Relativizes paths to aux files (#4792)

* Relativizes paths to aux files

* relativize code shifted to FileHelper

* changes

* Shortens text fields in Required Fields Tab

* Removing irrelevant changes

* Implemented requested changes

* Implemented changes

* Delete irrelevant code

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

@@ -1,8 +1,10 @@
 package org.jabref.gui.groups;
 
 import java.io.IOException;
+import java.nio.file.Path;
 import java.nio.file.Paths;
 import java.util.ArrayList;
+import java.util.List;
 import java.util.Optional;
 import java.util.regex.Pattern;
 import java.util.regex.PatternSyntaxException;
@@ -45,6 +47,7 @@
 import org.jabref.logic.l10n.Localization;
 import org.jabref.logic.search.SearchQuery;
 import org.jabref.logic.util.StandardFileType;
+import org.jabref.logic.util.io.FileUtil;
 import org.jabref.model.database.BibDatabase;
 import org.jabref.model.entry.FieldName;
 import org.jabref.model.entry.Keyword;
@@ -58,6 +61,7 @@
 import org.jabref.model.groups.SearchGroup;
 import org.jabref.model.groups.TexGroup;
 import org.jabref.model.groups.WordKeywordGroup;
+import org.jabref.model.metadata.MetaData;
 import org.jabref.model.strings.StringUtil;
 import org.jabref.preferences.JabRefPreferences;
 
@@ -90,6 +94,7 @@ class GroupDialog extends BaseDialog<AbstractGroup> {
     private final RadioButton unionButton = new RadioButton(Localization.lang("Include subgroups: When selected, view entries contained in this group or its subgroups"));
     private final DialogService dialogService;
     private final JabRefPreferences prefs;
+    private final BasePanel basePanel;
 
     // for KeywordGroup
     private final TextField keywordGroupSearchTerm = new TextField();
@@ -144,6 +149,7 @@ public GroupDialog(DialogService dialogService, BasePanel basePanel, JabRefPrefe
 
         this.dialogService = dialogService;
         this.prefs = prefs;
+        this.basePanel = basePanel;
 
         // set default values (overwritten if editedGroup != null)
         keywordGroupSearchField.setText(prefs.get(JabRefPreferences.GROUPS_DEFAULT_FIELD));
@@ -330,7 +336,7 @@ groupName, getContext(),
                         }
                     } else if (texRadioButton.isSelected()) {
                         resultingGroup = new TexGroup(groupName, getContext(),
-                                Paths.get(texGroupFilePath.getText().trim()), new DefaultAuxParser(new BibDatabase()), Globals.getFileUpdateMonitor());
+                                                      Paths.get(texGroupFilePath.getText().trim()), new DefaultAuxParser(new BibDatabase()), Globals.getFileUpdateMonitor(), basePanel.getBibDatabaseContext().getMetaData());
                     }
 
                     resultingGroup.setColor(colorField.getValue());
@@ -610,7 +616,21 @@ private void openBrowseDialog() {
             .addExtensionFilter(StandardFileType.AUX)
             .withDefaultExtension(StandardFileType.AUX)
             .withInitialDirectory(Globals.prefs.get(JabRefPreferences.WORKING_DIRECTORY)).build();
-        dialogService.showFileOpenDialog(fileDialogConfiguration).ifPresent(file -> texGroupFilePath.setText(file.toAbsolutePath().toString()));
+        dialogService.showFileOpenDialog(fileDialogConfiguration).ifPresent(file -> texGroupFilePath.setText(relativize(file.toAbsolutePath()).toString()));
+    }
+
+    private Path relativize(Path path) {
+        List<Path> fileDirectories = getFileDirectoriesAsPaths();
+        return FileUtil.relativize(path, fileDirectories);
+    }
+
+    private List<Path> getFileDirectoriesAsPaths() {
+        List<Path> fileDirs = new ArrayList<>();
+        MetaData metaData = basePanel.getBibDatabaseContext().getMetaData();
+        metaData.getLaTexFileDirectory(prefs.getFilePreferences().getUser())
+                .ifPresent(laTexFileDirectory -> fileDirs.add(laTexFileDirectory));
+
+        return fileDirs;
     }
 
