle.getTopLeft().getX() + rectangle.getWidth() > upperRightX) {
+                upperRightX = rectangle.getTopLeft().getX() + rectangle.getWidth();
+            }
+            if (rectangle.getTopLeft().getY() + rectangle.getHeight() > lowerLeftY) {
+                lowerLeftY = rectangle.getTopLeft().getY() + rectangle.getHeight();
+            }
+            if (rectangle.getTopLeft().getY() < upperRightY) {
+                upperRightY = rectangle.getTopLeft().getY();
+            }
+        }

        PDRectangle annotationPosition = new PDRectangle();
-        annotationPosition.setLowerLeftX(rectangle.getTopLeft().getX());
-        annotationPosition.setLowerLeftY(rectangle.getTopLeft().getY() + rectangle.getHeight());
-        annotationPosition.setUpperRightX(rectangle.getTopLeft().getX() + rectangle.getWidth());
-        annotationPosition.setUpperRightY(rectangle.getTopLeft().getY());
+        annotationPosition.setLowerLeftX(lowerLeftX);
+        annotationPosition.setLowerLeftY(lowerLeftY);
+        annotationPosition.setUpperRightX(upperRightX);
+        annotationPosition.setUpperRightY(upperRightY);
        return annotationPosition;
    }


-    private float[] toQuadPoints(Rectangle rectangle) {
+    private float[] toQuadPoints(List<Rectangle> rectangles) {
+
+        float[] quadPoints = new float[rectangles.size() * 8];
+        int i = 0;
+
+        for (Rectangle rectangle : rectangles) {
+            float[] quadPoint = toQuadPoint(rectangle);
+            for (int j = 0; j <= 7; j++) {
+                quadPoints[i + j] = quadPoint[j];
+            }
+            i += 8;
+        }
+        return quadPoints;
+    }
+
+
+    private float[] toQuadPoint(Rectangle rectangle) {

        // quadPoints is array of x,y coordinates in Z-like order (top-left, top-right, bottom-left,bottom-right)
        // of the area to be highlighted
        return new float[]{rectangle.getTopLeft().getX(), rectangle.getTopLeft().getY(), rectangle.getTopLeft()
-                .getX() + rectangle.getWidth(), rectangle.getTopLeft().getY(), rectangle.getTopLeft().getX(),
-                rectangle.getTopLeft()
+                .getX() + rectangle.getWidth(), rectangle.getTopLeft().getY(), rectangle.getTopLeft().getX(), rectangle.getTopLeft()
                .getY() + rectangle.getHeight(), rectangle.getTopLeft()
                .getX() + rectangle.getWidth(), rectangle.getTopLeft().getY() + rectangle.getHeight()};
    }
@@ -284,10 +394,13 @@ public class AnnotationHighlightService {
    }


-    private float[] getColor(Entity entity) {
+    private float[] getColor(Entity entity, boolean requestedToRemove) {

+        if (requestedToRemove) {
+            return dictionaryService.getRequestRemoveColor();
+        }
        if (!entity.isRedaction() && !isHint(entity)) {
-            return new float[]{0.627f, 0.627f, 0.627f};
+            return dictionaryService.getNotRedactedColor();
        }
        if (!dictionaryService.getEntryColors().containsKey(entity.getType())) {
            return dictionaryService.getDefaultColor();
@@ -296,6 +409,17 @@ public class AnnotationHighlightService {
    }


+    private float[] getColorForManualAdd(String type, Status status) {
+
+        if (status.equals(Status.REQUESTED)) {
+            return dictionaryService.getRequestAddColor();
+        } else if (status.equals(Status.DECLINED)){
+            return dictionaryService.getNotRedactedColor();
+        }
+        return getColor(type);
+    }
+
+
    private float[] getColor(String type) {

        if (!dictionaryService.getEntryColors().containsKey(type)) {
@@ -319,8 +443,7 @@ public class AnnotationHighlightService {
            return;
        }

-        PDPageContentStream contentStream = new PDPageContentStream(document, pdPage,
-                PDPageContentStream.AppendMode.APPEND, true);
+        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++) {
@@ -369,8 +492,7 @@ public class AnnotationHighlightService {
                if (cell != null) {
                    contentStream.setLineWidth(0.5f);
                    contentStream.setStrokingColor(Color.CYAN);
-                    contentStream.addRect((float) cell.getX(), (float) cell.getY(), (float) cell.getWidth(),
-                            (float) cell
+                    contentStream.addRect((float) cell.getX(), (float) cell.getY(), (float) cell.getWidth(), (float) cell
                            .getHeight());
                    contentStream.stroke();
                }
@@ -14,6 +14,7 @@ import java.io.InputStream;
 import java.io.InputStreamReader;
 import java.net.URL;
 import java.nio.charset.StandardCharsets;
+import java.time.OffsetDateTime;
 import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.List;
@@ -38,17 +39,20 @@ import org.springframework.context.annotation.Bean;
 import org.springframework.core.io.ClassPathResource;
 import org.springframework.test.context.junit4.SpringRunner;

