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

* upstream/master:
  Change location of some fields in the entry editor (#4448)
  Bump applicationinsights-core from 2.2.0 to 2.2.1 (#4488)
  Added feature to add server timezone when connecting to shared database (#4483)
  Bump applicationinsights-logging-log4j2 from 2.2.0 to 2.2.1 (#4487)
  fix save button
  Update archunit from 0.9.1 -> 0.9.2

CHANGELOG.md

@@ -11,6 +11,12 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 ## [Unreleased]
 
 ### Changed
+- We changed the location of some fields in the entry editor (you might need to reset your preferences for these changes to come into effect)
+  - Journal/Year/Month in biblatex mode -> Deprecated (if filled)
+  - DOI/URL: General -> Optional
+  - Internal fields like ranking, read status and priority: Other -> General
+  - Moreover, empty deprecated fields are no longer shown
+- Added server timezone parameter when connecting to a shared database.
 - We updated the dialog for setting up general fields.
 - URL field formatting is updated. All whitespace chars, located at the beginning/ending of the url, are trimmed automatically
 - We changed the behavior of the field formatting dialog such that the `bibtexkey` is not changed when formatting all fields or all text fields.

build.gradle

@@ -157,8 +157,8 @@ dependencies {
 
     errorproneJavac 'com.google.errorprone:javac:1.8.0-u20'
 
-    compile group: 'com.microsoft.azure', name: 'applicationinsights-core', version: '2.2.0'
-    compile group: 'com.microsoft.azure', name: 'applicationinsights-logging-log4j2', version: '2.2.0'
+    compile group: 'com.microsoft.azure', name: 'applicationinsights-core', version: '2.2.1'
+    compile group: 'com.microsoft.azure', name: 'applicationinsights-logging-log4j2', version: '2.2.1'
 
     testImplementation 'org.junit.jupiter:junit-jupiter-api:5.3.1'
     testCompile 'org.junit.jupiter:junit-jupiter-params:5.3.1'
@@ -174,8 +174,8 @@ dependencies {
     testCompile 'org.reflections:reflections:0.9.11'
     testCompile 'org.xmlunit:xmlunit-core:2.6.2'
     testCompile 'org.xmlunit:xmlunit-matchers:2.6.2'
-    testCompile 'com.tngtech.archunit:archunit-junit5-api:0.9.1'
-    testRuntime 'com.tngtech.archunit:archunit-junit5-engine:0.9.1'
+    testCompile 'com.tngtech.archunit:archunit-junit5-api:0.9.2'
+    testRuntime 'com.tngtech.archunit:archunit-junit5-engine:0.9.2'
     testCompile "org.testfx:testfx-core:4.0.+"
     testCompile "org.testfx:testfx-junit5:4.0.+"
 

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

@@ -1,6 +1,7 @@
 package org.jabref.gui.entryeditor;
 
 import java.util.Collection;
+import java.util.stream.Collectors;
 
 import javax.swing.undo.UndoManager;
 
@@ -25,6 +26,9 @@ public DeprecatedFieldsTab(BibDatabaseContext databaseContext, SuggestionProvide
 
     @Override
     protected Collection<String> determineFieldsToShow(BibEntry entry, EntryType entryType) {
-        return entryType.getDeprecatedFields();
+        return entryType.getDeprecatedFields()
+                        .stream()
+                        .filter(entry::hasField)
+                        .collect(Collectors.toList());
     }
 }

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

@@ -163,7 +163,14 @@ public boolean save() {
             panel.frame().output(Localization.lang("Saving library") + "...");
             panel.setSaving(true);
             return doSave();
+        } else {
+            Optional<Path> savePath = getSavePath();
+            if (savePath.isPresent()) {
+                saveAs(savePath.get());
+                return true;
+            }
         }
+
         return false;
     }
 

src/main/java/org/jabref/gui/shared/SharedDatabaseLoginDialog.fxml

@@ -52,6 +52,8 @@
                         <CheckBox fx:id="useSSL" mnemonicParsing="false" text="%Use SSL" GridPane.rowIndex="5" />
                         <TextField fx:id="fileKeystore" GridPane.columnIndex="1" GridPane.rowIndex="6" />
                         <Button fx:id="browseKeystore" mnemonicParsing="false" onAction="#showOpenKeystoreFileDialog" text="%Browse" GridPane.columnIndex="2" GridPane.rowIndex="6" />
+                        <Label text="%Server Timezone:" GridPane.rowIndex="8"/>
+                        <TextField fx:id="serverTimezone" GridPane.columnIndex="1" GridPane.columnSpan="2" GridPane.rowIndex="8" />
                         <GridPane>
                           <columnConstraints>
                             <ColumnConstraints hgrow="SOMETIMES" minWidth="10.0" prefWidth="100.0" />

src/main/java/org/jabref/gui/shared/SharedDatabaseLoginDialogView.java

@@ -43,6 +43,7 @@ public class SharedDatabaseLoginDialogView extends BaseDialog<Void> {
     @FXML private TextField fileKeystore;
     @FXML private PasswordField passwordKeystore;
     @FXML private Button browseKeystore;
+    @FXML private TextField serverTimezone;
 
