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

* upstream/master: Revised README.md (#4974) Switch Jsoup's StringUtil for JabRef's StringUtil (#4970) Remove UI ThreadList for maintable as it prevents sorting in maintable (#4964) fix map collision (#4962)
JabRef · May 17, 2019 · 888aa6f · 888aa6f
2 parents d3ce2e2 + 89d0f30
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diff --git a/README.md b/README.md
@@ -82,11 +82,11 @@ An explanation of donation possibilities and usage of donations is available at
 
 > Not a programmer? [Learn how to help.](http://contribute.jabref.org)
 
-Want to be part of a free and open-source project that tens of thousands scientist use every day?
-Check out our [issue tracker](https://github.com/JabRef/jabref/issues) to find something to work on.
-You are also welcome to contribute new features.
-To get your code included into JabRef, just fork JabRef and create a pull request.
-For details have a look at our [guidelines for contributing](CONTRIBUTING.md).
+Want to be part of a free and open-source project that tens of thousands scientist use every day? Check out the ways you can contribute, below:
+- For details on how to contribute, have a look at our [guidelines for contributing](CONTRIBUTING.md).
+- You are welcome to contribute new features. To get your code included into JabRef, just [fork](https://help.github.com/en/articles/fork-a-repo) the JabRef repository, make your changes, and create a [pull request](https://help.github.com/en/articles/about-pull-requests).
+- To work on existing JabRef issues, check out our [issue tracker](https://github.com/JabRef/jabref/issues). New to open source contributing? Look for issues with the ["good first issue"](https://github.com/JabRef/jabref/labels/good%20first%20issue) label to get started.
+
 We view pull requests as a collaborative process.
 Submit a pull request early to get feedback from the team on work in progress.
 We will discuss improvements with you and agree to merge them once the [developers](https://github.com/JabRef/jabref/blob/master/DEVELOPERS) approve.

diff --git a/build.gradle b/build.gradle
@@ -138,7 +138,7 @@ dependencies {
     // Cannot be updated to 9.*.* until Jabref works with Java 9
     compile 'org.controlsfx:controlsfx:8.40.15-SNAPSHOT'
 
-    compile 'org.jsoup:jsoup:1.11.3'
+    compile 'org.jsoup:jsoup:1.12.1'
     compile 'com.mashape.unirest:unirest-java:1.4.9'
 
     // >1.8.0-beta is required for java 9 compatibility

diff --git a/src/main/java/org/jabref/gui/externalfiles/FindFullTextAction.java b/src/main/java/org/jabref/gui/externalfiles/FindFullTextAction.java
@@ -69,14 +69,14 @@ public void execute() {
             }
         }
 
-        Task<Map<Optional<URL>, BibEntry>> findFullTextsTask = new Task<Map<Optional<URL>, BibEntry>>() {
+        Task<Map<BibEntry, Optional<URL>>> findFullTextsTask = new Task<Map<BibEntry, Optional<URL>>>() {
             @Override
-            protected Map<Optional<URL>, BibEntry> call() {
-                Map<Optional<URL>, BibEntry> downloads = new ConcurrentHashMap<>();
+            protected Map<BibEntry, Optional<URL>> call() {
+                Map<BibEntry, Optional<URL>> downloads = new ConcurrentHashMap<>();
                 int count = 0;
                 for (BibEntry entry : basePanel.getSelectedEntries()) {
                     FulltextFetchers fetchers = new FulltextFetchers(Globals.prefs.getImportFormatPreferences());
-                    downloads.put(fetchers.findFullTextPDF(entry), entry);
+                    downloads.put(entry, fetchers.findFullTextPDF(entry));
                     updateProgress(++count, basePanel.getSelectedEntries().size());
                 }
                 return downloads;
@@ -93,10 +93,10 @@ protected Map<Optional<URL>, BibEntry> call() {
         Globals.TASK_EXECUTOR.execute(findFullTextsTask);
     }
 
-    private void downloadFullTexts(Map<Optional<URL>, BibEntry> downloads) {
-        for (Map.Entry<Optional<URL>, BibEntry> download : downloads.entrySet()) {
-            BibEntry entry = download.getValue();
-            Optional<URL> result = download.getKey();
+    private void downloadFullTexts(Map<BibEntry, Optional<URL>> downloads) {
+        for (Map.Entry<BibEntry, Optional<URL>> download : downloads.entrySet()) {
+            BibEntry entry = download.getKey();
+            Optional<URL> result = download.getValue();
             if (result.isPresent()) {
                 Optional<Path> dir = basePanel.getBibDatabaseContext().getFirstExistingFileDir(Globals.prefs.getFilePreferences());
 

diff --git a/src/main/java/org/jabref/gui/maintable/MainTable.java b/src/main/java/org/jabref/gui/maintable/MainTable.java
@@ -36,7 +36,6 @@
 import org.jabref.gui.keyboard.KeyBindingRepository;
 import org.jabref.gui.undo.NamedCompound;
 import org.jabref.gui.undo.UndoableInsertEntry;
-import org.jabref.gui.util.BindingsHelper;
 import org.jabref.gui.util.CustomLocalDragboard;
 import org.jabref.gui.util.ViewModelTableRowFactory;
 import org.jabref.logic.l10n.Localization;
@@ -109,7 +108,7 @@ public MainTable(MainTableDataModel model, JabRefFrame frame,
         }
         this.getSelectionModel().setSelectionMode(SelectionMode.MULTIPLE);
 
