Fix annotating single letter entities

Pull request #43 : RED-264: Avoid phantom cells, by merging line till rounded value of biggest char height/width
Merge in RED/redaction-service from RED-264 to master * commit 'e1adcfb02c4c7d46140884b3d38f8daf1e1aae92': Added missing unittest RED-264: Avoid phantom cells, by merging line till rounded value of biggest char height/width
2020-09-29 15:10:52 +02:00 · 2020-09-29 15:04:20 +02:00 · 2020-09-29 14:54:35 +02:00 · 2020-09-29 14:21:42 +02:00 · 2020-09-29 14:15:21 +02:00 · 2020-09-29 13:54:32 +02:00
19 changed files with 257 additions and 106 deletions
@@ -5,7 +5,7 @@
  <parent>
    <groupId>com.atlassian.bamboo</groupId>
    <artifactId>bamboo-specs-parent</artifactId>
-    <version>7.0.4</version>
+    <version>7.1.2</version>
    <relativePath/>
  </parent>

@@ -34,4 +34,4 @@

  <!-- run 'mvn test' to perform offline validation of the plan -->
  <!-- run 'mvn -Ppublish-specs' to upload the plan to your Bamboo server -->
-</project>
+</project>
@@ -1,4 +1,4 @@
-FROM gin5/platform-base:5.2.0
+FROM red/base-image:1.0.0

 ARG PLATFORM_JAR

@@ -6,4 +6,4 @@ ENV PLATFORM_JAR ${PLATFORM_JAR}

 ENV USES_ELASTICSEARCH false

-COPY ["${PLATFORM_JAR}", "/"]
+COPY ["${PLATFORM_JAR}", "/"]
@@ -44,10 +44,10 @@ import lombok.extern.slf4j.Slf4j;
 public class PDFLinesTextStripper extends PDFTextStripper {

    @Getter
-    private float minCharWidth = Float.MAX_VALUE;
+    private int maxCharWidths;

    @Getter
-    private float minCharHeight = Float.MAX_VALUE;
+    private int maxCharHeight;

    @Getter
    private final List<TextPositionSequence> textPositionSequences = new ArrayList<>();
@@ -201,8 +201,16 @@ public class PDFLinesTextStripper extends PDFTextStripper {

        int startIndex = 0;
        for (int i = 0; i <= textPositions.size() - 1; i++) {
-            minCharWidth = Math.min(minCharWidth, textPositions.get(i).getWidthDirAdj());
-            minCharHeight = Math.min(minCharHeight, textPositions.get(i).getHeightDir());
+
+            int charHeight = (int) textPositions.get(i).getHeightDir();
+            if(charHeight > maxCharHeight){
+                maxCharHeight = charHeight;
+            }
+
+            int charWidth = (int) textPositions.get(i).getWidthDirAdj();
+            if(charWidth > maxCharWidths){
+                maxCharWidths = charWidth;
+            }

            if (i == 0 && textPositions.get(i).getUnicode().equals(" ")) {
                startIndex++;
@@ -241,8 +249,8 @@ public class PDFLinesTextStripper extends PDFTextStripper {
    @Override
    public String getText(PDDocument doc) throws IOException {

-        minCharWidth = Float.MAX_VALUE;
-        minCharHeight = Float.MAX_VALUE;
+        maxCharWidths = 0;
+        maxCharWidths = 0;
        textPositionSequences.clear();
        rulings.clear();
        graphicsPath.clear();
@@ -17,6 +17,6 @@ public class ParsedElements {
    private boolean landscape;
    private boolean rotated;

-    private float minCharWidth;
-    private float minCharHeight;
+    private float maxCharWidth;
+    private float maxCharHeight;
 }
@@ -9,9 +9,7 @@ import com.iqser.red.service.redaction.v1.model.Point;
 import com.iqser.red.service.redaction.v1.model.Rectangle;

 import lombok.Data;
-import lombok.Getter;
 import lombok.RequiredArgsConstructor;
-import lombok.Setter;

@Data
@RequiredArgsConstructor
@@ -19,10 +17,6 @@ public class TextPositionSequence implements CharSequence {

    private List<TextPosition> textPositions = new ArrayList<>();

-    @Getter
-    @Setter
-    private float[] annotationColor;
-
    private final int page;


