Implements #1664: group based on aux file

CHANGELOG.md

@@ -15,6 +15,7 @@ We refer to [GitHub issues](/~https://github.com/JabRef/jabref/issues) by using `#
 - We now show a small notification icon in the entry editor when we detect data inconsistency or other problems. [#3145](/~https://github.com/JabRef/jabref/issues/3145)
 - We added [oaDOI](https://oadoi.org/) as a fulltext provider, so that JabRef is now able to provide fulltexts for more than 90 million open-access articles.
 - We changed one default of [Cleanup entries dialog](http://help.jabref.org/en/CleanupEntries): Per default, the PDF are not moved to the default file directory anymore. [#3619](/~https://github.com/JabRef/jabref/issues/3619)
+- We added a new type of group that shows all items referenced in a given LaTeX file (actually the generated AUX file). [#1664](/~https://github.com/JabRef/jabref/issues/1664)
 - We added the export of the `translator` field to the according MS-Office XML field. [#1750, comment](/~https://github.com/JabRef/jabref/issues/1750#issuecomment-357350986)
 - We changed the import of the MS-Office XML fields `bookauthor` and `translator`. Both are now imported to their corresponding bibtex/biblatex fields.
 - We improved the export of the `address` and `location` field to the MS-Office XML fields. If the address field does not contain a comma, it is treated as single value and exported to the field `city`. [#1750, comment](/~https://github.com/JabRef/jabref/issues/1750#issuecomment-357539167) 

src/jmh/java/org/jabref/benchmarks/Benchmarks.java

@@ -27,6 +27,7 @@
 import org.jabref.model.groups.KeywordGroup;
 import org.jabref.model.groups.WordKeywordGroup;
 import org.jabref.model.metadata.MetaData;
+import org.jabref.model.util.DummyFileUpdateMonitor;
 import org.jabref.preferences.JabRefPreferences;
 
 import org.openjdk.jmh.Main;
@@ -73,7 +74,7 @@ public void init() throws Exception {
 
     @Benchmark
     public ParserResult parse() throws IOException {
-        BibtexParser parser = new BibtexParser(Globals.prefs.getImportFormatPreferences());
+        BibtexParser parser = new BibtexParser(Globals.prefs.getImportFormatPreferences(), new DummyFileUpdateMonitor());
         return parser.parse(new StringReader(bibtexString));
     }
 

src/main/java/org/jabref/Globals.java

@@ -7,15 +7,16 @@
 import org.jabref.gui.GlobalFocusListener;
 import org.jabref.gui.StateManager;
 import org.jabref.gui.keyboard.KeyBindingRepository;
+import org.jabref.gui.util.DefaultFileUpdateMonitor;
 import org.jabref.gui.util.DefaultTaskExecutor;
-import org.jabref.gui.util.FileUpdateMonitor;
 import org.jabref.gui.util.TaskExecutor;
 import org.jabref.logic.exporter.ExporterFactory;
 import org.jabref.logic.importer.ImportFormatReader;
 import org.jabref.logic.journals.JournalAbbreviationLoader;
 import org.jabref.logic.protectedterms.ProtectedTermsLoader;
 import org.jabref.logic.remote.server.RemoteListenerServerLifecycle;
 import org.jabref.logic.util.BuildInfo;
+import org.jabref.model.util.FileUpdateMonitor;
 import org.jabref.preferences.JabRefPreferences;
 
 import com.google.common.base.StandardSystemProperty;
@@ -54,7 +55,7 @@ public class Globals {
     private static KeyBindingRepository keyBindingRepository;
     // Background tasks
     private static GlobalFocusListener focusListener;
-    private static FileUpdateMonitor fileUpdateMonitor;
+    private static DefaultFileUpdateMonitor fileUpdateMonitor;
     private static TelemetryClient telemetryClient;
 
     private Globals() {
@@ -73,7 +74,7 @@ public static synchronized KeyBindingRepository getKeyPrefs() {
     public static void startBackgroundTasks() {
         Globals.focusListener = new GlobalFocusListener();
 