-import com.iqser.red.service.configuration.v1.api.model.DefaultColor;
+import com.iqser.red.service.configuration.v1.api.model.Colors;
 import com.iqser.red.service.configuration.v1.api.model.DictionaryResponse;
 import com.iqser.red.service.configuration.v1.api.model.RulesResponse;
 import com.iqser.red.service.configuration.v1.api.model.TypeResponse;
 import com.iqser.red.service.configuration.v1.api.model.TypeResult;
+import com.iqser.red.service.redaction.v1.model.Comment;
+import com.iqser.red.service.redaction.v1.model.IdRemoval;
 import com.iqser.red.service.redaction.v1.model.ManualRedactionEntry;
 import com.iqser.red.service.redaction.v1.model.ManualRedactions;
 import com.iqser.red.service.redaction.v1.model.Point;
 import com.iqser.red.service.redaction.v1.model.Rectangle;
 import com.iqser.red.service.redaction.v1.model.RedactionRequest;
 import com.iqser.red.service.redaction.v1.model.RedactionResult;
+import com.iqser.red.service.redaction.v1.model.Status;
 import com.iqser.red.service.redaction.v1.server.client.DictionaryClient;
 import com.iqser.red.service.redaction.v1.server.client.RulesClient;
 import com.iqser.red.service.redaction.v1.server.controller.RedactionController;
@@ -63,6 +67,7 @@ public class RedactionIntegrationTest {
    private static final String VERTEBRATES_CODE = "vertebrate";
    private static final String ADDRESS_CODE = "address";
    private static final String NAME_CODE = "name";
+    private static final String SPONSOR = "sponsor";
    private static final String NO_REDACTION_INDICATOR = "no_redaction_indicator";
    private static final String REDACTION_INDICATOR = "redaction_indicator";
    private static final String HINT_ONLY = "hint_only";
@@ -78,9 +83,10 @@ public class RedactionIntegrationTest {
    private DictionaryClient dictionaryClient;

    private final Map<String, List<String>> dictionary = new HashMap<>();
-    private final Map<String, float[]> typeColorMap = new HashMap<>();
+    private final Map<String, String> typeColorMap = new HashMap<>();
    private final Map<String, Boolean> hintTypeMap = new HashMap<>();
    private final Map<String, Boolean> caseInSensitiveMap = new HashMap<>();
+    private final Colors colors = new Colors();

    @TestConfiguration
    public static class RedactionIntegrationTestConfiguration {
@@ -117,11 +123,12 @@ public class RedactionIntegrationTest {
        when(dictionaryClient.getDictionaryForType(VERTEBRATES_CODE)).thenReturn(getDictionaryResponse(VERTEBRATES_CODE));
        when(dictionaryClient.getDictionaryForType(ADDRESS_CODE)).thenReturn(getDictionaryResponse(ADDRESS_CODE));
        when(dictionaryClient.getDictionaryForType(NAME_CODE)).thenReturn(getDictionaryResponse(NAME_CODE));
+        when(dictionaryClient.getDictionaryForType(SPONSOR)).thenReturn(getDictionaryResponse(SPONSOR));
        when(dictionaryClient.getDictionaryForType(NO_REDACTION_INDICATOR)).thenReturn(getDictionaryResponse(NO_REDACTION_INDICATOR));
        when(dictionaryClient.getDictionaryForType(REDACTION_INDICATOR)).thenReturn(getDictionaryResponse(REDACTION_INDICATOR));
        when(dictionaryClient.getDictionaryForType(HINT_ONLY)).thenReturn(getDictionaryResponse(HINT_ONLY));
        when(dictionaryClient.getDictionaryForType(MUST_REDACT)).thenReturn(getDictionaryResponse(MUST_REDACT));
-        when(dictionaryClient.getDefaultColor()).thenReturn(new DefaultColor(new float[]{1f, 0.502f, 0f}));
+        when(dictionaryClient.getColors()).thenReturn(colors);
    }


