Merge remote-tracking branch 'upstream/master' into writebackupToTemp

* upstream/master:
  Arch fix (#6825)

build.gradle

@@ -210,6 +210,7 @@ dependencies {
     testImplementation 'org.mockito:mockito-core:3.5.7'
     testImplementation 'org.xmlunit:xmlunit-core:2.7.0'
     testImplementation 'org.xmlunit:xmlunit-matchers:2.7.0'
+    testRuntime 'com.tngtech.archunit:archunit-junit5-engine:0.14.1'
     testImplementation 'com.tngtech.archunit:archunit-junit5-api:0.14.1'
     testImplementation "org.testfx:testfx-core:4.0.17-alpha-SNAPSHOT"
     testImplementation "org.testfx:testfx-junit5:4.0.17-alpha-SNAPSHOT"
@@ -442,6 +443,11 @@ test {
         excludeTags 'DatabaseTest', 'FetcherTest', 'GUITest'
     }
 
+    moduleOptions {
+        // TODO: Remove this as soon as archunit is modularized
+        runOnClasspath = true
+    }
+
     testLogging {
         // set options for log level LIFECYCLE
         // for debugging tests: add "STANDARD_OUT", "STANDARD_ERROR"

docs/adr/0015-allow-model-access-logic.md

@@ -0,0 +1,40 @@
+# Allow org.jabref.model to access org.jabref.logic
+
+## Context and Problem Statement
+
+- How to create a maintainable architecture?
+- How to split model, logic, and UI
+
+## Decision Drivers
+
+- New comers should find the architecture "split" natural
+- The architecture should be a help (and not a burden)
+
+## Considered Options
+
+- `org.jabref.model` uses `org.jabref.model` (and external libraries) only
+- `org.jabref.model` may use `org.jabref.logic` in defined cases
+- `org.jabref.model` and `org.jabref.logic` may access each other freely
+
+## Decision Outcome
+
+Chosen option: "`org.jabref.model` may use `org.jabref.logic` in defined cases", because comes out best \(see below\).
+
+## Pros and Cons of the Options
+
+### `org.jabref.model` uses `org.jabref.model` (and external libraries) only
+
+- Good, because clear separation of model and logic
+- Bad, because this leads to an [Anemic Domain Model](https://martinfowler.com/bliki/AnemicDomainModel.html)
+
+### `org.jabref.model` may use `org.jabref.logic` in defined cases
+
+- Good, because model and logic are still separated
+- Neutral, because each exception has to be discussed and agreed
+- Bad, because new comers have to be informed that there are certain (agreed) exceptions for model to access logic
+
+### `org.jabref.model` and `org.jabref.logic` may access each other freely
+
+- Bad, because may lead to spaghetti code
+- Bad, because coupling between model and logic is increased
+- Bad, because cohesion inside model is decreased

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

@@ -23,9 +23,9 @@
 import org.jabref.logic.importer.OpenDatabase;
 import org.jabref.logic.importer.ParserResult;
 import org.jabref.logic.l10n.Localization;
+import org.jabref.logic.shared.DatabaseNotSupportedException;
 import org.jabref.logic.shared.exception.InvalidDBMSConnectionPropertiesException;
 import org.jabref.logic.shared.exception.NotASharedDatabaseException;
-import org.jabref.model.database.shared.DatabaseNotSupportedException;
 import org.jabref.preferences.JabRefPreferences;
 
 import impl.org.controlsfx.skin.DecorationPane;

src/main/java/org/jabref/architecture/AllowedToUseLogic.java

@@ -0,0 +1,10 @@
+package org.jabref.architecture;
+
+/**
+ * Annotation to indicate that this logic class can be used in the model package.
+ */
+public @interface AllowedToUseLogic {
+
+    // The rationale
+    String value();
+}

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

@@ -3,9 +3,9 @@
 import java.nio.file.Path;
 
 import org.jabref.gui.auximport.AuxParserResultViewModel;
+import org.jabref.logic.auxparser.AuxParser;
+import org.jabref.logic.auxparser.AuxParserResult;
 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;
 