@@ -194,22 +188,18 @@ public class TextPositionSequence implements CharSequence {

    public Rectangle getRectangle() {

-        float height = textPositions.get(0).getHeightDir() + 2;
+        float height = getTextHeight();

-        float posXInit;
+        float posXInit = getX1();
        float posXEnd;
        float posYInit;
        float posYEnd;

        if (textPositions.get(0).getRotation() == 90) {
-
            posXEnd = textPositions.get(0).getYDirAdj() + 2;
-            posXInit = textPositions.get(0).getYDirAdj() - height;
-            posYInit = textPositions.get(0).getXDirAdj();
+            posYInit = getY1();
            posYEnd = textPositions.get(textPositions.size() - 1).getXDirAdj() - height + 4;
        } else {
-
-            posXInit = textPositions.get(0).getXDirAdj();
            posXEnd = textPositions.get(textPositions.size() - 1)
                    .getXDirAdj() + textPositions.get(textPositions.size() - 1).getWidth() + 1;
            posYInit = textPositions.get(0).getPageHeight() - textPositions.get(0).getYDirAdj() - 2;
@@ -220,4 +210,5 @@ public class TextPositionSequence implements CharSequence {
        return new Rectangle(new Point(posXInit, posYInit), posXEnd - posXInit, posYEnd - posYInit + height, page);
    }

+
 }
@@ -1,6 +1,8 @@
 package com.iqser.red.service.redaction.v1.server.redaction.model;

 import com.iqser.red.service.redaction.v1.server.classification.model.TextBlock;
+import com.iqser.red.service.redaction.v1.server.parsing.model.TextPositionSequence;
+import com.iqser.red.service.redaction.v1.server.redaction.utils.TextNormalizationUtilities;

 import lombok.RequiredArgsConstructor;
 import lombok.Value;
@@ -13,4 +15,29 @@ public class CellValue {

    int rowSpanStart;

+    @Override
+    public String toString() {
+
+        StringBuilder sb = new StringBuilder();
+
+
+            TextPositionSequence previous = null;
+            for (TextPositionSequence word : textBlock.getSequences()) {
+
+                if (previous != null) {
+                    if (Math.abs(previous.getY1() - word.getY1()) > word.getTextHeight()) {
+                        sb.append('\n');
+                    } else {
+                        sb.append(' ');
+                    }
+                }
+                sb.append(word.toString());
+                previous = word;
+            }
+
+        return TextNormalizationUtilities.removeHyphenLineBreaks(sb.toString())
+                .replaceAll("\n", " ")
+                .replaceAll(" {2}", " ");
+    }
+
 }
@@ -33,13 +33,14 @@ public class Section {
    private Map<String, CellValue> tabularData;


-    public boolean rowEquals(String headerName, String value){
-        String cleanHeaderName = headerName.replaceAll("\n", "")
-                .replaceAll(" ", "")
-                .replaceAll("-", "");
+    public boolean rowEquals(String headerName, String value) {

-        return tabularData != null && tabularData.containsKey(cleanHeaderName)
-                && tabularData.get(cleanHeaderName).getTextBlock().getText().equals(value);
+        String cleanHeaderName = headerName.replaceAll("\n", "").replaceAll(" ", "").replaceAll("-", "");
+
+        return tabularData != null && tabularData.containsKey(cleanHeaderName) && tabularData.get(cleanHeaderName)
+                .getTextBlock()
+                .getText()
+                .equals(value);
    }


@@ -172,25 +173,46 @@ public class Section {

    public void highlightCell(String cellHeader, int ruleNumber, String type) {

-        String cleanHeaderName = cellHeader.replaceAll("\n", "")
-                .replaceAll(" ", "")
-                .replaceAll("-", "");
+        annotateCell(cellHeader, ruleNumber, type, false, null);
+    }
+
+
+    public void redactCell(String cellHeader, int ruleNumber, String type, String reason) {
+
+        annotateCell(cellHeader, ruleNumber, type, true, reason);
+    }
+
+
+    public void redactNotCell(String cellHeader, int ruleNumber, String type, String reason) {
+
+        annotateCell(cellHeader, ruleNumber, type, false, reason);
+    }
+
+
+    private void annotateCell(String cellHeader, int ruleNumber, String type, boolean redact, String reason) {
+
+        String cleanHeaderName = cellHeader.replaceAll("\n", "").replaceAll(" ", "").replaceAll("-", "");

