Fix NullPointer exception in PDFALTOOutlineSaxHandler

grobid-core/src/main/java/org/grobid/core/document/DocumentNode.java

@@ -12,32 +12,33 @@
  */
 
 public class DocumentNode {
+    private Integer id = null;
+
     // Gorn address for tree structure
     private String address = null;
-
     // real numbering of the section, if any
-    private String realNumber = null;
 
+    private String realNumber = null;
     // normalized numbering of the section, if any
-    private String normalizedNumber = null;
 
+    private String normalizedNumber = null;
     // the string attached to this document level, e.g. section title
-    private String label = null;
 
+    private String label = null;
     // list of child document nodes
-    private List<DocumentNode> children = null;
 
+    private List<DocumentNode> children = null;
     // offset relatively to the document tokenization (so token offset, NOT character offset)
+
     public int startToken = -1;
     public int endToken = -1;
-
     // coordinates of the string attached to this document level, typically where an index link
     // action point in the document
-    private BoundingBox boundingBox = null;
 
+    private BoundingBox boundingBox = null;
     // parent document node, if null it is a root node
-    private DocumentNode father = null;
 
+    private DocumentNode father = null;
     public DocumentNode() {
     }
 
@@ -128,8 +129,8 @@ public String toString() {
     }
 
     public String toString(int tab) {
-        StringBuffer sb = new StringBuffer();
-        sb.append(address + " " + label + " " + startToken + " " + endToken + "\n");
+        StringBuilder sb = new StringBuilder();
+        sb.append(id).append(" ").append(address).append(" ").append(label).append(" ").append(startToken).append(" ").append(endToken).append("\n");
 
         if (children != null) {
             for (DocumentNode node : children) {
@@ -169,6 +170,7 @@ public DocumentNode getSpanningNode(int position) {
         }
     }
 
+
     /*public DocumentNode nextSlibing() {
          if ( (children != null) && (children.size() > 0) ) {
              return children.get(0);
@@ -182,5 +184,12 @@ else if (father == null) {
              }
          }
      }*/
+    public Integer getId() {
+        return id;
+    }
+
+    public void setId(Integer id) {
+        this.id = id;
+    }
 }
 

grobid-core/src/main/java/org/grobid/core/sax/PDFALTOOutlineSaxHandler.java

@@ -32,7 +32,7 @@ public class PDFALTOOutlineSaxHandler extends DefaultHandler {
 	private int currentParentId = -1;
 
 	private Map<Integer,DocumentNode> nodes = null;
-	
+
 	public PDFALTOOutlineSaxHandler(Document doc) {
 		this.doc = doc;
 	}
@@ -53,11 +53,24 @@ public void endElement(java.lang.String uri, java.lang.String localName,
 			java.lang.String qName) throws SAXException {
 
 		if (qName.equals("STRING")) {
-			label = getText();
+		    currentNode.setLabel(getText());
 		} else if (qName.equals("ITEM")) {
-			currentNode.setLabel(label);
-			currentNode.setBoundingBox(box);
-		}
+		    //The box could come from a nested element
+		    if (box != null) {
+                currentNode.setBoundingBox(box);
+		    }
+
+            box = null;
+            label = null;
+		} else if (qName.equals("TOCITEMLIST")) {
+		    currentParentId = -1;
+        } else if (qName.equals("LINK")) {
+		    // in case of nested item, we need to assign the box right away or we will lose it.
+            if (box != null) {
+                currentNode.setBoundingBox(box);
+            }
+            box = null;
+        }
 	}
 
 	public void startElement(String namespaceURI, String localName,
@@ -66,7 +79,7 @@ public void startElement(String namespaceURI, String localName,
 			// this is the document root
 			root = new DocumentNode();
 			nodes = new HashMap<Integer,DocumentNode>();
-		} if (qName.equals("ITEM")) {
+		} else if (qName.equals("ITEM")) {
 			currentNode = new DocumentNode();
 			// get the node id 
 			int length = atts.getLength();
@@ -78,7 +91,7 @@ public void startElement(String namespaceURI, String localName,
 				String value = atts.getValue(i);
 
