LaTeX integration latest changes (#5167)

* Update for adding latest changes (no final version)

* Fix small issues

* Update for improving code

* Add localization keys

* Update styles

* Remove unused code and improve exceptions handling

* Add latest improvements

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

@@ -291,7 +291,7 @@ private List<EntryEditorTab> createTabs() {
         tabs.add(sourceTab);
 
         // LaTeX citations tab
-        tabs.add(new LatexCitationsTab(databaseContext, preferencesService, taskExecutor));
+        tabs.add(new LatexCitationsTab(databaseContext, preferencesService, taskExecutor, dialogService));
 
         return tabs;
     }

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

@@ -1,16 +1,17 @@
 package org.jabref.gui.entryeditor;
 
-import java.nio.file.Path;
 import java.util.Optional;
 import java.util.stream.Collectors;
 
+import javafx.scene.control.Button;
 import javafx.scene.control.ProgressIndicator;
 import javafx.scene.control.ScrollPane;
 import javafx.scene.control.Tooltip;
 import javafx.scene.layout.StackPane;
 import javafx.scene.layout.VBox;
 import javafx.scene.text.Text;
 
+import org.jabref.gui.DialogService;
 import org.jabref.gui.icon.IconTheme;
 import org.jabref.gui.util.TaskExecutor;
 import org.jabref.logic.l10n.Localization;
@@ -27,8 +28,8 @@ public class LatexCitationsTab extends EntryEditorTab {
     private final ProgressIndicator progressIndicator;
 
     public LatexCitationsTab(BibDatabaseContext databaseContext, PreferencesService preferencesService,
-                             TaskExecutor taskExecutor) {
-        this.viewModel = new LatexCitationsTabViewModel(databaseContext, preferencesService, taskExecutor);
+                             TaskExecutor taskExecutor, DialogService dialogService) {
+        this.viewModel = new LatexCitationsTabViewModel(databaseContext, preferencesService, taskExecutor, dialogService);
         this.searchPane = new StackPane();
         this.progressIndicator = new ProgressIndicator();
 
@@ -62,14 +63,25 @@ private void setSearchPane() {
         });
     }
 
+    private VBox getLatexDirectoryBox() {
+        Text latexDirectoryText = new Text(String.format("%n%n%s: %s", Localization.lang("Current search directory"),
+                viewModel.directoryProperty().get()));
+        latexDirectoryText.setStyle("-fx-font-weight: bold;");
+        Button latexDirectoryButton = new Button(Localization.lang("Set LaTeX file directory"));
+        latexDirectoryButton.setOnAction(event -> viewModel.setLatexDirectory());
+
+        return new VBox(15, latexDirectoryText, latexDirectoryButton);
+    }
+
     private ScrollPane getCitationsPane() {
         Text titleText = new Text(Localization.lang("Citations found"));
         titleText.getStyleClass().add("recommendation-heading");
 
         VBox citationsBox = new VBox(20, titleText);
-        Path basePath = viewModel.directoryProperty().get();
         citationsBox.getChildren().addAll(viewModel.getCitationList().stream().map(
-                citation -> citation.getDisplayGraphic(basePath, Optional.empty())).collect(Collectors.toList()));
+                citation -> citation.getDisplayGraphic(viewModel.directoryProperty().get(), Optional.empty())).collect(Collectors.toList()));
+
+        citationsBox.getChildren().add(getLatexDirectoryBox());
 
         ScrollPane citationsPane = new ScrollPane();
         citationsPane.setContent(citationsBox);
@@ -82,13 +94,9 @@ private ScrollPane getNotFoundPane() {
         notFoundTitleText.getStyleClass().add("recommendation-heading");
 
         Text notFoundText = new Text(Localization.lang("No LaTeX files containing this entry were found."));
-        notFoundText.setStyle("-fx-font-size: 110%");
-
-        Text notFoundAdviceText = new Text(Localization.lang(
-                "You can set the LaTeX file directory in the 'Library properties' dialog."));
-        notFoundAdviceText.setStyle("-fx-font-weight: bold;");
+        notFoundText.setStyle("-fx-font-size: 110%;");
 
-        VBox notFoundBox = new VBox(20, notFoundTitleText, notFoundText, notFoundAdviceText);
+        VBox notFoundBox = new VBox(20, notFoundTitleText, notFoundText, getLatexDirectoryBox());
         ScrollPane notFoundPane = new ScrollPane();
         notFoundPane.setContent(notFoundBox);
 
