Pull request #84: Fixed 'Comparison method violates its general contract' by using QuickSort from PDFBox

Merge in RED/redaction-service from sortAlgorithm to master

* commit '000b145e710b8459e56223e77a9e19f4a7edd33e':
  Fixed 'Comparison method violates its general contract' by using QuickSort from PDFBox

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

@@ -5,15 +5,17 @@ import java.util.regex.Pattern;
 
 import org.springframework.stereotype.Service;
 
-import com.iqser.red.service.redaction.v1.server.classification.utils.PositionUtils;
 import com.iqser.red.service.redaction.v1.server.classification.model.Document;
 import com.iqser.red.service.redaction.v1.server.classification.model.Page;
 import com.iqser.red.service.redaction.v1.server.classification.model.TextBlock;
+import com.iqser.red.service.redaction.v1.server.classification.utils.PositionUtils;
 import com.iqser.red.service.redaction.v1.server.tableextraction.model.AbstractTextContainer;
 import com.iqser.red.service.redaction.v1.server.tableextraction.model.Rectangle;
 
 import lombok.RequiredArgsConstructor;
+import lombok.extern.slf4j.Slf4j;
 
+@Slf4j
 @Service
 @RequiredArgsConstructor
 public class ClassificationService {
@@ -28,7 +30,7 @@ public class ClassificationService {
 
         List<Float> headlineFontSizes = document.getFontSizeCounter().getHighterThanMostPopular();
 
-        System.out.println(document.getFontSizeCounter().getCountPerValue());
+        log.debug("Document FontSize counters are: {}", document.getFontSizeCounter().getCountPerValue());
 
         for (Page page : document.getPages()) {
             Rectangle btf = page.isLandscape() ? landscapeBodyTextFrame : bodyTextFrame;
@@ -39,6 +41,7 @@ public class ClassificationService {
 
 
     public void classifyPage(Rectangle bodyTextFrame, Page page, Document document, List<Float> headlineFontSizes) {
+
         for (AbstractTextContainer textBlock : page.getTextBlocks()) {
             if (textBlock instanceof TextBlock) {
                 classifyBlock((TextBlock) textBlock, bodyTextFrame, page, document, headlineFontSizes);
@@ -47,24 +50,33 @@ public class ClassificationService {
     }
 
 
-    public void classifyBlock(TextBlock textBlock, Rectangle bodyTextFrame, Page page, Document document, List<Float> headlineFontSizes) {
+    public void classifyBlock(TextBlock textBlock, Rectangle bodyTextFrame, Page page, Document document,
+                              List<Float> headlineFontSizes) {
+
         if (document.getFontSizeCounter().getMostPopular() == null) {
             // TODO Figure out why this happens.
             return;
         }
-        if (PositionUtils.isOverBodyTextFrame(bodyTextFrame, textBlock, page.isRotated()) && (document.getFontSizeCounter().getMostPopular() == null || textBlock.getHighestFontSize() <= document.getFontSizeCounter().getMostPopular())) {
+        if (PositionUtils.isOverBodyTextFrame(bodyTextFrame, textBlock, page.isRotated()) && (document.getFontSizeCounter()
+                .getMostPopular() == null || textBlock.getHighestFontSize() <= document.getFontSizeCounter()
+                .getMostPopular())) {
             textBlock.setClassification("Header");
 