        CellValue value = tabularData.get(cleanHeaderName);
        if (value == null) {
            log.warn("Could not find any data for {}.", cellHeader);
        } else {
-            Entity entity = new Entity(value.getTextBlock()
-                    .getText(), type, value.getRowSpanStart(), value.getRowSpanStart() + value.getTextBlock()
-                    .getText()
+            Entity entity = new Entity(value.toString(), type, value.getRowSpanStart(), value.getRowSpanStart() + value.toString()
                    .length(), headline, sectionNumber);
-            entity.setRedaction(false);
+            entity.setRedaction(redact);
            entity.setMatchedRule(ruleNumber);
-            entity.setRedactionReason(cellHeader);
-            entity.setTargetSequences(value.getTextBlock().getSequences()); // Make sure no other cells with same content are highlighted
-            entities.add(entity);
-        }
+            entity.setRedactionReason(reason);
+            entity.setTargetSequences(value.getTextBlock()
+                    .getSequences()); // Make sure no other cells with same content are highlighted

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

 }
@@ -27,9 +27,7 @@ import com.iqser.red.service.redaction.v1.server.tableextraction.model.Cell;
 import com.iqser.red.service.redaction.v1.server.tableextraction.model.Table;

 import lombok.RequiredArgsConstructor;
-import lombok.extern.slf4j.Slf4j;

-@Slf4j
@Service
@RequiredArgsConstructor
 public class EntityRedactionService {
@@ -72,7 +70,7 @@ public class EntityRedactionService {
                                    .replaceAll("-", "");
                            tabularData.put(headerName, new CellValue(cell.getTextBlocks().get(0), cellStart));
                        });
-                        start = start + cell.getTextBlocks().get(0).toString().length();
+                        start = start + cell.toString().length();
                        for (TextBlock textBlock : cell.getTextBlocks()) {
                            searchableRow.addAll(textBlock.getSequences());
                        }
@@ -21,7 +21,6 @@ import com.iqser.red.service.redaction.v1.server.tableextraction.model.AbstractT
 import com.iqser.red.service.redaction.v1.server.tableextraction.model.CleanRulings;
 import com.iqser.red.service.redaction.v1.server.tableextraction.service.RulingCleaningService;
 import com.iqser.red.service.redaction.v1.server.tableextraction.service.TableExtractionService;
-import com.iqser.red.service.redaction.v1.server.tableextraction.utils.Utils;

 import lombok.RequiredArgsConstructor;
 import lombok.extern.slf4j.Slf4j;
@@ -37,6 +36,7 @@ public class PdfSegmentationService {
    private final ClassificationService classificationService;
    private final SectionsBuilderService sectionsBuilderService;

+
    public Document parseDocument(PDDocument pdDocument) throws IOException {

        Document document = new Document();
@@ -56,19 +56,21 @@ public class PdfSegmentationService {
            int rotation = pdPage.getRotation();
            boolean isRotated = rotation != 0 && rotation != 360;

-            ParsedElements parsedElements = ParsedElements
-                    .builder()
+
+            ParsedElements parsedElements = ParsedElements.builder()
                    .rulings(stripper.getRulings())
                    .sequences(stripper.getTextPositionSequences())
-                    .minCharWidth(Utils.round(stripper.getMinCharWidth(), 2))
-                    .minCharHeight(Utils.round(stripper.getMinCharHeight(), 2))
+                    .maxCharWidth(stripper.getMaxCharWidths())
+                    .maxCharHeight(stripper.getMaxCharWidths())
                    .landscape(isLandscape)
                    .rotated(isRotated)
                    .build();

-            CleanRulings cleanRulings = rulingCleaningService.getCleanRulings(parsedElements.getRulings(), parsedElements.getMinCharWidth(), parsedElements.getMinCharHeight());
+            CleanRulings cleanRulings = rulingCleaningService.getCleanRulings(parsedElements.getRulings(), parsedElements
+                    .getMaxCharWidth(), parsedElements.getMaxCharHeight());

-            Page page = blockificationService.blockify(parsedElements.getSequences(), cleanRulings.getHorizontal(), cleanRulings.getVertical());
+            Page page = blockificationService.blockify(parsedElements.getSequences(), cleanRulings.getHorizontal(), cleanRulings
+                    .getVertical());
            page.setRotation(rotation);

            tableExtractionService.extractTables(cleanRulings, page);
@@ -91,7 +93,10 @@ public class PdfSegmentationService {

