Support Annotations Created by Foxit

CHANGELOG.md

@@ -29,9 +29,9 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - We fixed the IEEE Xplore web search functionality [#2789](https://github.com/JabRef/jabref/issues/2789)
 - We fixed an error in the CrossRef fetcher that occurred if one of the fetched entries had no title
 - We fixed an issue that prevented new entries to be automatically assigned to the currently selected group [#2783](https://github.com/JabRef/jabref/issues/2783).
-- We fixed a bug that only allowed parsing positive timezones from a FileAnnotation [#2839](https://github.com/JabRef/jabref/issues/22839)
+- We fixed a bug that only allowed parsing positive timezones from a FileAnnotation [#2839](https://github.com/JabRef/jabref/issues/2839)
 - We fixed a bug that did not allow the correct re-export of the MS-Office XML field `msbib-accessed` with a different date format [#2859](https://github.com/JabRef/jabref/issues/2859).
-
+- We fixed some bugs that prevented the display of FileAnnotations that were created using the Foxit Reader. [#2839, comment](https://github.com/JabRef/jabref/issues/2839#issuecomment-302058227).
 ### Removed
 
 

src/main/java/org/jabref/logic/pdf/PdfAnnotationImporter.java

@@ -1,6 +1,5 @@
 package org.jabref.logic.pdf;
 
-import java.awt.geom.Rectangle2D;
 import java.io.IOException;
 import java.nio.file.Files;
 import java.nio.file.Path;
@@ -18,13 +17,10 @@
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 import org.apache.pdfbox.cos.COSArray;
-import org.apache.pdfbox.cos.COSFloat;
 import org.apache.pdfbox.cos.COSName;
 import org.apache.pdfbox.pdmodel.PDDocument;
 import org.apache.pdfbox.pdmodel.PDPage;
-import org.apache.pdfbox.pdmodel.common.PDRectangle;
 import org.apache.pdfbox.pdmodel.interactive.annotation.PDAnnotation;
-import org.apache.pdfbox.util.PDFTextStripperByArea;
 
 public class PdfAnnotationImporter implements AnnotationImporter {
 
@@ -53,8 +49,8 @@ public List<FileAnnotation> importAnnotations(final Path path) {
                     if (!isSupportedAnnotationType(annotation)) {
                         continue;
                     }
-                    if (FileAnnotationType.UNDERLINE.toString().equals(annotation.getSubtype()) ||
-                            FileAnnotationType.HIGHLIGHT.toString().equals(annotation.getSubtype())) {
+
+                    if (FileAnnotationType.isMarkedFileAnnotationType(annotation.getSubtype())) {
                         annotationsList.add(createMarkedAnnotations(pageIndex, page, annotation));
                     } else {
                         FileAnnotation fileAnnotation = new FileAnnotation(annotation, pageIndex + 1);
@@ -71,6 +67,13 @@ public List<FileAnnotation> importAnnotations(final Path path) {
     }
 
     private boolean isSupportedAnnotationType(PDAnnotation annotation) {
+        if (annotation.getSubtype() == null) {
+            return false;
+        }
+        if ("Link".equals(annotation.getSubtype()) || "Widget".equals(annotation.getSubtype())) {
+            LOGGER.debug(annotation.getSubtype() + " is excluded from the supported file annotations");
+            return false;
+        }
         try {
             if (!Arrays.asList(FileAnnotationType.values()).contains(FileAnnotationType.valueOf(annotation.getSubtype()))) {
                 return false;
@@ -86,75 +89,34 @@ private FileAnnotation createMarkedAnnotations(int pageIndex, PDPage page, PDAnn
                 annotation.getDictionary().getString(COSName.T), FileAnnotation.extractModifiedTime(annotation.getModifiedDate()),
                 pageIndex + 1, annotation.getContents(), FileAnnotationType.valueOf(annotation.getSubtype().toUpperCase(Locale.ROOT)), Optional.empty());
 
-        try {
-            if (FileAnnotationType.HIGHLIGHT.toString().equals(annotation.getSubtype()) || FileAnnotationType.UNDERLINE.toString().equals(annotation.getSubtype())) {
-                annotation.setContents(extractMarkedText(page, annotation));
+        if (annotationBelongingToMarking.getAnnotationType().isLinkedFileAnnotationType()) {
+            try {
+                COSArray boundingBoxes = (COSArray) annotation.getDictionary().getDictionaryObject(COSName.getPDFName("QuadPoints"));
+                annotation.setContents(new TextExtractor(page, boundingBoxes).extractMarkedText());
+            } catch (IOException e) {
+                annotation.setContents("JabRef: Could not extract any marked text!");
             }
-        } catch (IOException e) {
-            annotation.setContents("JabRef: Could not extract any marked text!");
         }
 