@@ -132,6 +139,11 @@ public class RedactionIntegrationTest {
                        .stream()
                        .map(this::cleanDictionaryEntry)
                        .collect(Collectors.toSet()));
+        dictionary.computeIfAbsent(SPONSOR, v -> new ArrayList<>())
+                .addAll(ResourceLoader.load("dictionaries/sponsor_companies.txt")
+                        .stream()
+                        .map(this::cleanDictionaryEntry)
+                        .collect(Collectors.toSet()));
        dictionary.computeIfAbsent(VERTEBRATES_CODE, v -> new ArrayList<>())
                .addAll(ResourceLoader.load("dictionaries/vertebrates.txt")
                        .stream()
@@ -173,17 +185,19 @@ public class RedactionIntegrationTest {

    private void loadTypeForTest() {

-        typeColorMap.put(VERTEBRATES_CODE, new float[]{0, 1, 0});
-        typeColorMap.put(ADDRESS_CODE, new float[]{0, 1, 1});
-        typeColorMap.put(NAME_CODE, new float[]{1, 1, 0});
-        typeColorMap.put(NO_REDACTION_INDICATOR, new float[]{0.8f, 0, 0.8f});
-        typeColorMap.put(REDACTION_INDICATOR, new float[]{1, 0.502f, 0.1f});
-        typeColorMap.put(HINT_ONLY, new float[]{0.8f, 1, 0.8f});
-        typeColorMap.put(MUST_REDACT, new float[]{1, 0, 0});
+        typeColorMap.put(VERTEBRATES_CODE, "#00ff00");
+        typeColorMap.put(ADDRESS_CODE, "#00ffff");
+        typeColorMap.put(NAME_CODE, "#ffff00");
+        typeColorMap.put(SPONSOR, "#2c21fc");
+        typeColorMap.put(NO_REDACTION_INDICATOR, "#e600ff");
+        typeColorMap.put(REDACTION_INDICATOR, "#ff7700");
+        typeColorMap.put(HINT_ONLY, "#00fcb1");
+        typeColorMap.put(MUST_REDACT, "#ff0000");

        hintTypeMap.put(VERTEBRATES_CODE, true);
        hintTypeMap.put(ADDRESS_CODE, false);
        hintTypeMap.put(NAME_CODE, false);
+        hintTypeMap.put(SPONSOR, false);
        hintTypeMap.put(NO_REDACTION_INDICATOR, true);
        hintTypeMap.put(REDACTION_INDICATOR, true);
        hintTypeMap.put(HINT_ONLY, true);
@@ -192,10 +206,16 @@ public class RedactionIntegrationTest {
        caseInSensitiveMap.put(VERTEBRATES_CODE, true);
        caseInSensitiveMap.put(ADDRESS_CODE, false);
        caseInSensitiveMap.put(NAME_CODE, false);
+        caseInSensitiveMap.put(SPONSOR, false);
        caseInSensitiveMap.put(NO_REDACTION_INDICATOR, true);
        caseInSensitiveMap.put(REDACTION_INDICATOR, true);
        caseInSensitiveMap.put(HINT_ONLY, true);
        caseInSensitiveMap.put(MUST_REDACT, true);
+
+        colors.setDefaultColor("#acfc00");
+        colors.setNotRedacted("#cccccc");
+        colors.setRequestAdd("#04b093");
+        colors.setRequestRemove("#04b093");
    }


@@ -205,7 +225,7 @@ public class RedactionIntegrationTest {
                .stream()
                .map(typeColor -> TypeResult.builder()
                        .type(typeColor.getKey())
-                        .color(typeColor.getValue())
+                        .hexColor(typeColor.getValue())
                        .isHint(hintTypeMap.get(typeColor.getKey()))
                        .isCaseInsensitive(caseInSensitiveMap.get(typeColor.getKey()))
                        .build())
@@ -217,7 +237,7 @@ public class RedactionIntegrationTest {
    private DictionaryResponse getDictionaryResponse(String type) {

        return DictionaryResponse.builder()
-                .color(typeColorMap.get(type))
+                .hexColor(typeColorMap.get(type))
                .entries(dictionary.get(type))
                .isHint(hintTypeMap.get(type))
                .isCaseInsensitive(caseInSensitiveMap.get(type))
@@ -270,7 +290,7 @@ public class RedactionIntegrationTest {

        System.out.println("redactionTest");
        long start = System.currentTimeMillis();
-        ClassPathResource pdfFileResource = new ClassPathResource("files/Fludioxonil/50 Fludioxonil_RAR_01_Volume_1_2018-02-21.pdf");
+        ClassPathResource pdfFileResource = new ClassPathResource("files/Metolachlor/S-Metolachlor_RAR_01_Volume_1_2018-09-06.pdf");

        RedactionRequest request = RedactionRequest.builder()
                .document(IOUtils.toByteArray(pdfFileResource.getInputStream()))
@@ -320,9 +340,21 @@ public class RedactionIntegrationTest {
        ClassPathResource pdfFileResource = new ClassPathResource("files/Minimal Examples/Single Table.pdf");