-        Globals.fileUpdateMonitor = new FileUpdateMonitor();
+        Globals.fileUpdateMonitor = new DefaultFileUpdateMonitor();
         JabRefExecutorService.INSTANCE.executeInterruptableTask(Globals.fileUpdateMonitor, "FileUpdateMonitor");
 
         if (Globals.prefs.shouldCollectTelemetry()) {

src/main/java/org/jabref/JabRefGUI.java

@@ -205,7 +205,7 @@ private void openLastEditedDatabases() {
             }
 
             ParserResult parsedDatabase = OpenDatabase.loadDatabase(fileName,
-                    Globals.prefs.getImportFormatPreferences());
+                    Globals.prefs.getImportFormatPreferences(), Globals.getFileUpdateMonitor());
 
             if (parsedDatabase.isEmpty()) {
                 LOGGER.error(Localization.lang("Error opening file") + " '" + dbFile.getPath() + "'");

src/main/java/org/jabref/JabRefMain.java

@@ -144,7 +144,7 @@ private static void start(String[] args) {
 
         /* Build list of Import and Export formats */
         Globals.IMPORT_FORMAT_READER.resetImportFormats(Globals.prefs.getImportFormatPreferences(),
-                Globals.prefs.getXMPPreferences());
+                Globals.prefs.getXMPPreferences(), Globals.getFileUpdateMonitor());
         EntryTypes.loadCustomEntryTypes(preferences.loadCustomEntryTypes(BibDatabaseMode.BIBTEX),
                 preferences.loadCustomEntryTypes(BibDatabaseMode.BIBLATEX));
         Globals.exportFactory = ExporterFactory.create(Globals.prefs, Globals.journalAbbreviationLoader);

src/main/java/org/jabref/cli/ArgumentProcessor.java

@@ -130,7 +130,7 @@ private static Optional<ParserResult> importFile(Path file, String importFormat)
                 // * means "guess the format":
                 System.out.println(Localization.lang("Importing in unknown format") + ": " + file);
 
-                ImportFormatReader.UnknownFormatImport importResult = Globals.IMPORT_FORMAT_READER.importUnknownFormat(file);
+                ImportFormatReader.UnknownFormatImport importResult = Globals.IMPORT_FORMAT_READER.importUnknownFormat(file, Globals.getFileUpdateMonitor());
 
                 System.out.println(Localization.lang("Format used") + ": " + importResult.format);
                 return Optional.of(importResult.parserResult);
@@ -308,7 +308,7 @@ private List<ParserResult> importAndOpenFiles() {
                 boolean bibExtension = aLeftOver.toLowerCase(Locale.ENGLISH).endsWith("bib");
                 ParserResult pr = new ParserResult();
                 if (bibExtension) {
-                    pr = OpenDatabase.loadDatabase(aLeftOver, Globals.prefs.getImportFormatPreferences());
+                    pr = OpenDatabase.loadDatabase(aLeftOver, Globals.prefs.getImportFormatPreferences(), Globals.getFileUpdateMonitor());
                 }
 
                 if (!bibExtension || (pr.isEmpty())) {

src/main/java/org/jabref/cli/AuxCommandLine.java

@@ -1,7 +1,11 @@
 package org.jabref.cli;
 
-import org.jabref.logic.auxparser.AuxParser;
-import org.jabref.logic.auxparser.AuxParserResult;
+import java.nio.file.Paths;
+
+import org.jabref.gui.auximport.AuxParserResultViewModel;
+import org.jabref.logic.auxparser.DefaultAuxParser;
+import org.jabref.model.auxparser.AuxParser;
+import org.jabref.model.auxparser.AuxParserResult;
 import org.jabref.model.database.BibDatabase;
 import org.jabref.model.strings.StringUtil;
 
@@ -18,11 +22,11 @@ public BibDatabase perform() {
         BibDatabase subDatabase = null;
 
         if (!auxFile.isEmpty() && (database != null)) {
-            AuxParser auxParser = new AuxParser(auxFile, database);
-            AuxParserResult result = auxParser.parse();
+            AuxParser auxParser = new DefaultAuxParser(database);
+            AuxParserResult result = auxParser.parse(Paths.get(auxFile));
             subDatabase = result.getGeneratedBibDatabase();
             // print statistics
-            System.out.println(result.getInformation(true));
+            System.out.println(new AuxParserResultViewModel(result).getInformation(true));
         }
         return subDatabase;
     }

src/main/java/org/jabref/cli/CrossrefFetcherEvaluator.java

@@ -31,7 +31,7 @@ private CrossrefFetcherEvaluator() {
     public static void main(String[] args) throws IOException, InterruptedException {
         Globals.prefs = JabRefPreferences.getInstance();
         try (FileReader reader = new FileReader(args[0])) {
-            BibtexParser parser = new BibtexParser(Globals.prefs.getImportFormatPreferences());
+            BibtexParser parser = new BibtexParser(Globals.prefs.getImportFormatPreferences(), Globals.getFileUpdateMonitor());
             ParserResult result = parser.parse(reader);
             BibDatabase db = result.getDatabase();
 