         //Marked text that has a sticky note on it should be linked to the sticky note
         return new FileAnnotation(annotation, pageIndex + 1, annotationBelongingToMarking);
     }
 
-    private String extractMarkedText(PDPage page, PDAnnotation annotation) throws IOException {
-        //highlighted or underlined text has to be extracted by the rectangle calculated from the marking
-        PDFTextStripperByArea stripperByArea = new PDFTextStripperByArea();
-        COSArray quadsArray = (COSArray) annotation.getDictionary().getDictionaryObject(COSName.getPDFName("QuadPoints"));
-        String markedText = "";
-        for (int j = 1,
-             k = 0;
-             j <= (quadsArray.size() / 8);
-             j++) {
-
-            COSFloat upperLeftX = (COSFloat) quadsArray.get(k);
-            COSFloat upperLeftY = (COSFloat) quadsArray.get(1 + k);
-            COSFloat upperRightX = (COSFloat) quadsArray.get(2 + k);
-            COSFloat upperRightY = (COSFloat) quadsArray.get(3 + k);
-            COSFloat lowerLeftX = (COSFloat) quadsArray.get(4 + k);
-            COSFloat lowerLeftY = (COSFloat) quadsArray.get(5 + k);
-
-            k += 8;
-
-            float ulx = upperLeftX.floatValue() - 1;
-            float uly = upperLeftY.floatValue();
-            float width = upperRightX.floatValue() - lowerLeftX.floatValue();
-            float height = upperRightY.floatValue() - lowerLeftY.floatValue();
-
-            PDRectangle pageSize = page.getMediaBox();
-            uly = pageSize.getHeight() - uly;
-
-            Rectangle2D.Float rectangle = new Rectangle2D.Float(ulx, uly, width, height);
-            stripperByArea.addRegion("markedRegion", rectangle);
-            stripperByArea.extractRegions(page);
-            String markedTextInLine = stripperByArea.getTextForRegion("markedRegion");
-
-            if (j > 1) {
-                markedText = markedText.concat(markedTextInLine);
-            } else {
-                markedText = markedTextInLine;
-            }
-        }
-
-        return markedText.trim();
-    }
-
     private boolean validatePath(Path path) {
         Objects.requireNonNull(path);
 
         if (!path.toString().toLowerCase(Locale.ROOT).endsWith(".pdf")) {
-            LOGGER.warn(String.format("File %s does not end with .pdf!", path));
+            LOGGER.warn(String.format("File '%s' does not end with .pdf!", path));
             return false;
         }
 
         if (!Files.exists(path)) {
-            LOGGER.warn(String.format("File %s does not exist!", path));
+            LOGGER.warn(String.format("File '%s' does not exist!", path));
             return false;
         }
 
         if (!Files.isRegularFile(path) || !Files.isReadable(path)) {
-            LOGGER.warn(String.format("File %s is not readable!", path));
+            LOGGER.warn(String.format("File '%s' is not readable!", path));
             return false;
         }
 

