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

* upstream/master: Add oaDOI fulltext fetcher (#3581) Refactor export code to fix #3576 (#3578) Fix #3359: Automatically remove colon and apostrophe from key pattern (#3506)
JabRef · Jan 2, 2018 · d3daaa6 · d3daaa6
2 parents e71181a + b246b9c
commit d3daaa6
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -12,9 +12,11 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 ## [Unreleased]
 
 ### Changed
+- We added [oaDOI](https://oadoi.org/) as a fulltext provider, so that JabRef is now able to provide fulltexts for more than 90 million open-access articles.
 
 
 ### Fixed
+- We fixed the missing dot in the name of an exported file. [#3576](https://github.com/JabRef/jabref/issues/3576)
 
 ### Removed
 - We removed the Look and Feels from jgoodies, because these are not compatible with Java 9
@@ -126,6 +128,7 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
  - We fixed an issue where fetched entries from the ACM fetcher could not be imported. [#3500](https://github.com/JabRef/jabref/issues/3500)
  - We fixed an issue where custom data in combobox fields in the entry editor was not saved. [#3538](https://github.com/JabRef/jabref/issues/3538)
  - We fixed an issue where automatically found files were not added with a relative paths when the bib file is in the same directory as the files. [#3476](https://github.com/JabRef/jabref/issues/3476)
+ - We improved the key generator to remove certain illegal characters such as colons or apostrophes. [#3359](https://github.com/JabRef/jabref/issues/3359)
 
 
 ## [4.0] - 2017-10-04

diff --git a/src/main/java/org/jabref/Globals.java b/src/main/java/org/jabref/Globals.java
@@ -10,6 +10,7 @@
 import org.jabref.gui.util.DefaultTaskExecutor;
 import org.jabref.gui.util.FileUpdateMonitor;
 import org.jabref.gui.util.TaskExecutor;
+import org.jabref.logic.exporter.ExporterFactory;
 import org.jabref.logic.importer.ImportFormatReader;
 import org.jabref.logic.journals.JournalAbbreviationLoader;
 import org.jabref.logic.protectedterms.ProtectedTermsLoader;
@@ -48,6 +49,7 @@ public class Globals {
      * Manager for the state of the GUI.
      */
     public static StateManager stateManager = new StateManager();
+    public static ExporterFactory exportFactory;
     // Key binding preferences
     private static KeyBindingRepository keyBindingRepository;
     // Background tasks

diff --git a/src/main/java/org/jabref/JabRefMain.java b/src/main/java/org/jabref/JabRefMain.java
@@ -1,7 +1,6 @@
 package org.jabref;
 
 import java.net.Authenticator;
-import java.util.Map;
 
 import javax.swing.JFrame;
 import javax.swing.JOptionPane;
@@ -13,13 +12,10 @@
 
 import org.jabref.cli.ArgumentProcessor;
 import org.jabref.gui.remote.JabRefMessageHandler;
-import org.jabref.logic.exporter.ExportFormat;
-import org.jabref.logic.exporter.ExportFormats;
-import org.jabref.logic.exporter.SavePreferences;
+import org.jabref.logic.exporter.ExporterFactory;
 import org.jabref.logic.formatter.casechanger.ProtectTermsFormatter;
 import org.jabref.logic.journals.JournalAbbreviationLoader;
 import org.jabref.logic.l10n.Localization;
-import org.jabref.logic.layout.LayoutFormatterPreferences;
 import org.jabref.logic.net.ProxyAuthenticator;
 import org.jabref.logic.net.ProxyPreferences;
 import org.jabref.logic.net.ProxyRegisterer;
@@ -147,12 +143,7 @@ private static void start(String[] args) {
                 Globals.prefs.getXMPPreferences());
         EntryTypes.loadCustomEntryTypes(preferences.loadCustomEntryTypes(BibDatabaseMode.BIBTEX),
                 preferences.loadCustomEntryTypes(BibDatabaseMode.BIBLATEX));
-        Map<String, ExportFormat> customFormats = Globals.prefs.customExports.getCustomExportFormats(Globals.prefs,
-                Globals.journalAbbreviationLoader);
-        LayoutFormatterPreferences layoutPreferences = Globals.prefs
-                .getLayoutFormatterPreferences(Globals.journalAbbreviationLoader);
-        SavePreferences savePreferences = SavePreferences.loadForExportFromPreferences(Globals.prefs);
-        ExportFormats.initAllExports(customFormats, layoutPreferences, savePreferences);
+        Globals.exportFactory = ExporterFactory.create(Globals.prefs, Globals.journalAbbreviationLoader);
 
