Fix xref 0 entry index retrieval when reading file

DEVSIX-1428

Author: Benoit Lagae

kernel/src/main/java/com/itextpdf/kernel/pdf/PdfReader.java

@@ -830,6 +830,8 @@ protected PdfDictionary readXrefSection() throws IOException {
                 } else if (reference.checkState(PdfObject.READING) && reference.getGenNumber() == gen) {
                     reference.setOffset(pos);
                     reference.clearState(PdfObject.READING);
+                } else if (reference.objNr == 0 && pos != 0L) {
+                    reference.setIndex(pos);
                 } else {
                     continue;
                 }

kernel/src/main/java/com/itextpdf/kernel/pdf/PdfXrefTable.java

@@ -129,7 +129,6 @@ PdfIndirectReference createNewIndirectReference(PdfDocument document) {
     }
 
     protected void freeReference(PdfIndirectReference reference) {
-        reference.setOffset(0);
         reference.setState(PdfObject.FREE);
         if (!reference.checkState(PdfObject.FLUSHED)) {
             if (reference.refersTo != null) {

kernel/src/test/java/com/itextpdf/kernel/pdf/PdfXrefTableTest.java

@@ -0,0 +1,115 @@
+/*
+ * To change this license header, choose License Headers in Project Properties.
+ * To change this template file, choose Tools | Templates
+ * and open the template in the editor.
+ */
+package com.itextpdf.kernel.pdf;
+
+import com.itextpdf.test.ExtendedITextTest;
+import static com.itextpdf.test.ITextTest.createOrClearDestinationFolder;
+import com.itextpdf.test.annotations.type.IntegrationTest;
+
+import java.io.IOException;
+
+import org.junit.BeforeClass;
+import org.junit.Test;
+import org.junit.experimental.categories.Category;
+
+import junit.framework.Assert;
+
+/**
+ *
+ * @author benoit
+ */
+@Category(IntegrationTest.class)
+public class PdfXrefTableTest extends ExtendedITextTest {
+
+    public static final String sourceFolder = "./src/test/resources/com/itextpdf/kernel/pdf/PdfXrefTableTest/";
+    public static final String destinationFolder = "./target/test/com/itextpdf/kernel/pdf/PdfXrefTableTest/";
+
+    @BeforeClass
+    public static void beforeClass() {
+        createOrClearDestinationFolder(destinationFolder);
+    }
+
+    @Test
+    public void testCreateAndUpdateXMP() throws IOException {
+        String created = destinationFolder + "testCreateAndUpdateXMP_create.pdf";
+        String updated = destinationFolder + "testCreateAndUpdateXMP_update.pdf";
+        PdfDocument pdfDocument = new PdfDocument(new PdfWriter(created));
+        pdfDocument.addNewPage();
+
+        pdfDocument.getXmpMetadata(true); // create XMP metadata
+        pdfDocument.close();
+
+        pdfDocument = new PdfDocument(new PdfReader(created), new PdfWriter(updated));
+        pdfDocument.close();
+        pdfDocument = new PdfDocument(new PdfReader(updated));
+        PdfXrefTable xref = pdfDocument.getXref();
+        PdfIndirectReference freeRef = xref.get(xref.size() - 2); // 6
+
+        /*
+        Current xref structure:
+        xref
+        0 8
+        0000000006 65535 f % this is object 0; 6 refers to free object 6
+        0000000203 00000 n
+        0000000510 00000 n
+        0000000263 00000 n
+        0000000088 00000 n
+        0000000015 00000 n
+        0000000000 00001 f % this is object 6; 0 refers to free object 0; note generation number
+        0000000561 00000 n
+        */
+
+        Assert.assertTrue(freeRef.isFree());
+        Assert.assertEquals(xref.get(0).offsetOrIndex, freeRef.objNr);
+        Assert.assertEquals(1, freeRef.genNr);
+        pdfDocument.close();
+    }
+    
+    
+    @Test
+    public void testCreateAndUpdateTwiceXMP() throws IOException {
+        String created = destinationFolder + "testCreateAndUpdateTwiceXMP_create.pdf";
+        String updated = destinationFolder + "testCreateAndUpdateTwiceXMP_update.pdf";
+        String updatedAgain = destinationFolder + "testCreateAndUpdateTwiceXMP_updatedAgain.pdf";
+        PdfDocument pdfDocument = new PdfDocument(new PdfWriter(created));
+        pdfDocument.addNewPage();
+
+        pdfDocument.getXmpMetadata(true); // create XMP metadata
+        pdfDocument.close();
+
+        pdfDocument = new PdfDocument(new PdfReader(created), new PdfWriter(updated));
+        pdfDocument.close();
+        pdfDocument = new PdfDocument(new PdfReader(updated), new PdfWriter(updatedAgain));
+        pdfDocument.close();
+        pdfDocument = new PdfDocument(new PdfReader(updatedAgain));
+        PdfXrefTable xref = pdfDocument.getXref();
+        PdfIndirectReference freeRef1 = xref.get(xref.size() - 3); // 6
+        PdfIndirectReference freeRef2 = xref.get(xref.size() - 2); // 7
+        
+        /*
+        Current xref structure:
+        xref
+        0 9
+        0000000006 65535 f % this is object 0; 6 refers to free object 6
+        0000000203 00000 n
+        0000000510 00000 n
+        0000000263 00000 n
+        0000000088 00000 n
+        0000000015 00000 n
+        0000000007 00002 f % this is object 6; 7 refers to free object 7; note generation number
+        0000000000 00001 f % this is object 7; 0 refers to free object 0; note generation number
+        0000000561 00000 n
+        */
+
+        Assert.assertTrue(freeRef1.isFree());
+        Assert.assertEquals(xref.get(0).offsetOrIndex, freeRef1.objNr);
+        Assert.assertEquals(2, freeRef1.genNr);
+        Assert.assertTrue(freeRef2.isFree());
+        Assert.assertEquals(freeRef1.offsetOrIndex, freeRef2.objNr);
+        Assert.assertEquals(1, freeRef2.genNr);
+        pdfDocument.close();
+    }
+}