-        } else if (PositionUtils.isUnderBodyTextFrame(bodyTextFrame, textBlock) && (document.getFontSizeCounter().getMostPopular() == null || textBlock.getHighestFontSize() <= document.getFontSizeCounter().getMostPopular())) {
+        } else if (PositionUtils.isUnderBodyTextFrame(bodyTextFrame, textBlock) && (document.getFontSizeCounter()
+                .getMostPopular() == null || textBlock.getHighestFontSize() <= document.getFontSizeCounter()
+                .getMostPopular())) {
             textBlock.setClassification("Footer");
-        }  else if (page.getPageNumber() == 1
+        } else if (page.getPageNumber() == 1 && (!PositionUtils.isTouchingUnderBodyTextFrame(bodyTextFrame, textBlock) && PositionUtils
-                && (!PositionUtils.isTouchingUnderBodyTextFrame(bodyTextFrame, textBlock)
+                .getHeightDifferenceBetweenChunkWordAndDocumentWord(textBlock, document.getTextHeightCounter()
-                && PositionUtils.getHeightDifferenceBetweenChunkWordAndDocumentWord(textBlock, document.getTextHeightCounter().getMostPopular()) > 2.5 && textBlock.getHighestFontSize() > document.getFontSizeCounter().getMostPopular() || page.getTextBlocks().size() == 1)) {
+                        .getMostPopular()) > 2.5 && textBlock.getHighestFontSize() > document.getFontSizeCounter()
+                .getMostPopular() || page.getTextBlocks().size() == 1)) {
             if (!Pattern.matches("[0-9]+", textBlock.toString())) {
                 textBlock.setClassification("Title");
             }
-        }
+        } else if (PositionUtils.isWithinBodyTextFrame(bodyTextFrame, textBlock) && textBlock.getMostPopularWordFontSize() > document
-        else if (PositionUtils.isWithinBodyTextFrame(bodyTextFrame, textBlock) && textBlock.getMostPopularWordFontSize() > document.getFontSizeCounter().getMostPopular() && PositionUtils.getApproxLineCount(textBlock) < 4.9 && textBlock.getMostPopularWordStyle().equals("bold")) {
+                .getFontSizeCounter()
+                .getMostPopular() && PositionUtils.getApproxLineCount(textBlock) < 4.9 && textBlock.getMostPopularWordStyle()
+                .equals("bold")) {
 
             for (int i = 1; i <= headlineFontSizes.size(); i++) {
                 if (textBlock.getMostPopularWordFontSize() == headlineFontSizes.get(i - 1)) {
@@ -72,20 +84,34 @@ public class ClassificationService {
                     document.setHeadlines(true);
                 }
             }
-        }else if (!textBlock.getText().startsWith("Table ") && !textBlock.getText().startsWith("Figure ") && PositionUtils.isWithinBodyTextFrame(bodyTextFrame, textBlock) && textBlock.getMostPopularWordStyle().equals("bold") && !document.getFontStyleCounter().getMostPopular().equals("bold") && PositionUtils.getApproxLineCount(textBlock) < 2.9) {
+        } else if (!textBlock.getText().startsWith("Table ") && !textBlock.getText()
+                .startsWith("Figure ") && PositionUtils.isWithinBodyTextFrame(bodyTextFrame, textBlock) && textBlock.getMostPopularWordStyle()
+                .equals("bold") && !document.getFontStyleCounter()
+                .getMostPopular()
+                .equals("bold") && PositionUtils.getApproxLineCount(textBlock) < 2.9) {
             textBlock.setClassification("H " + (headlineFontSizes.size() + 1));
             document.setHeadlines(true);
-        }
+        } else if (PositionUtils.isWithinBodyTextFrame(bodyTextFrame, textBlock) && textBlock.getMostPopularWordFontSize() == document
-        else if (PositionUtils.isWithinBodyTextFrame(bodyTextFrame, textBlock) && textBlock.getMostPopularWordFontSize() == document.getFontSizeCounter().getMostPopular() && textBlock.getMostPopularWordStyle().equals("bold") && !document.getFontStyleCounter().getMostPopular().equals("bold")) {
+                .getFontSizeCounter()
+                .getMostPopular() && textBlock.getMostPopularWordStyle()
+                .equals("bold") && !document.getFontStyleCounter().getMostPopular().equals("bold")) {
             textBlock.setClassification("TextBlock Bold");
-        }
+        } else if (PositionUtils.isWithinBodyTextFrame(bodyTextFrame, textBlock) && textBlock.getMostPopularWordFont()
-        else if (PositionUtils.isWithinBodyTextFrame(bodyTextFrame, textBlock) && textBlock.getMostPopularWordFont().equals(document.getFontCounter().getMostPopular()) && textBlock.getMostPopularWordStyle().equals(document.getFontStyleCounter().getMostPopular()) && textBlock.getMostPopularWordFontSize() == document.getFontSizeCounter().getMostPopular()) {
+                .equals(document.getFontCounter().getMostPopular()) && textBlock.getMostPopularWordStyle()
+                .equals(document.getFontStyleCounter()
+                        .getMostPopular()) && textBlock.getMostPopularWordFontSize() == document.getFontSizeCounter()
+                .getMostPopular()) {
             textBlock.setClassification("TextBlock");
-        }
+        } else if (PositionUtils.isWithinBodyTextFrame(bodyTextFrame, textBlock) && textBlock.getMostPopularWordFontSize() == document
-        else if (PositionUtils.isWithinBodyTextFrame(bodyTextFrame, textBlock) && textBlock.getMostPopularWordFontSize() == document.getFontSizeCounter().getMostPopular() && textBlock.getMostPopularWordStyle().equals("italic") && !document.getFontStyleCounter().getMostPopular().equals("italic") && PositionUtils.getApproxLineCount(textBlock) < 2.9) {
+                .getFontSizeCounter()
+                .getMostPopular() && textBlock.getMostPopularWordStyle()
+                .equals("italic") && !document.getFontStyleCounter()
+                .getMostPopular()
+                .equals("italic") && PositionUtils.getApproxLineCount(textBlock) < 2.9) {
             textBlock.setClassification("TextBlock Italic");
-        } else if (PositionUtils.isWithinBodyTextFrame(bodyTextFrame, textBlock)){
+        } else if (PositionUtils.isWithinBodyTextFrame(bodyTextFrame, textBlock)) {
             textBlock.setClassification("TextBlock Unknown");
         }
     }
+
 }