        ManualRedactions manualRedactions = new ManualRedactions();
-        manualRedactions.setIdsToRemove(Set.of("0836727c3508a0b2ea271da69c04cc2f"));
+
+        Comment comment = Comment.builder()
+                .date(OffsetDateTime.now())
+                .user("TEST_USER")
+                .text("This is a comment test")
+                .build();
+        manualRedactions.setIdsToRemove(Set.of(IdRemoval.builder()
+                .id("0836727c3508a0b2ea271da69c04cc2f")
+                .status(Status.REQUESTED)
+                .comments(List.of(comment))
+                .build()));

        ManualRedactionEntry manualRedactionEntry = new ManualRedactionEntry();
+        manualRedactionEntry.setStatus(Status.REQUESTED);
+        manualRedactionEntry.setComments(List.of(comment));
        manualRedactionEntry.setType("name");
        manualRedactionEntry.setValue("O'Loughlin C.K.");
        manualRedactionEntry.setReason("Manual Redaction");
@@ -351,8 +383,7 @@ public class RedactionIntegrationTest {
    public void classificationTest() throws IOException {

        System.out.println("classificationTest");
-        ClassPathResource pdfFileResource = new ClassPathResource("files/Fludioxonil/51 " +
-                "Fludioxonil_RAR_02_Volume_2_2018-02-21.pdf");
+        ClassPathResource pdfFileResource = new ClassPathResource("files/Fludioxonil/51 Fludioxonil_RAR_02_Volume_2_2018-02-21.pdf");

        RedactionRequest request = RedactionRequest.builder()
                .document(IOUtils.toByteArray(pdfFileResource.getInputStream()))
@@ -370,8 +401,7 @@ public class RedactionIntegrationTest {
    public void sectionsTest() throws IOException {

        System.out.println("sectionsTest");
-        ClassPathResource pdfFileResource = new ClassPathResource("files/Fludioxonil/51 " +
-                "Fludioxonil_RAR_02_Volume_2_2018-02-21.pdf");
+        ClassPathResource pdfFileResource = new ClassPathResource("files/Fludioxonil/51 " + "Fludioxonil_RAR_02_Volume_2_2018-02-21.pdf");

        RedactionRequest request = RedactionRequest.builder()
                .document(IOUtils.toByteArray(pdfFileResource.getInputStream()))
@@ -389,7 +419,7 @@ public class RedactionIntegrationTest {
    public void htmlTablesTest() throws IOException {

        System.out.println("htmlTablesTest");
-        ClassPathResource pdfFileResource = new ClassPathResource("files/Metolachlor/S-Metolachlor_RAR_02_Volume_2_2018-09-06.pdf");
+        ClassPathResource pdfFileResource = new ClassPathResource("files/Minimal Examples/line_breaks.pdf");

        RedactionRequest request = RedactionRequest.builder()
                .document(IOUtils.toByteArray(pdfFileResource.getInputStream()))
@@ -407,8 +437,7 @@ public class RedactionIntegrationTest {
    public void htmlTableRotationTest() throws IOException {

        System.out.println("htmlTableRotationTest");
-        ClassPathResource pdfFileResource = new ClassPathResource("files/Metolachlor/S" +
-                "-Metolachlor_RAR_02_Volume_2_2018-09-06.pdf");
+        ClassPathResource pdfFileResource = new ClassPathResource("files/Metolachlor/S-Metolachlor_RAR_02_Volume_2_2018-09-06.pdf");

        RedactionRequest request = RedactionRequest.builder()
                .document(IOUtils.toByteArray(pdfFileResource.getInputStream()))
@@ -435,13 +464,35 @@ public class RedactionIntegrationTest {
        RedactionResult result = redactionController.redact(request);

        result.getRedactionLog().getRedactionLogEntry().forEach(entry -> {
-            if(!entry.isHint()){
+            if (!entry.isHint()) {
                assertThat(entry.getReason()).isEqualTo("Not redacted because row is not a vertebrate study");
            }
        });
    }


+    @Test
+    public void sponsorCompanyTest() throws IOException {
+
+        long start = System.currentTimeMillis();
+        ClassPathResource pdfFileResource = new ClassPathResource("files/Minimal Examples/sponsor_companies.pdf");
+
+        RedactionRequest request = RedactionRequest.builder()
+                .document(IOUtils.toByteArray(pdfFileResource.getInputStream()))
+                .build();
+        request.setFlatRedaction(false);
+
+        RedactionResult result = redactionController.redact(request);
+
+        try (FileOutputStream fileOutputStream = new FileOutputStream("/tmp/Redacted.pdf")) {
+            fileOutputStream.write(result.getDocument());
+        }
+        long end = System.currentTimeMillis();
+
+        System.out.println("duration: " + (end - start));
+        System.out.println("numberOfPages: " + result.getNumberOfPages());
+    }
+