     private String fromTextFlowToHTMLString(TextFlow textFlow) {

src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesDialog.fxml

@@ -26,6 +26,7 @@
                         <RowConstraints minHeight="10.0" prefHeight="30.0" vgrow="SOMETIMES" />
                         <RowConstraints minHeight="-Infinity" prefHeight="50.0" vgrow="SOMETIMES" />
                         <RowConstraints minHeight="10.0" prefHeight="30.0" vgrow="ALWAYS" />
+                        <RowConstraints minHeight="10.0" prefHeight="30.0" vgrow="ALWAYS" />
                         <RowConstraints minHeight="10.0" prefHeight="30.0" vgrow="SOMETIMES" />
                         <RowConstraints minHeight="-Infinity" prefHeight="50.0" vgrow="ALWAYS" />
                         <RowConstraints minHeight="10.0" prefHeight="30.0" vgrow="SOMETIMES" />
@@ -40,10 +41,13 @@
                         <Label text="%User-specific file directory" GridPane.rowIndex="3" />
                         <TextField fx:id="userSpecificFileDirectory" GridPane.columnIndex="1" GridPane.rowIndex="3" />
                         <Button fx:id="browseUserSpefiicFileDir" mnemonicParsing="false" onAction="#browseUserSpecificFileDirectory" text="%Browse" GridPane.columnIndex="2" GridPane.rowIndex="3" />
+                        <Label text="%LaTex file directory" GridPane.rowIndex="4" />
+                        <TextField fx:id="laTexFileDirectory" GridPane.columnIndex="1" GridPane.rowIndex="4" />
+                        <Button fx:id="browseLatexFileDir" mnemonicParsing="false" onAction="#browseLaTexFileDirectory" text="%Browse" GridPane.columnIndex="2" GridPane.rowIndex="4" />
                         <Label alignment="TOP_LEFT" styleClass="sectionHeader" text="%Override default file directories" GridPane.columnSpan="3" GridPane.rowIndex="1" />
-                        <Label alignment="TOP_LEFT" styleClass="sectionHeader" text="%Library protection" GridPane.columnSpan="3" GridPane.rowIndex="4" />
-                        <CheckBox fx:id="protect" mnemonicParsing="false" text="%Refuse to save the library before external changes have been reviewed." GridPane.columnSpan="3" GridPane.rowIndex="5" />
-                        <Label styleClass="sectionHeader" text="%Export sort order" GridPane.rowIndex="6" />
+                        <Label alignment="TOP_LEFT" styleClass="sectionHeader" text="%Library protection" GridPane.columnSpan="3" GridPane.rowIndex="5" />
+                        <CheckBox fx:id="protect" mnemonicParsing="false" text="%Refuse to save the library before external changes have been reviewed." GridPane.columnSpan="3" GridPane.rowIndex="6" />
+                        <Label styleClass="sectionHeader" text="%Export sort order" GridPane.rowIndex="7" />
                     </children>
                 </GridPane>
             </children>

src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesDialogView.java

@@ -1,6 +1,7 @@
 package org.jabref.gui.libraryproperties;
 
 import java.nio.charset.Charset;
+import java.nio.file.Paths;
 import java.util.Optional;
 
 import javax.inject.Inject;
@@ -36,6 +37,7 @@ public class LibraryPropertiesDialogView extends BaseDialog<Void> {
     @FXML private Button browseGeneralFileDir;
     @FXML private TextField userSpecificFileDirectory;
     @FXML private Button browseUserSpefiicFileDir;
+    @FXML private TextField laTexFileDirectory;
     @FXML private CheckBox protect;
     @Inject private PreferencesService preferencesService;
 
@@ -70,6 +72,7 @@ private void initialize() {
 
         generalFileDirectory.textProperty().bindBidirectional(viewModel.generalFileDirectoryPropertyProperty());
         userSpecificFileDirectory.textProperty().bindBidirectional(viewModel.userSpecificFileDirectoryProperty());
+        laTexFileDirectory.textProperty().bindBidirectional(viewModel.LaTexFileDirectoryProperty());
 
         encoding.itemsProperty().bind(viewModel.encodingsProperty());
         encoding.valueProperty().bindBidirectional(viewModel.selectedEncodingProperty());
@@ -112,6 +115,11 @@ public void browseUserSpecificFileDirectory(ActionEvent event) {
         viewModel.browseUserDir();
     }
 