         // Initialize protected terms loader
         Globals.protectedTermsLoader = new ProtectedTermsLoader(Globals.prefs.getProtectedTermsPreferences());

diff --git a/src/main/java/org/jabref/cli/ArgumentProcessor.java b/src/main/java/org/jabref/cli/ArgumentProcessor.java
@@ -18,16 +18,16 @@
 import org.jabref.gui.externalfiles.AutoSetLinks;
 import org.jabref.gui.importer.fetcher.EntryFetcher;
 import org.jabref.gui.importer.fetcher.EntryFetchers;
-import org.jabref.logic.bibtexkeypattern.BibtexKeyPatternUtil;
+import org.jabref.logic.bibtexkeypattern.BibtexKeyGenerator;
 import org.jabref.logic.exporter.BibDatabaseWriter;
 import org.jabref.logic.exporter.BibtexDatabaseWriter;
-import org.jabref.logic.exporter.ExportFormat;
-import org.jabref.logic.exporter.ExportFormats;
+import org.jabref.logic.exporter.Exporter;
+import org.jabref.logic.exporter.ExporterFactory;
 import org.jabref.logic.exporter.FileSaveSession;
-import org.jabref.logic.exporter.IExportFormat;
 import org.jabref.logic.exporter.SaveException;
 import org.jabref.logic.exporter.SavePreferences;
 import org.jabref.logic.exporter.SaveSession;
+import org.jabref.logic.exporter.TemplateExporter;
 import org.jabref.logic.importer.ImportException;
 import org.jabref.logic.importer.ImportFormatReader;
 import org.jabref.logic.importer.OpenDatabase;
@@ -47,7 +47,6 @@
 import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.database.BibDatabaseMode;
 import org.jabref.model.entry.BibEntry;
-import org.jabref.model.metadata.MetaData;
 import org.jabref.model.strings.StringUtil;
 import org.jabref.preferences.SearchPreferences;
 
@@ -250,7 +249,7 @@ private boolean exportMatches(List<ParserResult> loaded) {
                 formatName = data[2];
                 break;
             case 2:
-                //default ExportFormat: HTML table (with Abstract & BibTeX)
+                //default exporter: HTML table (with Abstract & BibTeX)
                 formatName = "tablerefsabsbib";
                 break;
             default:
@@ -261,14 +260,14 @@ private boolean exportMatches(List<ParserResult> loaded) {
             }
 
             //export new database
-            IExportFormat format = ExportFormats.getExportFormat(formatName);
-            if (format == null) {
+            Optional<Exporter> exporter = Globals.exportFactory.getExporterByName(formatName);
+            if (!exporter.isPresent()) {
                 System.err.println(Localization.lang("Unknown export format") + ": " + formatName);
             } else {
-                // We have an ExportFormat instance:
+                // We have an TemplateExporter instance:
                 try {
                     System.out.println(Localization.lang("Exporting") + ": " + data[1]);
-                    format.performExport(databaseContext, data[1],
+                    exporter.get().export(databaseContext, Paths.get(data[1]),
                             databaseContext.getMetaData().getEncoding().orElse(Globals.prefs.getDefaultEncoding()),
                             matches);
                 } catch (Exception ex) {
@@ -438,18 +437,17 @@ private void exportFile(List<ParserResult> loaded, String[] data) {
             Globals.prefs.fileDirForDatabase = databaseContext
                     .getFileDirectories(Globals.prefs.getFileDirectoryPreferences());
             System.out.println(Localization.lang("Exporting") + ": " + data[0]);
-            IExportFormat format = ExportFormats.getExportFormat(data[1]);
-            if (format == null) {
+            Optional<Exporter> exporter = Globals.exportFactory.getExporterByName(data[1]);
+            if (!exporter.isPresent()) {
                 System.err.println(Localization.lang("Unknown export format") + ": " + data[1]);
             } else {
-                // We have an ExportFormat instance:
+                // We have an exporter:
                 try {
-                    format.performExport(pr.getDatabaseContext(), data[0],
+                    exporter.get().export(pr.getDatabaseContext(), Paths.get(data[0]),
                             pr.getDatabaseContext().getMetaData().getEncoding()
                                     .orElse(Globals.prefs.getDefaultEncoding()),
                             pr.getDatabaseContext().getDatabase().getEntries());
                 } catch (Exception ex) {
-
                     System.err.println(Localization.lang("Could not export file") + " '" + data[0] + "': "
                             + Throwables.getStackTraceAsString(ex));
                 }
@@ -463,12 +461,12 @@ private void importPreferences() {
             Globals.prefs.importPreferences(cli.getPreferencesImport());
             EntryTypes.loadCustomEntryTypes(Globals.prefs.loadCustomEntryTypes(BibDatabaseMode.BIBTEX),
                     Globals.prefs.loadCustomEntryTypes(BibDatabaseMode.BIBLATEX));
-            Map<String, ExportFormat> customFormats = Globals.prefs.customExports.getCustomExportFormats(Globals.prefs,
+            Map<String, TemplateExporter> customExporters = Globals.prefs.customExports.getCustomExportFormats(Globals.prefs,
                     Globals.journalAbbreviationLoader);
             LayoutFormatterPreferences layoutPreferences = Globals.prefs
                     .getLayoutFormatterPreferences(Globals.journalAbbreviationLoader);
             SavePreferences savePreferences = SavePreferences.loadForExportFromPreferences(Globals.prefs);
-            ExportFormats.initAllExports(customFormats, layoutPreferences, savePreferences);
+            Globals.exportFactory = ExporterFactory.create(customExporters, layoutPreferences, savePreferences);
         } catch (JabRefException ex) {
             LOGGER.error("Cannot import preferences", ex);
         }
@@ -509,17 +507,11 @@ private void regenerateBibtexKeys(List<ParserResult> loaded) {
         for (ParserResult parserResult : loaded) {
             BibDatabase database = parserResult.getDatabase();
 