    }

+
+
    private void increaseDocumentStatistics(Page page, Document document) {
+
        if (!page.isLandscape()) {
            document.getFontSizeCounter().addAll(page.getFontSizeCounter().getCountPerValue());
        }
@@ -100,6 +105,7 @@ public class PdfSegmentationService {
        document.getFontStyleCounter().addAll(page.getFontStyleCounter().getCountPerValue());
    }

+
    private void buildPageStatistics(Page page) {

        // Collect all statistics for the page, except from blocks inside tables, as tables will always be added to BodyTextFrame.
@@ -42,7 +42,9 @@ public class SectionsBuilderService {
                if (prev != null && current.getClassification().startsWith("H ") || !document.isHeadlines()) {
                    Paragraph chunkBlock = buildTextBlock(chunkWords, lastHeadline);
                    chunkBlock.setHeadline(lastHeadline);
-                    lastHeadline = current.getText();
+                    if(document.isHeadlines()) {
+                        lastHeadline = current.getText();
+                    }
                    chunkBlockList.add(chunkBlock);
                    chunkWords = new ArrayList<>();
                    if (CollectionUtils.isNotEmpty(chunkBlock.getTables())) {
@@ -5,6 +5,8 @@ import java.util.ArrayList;
 import java.util.List;

 import com.iqser.red.service.redaction.v1.server.classification.model.TextBlock;
+import com.iqser.red.service.redaction.v1.server.parsing.model.TextPositionSequence;
+import com.iqser.red.service.redaction.v1.server.redaction.utils.TextNormalizationUtilities;

 import lombok.Data;
 import lombok.EqualsAndHashCode;
@@ -20,10 +22,10 @@ public class Cell extends Rectangle {

    private boolean isHeaderCell;

+
    public Cell(Point2D topLeft, Point2D bottomRight) {

-        super((float) topLeft.getY(), (float) topLeft.getX(), (float) (bottomRight.getX() - topLeft.getX()),
-                (float) (bottomRight
+        super((float) topLeft.getY(), (float) topLeft.getX(), (float) (bottomRight.getX() - topLeft.getX()), (float) (bottomRight
                .getY() - topLeft.getY()));
    }

@@ -33,4 +35,34 @@ public class Cell extends Rectangle {
        textBlocks.add(textBlock);
    }

-}
+
+    @Override
+    public String toString() {
+
+        StringBuilder sb = new StringBuilder();
+
+        TextPositionSequence previous = null;
+        for (TextBlock textBlock : textBlocks) {
+
+
+            for (TextPositionSequence word : textBlock.getSequences()) {
+
+                if (previous != null) {
+                    if (Math.abs(previous.getY1() - word.getY1()) > word.getTextHeight()) {
+                        sb.append('\n');
+                    } else {
+                        sb.append(' ');
+                    }
+                }
+                sb.append(word.toString());
+                previous = word;
+            }
+        }
+
+        return TextNormalizationUtilities.removeHyphenLineBreaks(sb.toString())
+                .replaceAll("\n", " ")
+                .replaceAll(" {2}", " ");
+    }
+
+}
+
@@ -18,9 +18,9 @@ import com.iqser.red.service.redaction.v1.server.tableextraction.utils.Utils;
@Service
 public class RulingCleaningService {

-    public CleanRulings getCleanRulings(List<Ruling> rulings, float minCharWidth, float minCharHeight){
+    public CleanRulings getCleanRulings(List<Ruling> rulings, float maxCharWidth, float maxCharHeight){
        if (!rulings.isEmpty()) {
-            snapPoints(rulings, minCharWidth , minCharHeight);
+            snapPoints(rulings, maxCharWidth , maxCharHeight);
        }

        List<Ruling> vrs = new ArrayList<>();
@@ -2,9 +2,11 @@ package com.iqser.red.service.redaction.v1.server.visualization.service;

 import java.awt.Color;
 import java.io.IOException;
+import java.util.ArrayList;
 import java.util.HashSet;
 import java.util.List;
 import java.util.Set;
+import java.util.stream.Collectors;