 				if ((name != null) && (value != null)) {
-					if (name.equals("id")) {
+					if (name.equalsIgnoreCase("id")) {
 						try {
 							currentId = Integer.parseInt(value);
 						} catch(Exception e) {
@@ -88,14 +101,16 @@ public void startElement(String namespaceURI, String localName,
 					}
 				}
 			}
-			//currentNode.setId(currentId);
+			currentNode.setId(currentId);
 			nodes.put(currentId,currentNode);
 			if (currentParentId != -1) {
 				DocumentNode father = nodes.get(currentParentId);
-				if (father == null)
-					System.out.println("Warning, father not yet encountered! id is " + currentParentId);
-				currentNode.setFather(father);
-				father.addChild(currentNode);
+                if (father == null)
+					LOGGER.warn("Father not yet encountered! id is " + currentParentId);
+                else {
+				    currentNode.setFather(father);
+				    father.addChild(currentNode);
+                }
 			} else {
 				// parent is the root node
 				currentNode.setFather(root);
@@ -197,7 +212,7 @@ public void startElement(String namespaceURI, String localName,
 			}
 
 			// create the bounding box
-			double x = left;
+            double x = left;
 			double y = right;
 			double width = -1.0;
 			double height = -1.0;
@@ -211,4 +226,4 @@ public void startElement(String namespaceURI, String localName,
 		accumulator.setLength(0);
 	}
 