    private static String loadFromClassPath(String path) {

@@ -449,8 +500,7 @@ public class RedactionIntegrationTest {
        if (resource == null) {
            throw new IllegalArgumentException("could not load classpath resource: drools/rules.drl");
        }
-        try (BufferedReader br = new BufferedReader(new InputStreamReader(resource.openStream(),
-                StandardCharsets.UTF_8))) {
+        try (BufferedReader br = new BufferedReader(new InputStreamReader(resource.openStream(), StandardCharsets.UTF_8))) {
            StringBuilder sb = new StringBuilder();
            String str;
            while ((str = br.readLine()) != null) {
@@ -35,7 +35,7 @@ import org.springframework.context.annotation.Bean;
 import org.springframework.core.io.ClassPathResource;
 import org.springframework.test.context.junit4.SpringRunner;

-import com.iqser.red.service.configuration.v1.api.model.DefaultColor;
+import com.iqser.red.service.configuration.v1.api.model.Colors;
 import com.iqser.red.service.configuration.v1.api.model.DictionaryResponse;
 import com.iqser.red.service.configuration.v1.api.model.RulesResponse;
 import com.iqser.red.service.configuration.v1.api.model.TypeResponse;
@@ -134,7 +134,35 @@ public class EntityRedactionServiceTest {
            Document classifiedDoc = pdfSegmentationService.parseDocument(pdDocument);
            entityRedactionService.processDocument(classifiedDoc, null);
            assertThat(classifiedDoc.getEntities()).hasSize(1); // one page
-            assertThat(classifiedDoc.getEntities().get(1)).hasSize(7);// 3 names, 1 address, 1 Y and 2 N entities
+            assertThat(classifiedDoc.getEntities().get(1)).hasSize(7);// 3 author cells, 1 address, 1 Y and 2 N entities
+        }
+    }
+
+
+    @Test
+    public void testNestedRedaction() throws IOException {
+
+        ClassPathResource pdfFileResource = new ClassPathResource("files/Minimal Examples/nested_redaction.pdf");
+
+        RedactionRequest redactionRequest = RedactionRequest.builder()
+                .document(IOUtils.toByteArray(pdfFileResource.getInputStream()))
+                .build();
+
+        DictionaryResponse dictionaryResponse = DictionaryResponse.builder()
+                .entries(Arrays.asList("Casey, H.W.", "O’Loughlin,  C.K.", "Salamon, C.M.", "Smith, S.H."))
+                .build();
+        when(dictionaryClient.getVersion()).thenReturn(DICTIONARY_VERSION.incrementAndGet());
+        when(dictionaryClient.getDictionaryForType(NAME_CODE)).thenReturn(dictionaryResponse);
+        DictionaryResponse addressResponse = DictionaryResponse.builder()
+                .entries(Collections.singletonList("Toxigenics, Inc., Decatur, IL 62526, USA"))
+                .build();
+        when(dictionaryClient.getDictionaryForType(ADDRESS_CODE)).thenReturn(addressResponse);
+
+        try (PDDocument pdDocument = PDDocument.load(new ByteArrayInputStream(redactionRequest.getDocument()))) {
+            Document classifiedDoc = pdfSegmentationService.parseDocument(pdDocument);
+            entityRedactionService.processDocument(classifiedDoc, null);
+            assertThat(classifiedDoc.getEntities()).hasSize(1); // one page
+            assertThat(classifiedDoc.getEntities().get(1)).hasSize(7);// 3 author cells, 1 address, 1 Y and 2 N entities
        }
    }

@@ -273,7 +301,7 @@ public class EntityRedactionServiceTest {
            entityRedactionService.processDocument(classifiedDoc, null);
            assertThat(classifiedDoc.getEntities()).hasSize(2); // two pages
            assertThat(classifiedDoc.getEntities().get(1).stream().filter(entity -> entity.getMatchedRule() == 9).count()).isEqualTo(8);
-            assertThat(classifiedDoc.getEntities().get(2).stream().filter(entity -> entity.getMatchedRule() == 9).count()).isEqualTo(4);
+            assertThat(classifiedDoc.getEntities().get(2).stream().filter(entity -> entity.getMatchedRule() == 9).count()).isEqualTo(5); // 2 names, 1 address, 2 Y
        }

