[WIP] Refactored around the FileAnnotationCache.

src/main/java/org/jabref/gui/BasePanel.java

@@ -206,7 +206,7 @@ public BasePanel(JabRefFrame frame, BibDatabaseContext bibDatabaseContext) {
         this.tableModel = new MainTableDataModel(getBibDatabaseContext());
 
         citationStyleCache = new CitationStyleCache(bibDatabaseContext);
-        annotationCache = new FileAnnotationCache();
+        annotationCache = new FileAnnotationCache(bibDatabaseContext);
 
         setupMainPanel();
 

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

@@ -0,0 +1,11 @@
+package org.jabref.logic.pdf;
+
+import java.util.List;
+
+import org.jabref.model.database.BibDatabaseContext;
+import org.jabref.model.pdf.FileAnnotation;
+
+public interface AnnotationImporter {
+
+    List<FileAnnotation> importAnnotations(final String path, final BibDatabaseContext context);
+}

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

@@ -0,0 +1,54 @@
+package org.jabref.logic.pdf;
+
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.stream.Collectors;
+
+import org.jabref.model.database.BibDatabaseContext;
+import org.jabref.model.entry.BibEntry;
+import org.jabref.model.entry.FieldName;
+import org.jabref.model.entry.FileField;
+import org.jabref.model.entry.ParsedFileField;
+import org.jabref.model.pdf.FileAnnotation;
+
+
+/**
+ * Here all PDF files attached to a BibEntry are scanned for annotations using a PdfAnnotationImporter.
+ */
+public class EntryAnnotationImporter {
+
+    private final BibEntry entry;
+
+    /**
+     * @param entry The BibEntry whose attached files are scanned for annotations.
+     */
+    public EntryAnnotationImporter(BibEntry entry) {
+        this.entry = entry;
+    }
+
+    /**
+     * Filter files with a web address containing "www."
+     *
+     * @return a list of file parsed files
+     */
+    public List<ParsedFileField> getFilteredFileList() {
+        return FileField.parse(this.entry.getField(FieldName.FILE).get()).stream()
+                .filter(parsedFileField -> parsedFileField.getLink().toLowerCase().endsWith(".pdf"))
+                .filter(parsedFileField -> !parsedFileField.getLink().contains("www.")).collect(Collectors.toList());
+    }
+
+    /**
+     * Reads the annotations from the files that are attached to a BibEntry.
+     *
+     * @param context The context is needed for the importer.
+     * @return Map from each PDF to a list of file annotations
+     */
+    public Map<String, List<FileAnnotation>> importAnnotationsFromFiles(BibDatabaseContext context) {
+        Map<String, List<FileAnnotation>> annotations = new HashMap<>();
+        AnnotationImporter importer = new PdfAnnotationImporter();
+        //import annotationsOfFiles if the selected files are valid which is checked in getFilteredFileList()
+        this.getFilteredFileList().forEach(parsedFileField -> annotations.put(parsedFileField.getLink(), importer.importAnnotations(parsedFileField.getLink(), context)));
+        return annotations;
+    }
+}

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

@@ -1,54 +1,41 @@
 package org.jabref.logic.pdf;
 
-import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
-import java.util.Optional;
 import java.util.concurrent.ExecutionException;
 
+import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.entry.BibEntry;
 import org.jabref.model.pdf.FileAnnotation;
 
 import com.google.common.cache.CacheBuilder;
 import com.google.common.cache.CacheLoader;
 import com.google.common.cache.LoadingCache;
 
+
 public class FileAnnotationCache {
 
     //cache size in entries
     private final static int CACHE_SIZE = 10;
     //the inner list holds the annotations per file, the outer collection maps this to a BibEntry.
     private LoadingCache<BibEntry, Map<String, List<FileAnnotation>>> annotationCache;
 
-    public FileAnnotationCache() {
+    public FileAnnotationCache(BibDatabaseContext context) {
         annotationCache = CacheBuilder.newBuilder().maximumSize(CACHE_SIZE).build(new CacheLoader<BibEntry, Map<String, List<FileAnnotation>>>() {
             @Override
-            public Map<String, List<FileAnnotation>> load(BibEntry notUsed) throws Exception {
-                // Automated reloading of entries is not supported.
-                return new HashMap<>();
+            public Map<String, List<FileAnnotation>> load(BibEntry entry) throws Exception {
+                return new EntryAnnotationImporter(entry).importAnnotationsFromFiles(context);
             }
         });
     }
 
-    public void addToCache(BibEntry entry, final Map<String, List<FileAnnotation>> annotations) {
-        annotationCache.put(entry, annotations);
-    }
-
     /**
      * Note that entry becomes the most recent entry in the cache
      *
      * @param entry entry for which to get the annotations
      * @return Map containing a list of annotations in a list for each file
      */
-    public Optional<Map<String, List<FileAnnotation>>> getFromCache(Optional<BibEntry> entry) {
-        Optional<Map<String, List<FileAnnotation>>> emptyAnnotation = Optional.empty();
-        try {
-            if (entry.isPresent() && annotationCache.get(entry.get()).size() > 0) {
-                return Optional.of(annotationCache.get(entry.get()));
-            }
-        } catch (ExecutionException failure) {
-            return emptyAnnotation;
-        }
-        return emptyAnnotation;
+    public Map<String, List<FileAnnotation>> getFromCache(BibEntry entry) throws ExecutionException {
+        return annotationCache.get(entry);
     }
 }