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

@@ -27,7 +27,9 @@ import com.iqser.red.service.redaction.v1.server.visualization.service.Annotatio
 import com.iqser.red.service.redaction.v1.server.visualization.service.PdfVisualisationService;
 
 import lombok.RequiredArgsConstructor;
+import lombok.extern.slf4j.Slf4j;
 
+@Slf4j
 @RestController
 @RequiredArgsConstructor
 public class RedactionController implements RedactionResource {
@@ -46,10 +48,15 @@ public class RedactionController implements RedactionResource {
             pdDocument.setAllSecurityToBeRemoved(true);
 
             Document classifiedDoc = pdfSegmentationService.parseDocument(pdDocument);
+
+            log.info("Document structure analysis successful, starting redaction analysis...");
+
             entityRedactionService.processDocument(classifiedDoc, redactionRequest.getManualRedactions());
             annotationHighlightService.highlight(pdDocument, classifiedDoc, redactionRequest.isFlatRedaction(), redactionRequest
                     .getManualRedactions());
 
+            log.info("Redaction analysis successful...");
+
             return convert(pdDocument, classifiedDoc.getPages()
                     .size(), classifiedDoc.getRedactionLogEntities(), classifiedDoc.getSectionGrid(), classifiedDoc.getDictionaryVersion(), classifiedDoc.getRulesVersion());
 