        pdfFileResource = new ClassPathResource("files/Minimal Examples/Header Propagation2.pdf");
@@ -335,7 +363,7 @@ public class EntityRedactionServiceTest {
                "    when\n" +
                "        Section(rowEquals(\"Vertebrate study Y/N\", \"N\") || rowEquals(\"Vertebrate study Y/N\", \"No\"))\n" +
                "    then\n" +
-                "        section.redactNot(\"name\", 8, \"Not redacted because row is not a vertebrate study\");\n" +
+                "        section.redactNotCell(\"Author(s)\", 8,  \"name\", \"Not redacted because row is not a vertebrate study\");\n" +
                "        section.redactNot(\"address\", 8, \"Not redacted because row is not a vertebrate study\");\n" +
                "        section.highlightCell(\"Vertebrate study Y/N\", 8, \"hint_only\");\n" +
                "    end\n" +
@@ -344,7 +372,7 @@ public class EntityRedactionServiceTest {
                "        Section(rowEquals(\"Vertebrate study Y/N\", \"Y\") || rowEquals(\"Vertebrate study Y/N\", " +
                "\"Yes\"))\n" +
                "    then\n" +
-                "        section.redact(\"name\", 9, \"Redacted because row is a vertebrate study\");\n" +
+                "        section.redactCell(\"Author(s)\", 9,  \"name\", \"Redacted because row is a vertebrate study\");\n" +
                "        section.redact(\"address\", 9, \"Redacted because row is a vertebrate study\");\n" +
                "        section.highlightCell(\"Vertebrate study Y/N\", 9, \"must_redact\");\n" +
                "    end";
@@ -352,12 +380,19 @@ public class EntityRedactionServiceTest {
        when(rulesClient.getRules()).thenReturn(new RulesResponse(tableRules));
        TypeResponse typeResponse = TypeResponse.builder()
                .types(Arrays.asList(
-                        TypeResult.builder().type(NAME_CODE).color(new float[]{1, 1, 0}).build(),
-                        TypeResult.builder().type(ADDRESS_CODE).color(new float[]{0, 1, 1}).build()))
+                        TypeResult.builder().type(NAME_CODE).hexColor("#ffff00").build(),
+                        TypeResult.builder().type(ADDRESS_CODE).hexColor("#00ffff").build()))
                .build();
        when(dictionaryClient.getVersion()).thenReturn(DICTIONARY_VERSION.incrementAndGet());
        when(dictionaryClient.getAllTypes()).thenReturn(typeResponse);
-        when(dictionaryClient.getDefaultColor()).thenReturn(new DefaultColor());
+
+        Colors colors = new Colors();
+        colors.setDefaultColor("#acfc00");
+        colors.setNotRedacted("#cccccc");
+        colors.setRequestAdd("#04b093");
+        colors.setRequestRemove("#04b093");
+
+        when(dictionaryClient.getColors()).thenReturn(colors);
    }


@@ -1,3 +1,2 @@
-Batches Produced at
 CTL
 determination of residues
@@ -0,0 +1,7 @@
+Monthey Syngenta Crop Protection AG, Basel, Switzerland
+Syngenta Crop Protection, Monthey, Switzerland
+Fine Organics Limited, Middlesbrough, United Kingdom
+Syngenta Monthey Switzerland
+Hunan Haili Chemical Industry Co., Ltd., Hunan, China
+Syngenta, Switzerland
+Syngenta Nantong, China
@@ -7,7 +7,7 @@ global Section section

 rule "1: Redacted because Section contains Vertebrate"
 	when
-		eval(section.contains("vertebrate")==true);
+		Section(matchesType("vertebrate"))
 	then
 		section.redact("name", 1, "Redacted because Section contains Vertebrate");
 		section.redact("address", 1, "Redacted because Section contains Vertebrate");
@@ -16,7 +16,7 @@ rule "1: Redacted because Section contains Vertebrate"

 rule "2: Not Redacted because Section contains no Vertebrate"
 	when
-		eval(section.contains("vertebrate")==false);
+		Section(!matchesType("vertebrate"))
 	then
 		section.redactNot("name", 2, "Not Redacted because Section contains no Vertebrate");
 		section.redactNot("address", 2, "Not Redacted because Section contains no Vertebrate");
@@ -25,7 +25,7 @@ rule "2: Not Redacted because Section contains no Vertebrate"

 rule "3: Do not redact Names and Addresses if no redaction Indicator is contained"
 	when
-		eval(section.contains("vertebrate")==true && section.contains("no_redaction_indicator")==true);
+		Section(matchesType("vertebrate"), matchesType("no_redaction_indicator"))
 	then
 		section.redactNot("name", 3, "Vertebrate was found, but also a no redaction indicator");
 		section.redactNot("address", 3, "Vertebrate was found, but also a no redaction indicator");
@@ -34,7 +34,7 @@ rule "3: Do not redact Names and Addresses if no redaction Indicator is containe

