Cleanup FindFile and asssociated tests

src/main/java/net/sf/jabref/external/AutoSetLinks.java

@@ -40,7 +40,7 @@ public class AutoSetLinks {
      * @param entries  the entries for which links should be set
      * @param databaseContext the database for which links are set
      */
-    public static void autoSetLinks(Collection<BibEntry> entries, BibDatabaseContext databaseContext) {
+    public static void autoSetLinks(List<BibEntry> entries, BibDatabaseContext databaseContext) {
         autoSetLinks(entries, null, null, null, databaseContext, null, null);
     }
 
@@ -69,7 +69,9 @@ public static void autoSetLinks(Collection<BibEntry> entries, BibDatabaseContext
      *                         parameter can be null, which means that no progress update will be shown.
      * @return the thread performing the automatically setting
      */
-    public static Runnable autoSetLinks(final Collection<BibEntry> entries, final NamedCompound ce, final Set<BibEntry> changedEntries, final FileListTableModel singleTableModel, final BibDatabaseContext databaseContext, final ActionListener callback, final JDialog diag) {
+    public static Runnable autoSetLinks(final List<BibEntry> entries, final NamedCompound ce,
+            final Set<BibEntry> changedEntries, final FileListTableModel singleTableModel,
+            final BibDatabaseContext databaseContext, final ActionListener callback, final JDialog diag) {
         final Collection<ExternalFileType> types = ExternalFileTypes.getInstance().getExternalFileTypeSelection();
         if (diag != null) {
             final JProgressBar prog = new JProgressBar(JProgressBar.HORIZONTAL, 0, types.size() - 1);
@@ -94,7 +96,7 @@ public void run() {
                 dirs.addAll(dirsS.stream().map(File::new).collect(Collectors.toList()));
 
                 // determine extensions
-                Collection<String> extensions = new ArrayList<>();
+                List<String> extensions = new ArrayList<>();
                 for (final ExternalFileType type : types) {
                     extensions.add(type.getExtension());
                 }
@@ -105,7 +107,8 @@ public void run() {
                     String regExp = Globals.prefs.get(JabRefPreferences.REG_EXP_SEARCH_EXPRESSION_KEY);
                     result = RegExpFileSearch.findFilesForSet(entries, extensions, dirs, regExp);
                 } else {
-                    result = FileUtil.findAssociatedFiles(entries, extensions, dirs, Globals.prefs);
+                    boolean autoLinkExactKeyOnly = Globals.prefs.getBoolean(JabRefPreferences.AUTOLINK_EXACT_KEY_ONLY);
+                    result = FileUtil.findAssociatedFiles(entries, extensions, dirs, autoLinkExactKeyOnly);
                 }
 
                 boolean foundAny = false;
@@ -210,7 +213,8 @@ public void run() {
      *                         parameter can be null, which means that no progress update will be shown.
      * @return the runnable able to perform the automatically setting
      */
-    public static Runnable autoSetLinks(final BibEntry entry, final FileListTableModel singleTableModel, final BibDatabaseContext databaseContext, final ActionListener callback, final JDialog diag) {
+    public static Runnable autoSetLinks(final BibEntry entry, final FileListTableModel singleTableModel,
+            final BibDatabaseContext databaseContext, final ActionListener callback, final JDialog diag) {
         return autoSetLinks(Collections.singletonList(entry), null, null, singleTableModel, databaseContext, callback,
                 diag);
     }

src/main/java/net/sf/jabref/external/ExternalFileTypes.java

@@ -1,7 +1,6 @@
 package net.sf.jabref.external;
 
 import java.util.ArrayList;
-import java.util.Collection;
 import java.util.List;
 import java.util.Optional;
 import java.util.Set;
@@ -104,7 +103,7 @@ public static List<ExternalFileType> getDefaultExternalFileTypes() {
         return list;
     }
 
-    public Collection<ExternalFileType> getExternalFileTypeSelection() {
+    public Set<ExternalFileType> getExternalFileTypeSelection() {
         return externalFileTypes;
     }
 

src/main/java/net/sf/jabref/external/RegExpFileSearch.java

@@ -19,7 +19,6 @@
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Arrays;
-import java.util.Collection;
 import java.util.Collections;
 import java.util.HashMap;
 import java.util.LinkedList;
@@ -63,8 +62,8 @@ public class RegExpFileSearch {
      * @param regExp The expression deciding which names are acceptable.
      * @return A map linking each given entry to a list of files matching the given criteria.
      */
-    public static Map<BibEntry, List<File>> findFilesForSet(Collection<BibEntry> entries,
-            Collection<String> extensions, List<File> directories, String regExp) {
+    public static Map<BibEntry, List<File>> findFilesForSet(List<BibEntry> entries, List<String> extensions,
+            List<File> directories, String regExp) {
 