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

@@ -33,14 +33,14 @@
 import org.jabref.logic.l10n.Localization;
 import org.jabref.logic.pdf.FileAnnotationCache;
 import org.jabref.logic.search.SearchQuery;
+import org.jabref.logic.shared.DatabaseLocation;
 import org.jabref.logic.util.UpdateField;
 import org.jabref.model.FieldChange;
 import org.jabref.model.database.BibDatabase;
 import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.database.event.BibDatabaseContextChangedEvent;
 import org.jabref.model.database.event.EntriesAddedEvent;
 import org.jabref.model.database.event.EntriesRemovedEvent;
-import org.jabref.model.database.shared.DatabaseLocation;
 import org.jabref.model.entry.BibEntry;
 import org.jabref.model.entry.event.EntriesEventSource;
 import org.jabref.model.entry.event.EntryChangedEvent;

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

@@ -128,13 +128,13 @@
 import org.jabref.logic.importer.ParserResult;
 import org.jabref.logic.importer.WebFetchers;
 import org.jabref.logic.l10n.Localization;
+import org.jabref.logic.shared.DatabaseLocation;
 import org.jabref.logic.undo.AddUndoableActionEvent;
 import org.jabref.logic.undo.UndoChangeEvent;
 import org.jabref.logic.undo.UndoRedoEvent;
 import org.jabref.logic.util.OS;
 import org.jabref.logic.util.io.FileUtil;
 import org.jabref.model.database.BibDatabaseContext;
-import org.jabref.model.database.shared.DatabaseLocation;
 import org.jabref.model.entry.BibEntry;
 import org.jabref.model.entry.field.SpecialField;
 import org.jabref.model.entry.field.StandardField;

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

@@ -1,7 +1,7 @@
 package org.jabref.gui.auximport;
 
+import org.jabref.logic.auxparser.AuxParserResult;
 import org.jabref.logic.l10n.Localization;
-import org.jabref.model.auxparser.AuxParserResult;
 
 public class AuxParserResultViewModel {
 

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

@@ -16,11 +16,11 @@
 import org.jabref.gui.JabRefFrame;
 import org.jabref.gui.util.BaseDialog;
 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.StandardFileType;
-import org.jabref.model.auxparser.AuxParser;
-import org.jabref.model.auxparser.AuxParserResult;
 import org.jabref.model.database.BibDatabase;
 import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.preferences.PreferencesService;

src/main/java/org/jabref/gui/citationkeypattern/CitationKeyPatternDialog.java

@@ -5,8 +5,8 @@
 import org.jabref.Globals;
 import org.jabref.gui.BasePanel;
 import org.jabref.gui.util.BaseDialog;
+import org.jabref.logic.citationkeypattern.AbstractCitationKeyPattern;
 import org.jabref.logic.l10n.Localization;
-import org.jabref.model.bibtexkeypattern.AbstractCitationKeyPattern;
 import org.jabref.model.metadata.MetaData;
 
 public class CitationKeyPatternDialog extends BaseDialog<Void> {

src/main/java/org/jabref/gui/citationkeypattern/CitationKeyPatternPanel.java

@@ -15,10 +15,10 @@
 import org.jabref.gui.actions.ActionFactory;
 import org.jabref.gui.actions.StandardActions;
 import org.jabref.gui.help.HelpAction;
+import org.jabref.logic.citationkeypattern.AbstractCitationKeyPattern;
+import org.jabref.logic.citationkeypattern.DatabaseCitationKeyPattern;
 import org.jabref.logic.help.HelpFile;
 import org.jabref.logic.l10n.Localization;
-import org.jabref.model.bibtexkeypattern.AbstractCitationKeyPattern;
-import org.jabref.model.bibtexkeypattern.DatabaseCitationKeyPattern;
 import org.jabref.model.database.BibDatabaseMode;
 import org.jabref.model.entry.BibEntryType;
 import org.jabref.model.entry.types.EntryType;