-        this.setItems(BindingsHelper.forUI(model.getEntriesFilteredAndSorted()));
+        this.setItems(model.getEntriesFilteredAndSorted());
         // Enable sorting
         model.getEntriesFilteredAndSorted().comparatorProperty().bind(this.comparatorProperty());
 

diff --git a/src/main/java/org/jabref/gui/maintable/MainTableDataModel.java b/src/main/java/org/jabref/gui/maintable/MainTableDataModel.java
@@ -22,10 +22,10 @@ public class MainTableDataModel {
     private final SortedList<BibEntryTableViewModel> entriesSorted;
 
     public MainTableDataModel(BibDatabaseContext context) {
-        ObservableList<BibEntry> allEntries = context.getDatabase().getEntries();
-
+        ObservableList<BibEntry> allEntries = BindingsHelper.forUI(context.getDatabase().getEntries());
+        
         ObservableList<BibEntryTableViewModel> entriesViewModel = BindingsHelper.mapBacked(allEntries, BibEntryTableViewModel::new);
-
+        
         entriesFiltered = new FilteredList<>(entriesViewModel);
         entriesFiltered.predicateProperty().bind(
                 Bindings.createObjectBinding(() -> this::isMatched,

diff --git a/src/main/java/org/jabref/logic/importer/IdBasedParserFetcher.java b/src/main/java/org/jabref/logic/importer/IdBasedParserFetcher.java
@@ -11,8 +11,8 @@
 import org.jabref.logic.net.URLDownload;
 import org.jabref.model.cleanup.Formatter;
 import org.jabref.model.entry.BibEntry;
+import org.jabref.model.strings.StringUtil;
 
-import org.jsoup.helper.StringUtil;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 

diff --git a/src/main/java/org/jabref/logic/importer/SearchBasedParserFetcher.java b/src/main/java/org/jabref/logic/importer/SearchBasedParserFetcher.java
@@ -11,8 +11,7 @@
 import org.jabref.logic.net.URLDownload;
 import org.jabref.model.cleanup.Formatter;
 import org.jabref.model.entry.BibEntry;
-
-import org.jsoup.helper.StringUtil;
+import org.jabref.model.strings.StringUtil;
 
 /**
  * Provides a convenient interface for search-based fetcher, which follow the usual three-step procedure:

diff --git a/src/main/java/org/jabref/logic/importer/fetcher/AstrophysicsDataSystem.java b/src/main/java/org/jabref/logic/importer/fetcher/AstrophysicsDataSystem.java
@@ -30,10 +30,10 @@
 import org.jabref.model.cleanup.FieldFormatterCleanup;
 import org.jabref.model.entry.BibEntry;
 import org.jabref.model.entry.FieldName;
+import org.jabref.model.strings.StringUtil;
 import org.jabref.model.util.DummyFileUpdateMonitor;
 
 import org.apache.http.client.utils.URIBuilder;
-import org.jsoup.helper.StringUtil;
 
 /**
  * Fetches data from the SAO/NASA Astrophysics Data System (http://www.adsabs.harvard.edu/)

diff --git a/src/main/java/org/jabref/logic/importer/fetcher/IsbnFetcher.java b/src/main/java/org/jabref/logic/importer/fetcher/IsbnFetcher.java
@@ -11,9 +11,9 @@
 import org.jabref.logic.importer.ImportFormatPreferences;
 import org.jabref.model.entry.BibEntry;
 import org.jabref.model.entry.FieldName;
+import org.jabref.model.strings.StringUtil;
 import org.jabref.model.util.OptionalUtil;
 
-import org.jsoup.helper.StringUtil;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 

diff --git a/src/main/java/org/jabref/logic/importer/fetcher/IsbnViaChimboriFetcher.java b/src/main/java/org/jabref/logic/importer/fetcher/IsbnViaChimboriFetcher.java
@@ -10,11 +10,11 @@
 import org.jabref.logic.importer.ImportFormatPreferences;
 import org.jabref.logic.importer.ParseException;
 import org.jabref.model.entry.BibEntry;
+import org.jabref.model.strings.StringUtil;
 
 import com.mashape.unirest.http.HttpResponse;
 import com.mashape.unirest.http.Unirest;
 import com.mashape.unirest.http.exceptions.UnirestException;
-import org.jsoup.helper.StringUtil;
 
 /**
  * Fetcher for ISBN using https://bibtex.chimbori.com/, which in turn uses Amazon's API.