Fix #2455: Add crossref as fetcher for everything (ID-, entry-, searc…

…h-based) (#2645) * Apply some post actions before displaying the file * Add changes in JabRefGUI * Add changelog entry * Refactor DOI fetcher * Move logic.identifier to model.entry.identifier * Move ArXiv identifier to model.entry.identifier * Do it * Add CrossRef as entry, search and id based fetcher * Move a few fetcher related things from gui to logic * Move MathSciNetId to identifier
JabRef · Mar 16, 2017 · d8f1d69 · d8f1d69
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -29,6 +29,7 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - The MS Office XML export now exports the field `volumes` and `pubstate`.
 - The integrity checker reports now if a journal is not found in the abbreviation list
 - Comments in PDF files can now be displayed inside JabRef in a separate tab
+- We are happy to welcome [CrossRef](https://www.crossref.org/) as a new member of our fetcher family. [#2455](https://github.com/JabRef/jabref/issues/2455)
 - We improved the UI customization possibilities:
     - It is now possible to customize the colors and the size of the icons (implements a [feature request in the forum](http://discourse.jabref.org/t/menu-and-buttons-with-a-dark-theme/405)).
     - Resizing the menu and label sizes has been improved.
@@ -61,6 +62,7 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
  - We fixed an issue where the "find unlinked files" functionality threw an error when only one PDF was imported but not assigned to an entry [#2577](https://github.com/JabRef/jabref/issues/2577)
  - We fixed issue where escaped braces were incorrectly counted when calculating brace balance in a field [#2561](https://github.com/JabRef/jabref/issues/2561)
  - We fixed an issue introduced with Version 3.8.2 where executing the `Rename PDFs`-cleanup operation moved the files to the file directory. [#2526](https://github.com/JabRef/jabref/issues/2526)
+ - We improved the performance when opening a big database that still used the old groups format. Fixes an [issue raised in the forum](http://discourse.jabref.org/t/v3-8-2-x64-windows-problem-saving-large-bib-libraries/456).
  - We fixed an issue where the `Move linked files to default file directory`- cleanup operation did not move the files to the location of the bib-file. [#2454](https://github.com/JabRef/jabref/issues/2454)
  - We fixed an issue where executing `Move file` on a selected file in the `general`-tab could overwrite an existing file. [#2385](https://github.com/JabRef/jabref/issues/2358)
  - We fixed an issue with importing groups and subgroups [#2600](https://github.com/JabRef/jabref/issues/2600)

diff --git a/src/main/java/org/jabref/cli/CrossrefFetcherEvaluator.java b/src/main/java/org/jabref/cli/CrossrefFetcherEvaluator.java
@@ -10,13 +10,14 @@
 import java.util.concurrent.atomic.AtomicInteger;
 
 import org.jabref.Globals;
-import org.jabref.logic.identifier.DOI;
+import org.jabref.logic.importer.FetcherException;
 import org.jabref.logic.importer.ParserResult;
 import org.jabref.logic.importer.fetcher.CrossRef;
 import org.jabref.logic.importer.fileformat.BibtexParser;
 import org.jabref.model.database.BibDatabase;
 import org.jabref.model.entry.BibEntry;
 import org.jabref.model.entry.FieldName;
+import org.jabref.model.entry.identifier.DOI;
 import org.jabref.preferences.JabRefPreferences;
 
 /**
@@ -52,22 +53,31 @@ public void run() {
                         Optional<DOI> origDOI = entry.getField(FieldName.DOI).flatMap(DOI::build);
                         if (origDOI.isPresent()) {
                             dois.incrementAndGet();
-                            Optional<DOI> crossrefDOI = CrossRef.findDOI(entry);
-                            if (crossrefDOI.isPresent()) {
-                                doiFound.incrementAndGet();
-                                if (origDOI.get().getDOI().equalsIgnoreCase(crossrefDOI.get().getDOI())) {
-                                    doiIdentical.incrementAndGet();
+                            try {
+                                Optional<DOI> crossrefDOI = new CrossRef().findIdentifier(entry);
+                                if (crossrefDOI.isPresent()) {
+                                    doiFound.incrementAndGet();
+                                    if (origDOI.get().getDOI().equalsIgnoreCase(crossrefDOI.get().getDOI())) {
+                                        doiIdentical.incrementAndGet();
+                                    } else {
+                                        System.out.println("DOI not identical for : " + entry);
+                                    }
                                 } else {
-                                    System.out.println("DOI not identical for : " + entry);
+                                    System.out.println("DOI not found for: " + entry);
                                 }
-                            } else {
-                                System.out.println("DOI not found for: " + entry);
+                            } catch (FetcherException e) {
+                                e.printStackTrace();
                             }
+
                         } else {
-                            Optional<DOI> crossrefDOI = CrossRef.findDOI(entry);
-                            if (crossrefDOI.isPresent()) {
-                                System.out.println("New DOI found for: " + entry);
-                                doiNew.incrementAndGet();
+                            try {
+                                Optional<DOI> crossrefDOI = new CrossRef().findIdentifier(entry);
+                                if (crossrefDOI.isPresent()) {
+                                    System.out.println("New DOI found for: " + entry);
+                                    doiNew.incrementAndGet();
+                                }
+                            } catch (FetcherException e) {
+                                e.printStackTrace();
                             }
                         }
                         countDownLatch.countDown();

diff --git a/src/main/java/org/jabref/gui/ClipBoardManager.java b/src/main/java/org/jabref/gui/ClipBoardManager.java
@@ -14,12 +14,12 @@
 import java.util.Optional;
 
 import org.jabref.Globals;
-import org.jabref.logic.identifier.DOI;
 import org.jabref.logic.importer.FetcherException;
 import org.jabref.logic.importer.fetcher.DoiFetcher;
 import org.jabref.logic.importer.fileformat.BibtexParser;
 import org.jabref.model.database.BibDatabase;
 import org.jabref.model.entry.BibEntry;
+import org.jabref.model.entry.identifier.DOI;
 