-}
+}

grobid-core/src/test/java/org/grobid/core/sax/PDFALTOOutlineSaxHandlerTest.java

@@ -0,0 +1,111 @@
+package org.grobid.core.sax;
+
+import org.grobid.core.document.Document;
+import org.grobid.core.document.DocumentSource;
+import org.grobid.core.document.DocumentNode;
+import org.junit.Before;
+import org.junit.Test;
+
+import javax.xml.parsers.SAXParser;
+import javax.xml.parsers.SAXParserFactory;
+
+import java.io.InputStream;
+
+import static org.easymock.EasyMock.createMock;
+import static org.hamcrest.CoreMatchers.is;
+import static org.hamcrest.CoreMatchers.nullValue;
+import static org.hamcrest.collection.IsCollectionWithSize.hasSize;
+import static org.junit.Assert.assertThat;
+import static org.junit.Assert.assertTrue;
+
+public class PDFALTOOutlineSaxHandlerTest {
+    SAXParserFactory spf = SAXParserFactory.newInstance();
+
+    PDFALTOOutlineSaxHandler target;
+    DocumentSource mockDocumentSource;
+    Document document;
+
+    @Before
+    public void setUp() throws Exception {
+
+        mockDocumentSource = createMock(DocumentSource.class);
+
+        document = Document.createFromText("");
+        target = new PDFALTOOutlineSaxHandler(document);
+    }
+
+    @Test
+    public void testParsing_pdf2XMLOutline_ShouldWork() throws Exception {
+        InputStream is = this.getClass().getResourceAsStream("pdfalto.xml_outline.xml");
+
+        SAXParser p = spf.newSAXParser();
+        p.parse(is, target);
+
+        DocumentNode root = target.getRootNode();
+        assertTrue(root.getChildren().size() > 0);
+        assertThat(root.getChildren(), hasSize(9));
+        assertThat(root.getChildren().get(0).getLabel(), is("Abstract"));
+        assertThat(root.getChildren().get(0).getChildren(), is(nullValue()));
+        assertThat(root.getChildren().get(0).getBoundingBox().getPage(), is(1));
+        //<LINK page="1" top="592.00" bottom="0.00" left="0.00" right="0.00"/>
+//        assertThat(root.getChildren().get(0).getBoundingBox().getY(), is(0.0));
+//        assertThat(root.getChildren().get(0).getBoundingBox().getHeight(), is(-1.0));
+//        assertThat(root.getChildren().get(0).getBoundingBox().getX(), is(0.0));
+//        assertThat(root.getChildren().get(0).getBoundingBox().getWidth(), is(0.0));
+    }
+
+    @Test
+    public void testParsing_pdf2XMLOutline_errorcase_ShouldWork() throws Exception {
+        InputStream is = this.getClass().getResourceAsStream("test_outline.xml");
+
+        SAXParser p = spf.newSAXParser();
+        p.parse(is, target);
+
+        DocumentNode root = target.getRootNode();
+        assertThat(root.getChildren(), hasSize(5));
+
+        assertThat(root.getChildren().get(0).getLabel(), is("A Identification"));
+        assertThat(root.getChildren().get(0).getChildren(), is(nullValue()));
+        //<LINK page="2" top="71.0000" bottom="0.0000" left="68.0000" right="0.0000"/>
+        assertThat(root.getChildren().get(0).getBoundingBox().getPage(), is(2));
+//        assertThat(root.getChildren().get(0).getBoundingBox().getY(), is(71.000));
+//        assertThat(root.getChildren().get(0).getBoundingBox().getHeight(), is(0.0));
+//        assertThat(root.getChildren().get(0).getBoundingBox().getX(), is(68.000));
+//        assertThat(root.getChildren().get(0).getBoundingBox().getWidth(), is(0.0));
+
+        assertThat(root.getChildren().get(1).getLabel(), is("B Résumé consolidé public."));
+        assertThat(root.getChildren().get(1).getChildren(), hasSize(1));
+        //<LINK page="2" top="377.000" bottom="0.0000" left="68.0000" right="0.0000"/>
+        assertThat(root.getChildren().get(1).getBoundingBox().getPage(), is(2));
+//        assertThat(root.getChildren().get(1).getBoundingBox().getY(), is(377.000));
+//        assertThat(root.getChildren().get(1).getBoundingBox().getHeight(), is(0.0));
+//        assertThat(root.getChildren().get(1).getBoundingBox().getX(), is(68.000));
+//        assertThat(root.getChildren().get(1).getBoundingBox().getWidth(), is(0.0));
+
+        assertThat(root.getChildren().get(1).getChildren(), hasSize(1));
+        assertThat(root.getChildren().get(1).getChildren().get(0).getLabel(), is("B.1 Résumé consolidé public en français"));
+        //<LINK page="2" top="412.000" bottom="0.0000" left="68.0000" right="0.0000"/>
+        assertThat(root.getChildren().get(1).getChildren().get(0).getBoundingBox().getPage(), is(2));
+//        assertThat(root.getChildren().get(1).getChildren().get(0).getBoundingBox().getY(), is(412.000));
+//        assertThat(root.getChildren().get(1).getChildren().get(0).getBoundingBox().getHeight(), is(0.0));
+//        assertThat(root.getChildren().get(1).getChildren().get(0).getBoundingBox().getX(), is(68.000));
+//        assertThat(root.getChildren().get(1).getChildren().get(0).getBoundingBox().getWidth(), is(0.0));
+
+        assertThat(root.getChildren().get(2).getLabel(), is("C Mémoire scientifique en français"));
+        assertThat(root.getChildren().get(2).getChildren(), hasSize(6));
+        assertThat(root.getChildren().get(2).getChildren().get(2).getLabel(), is("C.3 Approche scientifique et technique"));
+        assertThat(root.getChildren().get(3).getLabel(), is("D Liste des livrables"));
+        assertThat(root.getChildren().get(3).getChildren(), is(nullValue()));
+        assertThat(root.getChildren().get(4).getLabel(), is("E Impact du projet"));
+        assertThat(root.getChildren().get(4).getChildren(), hasSize(4));
+        assertThat(root.getChildren().get(4).getChildren().get(1).getLabel(), is("E.2 Liste des publications et communications"));
+        assertThat(root.getChildren().get(4).getChildren().get(2).getLabel(), is("E.3 Liste des autres valorisations scientifiques"));
+        //<LINK page="1" top="170.000" bottom="0.0000" left="68.0000" right="0.0000"/>
+        assertThat(root.getChildren().get(4).getChildren().get(2).getBoundingBox().getPage(), is(1));
+//        assertThat(root.getChildren().get(4).getChildren().get(2).getBoundingBox().getY(), is(170.000));
+//        assertThat(root.getChildren().get(4).getChildren().get(2).getBoundingBox().getHeight(), is(0.0));
+//        assertThat(root.getChildren().get(4).getChildren().get(2).getBoundingBox().getX(), is(68.000));
+//        assertThat(root.getChildren().get(4).getChildren().get(2).getBoundingBox().getWidth(), is(0.0));
+    }
+
+}