src/main/java/org/jabref/logic/pdf/TextExtractor.java

@@ -0,0 +1,86 @@
+package org.jabref.logic.pdf;
+
+import java.awt.geom.Rectangle2D;
+import java.io.IOException;
+import java.util.Objects;
+
+import org.apache.pdfbox.cos.COSArray;
+import org.apache.pdfbox.cos.COSFloat;
+import org.apache.pdfbox.cos.COSInteger;
+import org.apache.pdfbox.pdmodel.PDPage;
+import org.apache.pdfbox.pdmodel.common.PDRectangle;
+import org.apache.pdfbox.util.PDFTextStripperByArea;
+
+/**
+ * Extracts the text of marked annotations using bounding boxes.
+ */
+public final class TextExtractor {
+
+    private final COSArray boundingBoxes;
+    private final PDPage page;
+
+    /**
+     * @param page       the page the annotation is on, must not be null
+     * @param boundingBoxes the raw annotation, must not be null
+     */
+    public TextExtractor(PDPage page, COSArray boundingBoxes) {
+        this.page = Objects.requireNonNull(page);
+        this.boundingBoxes = Objects.requireNonNull(boundingBoxes);
+    }
+
+    /**
+     * Extracts the text of a marked annotation such as highlights, underlines, strikeouts etc.
+     *
+     * @return The text of the annotation
+     * @throws IOException If the PDFTextStripperByArea fails to initialize.
+     */
+    public String extractMarkedText() throws IOException {
+        // Text has to be extracted by the rectangle calculated from the marking
+        PDFTextStripperByArea stripperByArea = new PDFTextStripperByArea();
+        String markedText = "";
+
+        // Iterates over the array of segments. Each segment consists of 8 points forming a bounding box.
+        int totalSegments = boundingBoxes.size() / 8;
+        for (int currentSegment = 1, segmentPointer = 0; currentSegment <= totalSegments; currentSegment++, segmentPointer += 8) {
+            try {
+                stripperByArea.addRegion("markedRegion", calculateSegmentBoundingBox(boundingBoxes, segmentPointer));
+                stripperByArea.extractRegions(page);
+
+                markedText = markedText.concat(stripperByArea.getTextForRegion("markedRegion"));
+            } catch (IllegalArgumentException e) {
+                throw new IOException("Cannot read annotation coordinates!", e);
+            }
+        }
+
+        return markedText.trim();
+    }
+
+    private Rectangle2D calculateSegmentBoundingBox(COSArray quadsArray, int segmentPointer) {
+        // Extract coordinate values
+        float upperLeftX = toFloat(quadsArray.get(segmentPointer));
+        float upperLeftY = toFloat(quadsArray.get(segmentPointer + 1));
+        float upperRightX = toFloat(quadsArray.get(segmentPointer + 2));
+        float upperRightY = toFloat(quadsArray.get(segmentPointer + 3));
+        float lowerLeftX = toFloat(quadsArray.get(segmentPointer + 4));
+        float lowerLeftY = toFloat(quadsArray.get(segmentPointer + 5));
+
+        // Post-processing of the raw coordinates.
+        PDRectangle pageSize = page.getMediaBox();
+        float ulx = upperLeftX - 1; // It is magic.
+        float uly = pageSize.getHeight() - upperLeftY;
+        float width = upperRightX - lowerLeftX;
+        float height = upperRightY - lowerLeftY;
+
+        return new Rectangle2D.Float(ulx, uly, width, height);
+    }
+
+    private float toFloat(Object cosNumber) {
+        if (cosNumber instanceof COSFloat) {
+            return ((COSFloat) cosNumber).floatValue();
+        }
+        if (cosNumber instanceof COSInteger) {
+            return ((COSInteger) cosNumber).floatValue();
+        }
+        throw new IllegalArgumentException("The number type of the annotation is not supported!");
+    }
+}

src/main/java/org/jabref/model/pdf/FileAnnotationType.java

@@ -12,26 +12,28 @@
  */
 
 public enum FileAnnotationType {
-    TEXT("Text"),
-    HIGHLIGHT("Highlight"),
-    UNDERLINE("Underline"),
-    POLYGON("Polygon"),
-    POPUP("Popup"),
-    LINE("Line"),
-    CIRCLE("Circle"),
-    FREETEXT("FreeText"),
-    STRIKEOUT("Strikeout"),
-    LINK("Link"),
-    INK("Ink"),
-    UNKNOWN("Unknown"),
-    NONE("None");
+    TEXT("Text", false),
+    HIGHLIGHT("Highlight", true),
+    SQUIGGLY("Squiggly", true),
+    UNDERLINE("Underline", true),
+    STRIKEOUT("StrikeOut", true),
+    POLYGON("Polygon", false),
+    POPUP("Popup", false),
+    LINE("Line", false),
+    CIRCLE("Circle", false),
+    FREETEXT("FreeText", false),
+    INK("Ink", false),
+    UNKNOWN("Unknown", false),
+    NONE("None", false);
 
     private static final Log LOGGER = LogFactory.getLog(FileAnnotationType.class);
 
     private final String name;
+    private final boolean linkedFileAnnotationType;
 
-    FileAnnotationType(String name) {
+    FileAnnotationType(String name, boolean linkedFileAnnotationType) {
         this.name = name;
+        this.linkedFileAnnotationType = linkedFileAnnotationType;
     }
 
     /**
@@ -50,6 +52,24 @@ public static FileAnnotationType parse(PDAnnotation annotation) {
         }
     }
 