src/main/java/org/jabref/gui/cleanup/CleanupDialog.java

@@ -6,7 +6,7 @@
 import org.jabref.logic.cleanup.CleanupPreset;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.model.database.BibDatabaseContext;
-import org.jabref.model.metadata.FilePreferences;
+import org.jabref.preferences.FilePreferences;
 
 public class CleanupDialog extends BaseDialog<CleanupPreset> {
 

src/main/java/org/jabref/gui/cleanup/CleanupPresetPanel.java

@@ -14,11 +14,11 @@
 
 import org.jabref.gui.commonfxcontrols.FieldFormatterCleanupsPanel;
 import org.jabref.logic.cleanup.CleanupPreset;
+import org.jabref.logic.cleanup.FieldFormatterCleanups;
 import org.jabref.logic.l10n.Localization;
-import org.jabref.model.cleanup.FieldFormatterCleanups;
 import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.entry.field.StandardField;
-import org.jabref.model.metadata.FilePreferences;
+import org.jabref.preferences.FilePreferences;
 
 import com.airhacks.afterburner.views.ViewLoader;
 

src/main/java/org/jabref/gui/commonfxcontrols/CitationKeyPatternPanel.java

@@ -13,8 +13,8 @@
 
 import org.jabref.gui.icon.IconTheme;
 import org.jabref.gui.util.ValueTableCellFactory;
+import org.jabref.logic.citationkeypattern.AbstractCitationKeyPattern;
 import org.jabref.logic.l10n.Localization;
-import org.jabref.model.bibtexkeypattern.AbstractCitationKeyPattern;
 import org.jabref.model.entry.BibEntryType;
 import org.jabref.model.entry.types.EntryType;
 import org.jabref.preferences.PreferencesService;

src/main/java/org/jabref/gui/commonfxcontrols/CitationKeyPatternPanelViewModel.java

@@ -9,8 +9,8 @@
 import javafx.beans.property.SimpleObjectProperty;
 import javafx.collections.FXCollections;
 
+import org.jabref.logic.citationkeypattern.AbstractCitationKeyPattern;
 import org.jabref.logic.l10n.Localization;
-import org.jabref.model.bibtexkeypattern.AbstractCitationKeyPattern;
 import org.jabref.model.entry.BibEntryType;
 import org.jabref.model.entry.types.EntryType;
 import org.jabref.preferences.PreferencesService;

src/main/java/org/jabref/gui/commonfxcontrols/FieldFormatterCleanupsPanel.java

@@ -18,9 +18,9 @@
 import org.jabref.gui.util.FieldsUtil;
 import org.jabref.gui.util.ValueTableCellFactory;
 import org.jabref.gui.util.ViewModelListCellFactory;
+import org.jabref.logic.cleanup.FieldFormatterCleanup;
+import org.jabref.logic.cleanup.Formatter;
 import org.jabref.logic.l10n.Localization;
-import org.jabref.model.cleanup.FieldFormatterCleanup;
-import org.jabref.model.cleanup.Formatter;
 import org.jabref.model.entry.field.Field;
 
 import com.airhacks.afterburner.views.ViewLoader;

src/main/java/org/jabref/gui/commonfxcontrols/FieldFormatterCleanupsPanelViewModel.java

@@ -12,8 +12,8 @@
 import org.jabref.Globals;
 import org.jabref.gui.util.NoSelectionModel;
 import org.jabref.logic.cleanup.Cleanups;
-import org.jabref.model.cleanup.FieldFormatterCleanup;
-import org.jabref.model.cleanup.Formatter;
+import org.jabref.logic.cleanup.FieldFormatterCleanup;
+import org.jabref.logic.cleanup.Formatter;
 import org.jabref.model.entry.field.Field;
 import org.jabref.model.entry.field.FieldFactory;
 