 import org.apache.commons.collections4.CollectionUtils;
 import org.apache.pdfbox.pdmodel.PDDocument;
@@ -16,6 +18,7 @@ import org.apache.pdfbox.pdmodel.graphics.color.PDColor;
 import org.apache.pdfbox.pdmodel.graphics.color.PDDeviceRGB;
 import org.apache.pdfbox.pdmodel.interactive.annotation.PDAnnotation;
 import org.apache.pdfbox.pdmodel.interactive.annotation.PDAnnotationTextMarkup;
+import org.apache.pdfbox.text.TextPosition;
 import org.springframework.stereotype.Service;

 import com.iqser.red.service.redaction.v1.model.ManualRedactionEntry;
@@ -35,9 +38,7 @@ import com.iqser.red.service.redaction.v1.server.tableextraction.model.Cell;
 import com.iqser.red.service.redaction.v1.server.tableextraction.model.Table;

 import lombok.RequiredArgsConstructor;
-import lombok.extern.slf4j.Slf4j;

-@Slf4j
@Service
@RequiredArgsConstructor
 public class AnnotationHighlightService {
@@ -45,7 +46,8 @@ public class AnnotationHighlightService {
    private final DictionaryService dictionaryService;


-    public void highlight(PDDocument document, Document classifiedDoc, boolean flatRedaction, ManualRedactions manualRedactions) throws IOException {
+    public void highlight(PDDocument document, Document classifiedDoc, boolean flatRedaction,
+                          ManualRedactions manualRedactions) throws IOException {

        Set<Integer> manualRedactionPages = getManualRedactionPages(manualRedactions);

@@ -83,7 +85,8 @@ public class AnnotationHighlightService {
    }


-    private void addAnnotations(PDPage pdPage, Document classifiedDoc, boolean flatRedaction, ManualRedactions manualRedactions, int page) throws IOException {
+    private void addAnnotations(PDPage pdPage, Document classifiedDoc, boolean flatRedaction,
+                                ManualRedactions manualRedactions, int page) throws IOException {

        List<PDAnnotation> annotations = pdPage.getAnnotations();

@@ -107,11 +110,15 @@ public class AnnotationHighlightService {
                    redactionLogEntry.setManual(true);
                }

-                for (TextPositionSequence textPositions : entityPositionSequence.getSequences()) {
-
-                    Rectangle rectangle = textPositions.getRectangle();
-                    redactionLogEntry.getPositions().add(rectangle);
-                    annotations.add(createAnnotation(rectangle, entityPositionSequence.getId(), createAnnotationContent(entity), getColor(entity), !flatRedaction && !isHint(entity)));
+                if (CollectionUtils.isNotEmpty(entityPositionSequence.getSequences())) {
+                    for (Rectangle rectangle : 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)));
+                    }
                }
                redactionLogEntry.setId(entityPositionSequence.getId());
            }
@@ -120,7 +127,33 @@ public class AnnotationHighlightService {
    }


-    private void addManualAnnotations(PDPage pdPage, Document classifiedDoc, ManualRedactions manualRedactions, int page) throws IOException {
+    private List<Rectangle> getRectanglesPerLine(List<TextPosition> textPositions, int page) {
+
+        List<Rectangle> rectangles = new ArrayList<>();
+        if (textPositions.size() == 1) {
+            rectangles.add(new TextPositionSequence(textPositions, page).getRectangle());
+        } else {
+            float y = textPositions.get(0).getYDirAdj();
+            int startIndex = 0;
+            for (int i = 1; i < textPositions.size(); i++) {
+                float yDirAdj = textPositions.get(i).getYDirAdj();
+                if (yDirAdj != y) {
+                    rectangles.add(new TextPositionSequence(textPositions.subList(startIndex, i), page).getRectangle());
+                    y = yDirAdj;
+                    startIndex = i;
+                }
+            }
+            if (startIndex != textPositions.size() - 1) {
+                rectangles.add(new TextPositionSequence(textPositions.subList(startIndex, textPositions.size()), page).getRectangle());
+            }
+        }
+
+        return rectangles;
+    }
+
+
+    private void addManualAnnotations(PDPage pdPage, Document classifiedDoc, ManualRedactions manualRedactions,
+                                      int page) throws IOException {

        if (manualRedactions == null) {
            return;
@@ -143,8 +176,8 @@ public class AnnotationHighlightService {

                foundOnPage = true;