+    @FXML
+    void browseLaTexFileDirectory(ActionEvent event) {
+        viewModel.browseLaTexDir();
+    }
+
     private void storeSettings() {
         //FIXME: Move to viewModel until fieldFormatterCleanupsPanel is property implemented
         MetaData metaData = panel.getBibDatabaseContext().getMetaData();
@@ -134,6 +142,13 @@ private void storeSettings() {
             metaData.setUserFileDirectory(preferencesService.getUser(), text);
         }
 
+        text = viewModel.LaTexFileDirectoryProperty().getValue();
+        if (text.isEmpty()) {
+            metaData.clearLaTexFileDirectory(preferencesService.getUser());
+        } else {
+            metaData.setLaTexFileDirectory(preferencesService.getUser(), Paths.get(text));
+        }
+
         if (viewModel.libraryProtectedProperty().getValue()) {
             metaData.markAsProtected();
         } else {
@@ -165,7 +180,7 @@ private void storeSettings() {
 
         boolean changed = saveOrderConfigChanged || encodingChanged
                           || viewModel.generalFileDirChanged() || viewModel.userFileDirChanged()
-                          || viewModel.protectedValueChanged() || saveActionsChanged;
+                          || viewModel.protectedValueChanged() || saveActionsChanged || viewModel.LaTexFileDirChanged();
         // ... if so, mark base changed. Prevent the Undo button from removing
         // change marking:
         if (changed) {

src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesDialogViewModel.java

@@ -1,6 +1,7 @@
 package org.jabref.gui.libraryproperties;
 
 import java.nio.charset.Charset;
+import java.nio.file.Path;
 import java.util.Optional;
 
 import javafx.beans.property.BooleanProperty;
@@ -25,6 +26,7 @@ public class LibraryPropertiesDialogViewModel {
 
     private final StringProperty generalFileDirectoryProperty = new SimpleStringProperty("");
     private final StringProperty userSpecificFileDirectoryProperty = new SimpleStringProperty("");
+    private final StringProperty laTexFileDirectoryProperty = new SimpleStringProperty("");
     private final ListProperty<Charset> encodingsProperty = new SimpleListProperty<>(FXCollections.observableArrayList(Encodings.getCharsets()));
     private final ObjectProperty<Charset> selectedEncodingPropety = new SimpleObjectProperty<>(Encodings.getCharsets().get(0));
     private final BooleanProperty libraryProtectedProperty = new SimpleBooleanProperty();
@@ -36,6 +38,7 @@ public class LibraryPropertiesDialogViewModel {
 
     private final String oldUserSpecificFileDir;
     private final String oldGeneralFileDir;
+    private final String oldLaTexFileDir;
     private final boolean oldLibraryProtected;
 
     public LibraryPropertiesDialogViewModel(BasePanel panel, DialogService dialogService, PreferencesService preferencesService) {
@@ -59,8 +62,11 @@ public LibraryPropertiesDialogViewModel(BasePanel panel, DialogService dialogSer
         Optional<String> fileDI = metaData.getUserFileDirectory(preferencesService.getUser());
         fileDI.ifPresent(userSpecificFileDirectoryProperty::setValue);
 
+        metaData.getLaTexFileDirectory(preferencesService.getUser()).map(Path::toString).ifPresent(laTexFileDirectoryProperty::setValue);
+
         oldUserSpecificFileDir = generalFileDirectoryProperty.getValue();
         oldGeneralFileDir = userSpecificFileDirectoryProperty.getValue();
+        oldLaTexFileDir = laTexFileDirectoryProperty.getValue();
 
         libraryProtectedProperty.setValue(metaData.isProtected());
         oldLibraryProtected = libraryProtectedProperty.getValue();
@@ -74,6 +80,10 @@ public StringProperty userSpecificFileDirectoryProperty() {
         return this.userSpecificFileDirectoryProperty;
     }
 