src/main/java/org/jabref/gui/exporter/SaveDatabaseAction.java

@@ -30,12 +30,12 @@
 import org.jabref.logic.exporter.SavePreferences;
 import org.jabref.logic.l10n.Encodings;
 import org.jabref.logic.l10n.Localization;
+import org.jabref.logic.shared.DatabaseLocation;
 import org.jabref.logic.shared.prefs.SharedDatabasePreferences;
 import org.jabref.logic.util.DelayTaskThrottler;
 import org.jabref.logic.util.StandardFileType;
 import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.database.event.ChangePropagation;
-import org.jabref.model.database.shared.DatabaseLocation;
 import org.jabref.model.entry.BibEntryTypesManager;
 import org.jabref.preferences.JabRefPreferences;
 

src/main/java/org/jabref/gui/externalfiles/AutoSetFileLinksUtil.java

@@ -14,17 +14,17 @@
 import org.jabref.gui.undo.NamedCompound;
 import org.jabref.gui.undo.UndoableFieldChange;
 import org.jabref.gui.util.DefaultTaskExecutor;
+import org.jabref.logic.bibtex.FileFieldWriter;
 import org.jabref.logic.util.io.AutoLinkPreferences;
 import org.jabref.logic.util.io.FileFinder;
 import org.jabref.logic.util.io.FileFinders;
 import org.jabref.logic.util.io.FileUtil;
 import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.entry.BibEntry;
-import org.jabref.model.entry.FileFieldWriter;
 import org.jabref.model.entry.LinkedFile;
 import org.jabref.model.entry.field.StandardField;
-import org.jabref.model.metadata.FilePreferences;
 import org.jabref.model.util.FileHelper;
+import org.jabref.preferences.FilePreferences;
 
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;

src/main/java/org/jabref/gui/externalfiles/ExternalFilesEntryLinker.java

@@ -14,7 +14,7 @@
 import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.entry.BibEntry;
 import org.jabref.model.entry.LinkedFile;
-import org.jabref.model.metadata.FilePreferences;
+import org.jabref.preferences.FilePreferences;
 
 public class ExternalFilesEntryLinker {
 

src/main/java/org/jabref/gui/externalfiletype/ExternalFileTypes.java

@@ -11,7 +11,7 @@
 import java.util.TreeSet;
 
 import org.jabref.Globals;
-import org.jabref.model.entry.FileFieldWriter;
+import org.jabref.logic.bibtex.FileFieldWriter;
 import org.jabref.model.entry.LinkedFile;
 import org.jabref.model.strings.StringUtil;
 import org.jabref.model.util.FileHelper;

src/main/java/org/jabref/gui/fieldeditors/AbstractEditorViewModel.java

@@ -23,7 +23,6 @@
 import de.saxsys.mvvmfx.utils.validation.FunctionBasedValidator;
 import de.saxsys.mvvmfx.utils.validation.ValidationMessage;
 import de.saxsys.mvvmfx.utils.validation.Validator;
-import org.apache.commons.lang3.StringUtils;
 import org.controlsfx.control.textfield.AutoCompletionBinding;
 
 public class AbstractEditorViewModel extends AbstractViewModel {
@@ -66,10 +65,10 @@ public void bindToEntry(BibEntry entry) {
                 newValue -> {
                     if (newValue != null) {
                         // Controlsfx uses hardcoded \n for multiline fields, but JabRef stores them in OS Newlines format
-                        String oldValue = entry.getField(field).map(value -> value.replace(OS.NEWLINE, "\n")).orElse(null);
+                        String oldValue = entry.getField(field).map(value -> value.replace(OS.NEWLINE, "\n").trim()).orElse(null);
                         // Autosave and save action trigger the entry editor to reload the fields, so we have to
                         // check for changes here, otherwise the cursor position is annoyingly reset every few seconds
-                        if (!(newValue.trim()).equals(StringUtils.trim(oldValue))) {
+                        if (!(newValue.trim()).equals(oldValue)) {
                             entry.setField(field, newValue);
                             UndoManager undoManager = JabRefGUI.getMainFrame().getUndoManager();
                             undoManager.addEdit(new UndoableFieldChange(entry, field, oldValue, newValue));

