Update many files and revert tests to a previous version

Author: davidemdot

build.gradle

@@ -111,6 +111,8 @@ dependencies {
     compile 'org.apache.pdfbox:fontbox:2.0.17'
     compile 'org.apache.pdfbox:xmpbox:2.0.17'
 
+    compile group: 'org.apache.commons', name: 'commons-csv', version: '1.7'
+
     compile group: 'org.apache.tika', name: 'tika-core', version: '1.22'
 
     // required for reading write-protected PDFs - see https://github.com/JabRef/jabref/pull/942#issuecomment-209252635

scripts/convert_txt2csv.py

@@ -26,5 +26,5 @@
     df = pd.read_csv(fileName + ".txt", sep=separator, skiprows=commented_lines, header=None, engine="python", skipinitialspace=True, index_col=0, names=["Name", "Abbrev"])
     df.index = df.index.str.strip()
     df = df.Abbrev.str.split(";", expand=True)
-    df.to_csv(fileName + ".csv", sep="\t", header=False)
+    df.to_csv(fileName + ".csv", sep=";", header=False)
     print(fileName + ".csv")

src/main/java/module-info.java

@@ -65,4 +65,5 @@
     requires de.saxsys.mvvmfx.validation;
     requires richtextfx;
     requires unirest.java;
+    requires commons.csv;
 }

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

@@ -46,6 +46,7 @@
 import org.jabref.gui.externalfiletype.ExternalFileTypes;
 import org.jabref.gui.importer.actions.AppendDatabaseAction;
 import org.jabref.gui.journals.AbbreviateAction;
+import org.jabref.gui.journals.AbbreviationType;
 import org.jabref.gui.journals.UnabbreviateAction;
 import org.jabref.gui.maintable.MainTable;
 import org.jabref.gui.maintable.MainTableDataModel;
@@ -365,9 +366,9 @@ private void setupActions() {
 
         actions.put(Actions.WRITE_XMP, new WriteXMPAction(this)::execute);
 
-        actions.put(Actions.ABBREVIATE_ISO, new AbbreviateAction(this, 0));
-        actions.put(Actions.ABBREVIATE_MEDLINE, new AbbreviateAction(this, 1));
-        actions.put(Actions.ABBREVIATE_SHORTEST, new AbbreviateAction(this, 2));
+        actions.put(Actions.ABBREVIATE_DEFAULT, new AbbreviateAction(this, AbbreviationType.DEFAULT));
+        actions.put(Actions.ABBREVIATE_MEDLINE, new AbbreviateAction(this, AbbreviationType.MEDLINE));
+        actions.put(Actions.ABBREVIATE_SHORTEST_UNIQUE, new AbbreviateAction(this, AbbreviationType.SHORTEST_UNIQUE));
         actions.put(Actions.UNABBREVIATE, new UnabbreviateAction(this));
 
         actions.put(Actions.DOWNLOAD_FULL_TEXT, new FindFullTextAction(this)::execute);

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

@@ -783,9 +783,9 @@ private MenuBar createMenu() {
                 pushToApplicationMenuItem,
 
                 factory.createSubMenu(StandardActions.ABBREVIATE,
-                        factory.createMenuItem(StandardActions.ABBREVIATE_ISO, new OldDatabaseCommandWrapper(Actions.ABBREVIATE_ISO, this, stateManager)),
+                        factory.createMenuItem(StandardActions.ABBREVIATE_DEFAULT, new OldDatabaseCommandWrapper(Actions.ABBREVIATE_DEFAULT, this, stateManager)),
                         factory.createMenuItem(StandardActions.ABBREVIATE_MEDLINE, new OldDatabaseCommandWrapper(Actions.ABBREVIATE_MEDLINE, this, stateManager)),
-                        factory.createMenuItem(StandardActions.ABBREVIATE_SHORTEST, new OldDatabaseCommandWrapper(Actions.ABBREVIATE_SHORTEST, this, stateManager))),
+                        factory.createMenuItem(StandardActions.ABBREVIATE_SHORTEST_UNIQUE, new OldDatabaseCommandWrapper(Actions.ABBREVIATE_SHORTEST_UNIQUE, this, stateManager))),
 
                 factory.createMenuItem(StandardActions.UNABBREVIATE, new OldDatabaseCommandWrapper(Actions.UNABBREVIATE, this, stateManager))
         );

src/main/java/org/jabref/gui/actions/Actions.java

@@ -6,9 +6,9 @@
 @Deprecated
 public enum Actions {
 
-    ABBREVIATE_ISO,
+    ABBREVIATE_DEFAULT,
     ABBREVIATE_MEDLINE,
-    ABBREVIATE_SHORTEST,
+    ABBREVIATE_SHORTEST_UNIQUE,
     ADD_FILE_LINK,
     CLEANUP,
     COPY,

src/main/java/org/jabref/gui/actions/StandardActions.java

@@ -94,9 +94,9 @@ public enum StandardActions implements Action {
     COPY_LINKED_FILES(Localization.lang("Copy linked files to folder...")),
     COPY_DOI(Localization.lang("Copy DOI url")),
     ABBREVIATE(Localization.lang("Abbreviate journal names")),
-    ABBREVIATE_ISO("ISO", Localization.lang("Abbreviate journal names of the selected entries (ISO abbreviation)"), KeyBinding.ABBREVIATE),
+    ABBREVIATE_DEFAULT("DEFAULT", Localization.lang("Abbreviate journal names of the selected entries (DEFAULT abbreviation)"), KeyBinding.ABBREVIATE),
     ABBREVIATE_MEDLINE("MEDLINE", Localization.lang("Abbreviate journal names of the selected entries (MEDLINE abbreviation)")),
-    ABBREVIATE_SHORTEST("SHORTEST", Localization.lang("Abbreviate journal names of the selected entries (SHORTEST abbreviation)")),
+    ABBREVIATE_SHORTEST_UNIQUE("SHORTEST UNIQUE", Localization.lang("Abbreviate journal names of the selected entries (SHORTEST UNIQUE abbreviation)")),
     UNABBREVIATE(Localization.lang("Unabbreviate journal names"), Localization.lang("Unabbreviate journal names of the selected entries"), KeyBinding.UNABBREVIATE),
 