+    /**
+     * Determines if a String is a supported marked FileAnnotation type.
+     *
+     * @param annotationType a type descriptor
+     * @return true if annotationType is a supported marked FileAnnotation type
+     */
+    public static boolean isMarkedFileAnnotationType(String annotationType) {
+        try {
+            return FileAnnotationType.valueOf(annotationType.toUpperCase(Locale.ROOT)).linkedFileAnnotationType;
+        } catch (IllegalArgumentException e) {
+            return false;
+        }
+    }
+
+    public boolean isLinkedFileAnnotationType() {
+        return linkedFileAnnotationType;
+    }
+
     public String toString() {
         return this.name;
     }

src/test/java/org/jabref/logic/pdf/PdfAnnotationImporterTest.java

@@ -16,6 +16,21 @@ public class PdfAnnotationImporterTest {
 
     private final AnnotationImporter importer = new PdfAnnotationImporter();
 
+    @Test
+    public void invalidPath() {
+        assertEquals(Collections.emptyList(), importer.importAnnotations(Paths.get("/asdf/does/not/exist.pdf")));
+    }
+
+    @Test
+    public void invalidDirectory() {
+        assertEquals(Collections.emptyList(), importer.importAnnotations(Paths.get("src/test/resources/pdfs")));
+    }
+
+    @Test
+    public void invalidDocumentType() {
+        assertEquals(Collections.emptyList(), importer.importAnnotations(Paths.get("src/test/resources/pdfs/write-protected.docx")));
+    }
+
     @Test
     public void noAnnotationsWriteProtected() {
         assertEquals(Collections.emptyList(), importer.importAnnotations(Paths.get("src/test/resources/pdfs/write-protected.pdf")));
@@ -54,6 +69,16 @@ public void popupNoteMinimal() {
                 importer.importAnnotations(Paths.get("src/test/resources/pdfs/minimal-popup.pdf")));
     }
 
+    @Test
+    public void highlightMinimalFoxit() {
+        final FileAnnotation expectedLinkedAnnotation = new FileAnnotation("lynyus", LocalDateTime.of(2017, 5, 31, 15, 16, 1), 1,
+                "this is a foxit highlight", FileAnnotationType.HIGHLIGHT, Optional.empty());
+        final FileAnnotation expected = new FileAnnotation("lynyus", LocalDateTime.of(2017, 5, 31, 15, 16, 1), 1,
+                "Hello", FileAnnotationType.HIGHLIGHT, Optional.of(expectedLinkedAnnotation));
+        assertEquals(Collections.singletonList(expected),
+                importer.importAnnotations(Paths.get("src/test/resources/pdfs/minimal-foxithighlight.pdf")));
+    }
+
     @Test
     public void highlightNoNoteMinimal() {
         final FileAnnotation expectedLinkedAnnotation = new FileAnnotation("Linus Dietz", LocalDateTime.of(2017, 3, 12, 20, 28, 39), 1,
@@ -65,6 +90,29 @@ public void highlightNoNoteMinimal() {
                 importer.importAnnotations(Paths.get("src/test/resources/pdfs/minimal-highlight-no-note.pdf")));
     }
 
+    @Test
+    public void squigglyWithNoteMinimal() {
+        final FileAnnotation expectedLinkedAnnotation = new FileAnnotation("lynyus", LocalDateTime.of(2017, 6, 1, 2, 40, 25), 1,
+                "Squiggly note", FileAnnotationType.SQUIGGLY, Optional.empty());
+        final FileAnnotation expected = new FileAnnotation("lynyus", LocalDateTime.of(2017, 6, 1, 2, 40, 25), 1,
+                "ello", FileAnnotationType.SQUIGGLY, Optional.of(expectedLinkedAnnotation));
+
+        assertEquals(Collections.singletonList(expected),
+                importer.importAnnotations(Paths.get("src/test/resources/pdfs/minimal-squiggly.pdf")));
+    }
+
+    @Test
+
+    public void strikeoutWithNoteMinimal() {
+        final FileAnnotation expectedLinkedAnnotation = new FileAnnotation("lynyus", LocalDateTime.of(2017, 6, 1, 13, 2, 3), 1,
+                "striked out", FileAnnotationType.STRIKEOUT, Optional.empty());
+        final FileAnnotation expected = new FileAnnotation("lynyus", LocalDateTime.of(2017, 6, 1, 13, 2, 3), 1,
+                "World", FileAnnotationType.STRIKEOUT, Optional.of(expectedLinkedAnnotation));
+
+        assertEquals(Collections.singletonList(expected),
+                importer.importAnnotations(Paths.get("src/test/resources/pdfs/minimal-strikeout.pdf")));
+    }
+
     @Test
     public void highlightWithNoteMinimal() {
         final FileAnnotation expectedLinkedAnnotation = new FileAnnotation("Linus Dietz", LocalDateTime.of(2017, 3, 12, 20, 32, 2), 1,