     @Inject private DialogService dialogService;
 
@@ -83,6 +84,7 @@ private void initialize() {
         user.textProperty().bindBidirectional(viewModel.userProperty());
         password.textProperty().bindBidirectional(viewModel.passwordProperty());
         port.textProperty().bindBidirectional(viewModel.portProperty());
+        serverTimezone.textProperty().bindBidirectional(viewModel.serverTimezoneProperty());
         databaseType.valueProperty().bindBidirectional(viewModel.selectedDbmstypeProperty());
 
         folder.textProperty().bindBidirectional(viewModel.folderProperty());

src/main/java/org/jabref/gui/shared/SharedDatabaseLoginDialogViewModel.java

@@ -69,6 +69,7 @@ public class SharedDatabaseLoginDialogViewModel extends AbstractViewModel {
     private final StringProperty keystore = new SimpleStringProperty("");
     private final BooleanProperty useSSL = new SimpleBooleanProperty();
     private final StringProperty keyStorePasswordProperty = new SimpleStringProperty("");
+    private final StringProperty serverTimezone = new SimpleStringProperty("");
 
     private final JabRefFrame frame;
     private final DialogService dialogService;
@@ -118,6 +119,7 @@ public void openDatabase() {
         connectionProperties.setPassword(password.getValue());
         connectionProperties.setUseSSL(useSSL.getValue());
         connectionProperties.setKeyStore(keystore.getValue());
+        connectionProperties.setServerTimezone(serverTimezone.getValue());
 
         setupKeyStore();
         openSharedDatabase(connectionProperties);
@@ -200,6 +202,7 @@ private void setPreferences() {
         prefs.setUser(user.getValue());
         prefs.setUseSSL(useSSL.getValue());
         prefs.setKeystoreFile(keystore.getValue());
+        prefs.setServerTimezone(serverTimezone.getValue());
 
         if (rememberPassword.get()) {
             try {
@@ -364,4 +367,6 @@ public ValidationStatus keystoreValidation() {
     public ValidationStatus formValidation() {
         return formValidator.getValidationStatus();
     }
+
+    public StringProperty serverTimezoneProperty() { return serverTimezone; }
 }

src/main/java/org/jabref/logic/integrity/NoBibtexFieldChecker.java

@@ -10,7 +10,6 @@
 import org.jabref.model.entry.BiblatexEntryTypes;
 import org.jabref.model.entry.BibtexEntryTypes;
 import org.jabref.model.entry.FieldName;
-import org.jabref.model.entry.InternalBibtexFields;
 
 /**
  * This checker checks whether the entry does not contain any field appearing only in biblatex (and not in BibTeX)
@@ -20,23 +19,23 @@ public class NoBibtexFieldChecker implements Checker {
     private List<String> getAllBiblatexOnlyFields() {
         Set<String> allBibtexFields = BibtexEntryTypes.ALL.stream().flatMap(type -> type.getAllFields().stream()).collect(Collectors.toSet());
         return BiblatexEntryTypes.ALL.stream()
-                .flatMap(type -> type.getAllFields().stream())
-                .filter(fieldName -> !allBibtexFields.contains(fieldName))
-                // these fields are displayed by JabRef as default
-                .filter(fieldName -> !InternalBibtexFields.DEFAULT_GENERAL_FIELDS.contains(fieldName))
-                .filter(fieldName -> !fieldName.equals(FieldName.ABSTRACT))
-                .filter(fieldName -> !fieldName.equals(FieldName.REVIEW))
-                .sorted()
-                .collect(Collectors.toList());
+                                     .flatMap(type -> type.getAllFields().stream())
+                                     .filter(fieldName -> !allBibtexFields.contains(fieldName))
+                                     // these fields are displayed by JabRef as default
+                                     .filter(fieldName -> !fieldName.equals(FieldName.ABSTRACT))
+                                     .filter(fieldName -> !fieldName.equals(FieldName.COMMENT))
+                                     .filter(fieldName -> !fieldName.equals(FieldName.DOI))
+                                     .filter(fieldName -> !fieldName.equals(FieldName.URL))
+                                     .sorted()
+                                     .collect(Collectors.toList());
     }
 
     @Override
     public List<IntegrityMessage> check(BibEntry entry) {
         // non-static initalization of ALL_BIBLATEX_ONLY_FIELDS as the user can customize the entry types during runtime
         final List<String> allBiblatexOnlyFields = getAllBiblatexOnlyFields();
         return entry.getFieldNames().stream()
-                .filter(name ->  allBiblatexOnlyFields.contains(name))
-                .map(name -> new IntegrityMessage(Localization.lang("biblatex field only"), entry, name)).collect(Collectors.toList());
+                    .filter(allBiblatexOnlyFields::contains)
+                    .map(name -> new IntegrityMessage(Localization.lang("biblatex field only"), entry, name)).collect(Collectors.toList());
     }
-
 }

src/main/java/org/jabref/logic/shared/DBMSConnectionProperties.java

@@ -28,6 +28,7 @@ public class DBMSConnectionProperties implements DatabaseConnectionProperties {
     private String user;
     private String password;
     private boolean useSSL;
+    private String serverTimezone;
 