+    public StringProperty LaTexFileDirectoryProperty() {
+        return this.laTexFileDirectoryProperty;
+    }
+
     public ListProperty<Charset> encodingsProperty() {
         return this.encodingsProperty;
     }
@@ -90,6 +100,10 @@ public void browseUserDir() {
         dialogService.showDirectorySelectionDialog(directoryDialogConfiguration).ifPresent(dir -> userSpecificFileDirectoryProperty.setValue(dir.toAbsolutePath().toString()));
     }
 
+    public void browseLaTexDir() {
+        dialogService.showDirectorySelectionDialog(directoryDialogConfiguration).ifPresent(dir -> laTexFileDirectoryProperty.setValue(dir.toAbsolutePath().toString()));
+    }
+
     public BooleanProperty libraryProtectedProperty() {
         return this.libraryProtectedProperty;
     }
@@ -102,6 +116,10 @@ public boolean userFileDirChanged() {
         return !oldUserSpecificFileDir.equals(userSpecificFileDirectoryProperty.getValue());
     }
 
+    public boolean LaTexFileDirChanged() {
+        return !oldLaTexFileDir.equals(laTexFileDirectoryProperty.getValue());
+    }
+
     public boolean protectedValueChanged() {
         return !oldLibraryProtected == libraryProtectedProperty.getValue();
     }
@@ -113,4 +131,5 @@ public BooleanProperty encodingDisableProperty() {
     public BooleanProperty protectDisableProperty() {
         return protectDisableProperty;
     }
+
 }

src/main/java/org/jabref/logic/exporter/MetaDataSerializer.java

@@ -43,6 +43,8 @@ public static Map<String, String> getSerializedStringMap(MetaData metaData,
                 path -> stringyMetaData.put(MetaData.FILE_DIRECTORY, Collections.singletonList(path.trim())));
         metaData.getUserFileDirectories().forEach((user, path) -> stringyMetaData
                 .put(MetaData.FILE_DIRECTORY + '-' + user, Collections.singletonList(path.trim())));
+        metaData.getLaTexFileDirectories().forEach((user, path) -> stringyMetaData
+                .put(MetaData.FILE_DIRECTORY + "Latex-" + user, Collections.singletonList(path.toString().trim())));
 
         for (ContentSelector selector: metaData.getContentSelectorList()) {
                 stringyMetaData.put(MetaData.SELECTOR_META_PREFIX + selector.getFieldName(), selector.getValues());

src/main/java/org/jabref/logic/importer/util/GroupsParser.java

@@ -24,6 +24,7 @@
 import org.jabref.model.groups.SearchGroup;
 import org.jabref.model.groups.TexGroup;
 import org.jabref.model.groups.WordKeywordGroup;
+import org.jabref.model.metadata.MetaData;
 import org.jabref.model.strings.StringUtil;
 import org.jabref.model.util.FileUpdateMonitor;
 
@@ -35,7 +36,7 @@ public class GroupsParser {
     private GroupsParser() {
     }
 
-    public static GroupTreeNode importGroups(List<String> orderedData, Character keywordSeparator, FileUpdateMonitor fileMonitor)
+    public static GroupTreeNode importGroups(List<String> orderedData, Character keywordSeparator, FileUpdateMonitor fileMonitor, MetaData metaData)
             throws ParseException {
         try {
             GroupTreeNode cursor = null;
@@ -52,7 +53,7 @@ public static GroupTreeNode importGroups(List<String> orderedData, Character key
                     throw new ParseException("Expected \"" + string + "\" to contain whitespace");
                 }
                 int level = Integer.parseInt(string.substring(0, spaceIndex));
-                AbstractGroup group = GroupsParser.fromString(string.substring(spaceIndex + 1), keywordSeparator, fileMonitor);
+                AbstractGroup group = GroupsParser.fromString(string.substring(spaceIndex + 1), keywordSeparator, fileMonitor, metaData);
                 GroupTreeNode newNode = GroupTreeNode.fromGroup(group);
                 if (cursor == null) {
                     // create new root
@@ -84,7 +85,7 @@ public static GroupTreeNode importGroups(List<String> orderedData, Character key
      * @throws ParseException If an error occurred and a group could not be created,
      *                        e.g. due to a malformed regular expression.
      */
-    public static AbstractGroup fromString(String s, Character keywordSeparator, FileUpdateMonitor fileMonitor)
+    public static AbstractGroup fromString(String s, Character keywordSeparator, FileUpdateMonitor fileMonitor, MetaData metaData)
             throws ParseException {
         if (s.startsWith(MetadataSerializationConfiguration.KEYWORD_GROUP_ID)) {
             return keywordGroupFromString(s, keywordSeparator);
@@ -108,21 +109,21 @@ public static AbstractGroup fromString(String s, Character keywordSeparator, Fil
             return automaticKeywordGroupFromString(s);
         }
         if (s.startsWith(MetadataSerializationConfiguration.TEX_GROUP_ID)) {
-            return texGroupFromString(s, fileMonitor);
+            return texGroupFromString(s, fileMonitor, metaData);
         }
 