 rule "4: Redact Names and Addresses if no_redaction_indicator and redaction_indicator is contained"
 	when
-		eval(section.contains("vertebrate")==true && section.contains("no_redaction_indicator")==true && section.contains("redaction_indicator")==true);
+		Section(matchesType("vertebrate"), matchesType("no_redaction_indicator"), matchesType("redaction_indicator"))
 	then
 		section.redact("name", 4, "Vertebrate was found and no_redaction_indicator and redaction_indicator");
 		section.redact("address", 4, "Vertebrate was found and no_redaction_indicator and redaction_indicator");
@@ -43,15 +43,16 @@ rule "4: Redact Names and Addresses if no_redaction_indicator and redaction_indi

 rule "5: Do not redact in guideline sections"
 	when
-		eval(section.headlineContainsWord("guideline") || section.headlineContainsWord("Guidance"));
+		Section(headlineContainsWord("guideline") || headlineContainsWord("Guidance"))
 	then
 		section.redactNot("name", 5, "Section is a guideline section.");
 		section.redactNot("address", 5, "Section is a guideline section.");
 	end

+
 rule "6: Redact contact information if applicant is found"
 	when
-		eval(section.headlineContainsWord("applicant") || section.getText().contains("Applicant") || section.headlineContainsWord("Primary contact") || section.headlineContainsWord("Alternative contact"));
+		Section(headlineContainsWord("applicant") || text.contains("Applicant") || headlineContainsWord("Primary contact") || headlineContainsWord("Alternative contact"))
 	then
 		section.redactLineAfter("Name:", "address", 6, "Applicant information was found");
 		section.redactBetween("Address:", "Contact", "address", 6, "Applicant information was found");
@@ -78,7 +79,7 @@ rule "6: Redact contact information if applicant is found"

 rule "7: Redact contact information if Producer is found"
 	when
-		eval(section.getText().toLowerCase().contains("producer of the plant protection") || section.getText().toLowerCase().contains("producer of the active substance") || section.getText().contains("Manufacturer of the active substance") || section.getText().contains("Manufacturer:") || section.getText().contains("Producer or producers of the active substance"));
+		Section(text.toLowerCase().contains("producer of the plant protection") || text.toLowerCase().contains("producer of the active substance") || text.contains("Manufacturer of the active substance") || text.contains("Manufacturer:") || text.contains("Producer or producers of the active substance"))
 	then
 		section.redactLineAfter("Name:", "address", 7, "Producer was found");
 		section.redactBetween("Address:", "Contact", "address", 7, "Producer was found");
@@ -109,7 +110,7 @@ rule "8: Not redacted because Vertebrate Study = N"