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

@@ -6,6 +6,7 @@
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.List;
+import java.util.Locale;
 import java.util.Optional;
 
 import org.jabref.logic.util.io.FileUtil;
@@ -24,14 +25,10 @@
 import org.apache.pdfbox.pdmodel.interactive.annotation.PDAnnotation;
 import org.apache.pdfbox.util.PDFTextStripperByArea;
 
-public class PdfAnnotationImporterImpl implements AnnotationImporterInterface {
+import static org.jabref.gui.importer.actions.OpenDatabaseAction.LOGGER;
 
-    private List pdfPages;
-    private PDPage page;
+public class PdfAnnotationImporter implements AnnotationImporter {
 
-    public PdfAnnotationImporterImpl() {
-
-    }
 
     /**
      * Imports the comments from a pdf specified by its path
@@ -62,12 +59,12 @@ public List<FileAnnotation> importAnnotations(final String path, final BibDataba
             }
 
         } catch (IOException e) {
-            e.printStackTrace();
+            LOGGER.error(String.format("Failed to read file %s.", path) , e);
         }
 
-        pdfPages = document.getDocumentCatalog().getAllPages();
+        List pdfPages = document.getDocumentCatalog().getAllPages();
         for (int i = 0; i < pdfPages.size(); i++) {
-            page = (PDPage) pdfPages.get(i);
+            PDPage page = (PDPage) pdfPages.get(i);
             try {
                 for (PDAnnotation annotation : page.getAnnotations()) {
 
@@ -82,7 +79,10 @@ public List<FileAnnotation> importAnnotations(final String path, final BibDataba
                         PDFTextStripperByArea stripperByArea = new PDFTextStripperByArea();
                         COSArray quadsArray = (COSArray) annotation.getDictionary().getDictionaryObject(COSName.getPDFName("QuadPoints"));
                         String highlightedText = null;
-                        for (int j = 1, k = 0; j <= (quadsArray.size() / 8); j++) {
+                        for (int j = 1,
+                             k = 0;
+                             j <= (quadsArray.size() / 8);
+                             j++) {
 
                             COSFloat upperLeftX = (COSFloat) quadsArray.get(k);
                             COSFloat upperLeftY = (COSFloat) quadsArray.get(1 + k);
@@ -124,14 +124,13 @@ public List<FileAnnotation> importAnnotations(final String path, final BibDataba
                         annotationsList.add(new FileAnnotation(annotation, i + 1));
                     }
                 }
-            } catch (IOException e1) {
-                e1.printStackTrace();
+            } catch (IOException e) {
+                LOGGER.error(String.format("Failed to read file %s.", path) , e);
             }
         }
         try {
             document.close();
-        } catch (IOException e) {
-            e.printStackTrace();
+        } catch (IOException ignored) {
         }
         return annotationsList;
     }
@@ -144,7 +143,7 @@ public List<FileAnnotation> importAnnotations(final String path, final BibDataba
      */
     public PDDocument importPdfFile(final String path) throws IOException {
 
-            if(path.toLowerCase().endsWith(".pdf")){
+            if(path.toLowerCase(Locale.ROOT).endsWith(".pdf")){
                return PDDocument.load("/"+ path);
             }
         return null;

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

@@ -16,7 +16,7 @@ public class FileAnnotation {
     private FileAnnotation linkedFileAnnotation;
     private final static int ABBREVIATED_ANNOTATION_NAME_LENGTH = 45;
 
-    private boolean linkedComment;
+    private boolean linkedAnnotation;
 
     public FileAnnotation(final String commentId, final String author, final String date, final int page,
                           final String content, final String annotationType) {
@@ -56,8 +56,8 @@ private String abbreviateAnnotationName(final String annotationName ){
     public void linkComments(FileAnnotation commentToLinkTo){
         linkedFileAnnotation = commentToLinkTo;
         commentToLinkTo.setLinkedFileAnnotation(this);
-        commentToLinkTo.setLinkedComment(true);
-        linkedComment = true;
+        commentToLinkTo.setLinkedAnnotation(true);
+        linkedAnnotation = true;
     }
 
     @Override
@@ -117,11 +117,11 @@ public String getAnnotationType() {
         return annotationType;
     }
 
-    public boolean hasLinkedComment() {
-        return linkedComment;
+    public boolean hasLinkedAnnotation() {
+        return linkedAnnotation;
     }
 
-    public void setLinkedComment(boolean linkedComment) {
-        this.linkedComment = linkedComment;
+    public void setLinkedAnnotation(boolean linkedAnnotation) {
+        this.linkedAnnotation = linkedAnnotation;
     }
 }