-                PDAnnotationTextMarkup highlight = createAnnotation(rectangle, id, createAnnotationContent(manualRedactionEntry), getColor(manualRedactionEntry
-                        .getType()), true);
+                PDAnnotationTextMarkup highlight = createAnnotation(rectangle, id,
+                        createAnnotationContent(manualRedactionEntry), getColor(manualRedactionEntry.getType()), true);
                annotations.add(highlight);

                redactionLogEntry.getPositions().add(rectangle);
@@ -188,7 +221,8 @@ public class AnnotationHighlightService {
    }


-    private PDAnnotationTextMarkup createAnnotation(Rectangle rectangle, String id, String content, float[] color, boolean popup) {
+    private PDAnnotationTextMarkup createAnnotation(Rectangle rectangle, String id, String content, float[] color,
+                                                    boolean popup) {

        PDAnnotationTextMarkup annotation = new PDAnnotationTextMarkup(PDAnnotationTextMarkup.SUB_TYPE_HIGHLIGHT);
        annotation.constructAppearances();
@@ -206,25 +240,15 @@ public class AnnotationHighlightService {

    private String createAnnotationContent(Entity entity) {

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


    private String createAnnotationContent(ManualRedactionEntry entry) {

-        return new StringBuilder().append("\nManual Redaction")
-                .append("\n\nIn Section : \"")
-                .append(entry.getSection())
-                .append("\"")
-                .toString();
+        return "\nManual Redaction" + "\n\nIn Section : \"" + entry.getSection() + "\"";
    }


@@ -244,7 +268,8 @@ public class AnnotationHighlightService {
        // 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()};
    }
@@ -255,10 +280,7 @@ public class AnnotationHighlightService {
        if (!entity.isRedaction()) {
            return false;
        }
-        if (isHint(entity)) {
-            return false;
-        }
-        return true;
+        return !isHint(entity);
    }


@@ -286,20 +308,19 @@ public class AnnotationHighlightService {
    private boolean isHint(Entity entity) {

        List<String> hintTypes = dictionaryService.getHintTypes();
-        if (CollectionUtils.isNotEmpty(hintTypes) && hintTypes.contains(entity.getType())) {
-            return true;
-        }
-        return false;
+        return CollectionUtils.isNotEmpty(hintTypes) && hintTypes.contains(entity.getType());
    }


-    private void drawSectionFrames(PDDocument document, Document classifiedDoc, boolean flatRedaction, PDPage pdPage, int page) throws IOException {
+    private void drawSectionFrames(PDDocument document, Document classifiedDoc, boolean flatRedaction, PDPage pdPage,
+                                   int page) throws IOException {

        if (flatRedaction) {
            return;
        }

-        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++) {
@@ -348,7 +369,8 @@ 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();
                }
@@ -1,5 +1,6 @@
 package com.iqser.red.service.redaction.v1.server;

+import static org.assertj.core.api.Assertions.assertThat;
 import static org.mockito.Mockito.when;
 import static org.springframework.boot.test.context.SpringBootTest.WebEnvironment.DEFINED_PORT;

@@ -269,7 +270,7 @@ public class RedactionIntegrationTest {

        System.out.println("redactionTest");
        long start = System.currentTimeMillis();
-        ClassPathResource pdfFileResource = new ClassPathResource("files/new/Thiabendazole DAR Addendum for ED_April_2020.pdf");
+        ClassPathResource pdfFileResource = new ClassPathResource("files/Fludioxonil/50 Fludioxonil_RAR_01_Volume_1_2018-02-21.pdf");

        RedactionRequest request = RedactionRequest.builder()
                .document(IOUtils.toByteArray(pdfFileResource.getInputStream()))
@@ -388,8 +389,7 @@ public class RedactionIntegrationTest {
    public void htmlTablesTest() throws IOException {

        System.out.println("htmlTablesTest");
-        ClassPathResource pdfFileResource = new ClassPathResource("files/Fludioxonil/51 " +
-                "Fludioxonil_RAR_02_Volume_2_2018-02-21.pdf");
+        ClassPathResource pdfFileResource = new ClassPathResource("files/Metolachlor/S-Metolachlor_RAR_02_Volume_2_2018-09-06.pdf");

        RedactionRequest request = RedactionRequest.builder()
                .document(IOUtils.toByteArray(pdfFileResource.getInputStream()))
@@ -422,6 +422,27 @@ public class RedactionIntegrationTest {
    }