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;

diff --git a/src/main/java/org/jabref/gui/EntryTypeDialog.java b/src/main/java/org/jabref/gui/EntryTypeDialog.java
@@ -27,10 +27,10 @@
 import javax.swing.SwingWorker;
 
 import org.jabref.Globals;
-import org.jabref.gui.importer.fetcher.EntryFetchers;
 import org.jabref.gui.keyboard.KeyBinding;
 import org.jabref.logic.importer.FetcherException;
 import org.jabref.logic.importer.IdBasedFetcher;
+import org.jabref.logic.importer.WebFetchers;
 import org.jabref.logic.importer.fetcher.DoiFetcher;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.model.EntryTypes;
@@ -53,36 +53,14 @@
 public class EntryTypeDialog extends JDialog implements ActionListener {
 
     private static final Log LOGGER = LogFactory.getLog(EntryTypeDialog.class);
-
+    private static final int COLUMN = 3;
+    private final JabRefFrame frame;
+    private final CancelAction cancelAction = new CancelAction();
     private EntryType type;
     private SwingWorker<Optional<BibEntry>, Void> fetcherWorker = new FetcherWorker();
     private JButton generateButton;
     private JTextField idTextField;
     private JComboBox<String> comboBox;
-    private final JabRefFrame frame;
-    private static final int COLUMN = 3;
-
-    private final CancelAction cancelAction = new CancelAction();
-
-    static class TypeButton extends JButton implements Comparable<TypeButton> {
-
-        private final EntryType type;
-
-
-        TypeButton(String label, EntryType type) {
-            super(label);
-            this.type = type;
-        }
-
-        @Override
-        public int compareTo(TypeButton o) {
-            return type.getName().compareTo(o.type.getName());
-        }
-
-        public EntryType getType() {
-            return type;
-        }
-    }
 
     public EntryTypeDialog(JabRefFrame frame) {
         // modal dialog
@@ -186,7 +164,7 @@ private JPanel createIdFetcherPanel() {
         idTextField = new JTextField("");
         comboBox = new JComboBox<>();
 
-        EntryFetchers.getIdFetchers(Globals.prefs.getImportFormatPreferences()).forEach(fetcher -> comboBox.addItem(fetcher.getName()));
+        WebFetchers.getIdBasedFetchers(Globals.prefs.getImportFormatPreferences()).forEach(fetcher -> comboBox.addItem(fetcher.getName()));
         // set DOI as default
         comboBox.setSelectedItem(DoiFetcher.name);
 
@@ -263,6 +241,25 @@ public EntryType getChoice() {
         return type;
     }
 
+    static class TypeButton extends JButton implements Comparable<TypeButton> {
+
+        private final EntryType type;
+
+
+        TypeButton(String label, EntryType type) {
+            super(label);
+            this.type = type;
+        }
+
+        @Override
+        public int compareTo(TypeButton o) {
+            return type.getName().compareTo(o.type.getName());
+        }
+
+        public EntryType getType() {
+            return type;
+        }
+    }
 
     class CancelAction extends AbstractAction {
         public CancelAction() {
@@ -290,7 +287,7 @@ protected Optional<BibEntry> doInBackground() throws Exception {
                 generateButton.setText(Localization.lang("Searching..."));
             });
             searchID = idTextField.getText().trim();
-            fetcher = EntryFetchers.getIdFetchers(Globals.prefs.getImportFormatPreferences()).get(comboBox.getSelectedIndex());
+            fetcher = WebFetchers.getIdBasedFetchers(Globals.prefs.getImportFormatPreferences()).get(comboBox.getSelectedIndex());
             if (!searchID.isEmpty()) {
                 try {
                     bibEntry = fetcher.performSearchById(searchID);

diff --git a/src/main/java/org/jabref/gui/actions/CopyDoiUrlAction.java b/src/main/java/org/jabref/gui/actions/CopyDoiUrlAction.java
@@ -8,8 +8,8 @@
 
 import org.jabref.JabRefGUI;
 import org.jabref.gui.ClipBoardManager;
-import org.jabref.logic.identifier.DOI;
 import org.jabref.logic.l10n.Localization;
+import org.jabref.model.entry.identifier.DOI;
 
 /**
  * Copies the doi url to the clipboard

diff --git a/src/main/java/org/jabref/gui/desktop/JabRefDesktop.java b/src/main/java/org/jabref/gui/desktop/JabRefDesktop.java
@@ -29,14 +29,14 @@
 import org.jabref.gui.filelist.FileListEntryEditor;
 import org.jabref.gui.filelist.FileListTableModel;
 import org.jabref.gui.undo.UndoableFieldChange;
-import org.jabref.logic.identifier.DOI;
-import org.jabref.logic.identifier.Eprint;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.logic.util.OS;
 import org.jabref.logic.util.io.FileUtil;
 import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.entry.BibEntry;
 import org.jabref.model.entry.FieldName;
+import org.jabref.model.entry.identifier.DOI;
+import org.jabref.model.entry.identifier.Eprint;
 import org.jabref.preferences.JabRefPreferences;
 
 import org.apache.commons.logging.Log;