         Map<BibEntry, List<File>> res = new HashMap<>();
         for (BibEntry entry : entries) {
@@ -82,8 +81,8 @@ public static Map<BibEntry, List<File>> findFilesForSet(Collection<BibEntry> ent
      * @param regularExpression The expression deciding which names are acceptable.
      * @return A list of files paths matching the given criteria.
      */
-    private static List<File> findFiles(BibEntry entry, Collection<String> extensions,
-            Collection<File> directories, String regularExpression) {
+    private static List<File> findFiles(BibEntry entry, List<String> extensions, List<File> directories,
+            String regularExpression) {
 
         String extensionRegExp = '(' + String.join("|", extensions) + ')';
 
@@ -128,8 +127,7 @@ private static List<File> findFiles(BibEntry entry, Collection<String> extension
      * @return Will return the first file found to match the given criteria or
      *         null if none was found.
      */
-    private static List<File> findFile(BibEntry entry, Collection<File> dirs, String file,
-            String extensionRegExp) {
+    private static List<File> findFile(BibEntry entry, List<File> dirs, String file, String extensionRegExp) {
         List<File> res = new ArrayList<>();
         for (File directory : dirs) {
             res.addAll(findFile(entry, directory.getPath(), file, extensionRegExp));

src/main/java/net/sf/jabref/external/SynchronizeFileField.java

@@ -132,7 +132,7 @@ public void run() {
 
         // First we try to autoset fields
         if (autoSet) {
-            Collection<BibEntry> entries = new ArrayList<>(sel);
+            List<BibEntry> entries = new ArrayList<>(sel);
 
             // Start the automatically setting process:
             Runnable r = AutoSetLinks.autoSetLinks(entries, ce, changedEntries, null, panel.getBibDatabaseContext(), null, null);

src/main/java/net/sf/jabref/gui/BasePanel.java

@@ -38,6 +38,7 @@
 import java.util.Map;
 import java.util.Objects;
 import java.util.Optional;
+import java.util.Set;
 import java.util.TimerTask;
 
 import javax.swing.AbstractAction;
@@ -2402,9 +2403,9 @@ public Optional<String> searchAndOpen() {
                 of stuff below. It is now disabled by default. */
 
             // see if we can fall back to a filename based on the bibtex key
-            final Collection<BibEntry> entries = Collections.singleton(entry);
+            final List<BibEntry> entries = Collections.singletonList(entry);
 
-            final Collection<ExternalFileType> types = ExternalFileTypes.getInstance().getExternalFileTypeSelection();
+            final Set<ExternalFileType> types = ExternalFileTypes.getInstance().getExternalFileTypeSelection();
             final List<File> dirs = new ArrayList<>();
             if (!basePanel.getBibDatabaseContext().getFileDirectory().isEmpty()) {
                 final List<String> mdDirs = basePanel.getBibDatabaseContext().getFileDirectory();
@@ -2423,7 +2424,8 @@ public Optional<String> searchAndOpen() {
                 String regExp = Globals.prefs.get(JabRefPreferences.REG_EXP_SEARCH_EXPRESSION_KEY);
                 result = RegExpFileSearch.findFilesForSet(entries, extensions, dirs, regExp);
             } else {
-                result = FileUtil.findAssociatedFiles(entries, extensions, dirs, Globals.prefs);
+                boolean autoLinkExactKeyOnly = Globals.prefs.getBoolean(JabRefPreferences.AUTOLINK_EXACT_KEY_ONLY);
+                result = FileUtil.findAssociatedFiles(entries, extensions, dirs, autoLinkExactKeyOnly);
             }
             if (result.containsKey(entry)) {
                 final List<File> res = result.get(entry);

src/main/java/net/sf/jabref/gui/fieldeditors/FileListEditor.java

@@ -29,7 +29,6 @@
 import java.nio.file.Path;
 import java.nio.file.Paths;
 import java.util.ArrayList;
-import java.util.Collection;
 import java.util.List;
 import java.util.Optional;
 
@@ -434,8 +433,7 @@ private boolean editListEntry(FileListEntry entry, boolean openBrowse) {
     public void autoSetLinks() {
         auto.setEnabled(false);
 