     MANAGE_CUSTOM_EXPORTS(Localization.lang("Manage custom exports")),

src/main/java/org/jabref/gui/journals/AbbreviateAction.java

@@ -29,11 +29,11 @@ public class AbbreviateAction implements BaseAction {
 
     private static final Logger LOGGER = LoggerFactory.getLogger(AbbreviateAction.class);
     private final BasePanel panel;
-    private final int abbrvType;
+    private final AbbreviationType abbreviationType;
 
-    public AbbreviateAction(BasePanel panel, int abbrvType) {
+    public AbbreviateAction(BasePanel panel, AbbreviationType abbreviationType) {
         this.panel = panel;
-        this.abbrvType = abbrvType;
+        this.abbreviationType = abbreviationType;
     }
 
     @Override
@@ -49,7 +49,7 @@ private String abbreviate() {
         List<BibEntry> entries = panel.getSelectedEntries();
         UndoableAbbreviator undoableAbbreviator = new UndoableAbbreviator(
                 Globals.journalAbbreviationLoader.getRepository(Globals.prefs.getJournalAbbreviationPreferences()),
-                abbrvType);
+                abbreviationType);
 
         NamedCompound ce = new NamedCompound(Localization.lang("Abbreviate journal names"));
         Set<Callable<Boolean>> tasks = new HashSet<>();

src/main/java/org/jabref/gui/journals/AbbreviationType.java

@@ -0,0 +1,10 @@
+package org.jabref.gui.journals;
+
+/**
+ * Defines the different abbreviation types that JabRef can operate with
+ */
+public enum AbbreviationType {
+        DEFAULT,
+        MEDLINE,
+        SHORTEST_UNIQUE
+}

src/main/java/org/jabref/gui/journals/AbbreviationViewModel.java

@@ -10,25 +10,24 @@
 import org.jabref.logic.journals.Abbreviation;
 
 /**
- * This class provides a view model for abbreviation objects which can also
- * define placeholder objects of abbreviations. This is indicated by using the
- * {@code pseudoAbbreviation} property.
+ * This class provides a view model for abbreviation objects which can also define placeholder objects of abbreviations.
+ * This is indicated by using the {@code pseudoAbbreviation} property.
  */
 public class AbbreviationViewModel {
 
     private final Abbreviation abbreviationObject;
     private final StringProperty name = new SimpleStringProperty("");
     private final StringProperty abbreviation = new SimpleStringProperty("");
-    private final StringProperty shortestUnique = new SimpleStringProperty("");
+    private final StringProperty shortestUniqueAbbreviation = new SimpleStringProperty("");
     private final BooleanProperty pseudoAbbreviation = new SimpleBooleanProperty();
 
     public AbbreviationViewModel(Abbreviation abbreviation) {
         this.abbreviationObject = abbreviation;
-        pseudoAbbreviation.set(this.abbreviationObject == null);
+        this.pseudoAbbreviation.set(this.abbreviationObject == null);
         if (this.abbreviationObject != null) {
             this.name.bindBidirectional(this.abbreviationObject.nameProperty());
             this.abbreviation.bindBidirectional(this.abbreviationObject.abbreviationProperty());
-            this.shortestUnique.bindBidirectional(this.abbreviationObject.shortestUniqueProperty());
+            this.shortestUniqueAbbreviation.bindBidirectional(this.abbreviationObject.shortestUniqueAbbreviationProperty());
         } else {
             this.name.set("Add new Abbreviation");
         }
@@ -38,28 +37,28 @@ public Abbreviation getAbbreviationObject() {
         return this.abbreviationObject;
     }
 
-    public void setName(String name) {
-        this.name.set(name);
+    public String getName() {
+        return this.name.get();
     }
 
-    public void setAbbreviation(String abbreviation) {
-        this.abbreviation.set(abbreviation);
+    public void setName(String name) {
+        this.name.set(name);
     }
 
-    public void setShortestUnique(String shortestUnique) {
-        this.shortestUnique.set(shortestUnique);
+    public String getAbbreviation() {
+        return this.abbreviation.get();
     }
 
-    public String getName() {
-        return this.name.get();
+    public void setAbbreviation(String abbreviation) {
+        this.abbreviation.set(abbreviation);
     }
 
-    public String getAbbreviation() {
-        return this.abbreviation.get();
+    public String getShortestUniqueAbbreviation() {
+        return this.shortestUniqueAbbreviation.get();
     }
 
-    public String getShortestUnique() {
-        return this.shortestUnique.get();
+    public void setShortestUniqueAbbreviation(String shortestUniqueAbbreviation) {
+        this.shortestUniqueAbbreviation.set(shortestUniqueAbbreviation);
     }
 
     public boolean isPseudoAbbreviation() {
@@ -74,8 +73,8 @@ public StringProperty abbreviationProperty() {
         return this.abbreviation;
     }
 
-    public StringProperty shortestUniqueProperty() {
-        return this.shortestUnique;
+    public StringProperty shortestUniqueAbbreviationProperty() {
+        return this.shortestUniqueAbbreviation;
     }
 
     public BooleanProperty isPseudoAbbreviationProperty() {