+    @Test
+    public void phantomCellsDocumentTest() throws IOException {
+
+        ClassPathResource pdfFileResource = new ClassPathResource("files/Minimal Examples/Phantom Cells.pdf");
+
+        RedactionRequest request = RedactionRequest.builder()
+                .document(IOUtils.toByteArray(pdfFileResource.getInputStream()))
+                .build();
+        request.setFlatRedaction(false);
+
+        RedactionResult result = redactionController.redact(request);
+
+        result.getRedactionLog().getRedactionLogEntry().forEach(entry -> {
+            if(!entry.isHint()){
+                assertThat(entry.getReason()).isEqualTo("Not redacted because row is not a vertebrate study");
+            }
+        });
+    }
+
+
+
    private static String loadFromClassPath(String path) {

        URL resource = ResourceLoader.class.getClassLoader().getResource(path);
@@ -275,6 +275,27 @@ public class EntityRedactionServiceTest {
            assertThat(classifiedDoc.getEntities().get(1).stream().filter(entity -> entity.getMatchedRule() == 9).count()).isEqualTo(8);
            assertThat(classifiedDoc.getEntities().get(2).stream().filter(entity -> entity.getMatchedRule() == 9).count()).isEqualTo(4);
        }
+
+        pdfFileResource = new ClassPathResource("files/Minimal Examples/Header Propagation2.pdf");
+
+        dictionaryResponse = DictionaryResponse.builder()
+                .entries(Arrays.asList("Tribolet, R.", "Muir, G.", "Kühne-Thu, H.", "Close, C."))
+                .build();
+
+        when(dictionaryClient.getVersion()).thenReturn(DICTIONARY_VERSION.incrementAndGet());
+        when(dictionaryClient.getDictionaryForType(NAME_CODE)).thenReturn(dictionaryResponse);
+        addressResponse = DictionaryResponse.builder()
+                .entries(Collections.singletonList("Novartis Crop Protection AG, Basel, Switzerland"))
+                .build();
+        when(dictionaryClient.getDictionaryForType(ADDRESS_CODE)).thenReturn(addressResponse);
+
+        try (PDDocument pdDocument = PDDocument.load(pdfFileResource.getInputStream())) {
+            Document classifiedDoc = pdfSegmentationService.parseDocument(pdDocument);
+            entityRedactionService.processDocument(classifiedDoc, null);
+            assertThat(classifiedDoc.getEntities()).hasSize(1); // one page
+            assertThat(classifiedDoc.getEntities().get(1).stream().filter(entity -> entity.getMatchedRule() == 9).count()).isEqualTo(3);
+            assertThat(classifiedDoc.getEntities().get(1).stream().filter(entity -> entity.getMatchedRule() == 8).count()).isEqualTo(8);
+        }
    }


@@ -312,7 +333,7 @@ public class EntityRedactionServiceTest {
                "global Section section\n" +
                "rule \"8: Not redacted because Vertebrate Study = N\"\n" +
                "    when\n" +
-                "        Section(rowEquals(\"Vertebrate study Y/N\", \"N\"))\n" +
+                "        Section(rowEquals(\"Vertebrate study Y/N\", \"N\") || rowEquals(\"Vertebrate study Y/N\", \"No\"))\n" +
                "    then\n" +
                "        section.redactNot(\"name\", 8, \"Not redacted because row is not a vertebrate study\");\n" +
                "        section.redactNot(\"address\", 8, \"Not redacted because row is not a vertebrate study\");\n" +
@@ -320,7 +341,8 @@ public class EntityRedactionServiceTest {
                "    end\n" +
                "rule \"9: Redact Authors and Addresses in Reference Table, if it is a Vertebrate study\"\n" +
                "    when\n" +
-                "        Section(rowEquals(\"Vertebrate study Y/N\", \"Y\"))\n" +
+                "        Section(rowEquals(\"Vertebrate study Y/N\", \"Y\") || rowEquals(\"Vertebrate study Y/N\", " +
+                "\"Yes\"))\n" +
                "    then\n" +
                "        section.redact(\"name\", 9, \"Redacted because row is a vertebrate study\");\n" +
                "        section.redact(\"address\", 9, \"Redacted because row is a vertebrate study\");\n" +
@@ -99,9 +99,9 @@ rule "7: Redact contact information if Producer is found"