src/main/java/org/jabref/gui/fieldeditors/LinkedFileViewModel.java

@@ -45,10 +45,10 @@
 import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.entry.BibEntry;
 import org.jabref.model.entry.LinkedFile;
-import org.jabref.model.metadata.FilePreferences;
 import org.jabref.model.strings.StringUtil;
 import org.jabref.model.util.FileHelper;
 import org.jabref.model.util.OptionalUtil;
+import org.jabref.preferences.FilePreferences;
 
 import de.saxsys.mvvmfx.utils.validation.FunctionBasedValidator;
 import de.saxsys.mvvmfx.utils.validation.ValidationMessage;

src/main/java/org/jabref/gui/fieldeditors/LinkedFilesEditorViewModel.java

@@ -27,14 +27,14 @@
 import org.jabref.gui.util.BindingsHelper;
 import org.jabref.gui.util.FileDialogConfiguration;
 import org.jabref.gui.util.TaskExecutor;
+import org.jabref.logic.bibtex.FileFieldWriter;
 import org.jabref.logic.importer.FulltextFetchers;
+import org.jabref.logic.importer.util.FileFieldParser;
 import org.jabref.logic.integrity.FieldCheckers;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.logic.util.io.FileUtil;
 import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.entry.BibEntry;
-import org.jabref.model.entry.FileFieldParser;
-import org.jabref.model.entry.FileFieldWriter;
 import org.jabref.model.entry.LinkedFile;
 import org.jabref.model.entry.field.Field;
 import org.jabref.model.util.FileHelper;

src/main/java/org/jabref/gui/fieldeditors/contextmenu/CaseChangeMenu.java

@@ -11,10 +11,10 @@
 import javafx.scene.control.Tooltip;
 
 import org.jabref.Globals;
+import org.jabref.logic.cleanup.Formatter;
 import org.jabref.logic.formatter.Formatters;
 import org.jabref.logic.formatter.casechanger.ProtectTermsFormatter;
 import org.jabref.logic.l10n.Localization;
-import org.jabref.model.cleanup.Formatter;
 
 class CaseChangeMenu extends Menu {
 

src/main/java/org/jabref/gui/fieldeditors/contextmenu/ConversionMenu.java

@@ -6,9 +6,9 @@
 import javafx.scene.control.Menu;
 import javafx.scene.control.Tooltip;
 
+import org.jabref.logic.cleanup.Formatter;
 import org.jabref.logic.formatter.Formatters;
 import org.jabref.logic.l10n.Localization;
-import org.jabref.model.cleanup.Formatter;
 
 /**
  * Menu to show up on right-click in a text field for converting text formats

src/main/java/org/jabref/gui/fieldeditors/contextmenu/ProtectedTermsMenu.java

@@ -9,11 +9,11 @@
 import javafx.scene.control.TextInputControl;
 
 import org.jabref.Globals;
+import org.jabref.logic.cleanup.Formatter;
 import org.jabref.logic.formatter.casechanger.ProtectTermsFormatter;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.logic.protectedterms.ProtectedTermsList;
 import org.jabref.logic.protectedterms.ProtectedTermsLoader;
-import org.jabref.model.cleanup.Formatter;
 
 class ProtectedTermsMenu extends Menu {
 

src/main/java/org/jabref/gui/importer/ImportEntriesViewModel.java

@@ -29,17 +29,12 @@
 import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.entry.BibEntry;
 import org.jabref.model.entry.LinkedFile;
-import org.jabref.model.metadata.FilePreferences;
 import org.jabref.model.util.FileUpdateMonitor;
+import org.jabref.preferences.FilePreferences;
 import org.jabref.preferences.PreferencesService;
 
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
 public class ImportEntriesViewModel extends AbstractViewModel {
 
-    private static final Logger LOGGER = LoggerFactory.getLogger(ImportEntriesViewModel.class);
-
     private final StringProperty message;
     private final TaskExecutor taskExecutor;
     private final BibDatabaseContext databaseContext;