Rewrite loading pdf file to use convenience method

Author: Braunch

src/main/java/net/sf/jabref/gui/entryeditor/PdfCommentsTab.java

@@ -69,8 +69,6 @@ private void setUpPdfCommentsTab() {
             String pdfPath = field.get().replaceFirst(".*?:", System.getProperty("file.separator")).replaceAll(":PDF", "");
             HashMap<String, String> importedNotes = commentImporter.importNotes(pdfPath);
             importedNotes.values().stream().forEach((note) -> listModel.addElement(note));
-
-            //TODO add context information for importedNotes
         }
 
         commentScrollPane.setPreferredSize(new Dimension(450,200));

src/main/java/net/sf/jabref/logic/pdf/PdfCommentImporter.java

@@ -2,9 +2,17 @@
 
 import java.io.File;
 import java.io.IOException;
+import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.List;
 
+import net.sf.jabref.BibDatabaseContext;
+import net.sf.jabref.Globals;
+import net.sf.jabref.logic.util.io.FileUtil;
+import net.sf.jabref.model.entry.BibEntry;
+
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
 import org.apache.pdfbox.pdmodel.PDDocument;
 import org.apache.pdfbox.pdmodel.PDPage;
 import org.apache.pdfbox.pdmodel.interactive.annotation.PDAnnotation;
@@ -13,38 +21,48 @@ public class PdfCommentImporter {
 
     private List pdfPages;
     private PDPage page;
+
+    private Log logger = LogFactory.getLog(PdfCommentImporter.class);
+
     public PdfCommentImporter() {
 
     }
 
     /**
      * Imports the comments from a pdf specified by its URI
-     * @param pathToPDF the URI specifying the document
-     * @return a hasmap with the unique name as key and the notes content as value
+     *
+     * @param document a PDDocument to get the annotations from
+     * @return a hashmap with the unique name as key and the notes content as value
      */
-    public HashMap<String, String> importNotes(final String pathToPDF){
+    public HashMap<String, String> importNotes(final PDDocument document) {
 
-        PDDocument pdf;
         HashMap<String, String> annotationsMap = new HashMap<>();
-        try {
-            pdf = importPdfFile(pathToPDF);
 
-            pdfPages = pdf.getDocumentCatalog().getAllPages();
-            for(int i = 0; i < pdfPages.size(); i++){
-                page = (PDPage) pdfPages.get(i);
-                for(PDAnnotation annotation : page.getAnnotations()){
+        pdfPages = document.getDocumentCatalog().getAllPages();
+        for (int i = 0; i < pdfPages.size(); i++) {
+            page = (PDPage) pdfPages.get(i);
+            try {
+                for (PDAnnotation annotation : page.getAnnotations()) {
                     annotationsMap.put(annotation.getAnnotationName(), annotation.getContents());
                 }
+            } catch (IOException e1) {
+                e1.printStackTrace();
             }
-
-        } catch (IOException e) {
-            e.printStackTrace();
         }
         return annotationsMap;
     }
 
-    private PDDocument importPdfFile(final String pathToPDF) throws IOException {
-        File file = new File(pathToPDF);
-        return PDDocument.load(file);
+    private List<PDDocument> importPdfFile(final List<BibEntry> entryList, final BibDatabaseContext bibDatabaseContext) throws IOException {
+
+        final List<File> files = FileUtil.getListOfLinkedFiles(entryList,
+                bibDatabaseContext.getFileDirectory(Globals.prefs.getFileDirectoryPreferences()));
+
+        ArrayList<PDDocument> documents = new ArrayList<>();
+        for(File linkedFile : files){
+            if(linkedFile.getName().toLowerCase().endsWith(".pdf")){
+                documents.add(PDDocument.load(linkedFile));
+            }
+        }
+        return documents;
     }
 }