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

@@ -0,0 +1,111 @@
+package com.iqser.red.service.redaction.v1.server.tableextraction.utils;
+
+import java.util.ArrayDeque;
+import java.util.Comparator;
+import java.util.Deque;
+import java.util.List;
+
+/**
+ * Copied and minimal modified from PDFBox.
+ */
+public final class QuickSort {
+
+    private QuickSort() {
+
+    }
+
+
+    private static final Comparator<? extends Comparable> OBJCOMP = new Comparator<Comparable>() {
+        @Override
+        public int compare(Comparable object1, Comparable object2) {
+
+            return object1.compareTo(object2);
+        }
+    };
+
+
+    /**
+     * Sorts the given list using the given comparator.
+     *
+     * @param <T>  type of the objects to be sorted.
+     * @param list list to be sorted
+     * @param cmp  comparator used to compare the objects within the list
+     */
+    public static <T> void sort(List<T> list, Comparator<? super T> cmp) {
+
+        int size = list.size();
+        if (size < 2) {
+            return;
+        }
+        quicksort(list, cmp);
+    }
+
+
+    /**
+     * Sorts the given list using compareTo as comparator.
+     *
+     * @param <T>  type of the objects to be sorted.
+     * @param list list to be sorted
+     */
+    public static <T extends Comparable> void sort(List<T> list) {
+
+        sort(list, (Comparator<T>) OBJCOMP);
+    }
+
+
+    private static <T> void quicksort(List<T> list, Comparator<? super T> cmp) {
+
+        Deque<Integer> stack = new ArrayDeque<Integer>();
+        stack.push(0);
+        stack.push(list.size());
+        while (!stack.isEmpty()) {
+            int right = stack.pop();
+            int left = stack.pop();
+            if (right - left < 2) {
+                continue;
+            }
+            int p = left + ((right - left) / 2);
+            p = partition(list, cmp, p, left, right);
+
+            stack.push(p + 1);
+            stack.push(right);
+
+            stack.push(left);
+            stack.push(p);
+        }
+    }
+
+
+    private static <T> int partition(List<T> list, Comparator<? super T> cmp, int p, int start, int end) {
+
+        int l = start;
+        int h = end - 2;
+        T piv = list.get(p);
+        swap(list, p, end - 1);
+
+        while (l < h) {
+            if (cmp.compare(list.get(l), piv) <= 0) {
+                l++;
+            } else if (cmp.compare(piv, list.get(h)) <= 0) {
+                h--;
+            } else {
+                swap(list, l, h);
+            }
+        }
+        int idx = h;
+        if (cmp.compare(list.get(h), piv) < 0) {
+            idx++;
+        }
+        swap(list, end - 1, idx);
+        return idx;
+    }
+
+
+    private static <T> void swap(List<T> list, int i, int j) {
+
+        T tmp = list.get(i);
+        list.set(i, list.get(j));
+        list.set(j, tmp);
+    }
+
+}

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

@@ -1,7 +1,6 @@
 package com.iqser.red.service.redaction.v1.server.tableextraction.utils;
 
 import java.math.BigDecimal;
-import java.util.Collections;
 import java.util.Comparator;
 import java.util.List;
 
@@ -13,23 +12,29 @@ public class Utils {
 
     private final static float EPSILON = 0.1f;
 
+
     public static boolean feq(double f1, double f2) {
+
         return (Math.abs(f1 - f2) < EPSILON);
     }
 
+
     public static float round(double d, int decimalPlace) {
+
         BigDecimal bd = BigDecimal.valueOf(d);
         bd = bd.setScale(decimalPlace, BigDecimal.ROUND_HALF_UP);
         return bd.floatValue();
     }
 
-	public static <T> void sort(List<T> list, Comparator<? super T> comparator) {
+
+    public static <T> void sort(List<T> list, Comparator<? super T> comparator) {
+
         try {
-            Collections.sort(list, comparator);
+            QuickSort.sort(list, comparator);
-        } catch (IllegalArgumentException e){
+        } catch (IllegalArgumentException e) {
-            //TODO Figure out why this happens.
+            // This should not happen since we use QuickSort from PDFBox
             log.warn(e.getMessage());
         }
-	}
+    }
 
 }

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

@@ -331,6 +331,7 @@ public class RedactionIntegrationTest {
     @Test
     public void noExceptionShouldBeThrownForAnyFiles() throws IOException {
 
+        long start = System.currentTimeMillis();
         System.out.println("noExceptionShouldBeThrownForAnyFiles");
         ClassLoader loader = getClass().getClassLoader();
         URL url = loader.getResource("files");
@@ -356,6 +357,10 @@ public class RedactionIntegrationTest {
             });
         }
 
+        long end = System.currentTimeMillis();
+
+        System.out.println("duration: " + (end - start));
+
     }
 
 
@@ -382,7 +387,7 @@ public class RedactionIntegrationTest {
 
         System.out.println("redactionTest");
         long start = System.currentTimeMillis();
-        ClassPathResource pdfFileResource = new ClassPathResource("files/Fludioxonil/52 Fludioxonil_RAR_07_Volume_3CA_B-5_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()))