@@ -103,7 +111,7 @@ private ScrollPane getErrorPane() {
         Text errorMessageText = new Text(viewModel.searchErrorProperty().get());
         errorMessageText.setStyle("-fx-font-family: monospace;-fx-font-size: 120%;");
 
-        VBox errorBox = new VBox(20, errorTitleText, errorMessageText);
+        VBox errorBox = new VBox(20, errorTitleText, errorMessageText, getLatexDirectoryBox());
         ScrollPane errorPane = new ScrollPane();
         errorPane.setContent(errorBox);
 

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

@@ -3,7 +3,9 @@
 import java.io.IOException;
 import java.nio.file.Files;
 import java.nio.file.Path;
+import java.util.ArrayList;
 import java.util.List;
+import java.util.Map;
 import java.util.Optional;
 import java.util.concurrent.Future;
 import java.util.stream.Collectors;
@@ -18,8 +20,10 @@
 import javafx.collections.ObservableList;
 
 import org.jabref.gui.AbstractViewModel;
+import org.jabref.gui.DialogService;
 import org.jabref.gui.texparser.CitationViewModel;
 import org.jabref.gui.util.BackgroundTask;
+import org.jabref.gui.util.DirectoryDialogConfiguration;
 import org.jabref.gui.util.TaskExecutor;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.logic.texparser.DefaultTexParser;
@@ -45,17 +49,20 @@ enum Status {
     private final BibDatabaseContext databaseContext;
     private final PreferencesService preferencesService;
     private final TaskExecutor taskExecutor;
+    private final DialogService dialogService;
     private final ObjectProperty<Path> directory;
     private final ObservableList<CitationViewModel> citationList;
     private final ObjectProperty<Status> status;
     private final StringProperty searchError;
     private Future<?> searchTask;
+    private TexParserResult texParserResult;
 
     public LatexCitationsTabViewModel(BibDatabaseContext databaseContext, PreferencesService preferencesService,
-                                      TaskExecutor taskExecutor) {
+                                      TaskExecutor taskExecutor, DialogService dialogService) {
         this.databaseContext = databaseContext;
         this.preferencesService = preferencesService;
         this.taskExecutor = taskExecutor;
+        this.dialogService = dialogService;
         this.directory = new SimpleObjectProperty<>(null);
         this.citationList = FXCollections.observableArrayList();
         this.status = new SimpleObjectProperty<>(Status.IN_PROGRESS);
@@ -95,7 +102,7 @@ private void startSearch(String citeKey) {
                                    .onRunning(() -> status.set(Status.IN_PROGRESS))
                                    .onSuccess(status::set)
                                    .onFailure(error -> {
-                                       searchError.set(String.format("%s%n%n%s", error.getMessage(), error.getCause()));
+                                       searchError.set(error.getMessage());
                                        status.set(Status.ERROR);
                                    })
                                    .executeWith(taskExecutor);
@@ -111,23 +118,53 @@ private void cancelSearch() {
     }
 
     private Status searchAndParse(String citeKey) throws IOException {
-        directory.set(databaseContext.getMetaData().getLaTexFileDirectory(preferencesService.getUser())
-                                     .orElseGet(preferencesService::getWorkingDir));
-        List<Path> texFiles;
-        try (Stream<Path> filesStream = Files.walk(directory.get())) {
-            texFiles = filesStream.filter(path -> path.toFile().isFile() && path.toString().endsWith(TEX_EXT))
-                                  .collect(Collectors.toList());
-        } catch (IOException e) {
-            LOGGER.error("Error searching files", e);
-            throw new IOException("Error searching files", e);
+        Path newDirectory = databaseContext.getMetaData().getLaTexFileDirectory(preferencesService.getUser())
+                                           .orElseGet(preferencesService::getWorkingDir);
+
+        if (texParserResult == null || !newDirectory.equals(directory.get())) {
+            directory.set(newDirectory);
+
+            if (Files.notExists(newDirectory)) {
+                throw new IOException(String.format("Current search directory does not exist: %s", newDirectory));
+            }
+
+            List<Path> texFiles = searchDirectory(newDirectory, new ArrayList<>());
+            texParserResult = new DefaultTexParser().parse(texFiles);
         }
 
-        TexParserResult texParserResult = new DefaultTexParser().parse(citeKey, texFiles);
-        citationList.setAll(texParserResult.getCitations().values().stream().map(CitationViewModel::new).collect(Collectors.toList()));
+        citationList.setAll(texParserResult.getCitationsByKey(citeKey).stream().map(CitationViewModel::new).collect(Collectors.toList()));
 
         return citationList.isEmpty() ? Status.NO_RESULTS : Status.CITATIONS_FOUND;
     }
 