src/main/java/org/jabref/cli/XMPUtilMain.java

@@ -87,7 +87,7 @@ public static void main(String[] args) throws IOException, TransformerException
             } else if (args[0].endsWith(".bib")) {
                 // Read from BIB and write as XMP
                 try (FileReader fr = new FileReader(args[0])) {
-                    ParserResult result = new BibtexParser(importFormatPreferences).parse(fr);
+                    ParserResult result = new BibtexParser(importFormatPreferences, Globals.getFileUpdateMonitor()).parse(fr);
                     Collection<BibEntry> entries = result.getDatabase().getEntries();
 
                     if (entries.isEmpty()) {
@@ -114,7 +114,7 @@ public static void main(String[] args) throws IOException, TransformerException
             }
 
             if (args[0].endsWith(".bib") && args[1].endsWith(".pdf")) {
-                ParserResult result = new BibtexParser(importFormatPreferences).parse(new FileReader(args[0]));
+                ParserResult result = new BibtexParser(importFormatPreferences, Globals.getFileUpdateMonitor()).parse(new FileReader(args[0]));
 
                 Collection<BibEntry> entries = result.getDatabase().getEntries();
 
@@ -135,7 +135,7 @@ public static void main(String[] args) throws IOException, TransformerException
                 break;
             }
 
-            ParserResult result = new BibtexParser(importFormatPreferences).parse(new FileReader(args[1]));
+            ParserResult result = new BibtexParser(importFormatPreferences, Globals.getFileUpdateMonitor()).parse(new FileReader(args[1]));
 
             Optional<BibEntry> bibEntry = result.getDatabase().getEntryByKey(args[0]);
 

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

@@ -4,7 +4,7 @@
 
 import org.jabref.Globals;
 import org.jabref.gui.keyboard.KeyBindingRepository;
-import org.jabref.gui.util.FileUpdateMonitor;
+import org.jabref.gui.util.DefaultFileUpdateMonitor;
 import org.jabref.gui.util.TaskExecutor;
 import org.jabref.logic.journals.JournalAbbreviationLoader;
 import org.jabref.preferences.PreferencesService;
@@ -36,7 +36,7 @@ private static Object createDependency(Class<?> clazz) {
             return Globals.journalAbbreviationLoader;
         } else if (clazz == StateManager.class) {
             return Globals.stateManager;
-        } else if (clazz == FileUpdateMonitor.class) {
+        } else if (clazz == DefaultFileUpdateMonitor.class) {
             return Globals.getFileUpdateMonitor();
         } else {
             try {

src/main/java/org/jabref/gui/auximport/AuxParserResultViewModel.java

@@ -0,0 +1,38 @@
+package org.jabref.gui.auximport;
+
+import org.jabref.logic.l10n.Localization;
+import org.jabref.model.auxparser.AuxParserResult;
+
+public class AuxParserResultViewModel {
+
+    private AuxParserResult auxParserResult;
+
+    public AuxParserResultViewModel(AuxParserResult auxParserResult) {
+        this.auxParserResult = auxParserResult;
+    }
+
+    /**
+     * Prints parsing statistics
+     */
+    public String getInformation(boolean includeMissingEntries) {
+        StringBuilder result = new StringBuilder();
+
+        result.append(Localization.lang("keys in library")).append(' ').append(this.auxParserResult.getMasterDatabase().getEntryCount()).append('\n')
+                .append(Localization.lang("found in AUX file")).append(' ').append(this.auxParserResult.getFoundKeysInAux()).append('\n')
+                .append(Localization.lang("resolved")).append(' ').append(this.auxParserResult.getResolvedKeysCount()).append('\n')
+                .append(Localization.lang("not found")).append(' ').append(this.auxParserResult.getUnresolvedKeysCount()).append('\n')
+                .append(Localization.lang("crossreferenced entries included")).append(' ')
+                .append(this.auxParserResult.getCrossRefEntriesCount()).append(Localization.lang("strings included")).append(' ')
+                .append(this.auxParserResult.getInsertedStrings()).append('\n');
+
+        if (includeMissingEntries && (this.auxParserResult.getUnresolvedKeysCount() > 0)) {
+            for (String entry : this.auxParserResult.getUnresolvedKeys()) {
+                result.append(entry).append('\n');
+            }
+        }
+        if (this.auxParserResult.getNestedAuxCount() > 0) {
+            result.append(Localization.lang("nested AUX files")).append(' ').append(this.auxParserResult.getNestedAuxCount());
+        }
+        return result.toString();
+    }
+}