 rule "9: Redact if must redact entry is found"
 	when
-		eval(section.contains("must_redact")==true);
+		Section(matchesType("must_redact"))
 	then
 		section.redact("name", 9, "must_redact entry was found.");
 		section.redact("address", 9, "must_redact entry was found.");
@@ -124,3 +125,10 @@ rule "10: Redact Authors and Addresses in Reference Table if it is a Vertebrate
        section.redact("address", 10, "Redacted because row is a vertebrate study");
        section.highlightCell("Vertebrate study Y/N", 10, "must_redact");
    end
+
+rule "11: Redact sponsor company"
+    when
+        Section(text.toLowerCase().contains("batches produced at"))
+    then
+        section.redactIfPrecededBy("batches produced at", "sponsor", 11, "Redacted because it represents a sponsor company");
+    end
Author	SHA1	Message	Date
Dominique Eiflaender	268dd0200e	Pull request #55 : RED-413: Added user to manual redactions, approved flag to Status.APPROVED Merge in RED/redaction-service from RED-413 to master * commit '638c4f9c65d35406bba1fd33e20c3bae8a6e6a13': RED-413: Added user to manual redactions, approved flag to Status.APPROVED	2020-10-12 12:32:30 +02:00
deiflaender	638c4f9c65	RED-413: Added user to manual redactions, approved flag to Status.APPROVED	2020-10-12 12:21:18 +02:00
Dominique Eiflaender	8f12695f16	Pull request #54 : RED-414: Ids for manual redactions and comments must be created in file-management-service Merge in RED/redaction-service from RED-414 to master * commit '79db6e4bf9d821fe4716a6da31d3f6d6fcaff05b': RED-414: Ids for manual redactions and comments must be created in file-management-service	2020-10-09 12:17:38 +02:00
deiflaender	79db6e4bf9	RED-414: Ids for manual redactions and comments must be created in file-management-service	2020-10-09 12:06:19 +02:00
Dominique Eiflaender	c8eac2ca3d	Pull request #53 : RED-240: Use HexColors instead of float[], RED-380: Load all system colors from dictionary-service Merge in RED/redaction-service from RED-240 to master * commit 'a01651b8278ed09f9409d6ec2e1615680bc846cb': RED-240: Use HexColors instead of float[], RED-380: Load all system colors from dictionary-service	2020-10-08 12:05:42 +02:00
deiflaender	a01651b827	RED-240: Use HexColors instead of float[], RED-380: Load all system colors from dictionary-service	2020-10-08 11:51:35 +02:00
Dominique Eiflaender	943d40366e	Pull request #52 : RED-391: Support comments and approval of manual redactions, RED-385: Improve annotation IDs in PDFs Merge in RED/redaction-service from RED-391 to master * commit '365158a0084b2034aca91e6f77eb9df42bbcb246': RED-391: Support comments and approval of manual redactions, RED-385: Improve annotation IDs in PDFs	2020-10-05 15:36:06 +02:00
deiflaender	365158a008	RED-391: Support comments and approval of manual redactions, RED-385: Improve annotation IDs in PDFs	2020-10-05 15:14:23 +02:00
Thierry Goeckel	e76b893c8d	Pull request #51 : RED-104 Merge in RED/redaction-service from RED-104 to master * commit 'fa29f56d98d05fd348dd27e3bbb1098851c238bd': Test line break fix	2020-10-05 11:02:56 +02:00
Thierry Goeckel	d91612a69a	Pull request #50 : Make sure section and table char indices match Merge in RED/redaction-service from RED-381 to master * commit '9a965dd68a72285af6bf6a28ec6aa67358c35dba': Make sure section and table char indices match	2020-10-05 11:02:44 +02:00
Thierry Göckel	fa29f56d98	Test line break fix	2020-10-02 18:11:58 +02:00
Thierry Göckel	9a965dd68a	Make sure section and table char indices match	2020-10-02 17:54:31 +02:00
Dominique Eiflaender	0f4838e60d	Pull request #49 : RED-373: Fixed multiline annotations view in pdftron Merge in RED/redaction-service from RED-373-2 to master * commit 'a4e012762e1adda234decc1137f221cfd70498d3': RED-373: Fixed multiline annotations view in pdftron	2020-10-01 15:31:25 +02:00
deiflaender	a4e012762e	RED-373: Fixed multiline annotations view in pdftron	2020-10-01 15:19:57 +02:00
Dominique Eiflaender	0c1d8ba33d	Pull request #48 : RED-372: Suffix cross page annotations with -1, -2, etc., to avoid duplicate annotation ids Merge in RED/redaction-service from RED-372 to master * commit 'ecdfd29803e09ac57cc74b19408db54d9a8247a7': RED-372: Suffix cross page annotations with -1, -2, etc., to avoid duplicate annotation ids	2020-10-01 13:01:24 +02:00
deiflaender	ecdfd29803	RED-372: Suffix cross page annotations with -1, -2, etc., to avoid duplicate annotation ids	2020-10-01 12:48:44 +02:00
Dominique Eiflaender	107dbe1910	Pull request #47 : RED-373: Use a single multiline annotation instead of seperate annotations per line for one Entity Merge in RED/redaction-service from RED-373 to master * commit 'dd02296face3c32bf7675301cf9969103e65f52f': Changed formating RED-373: Use a single multiline annotation instead of seperate annotations per line for one Entity	2020-10-01 12:47:58 +02:00
deiflaender	dd02296fac	Changed formating	2020-10-01 11:55:38 +02:00
Thierry Goeckel	589458a112	Pull request #46 : Add rule redacting sponsor companies if preceded by prefix Merge in RED/redaction-service from RED-301 to master * commit '6a8f3665198ec2d7452ed0dac43b9a7d220c8bc5': Remove entries from must_redact dict, add test and refactor rules Add rule redacting sponsor companies if preceded by prefix	2020-10-01 11:44:41 +02:00
deiflaender	ce22121802	RED-373: Use a single multiline annotation instead of seperate annotations per line for one Entity	2020-10-01 11:15:28 +02:00
Thierry Göckel	6a8f366519	Remove entries from must_redact dict, add test and refactor rules	2020-09-30 16:08:56 +02:00
Thierry Göckel	cec5fd3d5e	Add rule redacting sponsor companies if preceded by prefix	2020-09-30 14:13:17 +02:00
Dominique Eiflaender	99bde2956f	Pull request #45 : RED-277: Upgraded to pdfbox 2.0.21 Merge in RED/redaction-service from RED-277 to master * commit 'ecc303e79e82ed698f1c8bdd37dbd521335428bc': RED-277: Upgraded to pdfbox 2.0.21	2020-09-29 16:17:32 +02:00
deiflaender	ecc303e79e	RED-277: Upgraded to pdfbox 2.0.21	2020-09-29 15:18:58 +02:00
Dominique Eiflaender	384cd1d0dc	Pull request #44 : Fix annotating single letter entities Merge in RED/redaction-service from bugfix/single-letter-annotations to master * commit '8e5ff318106e700e28abd14a0eb1337d3a44c109': Fix annotating single letter entities	2020-09-29 15:17:51 +02:00