     //Not needed for connection, but stored for future login
     private String keyStore;
@@ -41,14 +42,15 @@ public DBMSConnectionProperties(SharedDatabasePreferences prefs) {
     }
 
     public DBMSConnectionProperties(DBMSType type, String host, int port, String database, String user,
-                                    String password, boolean useSSL) {
+                                    String password, boolean useSSL, String serverTimezone) {
         this.type = type;
         this.host = host;
         this.port = port;
         this.database = database;
         this.user = user;
         this.password = password;
         this.useSSL = useSSL;
+        this.serverTimezone = serverTimezone;
     }
 
     @Override
@@ -118,6 +120,11 @@ public String getUrl() {
         return type.getUrl(host, port, database);
     }
 
+    @Override
+    public String getServerTimezone() { return serverTimezone; }
+
+    public void setServerTimezone(String serverTimezone) { this.serverTimezone = serverTimezone; }
+
     /**
      * Returns username, password and ssl as Properties Object
      * @return Properties with values for user, password and ssl
@@ -126,6 +133,7 @@ public Properties asProperties() {
         Properties props = new Properties();
         props.setProperty("user", user);
         props.setProperty("password", password);
+        props.setProperty("serverTimezone", serverTimezone);
 
         if (useSSL) {
             props.setProperty("ssl", Boolean.toString(useSSL));
@@ -161,7 +169,9 @@ public boolean equals(Object obj) {
                && Objects.equals(port, properties.getPort())
                && Objects.equals(database, properties.getDatabase())
                && Objects.equals(user, properties.getUser())
-               && Objects.equals(useSSL, properties.isUseSSL());
+               && Objects.equals(useSSL, properties.isUseSSL())
+               && Objects.equals(serverTimezone, properties.getServerTimezone());
+
     }
 
     @Override
@@ -184,6 +194,7 @@ private void setFromPreferences(SharedDatabasePreferences prefs) {
         prefs.getPort().ifPresent(thePort -> this.port = Integer.parseInt(thePort));
         prefs.getName().ifPresent(theDatabase -> this.database = theDatabase);
         prefs.getKeyStoreFile().ifPresent(theKeystore -> this.keyStore = theKeystore);
+        prefs.getServerTimezone().ifPresent(theServerTimezone -> this.serverTimezone = theServerTimezone);
         this.setUseSSL(prefs.isUseSSL());
 
         if (prefs.getUser().isPresent()) {

src/main/java/org/jabref/logic/shared/prefs/SharedDatabasePreferences.java

@@ -32,6 +32,7 @@ public class SharedDatabasePreferences {
     private static final String SHARED_DATABASE_REMEMBER_PASSWORD = "sharedDatabaseRememberPassword";
     private static final String SHARED_DATABASE_USE_SSL = "sharedDatabaseUseSSL";
     private static final String SHARED_DATABASE_KEYSTORE_FILE = "sharedDatabaseKeyStoreFile";
+    private static final String SHARED_DATABASE_SERVER_TIMEZONE = "sharedDatabaseServerTimezone";
 
     // This {@link Preferences} is used only for things which should not appear in real JabRefPreferences due to security reasons.
     private final Preferences internalPrefs;
@@ -72,6 +73,10 @@ public Optional<String> getKeyStoreFile() {
         return getOptionalValue(SHARED_DATABASE_KEYSTORE_FILE);
     }
 
+    public Optional<String> getServerTimezone() {
+        return getOptionalValue(SHARED_DATABASE_SERVER_TIMEZONE);
+    }
+
     public boolean getRememberPassword() {
         return internalPrefs.getBoolean(SHARED_DATABASE_REMEMBER_PASSWORD, false);
     }
@@ -116,6 +121,10 @@ public void setKeystoreFile(String keystoreFile) {
         internalPrefs.put(SHARED_DATABASE_KEYSTORE_FILE, keystoreFile);
     }
 
+    public void setServerTimezone(String serverTimezone) {
+        internalPrefs.put(SHARED_DATABASE_SERVER_TIMEZONE, serverTimezone);
+    }
+
     public void clearPassword() {
         internalPrefs.remove(SHARED_DATABASE_PASSWORD);
     }
@@ -142,6 +151,7 @@ public void putAllDBMSConnectionProperties(DatabaseConnectionProperties properti
         setUser(properties.getUser());
         setUseSSL(properties.isUseSSL());
         setKeystoreFile(properties.getKeyStore());
+        setServerTimezone(properties.getServerTimezone());
 
         try {
             setPassword(new Password(properties.getPassword().toCharArray(), properties.getUser()).encrypt());

src/main/java/org/jabref/model/database/shared/DatabaseConnectionProperties.java

@@ -20,4 +20,6 @@ public interface DatabaseConnectionProperties {
 
     boolean isUseSSL();
 
+    String getServerTimezone();
+
 }