src/main/java/org/jabref/gui/auximport/FromAuxDialog.java

@@ -3,6 +3,7 @@
 import java.awt.BorderLayout;
 import java.awt.event.ActionEvent;
 import java.nio.file.Path;
+import java.nio.file.Paths;
 import java.util.Optional;
 
 import javax.swing.AbstractAction;
@@ -29,10 +30,11 @@
 import org.jabref.gui.keyboard.KeyBinding;
 import org.jabref.gui.util.DefaultTaskExecutor;
 import org.jabref.gui.util.FileDialogConfiguration;
-import org.jabref.logic.auxparser.AuxParser;
-import org.jabref.logic.auxparser.AuxParserResult;
+import org.jabref.logic.auxparser.DefaultAuxParser;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.logic.util.FileType;
+import org.jabref.model.auxparser.AuxParser;
+import org.jabref.model.auxparser.AuxParserResult;
 import org.jabref.model.database.BibDatabase;
 import org.jabref.preferences.JabRefPreferences;
 
@@ -62,7 +64,7 @@ public class FromAuxDialog extends JabRefDialog {
 
     private boolean generatePressed;
 
-    private AuxParser auxParser;
+    private AuxParserResult auxParserResult;
 
     private final JabRefFrame parentFrame;
 
@@ -207,15 +209,15 @@ private void parseActionPerformed() {
         String auxName = auxFileField.getText();
 
         if ((auxName != null) && (refBase != null) && !auxName.isEmpty()) {
-            auxParser = new AuxParser(auxName, refBase);
-            AuxParserResult result = auxParser.parse();
-            notFoundList.setListData(result.getUnresolvedKeys().toArray(new String[result.getUnresolvedKeys().size()]));
-            statusInfos.append(result.getInformation(false));
+            AuxParser auxParser = new DefaultAuxParser(refBase);
+            auxParserResult = auxParser.parse(Paths.get(auxName));
+            notFoundList.setListData(auxParserResult.getUnresolvedKeys().toArray(new String[auxParserResult.getUnresolvedKeys().size()]));
+            statusInfos.append(new AuxParserResultViewModel(auxParserResult).getInformation(false));
 
             generateButton.setEnabled(true);
 
             // the generated database contains no entries -> no active generate-button
-            if (!result.getGeneratedBibDatabase().hasEntries()) {
+            if (!auxParserResult.getGeneratedBibDatabase().hasEntries()) {
                 statusInfos.append("\n" + Localization.lang("empty library"));
                 generateButton.setEnabled(false);
             }
@@ -231,7 +233,7 @@ public boolean generatePressed() {
     }
 
     public BibDatabase getGenerateDB() {
-        return auxParser.parse().getGeneratedBibDatabase();
+        return auxParserResult.getGeneratedBibDatabase();
     }
 
 }

src/main/java/org/jabref/gui/collab/ChangeScanner.java

@@ -123,11 +123,11 @@ public void run() {
 
             // Parse the temporary file.
             ImportFormatPreferences importFormatPreferences = Globals.prefs.getImportFormatPreferences();
-            ParserResult result = OpenDatabase.loadDatabase(tempFile.toFile(), importFormatPreferences);
+            ParserResult result = OpenDatabase.loadDatabase(tempFile.toFile(), importFormatPreferences, Globals.getFileUpdateMonitor());
             databaseInTemp = result.getDatabaseContext();
 
             // Parse the modified file.
-            result = OpenDatabase.loadDatabase(file, importFormatPreferences);
+            result = OpenDatabase.loadDatabase(file, importFormatPreferences, Globals.getFileUpdateMonitor());
             BibDatabaseContext databaseOnDisk = result.getDatabaseContext();
 
             // Start looking at changes.

src/main/java/org/jabref/gui/collab/DatabaseChangeMonitor.java

@@ -10,11 +10,11 @@
 import org.jabref.JabRefExecutorService;
 import org.jabref.gui.BasePanel;
 import org.jabref.gui.SidePaneManager;
-import org.jabref.gui.util.FileUpdateListener;
-import org.jabref.gui.util.FileUpdateMonitor;
 import org.jabref.logic.util.io.FileBasedLock;
 import org.jabref.logic.util.io.FileUtil;
 import org.jabref.model.database.BibDatabaseContext;
+import org.jabref.model.util.FileUpdateListener;
+import org.jabref.model.util.FileUpdateMonitor;
 
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;

src/main/java/org/jabref/gui/entryeditor/EntryEditor.java

@@ -167,7 +167,7 @@ private List<EntryEditorTab> createTabs() {
         tabs.add(new RelatedArticlesTab(Globals.prefs));
 