         throw new ParseException("Unknown group: " + s);
     }
 
-    private static AbstractGroup texGroupFromString(String string, FileUpdateMonitor fileMonitor) throws ParseException {
+    private static AbstractGroup texGroupFromString(String string, FileUpdateMonitor fileMonitor, MetaData metaData) throws ParseException {
         QuotedStringTokenizer tok = new QuotedStringTokenizer(string.substring(MetadataSerializationConfiguration.TEX_GROUP_ID
                 .length()), MetadataSerializationConfiguration.GROUP_UNIT_SEPARATOR, MetadataSerializationConfiguration.GROUP_QUOTE_CHAR);
 
         String name = StringUtil.unquote(tok.nextToken(), MetadataSerializationConfiguration.GROUP_QUOTE_CHAR);
         GroupHierarchyType context = GroupHierarchyType.getByNumberOrDefault(Integer.parseInt(tok.nextToken()));
         try {
             Path path = Paths.get(tok.nextToken());
-            TexGroup newGroup = new TexGroup(name, context, path, new DefaultAuxParser(new BibDatabase()), fileMonitor);
+            TexGroup newGroup = new TexGroup(name, context, path, new DefaultAuxParser(new BibDatabase()), fileMonitor, metaData);
             addGroupDetails(tok, newGroup);
             return newGroup;
         } catch (InvalidPathException | IOException ex) {

src/main/java/org/jabref/logic/importer/util/MetaDataParser.java

@@ -3,6 +3,8 @@
 import java.io.IOException;
 import java.io.Reader;
 import java.io.StringReader;
+import java.nio.file.Path;
+import java.nio.file.Paths;
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.HashMap;
@@ -60,12 +62,18 @@ public MetaData parse(MetaData metaData, Map<String, String> data, Character key
             } else if (entry.getKey().startsWith(MetaData.SELECTOR_META_PREFIX)) {
                 metaData.addContentSelector(ContentSelectors.parse(entry.getKey().substring(MetaData.SELECTOR_META_PREFIX.length()), StringUtil.unquote(entry.getValue(), MetaData.ESCAPE_CHARACTER)));
                 continue;
+            } else if (entry.getKey().startsWith(MetaData.FILE_DIRECTORY + "Latex-")) {
+                // The user name comes directly after "FILE_DIRECTORYLatex-"
+                String user = entry.getKey().substring(MetaData.FILE_DIRECTORY.length() + 6);
+                Path path = Paths.get(getSingleItem(value)).normalize();
+                metaData.setLaTexFileDirectory(user, path);
+                continue;
             }
 
             switch (entry.getKey()) {
                 case MetaData.GROUPSTREE:
                 case MetaData.GROUPSTREE_LEGACY:
-                    metaData.setGroups(GroupsParser.importGroups(value, keywordSeparator, fileMonitor));
+                    metaData.setGroups(GroupsParser.importGroups(value, keywordSeparator, fileMonitor, metaData));
                     break;
                 case MetaData.SAVE_ACTIONS:
                     metaData.setSaveActions(Cleanups.parse(value));

src/main/java/org/jabref/model/database/BibDatabaseContext.java

@@ -185,7 +185,7 @@ public Optional<Path> getFirstExistingFileDir(FilePreferences preferences) {
      * metadata can specify a general directory and/or a user-specific directory or the preferences can specify one. <p>
      * The settings are prioritized in the following order and the first defined setting is used:
      * <ol>
-     *     <li>metdata</li>
+     *     <li>metadata</li>
      *     <li>user-specific directory</li>
      *     <li>preferences directory</li>
      *     <li>BIB file directory</li>