 rule "8: Not redacted because Vertebrate Study = N"
    when
-        Section(rowEquals("Vertebrate study Y/N", "N"))
+        Section(rowEquals("Vertebrate study Y/N", "N") || rowEquals("Vertebrate study Y/N", "No"))
    then
-        section.redactNot("name", 8, "Not redacted because row is not a vertebrate study");
+        section.redactNotCell("Author(s)", 8, "name", "Not redacted because row is not a vertebrate study");
        section.redactNot("address", 8, "Not redacted because row is not a vertebrate study");
        section.highlightCell("Vertebrate study Y/N", 8, "hint_only");
    end
@@ -118,9 +118,9 @@ rule "9: Redact if must redact entry is found"

 rule "10: Redact Authors and Addresses in Reference Table if it is a Vertebrate study"
    when
-        Section(rowEquals("Vertebrate study Y/N", "Y"))
+        Section(rowEquals("Vertebrate study Y/N", "Y") || rowEquals("Vertebrate study Y/N", "Yes"))
    then
-        section.redact("name", 10, "Redacted because row is a vertebrate study");
+        section.redactCell("Author(s)", 10, "name", "Redacted because row is a vertebrate study");
        section.redact("address", 10, "Redacted because row is a vertebrate study");
        section.highlightCell("Vertebrate study Y/N", 10, "must_redact");
    end
Author	SHA1	Message	Date
Thierry Göckel	8e5ff31810	Fix annotating single letter entities	2020-09-29 15:10:52 +02:00
Dominique Eiflaender	8b1574845c	Pull request #43 : RED-264: Avoid phantom cells, by merging line till rounded value of biggest char height/width Merge in RED/redaction-service from RED-264 to master * commit 'e1adcfb02c4c7d46140884b3d38f8daf1e1aae92': Added missing unittest RED-264: Avoid phantom cells, by merging line till rounded value of biggest char height/width	2020-09-29 15:04:20 +02:00
deiflaender	e1adcfb02c	Added missing unittest	2020-09-29 14:54:35 +02:00
deiflaender	11164219c5	RED-264: Avoid phantom cells, by merging line till rounded value of biggest char height/width	2020-09-29 14:21:42 +02:00
Thierry Goeckel	c9516205fe	Pull request #42 : RED-318 Merge in RED/redaction-service from RED-318 to master * commit 'f5790bccab3fb8dce66aeb9fbe501655ae6b86c3': Log entries and manual redaction require one position per line Annotate line by line Refactor multiple positions to one Merge rectangles for single annotation/redaction log entry	2020-09-29 14:15:21 +02:00
Thierry Göckel	f5790bccab	Log entries and manual redaction require one position per line	2020-09-29 13:54:32 +02:00
Thierry Göckel	74e63ca292	Annotate line by line	2020-09-29 13:43:16 +02:00
Thierry Göckel	6638f0cf9e	Refactor multiple positions to one	2020-09-28 17:47:55 +02:00
Thierry Göckel	5448153096	Merge rectangles for single annotation/redaction log entry	2020-09-28 17:31:40 +02:00
Dominique Eiflaender	03274ba1ab	Pull request #41 : RED-299: Redact complete Author(s) Field in Vertebrate study tables Merge in RED/redaction-service from RED-299 to master * commit '664b9b420605cb1adf1113b34c52a45e8024dbbc': RED-299: Redact complete Author(s) Field in Vertebrate study tables	2020-09-23 15:34:46 +02:00
deiflaender	664b9b4206	RED-299: Redact complete Author(s) Field in Vertebrate study tables	2020-09-23 15:20:52 +02:00
Thierry Goeckel	564d74e39d	Pull request #40 : Test modified rules 8 and 10 Merge in RED/redaction-service from RED-288 to master * commit 'cfb7554c618b9482f529b8183bc0f1f95df7d00f': Test modified rules 8 and 9	2020-09-23 11:44:35 +02:00
Thierry Göckel	cfb7554c61	Test modified rules 8 and 9	2020-09-22 21:36:05 +02:00
Christoph Schabert	ee40064b32	Pull request #39 : RED-316: Switch to new red base image Merge in RED/redaction-service from RED-316 to master * commit 'f2fafc3db2ab8825eb4a2136e8eab28a12dbc2e6': Switch to rootless base-image Upgrade bamboo-specs to 7.1.2	2020-09-16 08:59:45 +02:00
Christoph Schabert	f2fafc3db2	Switch to rootless base-image	2020-09-15 16:02:08 +02:00
Christoph Schabert	d5b0638f11	Upgrade bamboo-specs to 7.1.2	2020-09-15 16:01:26 +02:00