+    private List<Path> searchDirectory(Path directory, List<Path> texFiles) {
+        Map<Boolean, List<Path>> fileListPartition;
+        try (Stream<Path> filesStream = Files.list(directory)) {
+            fileListPartition = filesStream.collect(Collectors.partitioningBy(path -> path.toFile().isDirectory()));
+        } catch (IOException e) {
+            LOGGER.error(String.format("Error searching files: %s", e.getMessage()));
+            return texFiles;
+        }
+
+        List<Path> subDirectories = fileListPartition.get(true);
+        List<Path> files = fileListPartition.get(false)
+                                            .stream()
+                                            .filter(path -> path.toString().endsWith(TEX_EXT))
+                                            .collect(Collectors.toList());
+        texFiles.addAll(files);
+        subDirectories.forEach(subDirectory -> searchDirectory(subDirectory, texFiles));
+
+        return texFiles;
+    }
+
+    public void setLatexDirectory() {
+        DirectoryDialogConfiguration directoryDialogConfiguration = new DirectoryDialogConfiguration.Builder()
+                .withInitialDirectory(directory.get()).build();
+
+        dialogService.showDirectorySelectionDialog(directoryDialogConfiguration).ifPresent(selectedDirectory ->
+                databaseContext.getMetaData().setLaTexFileDirectory(preferencesService.getUser(), selectedDirectory.toAbsolutePath()));
+    }
+
     public boolean shouldShow() {
         return preferencesService.getEntryEditorPreferences().shouldShowLatexCitationsTab();
     }

src/main/java/org/jabref/gui/texparser/ParseTexDialogViewModel.java

@@ -34,9 +34,12 @@
 import de.saxsys.mvvmfx.utils.validation.FunctionBasedValidator;
 import de.saxsys.mvvmfx.utils.validation.ValidationMessage;
 import de.saxsys.mvvmfx.utils.validation.ValidationStatus;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 public class ParseTexDialogViewModel extends AbstractViewModel {
 
+    private static final Logger LOGGER = LoggerFactory.getLogger(ParseTexDialogViewModel.class);
     private static final String TEX_EXT = ".tex";
     private final DialogService dialogService;
     private final TaskExecutor taskExecutor;
@@ -131,7 +134,7 @@ public void searchButtonClicked() {
 
     private FileNodeViewModel searchDirectory(Path directory) throws IOException {
         if (directory == null || !directory.toFile().exists() || !directory.toFile().isDirectory()) {
-            throw new IOException("Error searching an invalid directory");
+            throw new IOException(String.format("Error searching files: %s", directory));
         }
 
         FileNodeViewModel parent = new FileNodeViewModel(directory);
@@ -140,7 +143,8 @@ private FileNodeViewModel searchDirectory(Path directory) throws IOException {
         try (Stream<Path> filesStream = Files.list(directory)) {
             fileListPartition = filesStream.collect(Collectors.partitioningBy(path -> path.toFile().isDirectory()));
         } catch (IOException e) {
-            throw new IOException("Error searching files", e);
+            LOGGER.error(String.format("Error searching files: %s", e.getMessage()));
+            return parent;
         }
 
         List<Path> subDirectories = fileListPartition.get(true);

src/main/java/org/jabref/logic/texparser/DefaultTexParser.java

@@ -2,6 +2,7 @@
 
 import java.io.IOException;
 import java.io.LineNumberReader;
+import java.io.UncheckedIOException;
 import java.nio.channels.ClosedChannelException;
 import java.nio.file.Files;
 import java.nio.file.Path;
@@ -58,56 +59,47 @@ public TexParserResult getTexParserResult() {
 
     @Override
     public TexParserResult parse(String citeString) {
-        matchCitation(null, Paths.get(""), 1, citeString);
+        matchCitation(Paths.get(""), 1, citeString);
         return texParserResult;
     }
 
     @Override
     public TexParserResult parse(Path texFile) {
-        return parse(null, Collections.singletonList(texFile));
+        return parse(Collections.singletonList(texFile));
     }
 