-        Collection<BibEntry> entries = new ArrayList<>();
-        entries.addAll(frame.getCurrentBasePanel().getSelectedEntries());
+        List<BibEntry> entries = new ArrayList<>(frame.getCurrentBasePanel().getSelectedEntries());
 
         // filesystem lookup
         JDialog dialog = new JDialog(frame, true);

src/main/java/net/sf/jabref/logic/util/io/FileFinder.java

@@ -1,43 +1,47 @@
 package net.sf.jabref.logic.util.io;
 
 import java.io.File;
-import java.util.Collection;
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.attribute.BasicFileAttributes;
 import java.util.HashSet;
+import java.util.List;
+import java.util.Objects;
 import java.util.Set;
+import java.util.function.BiPredicate;
+import java.util.stream.Collectors;
+import java.util.stream.Stream;
+
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
 
 public class FileFinder {
 
-    public static Set<File> findFiles(Collection<String> extensions, Collection<File> directories) {
-        Set<File> result = new HashSet<>();
+    private static final Log LOGGER = LogFactory.getLog(FileFinder.class);
 
-        for (File directory : directories) {
-            result.addAll(FileFinder.findFiles(extensions, directory));
-        }
 
-        return result;
-    }
+    public static Set<File> findFiles(List<String> extensions, List<File> directories) {
+
+        Objects.requireNonNull(directories, "Directories must not be null!");
+        Objects.requireNonNull(extensions, "Extensions must not be null!");
+
+        BiPredicate<Path, BasicFileAttributes> isDirectoryAndContainsExtension = (path,
+                attr) -> !Files.isDirectory(path)
+                        && extensions.contains(FileUtil.getFileExtension(path.toFile()).orElse(""));
 
-    private static Collection<? extends File> findFiles(Collection<String> extensions, File directory) {
         Set<File> result = new HashSet<>();
+        for (File directory : directories) {
 
-        File[] children = directory.listFiles();
-        if (children == null) {
-            return result; // No permission?
-        }
+            try (Stream<File> files = Files.find(directory.toPath(), Integer.MAX_VALUE, isDirectoryAndContainsExtension)
+                    .map(x -> x.toFile())) {
+                result.addAll(files.collect(Collectors.toSet()));
 
-        for (File child : children) {
-            if (child.isDirectory()) {
-                result.addAll(FileFinder.findFiles(extensions, child));
-            } else {
-                FileUtil.getFileExtension(child).ifPresent(extension -> {
-                    if (extensions.contains(extension)) {
-                        result.add(child);
-                    }
-                });
+            } catch (IOException e) {
+                LOGGER.error("Problem in finding files", e);
             }
         }
-
         return result;
-    }
 
+    }
 }

src/main/java/net/sf/jabref/logic/util/io/FileUtil.java

@@ -24,7 +24,6 @@
 import java.io.StringReader;
 import java.util.ArrayList;
 import java.util.Arrays;
-import java.util.Collection;
 import java.util.Collections;
 import java.util.HashMap;
 import java.util.List;
@@ -317,8 +316,8 @@ private static File shortenFileName(File fileName, String directory) {
         }
     }
 
-    public static Map<BibEntry, List<File>> findAssociatedFiles(Collection<BibEntry> entries,
-            Collection<String> extensions, Collection<File> directories, JabRefPreferences prefs) {
+    public static Map<BibEntry, List<File>> findAssociatedFiles(List<BibEntry> entries,
+            List<String> extensions, List<File> directories, boolean autolinkExactKeyOnly) {
         Map<BibEntry, List<File>> result = new HashMap<>();
 
         // First scan directories
@@ -329,7 +328,6 @@ public static Map<BibEntry, List<File>> findAssociatedFiles(Collection<BibEntry>
             result.put(entry, new ArrayList<>());
         }
 
-        boolean exactOnly = prefs.getBoolean(JabRefPreferences.AUTOLINK_EXACT_KEY_ONLY);
         // Now look for keys
         nextFile: for (File file : filesWithExtension) {
 
@@ -345,7 +343,7 @@ public static Map<BibEntry, List<File>> findAssociatedFiles(Collection<BibEntry>
             }
             // If we get here, we didn't find any exact matches. If non-exact
             // matches are allowed, try to find one:
-            if (!exactOnly) {
+            if (!autolinkExactKeyOnly) {
                 for (BibEntry entry : entries) {
                     String citeKey = entry.getCiteKey();
                     if ((citeKey != null) && !citeKey.isEmpty() && name.startsWith(citeKey)) {