         // Source tab
-        sourceTab = new SourceTab(bibDatabaseContext, undoManager, Globals.prefs.getLatexFieldFormatterPreferences(), Globals.prefs);
+        sourceTab = new SourceTab(bibDatabaseContext, undoManager, Globals.prefs.getLatexFieldFormatterPreferences(), Globals.prefs, Globals.getFileUpdateMonitor());
         tabs.add(sourceTab);
         return tabs;
     }

src/main/java/org/jabref/gui/entryeditor/SourceTab.java

@@ -32,6 +32,7 @@
 import org.jabref.model.database.BibDatabaseMode;
 import org.jabref.model.entry.BibEntry;
 import org.jabref.model.entry.InternalBibtexFields;
+import org.jabref.model.util.FileUpdateMonitor;
 import org.jabref.preferences.JabRefPreferences;
 
 import de.saxsys.mvvmfx.utils.validation.ObservableRuleBasedValidator;
@@ -51,15 +52,17 @@ public class SourceTab extends EntryEditorTab {
     private UndoManager undoManager;
     private final ObjectProperty<ValidationMessage> sourceIsValid = new SimpleObjectProperty<>();
     private final ObservableRuleBasedValidator sourceValidator = new ObservableRuleBasedValidator(sourceIsValid);
+    private FileUpdateMonitor fileMonitor;
 
-    public SourceTab(BibDatabaseContext bibDatabaseContext, CountingUndoManager undoManager, LatexFieldFormatterPreferences fieldFormatterPreferences, JabRefPreferences preferences) {
+    public SourceTab(BibDatabaseContext bibDatabaseContext, CountingUndoManager undoManager, LatexFieldFormatterPreferences fieldFormatterPreferences, JabRefPreferences preferences, FileUpdateMonitor fileMonitor) {
         this.mode = bibDatabaseContext.getMode();
         this.setText(Localization.lang("%0 source", mode.getFormattedName()));
         this.setTooltip(new Tooltip(Localization.lang("Show/edit %0 source", mode.getFormattedName())));
         this.setGraphic(IconTheme.JabRefIcon.SOURCE.getGraphicNode());
         this.undoManager = undoManager;
         this.fieldFormatterPreferences = fieldFormatterPreferences;
         this.preferences = preferences;
+        this.fileMonitor = fileMonitor;
     }
 
     private static String getSourceString(BibEntry entry, BibDatabaseMode type, LatexFieldFormatterPreferences fieldFormatterPreferences) throws IOException {
@@ -119,7 +122,7 @@ private void storeSource(String text) {
             return;
         }
 
-        BibtexParser bibtexParser = new BibtexParser(preferences.getImportFormatPreferences());
+        BibtexParser bibtexParser = new BibtexParser(preferences.getImportFormatPreferences(), fileMonitor);
         try {
             ParserResult parserResult = bibtexParser.parse(new StringReader(text));
             BibDatabase database = parserResult.getDatabase();

src/main/java/org/jabref/gui/entryeditor/fileannotationtab/FileAnnotationTabController.java

@@ -19,11 +19,11 @@
 import javafx.scene.text.Text;
 
 import org.jabref.gui.AbstractController;
-import org.jabref.gui.util.FileUpdateMonitor;
 import org.jabref.gui.util.ViewModelListCellFactory;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.logic.pdf.FileAnnotationCache;
 import org.jabref.model.entry.BibEntry;
+import org.jabref.model.util.FileUpdateMonitor;
 
 import org.fxmisc.easybind.EasyBind;
 

src/main/java/org/jabref/gui/entryeditor/fileannotationtab/FileAnnotationTabViewModel.java

@@ -18,13 +18,13 @@
 import org.jabref.gui.AbstractViewModel;
 import org.jabref.gui.ClipBoardManager;
 import org.jabref.gui.util.DefaultTaskExecutor;
-import org.jabref.gui.util.FileUpdateListener;
-import org.jabref.gui.util.FileUpdateMonitor;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.logic.pdf.FileAnnotationCache;
 import org.jabref.logic.util.OS;
 import org.jabref.model.entry.BibEntry;
 import org.jabref.model.pdf.FileAnnotation;
+import org.jabref.model.util.FileUpdateListener;
+import org.jabref.model.util.FileUpdateMonitor;
 
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;

src/main/java/org/jabref/gui/groups/GroupDescriptions.java

@@ -94,7 +94,6 @@ public static String getShortDescriptionAllEntriesGroup() {
     }
 
     public static String getShortDescription(SearchGroup searchGroup, boolean showDynamic) {
-
         StringBuilder sb = new StringBuilder();
         sb.append("<b>");
         if (showDynamic) {