     @Override
     public TexParserResult parse(List<Path> texFiles) {
-        return parse(null, texFiles);
-    }
-
-    /**
-     * Parse a list of TEX files for searching a given entry.
-     *
-     * @param entryKey String that contains the entry key we are searching (null for all entries)
-     * @param texFiles List of Path objects linked to a TEX file
-     * @return a TexParserResult, which contains all data related to the bibliographic entries
-     */
-    public TexParserResult parse(String entryKey, List<Path> texFiles) {
         texParserResult.addFiles(texFiles);
 
         List<Path> referencedFiles = new ArrayList<>();
 
         for (Path file : texFiles) {
+            if (Files.notExists(file)) {
+                LOGGER.error(String.format("File does not exist: %s", file));
+                continue;
+            }
+
             try (LineNumberReader lineNumberReader = new LineNumberReader(Files.newBufferedReader(file))) {
                 for (String line = lineNumberReader.readLine(); line != null; line = lineNumberReader.readLine()) {
                     // Skip comments and blank lines.
                     if (line.isEmpty() || line.charAt(0) == '%') {
                         continue;
                     }
-                    // Skip the citation matching if the line does not contain the given entry to speed up the parsing.
-                    if (entryKey == null || line.contains(entryKey)) {
-                        matchCitation(entryKey, file, lineNumberReader.getLineNumber(), line);
-                    }
+                    matchCitation(file, lineNumberReader.getLineNumber(), line);
                     matchNestedFile(file, texFiles, referencedFiles, line);
                 }
             } catch (ClosedChannelException e) {
-                LOGGER.info("Parsing has been interrupted");
-                return texParserResult;
-            } catch (IOException e) {
-                LOGGER.error("Error opening a TEX file", e);
+                LOGGER.error("Parsing has been interrupted");
+                return null;
+            } catch (IOException | UncheckedIOException e) {
+                LOGGER.error(String.format("Error searching files: %s", e.getMessage()));
             }
         }
 
         // Parse all files referenced by TEX files, recursively.
         if (!referencedFiles.isEmpty()) {
-            parse(entryKey, referencedFiles);
+            parse(referencedFiles);
         }
 
         return texParserResult;
@@ -116,12 +108,11 @@ public TexParserResult parse(String entryKey, List<Path> texFiles) {
     /**
      * Find cites along a specific line and store them.
      */
-    private void matchCitation(String entryKey, Path file, int lineNumber, String line) {
+    private void matchCitation(Path file, int lineNumber, String line) {
         Matcher citeMatch = CITE_PATTERN.matcher(line);
 
         while (citeMatch.find()) {
             Arrays.stream(citeMatch.group(CITE_GROUP).split(","))
-                  .filter(key -> entryKey == null || key.equals(entryKey))
                   .forEach(key -> texParserResult.addKey(key, file, lineNumber, citeMatch.start(), citeMatch.end(), line));
         }
     }
@@ -133,16 +124,12 @@ private void matchNestedFile(Path file, List<Path> texFiles, List<Path> referenc
         Matcher includeMatch = INCLUDE_PATTERN.matcher(line);
 
         while (includeMatch.find()) {
-            StringBuilder include = new StringBuilder(includeMatch.group(INCLUDE_GROUP));
-
-            if (!include.toString().endsWith(TEX_EXT)) {
-                include.append(TEX_EXT);
-            }
+            String include = includeMatch.group(INCLUDE_GROUP);
 
-            Path folder = file.getParent();
-            Path inputFile = (folder == null)
-                    ? Paths.get(include.toString())
-                    : folder.resolve(include.toString());
+            Path inputFile = file.toAbsolutePath().getParent().resolve(
+                    include.endsWith(TEX_EXT)
+                            ? include
+                            : String.format("%s%s", include, TEX_EXT));
 
             if (!texFiles.contains(inputFile)) {
                 referencedFiles.add(inputFile);

src/main/resources/l10n/JabRef_en.properties

@@ -2120,5 +2120,6 @@ Search\ citations\ for\ this\ entry\ in\ LaTeX\ files=Search citations for this
 Citations\ found=Citations found
 No\ citations\ found=No citations found
 No\ LaTeX\ files\ containing\ this\ entry\ were\ found.=No LaTeX files containing this entry were found.
-You\ can\ set\ the\ LaTeX\ file\ directory\ in\ the\ 'Library\ properties'\ dialog.=You can set the LaTeX file directory in the 'Library properties' dialog.
 Selected\ entry\ does\ not\ have\ an\ associated\ BibTeX\ key.=Selected entry does not have an associated BibTeX key.
+Current\ search\ directory=Current search directory
+Set\ LaTeX\ file\ directory=Set LaTeX file directory