-            MetaData metaData = parserResult.getMetaData();
-            if (metaData != null) {
-                LOGGER.info(Localization.lang("Regenerating BibTeX keys according to metadata"));
-                for (BibEntry entry : database.getEntries()) {
-                    // try to make a new label
-                    BibtexKeyPatternUtil.makeAndSetLabel(
-                            metaData.getCiteKeyPattern(Globals.prefs.getBibtexKeyPatternPreferences().getKeyPattern()),
-                            database, entry, Globals.prefs.getBibtexKeyPatternPreferences());
-                }
-            } else {
-                LOGGER.info(Localization.lang("No meta data present in BIB file. Cannot regenerate BibTeX keys"));
+            LOGGER.info(Localization.lang("Regenerating BibTeX keys according to metadata"));
+
+            BibtexKeyGenerator keyGenerator = new BibtexKeyGenerator(parserResult.getDatabaseContext(), Globals.prefs.getBibtexKeyPatternPreferences());
+            for (BibEntry entry : database.getEntries()) {
+                keyGenerator.generateAndSetKey(entry);
             }
         }
     }

diff --git a/src/main/java/org/jabref/cli/JabRefCLI.java b/src/main/java/org/jabref/cli/JabRefCLI.java
@@ -4,7 +4,6 @@
 import java.util.List;
 
 import org.jabref.Globals;
-import org.jabref.logic.exporter.ExportFormats;
 import org.jabref.logic.l10n.Localization;
 
 import org.apache.commons.cli.CommandLine;
@@ -246,7 +245,7 @@ public void printUsage() {
         String importFormats = Globals.IMPORT_FORMAT_READER.getImportFormatList();
         String importFormatsList = String.format("%s:%n%s%n", Localization.lang("Available import formats"), importFormats);
 
-        String outFormats = ExportFormats.getConsoleExportList(70, 20, "");
+        String outFormats = Globals.exportFactory.getExportersAsString(70, 20, "");
         String outFormatsList = String.format("%s: %s%n", Localization.lang("Available export formats"), outFormats);
 
         String footer = '\n' + importFormatsList + outFormatsList + "\nPlease report issues at https://github.com/JabRef/jabref/issues.";

diff --git a/src/main/java/org/jabref/gui/BasePanel.java b/src/main/java/org/jabref/gui/BasePanel.java
@@ -102,7 +102,7 @@
 import org.jabref.gui.worker.CitationStyleToClipboardWorker;
 import org.jabref.gui.worker.MarkEntriesAction;
 import org.jabref.gui.worker.SendAsEMailAction;
-import org.jabref.logic.bibtexkeypattern.BibtexKeyPatternUtil;
+import org.jabref.logic.bibtexkeypattern.BibtexKeyGenerator;
 import org.jabref.logic.citationstyle.CitationStyleCache;
 import org.jabref.logic.citationstyle.CitationStyleOutputFormat;
 import org.jabref.logic.exporter.BibtexDatabaseWriter;
@@ -116,13 +116,12 @@
 import org.jabref.logic.layout.LayoutHelper;
 import org.jabref.logic.pdf.FileAnnotationCache;
 import org.jabref.logic.search.SearchQuery;
-import org.jabref.logic.util.FileExtensions;
+import org.jabref.logic.util.FileType;
 import org.jabref.logic.util.UpdateField;
 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.FieldChange;
-import org.jabref.model.bibtexkeypattern.AbstractBibtexKeyPattern;
 import org.jabref.model.database.BibDatabase;
 import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.database.KeyCollisionException;
@@ -140,6 +139,7 @@
 import org.jabref.model.entry.event.EntryEventSource;
 import org.jabref.model.entry.specialfields.SpecialField;
 import org.jabref.model.entry.specialfields.SpecialFieldValue;
+import org.jabref.model.strings.StringUtil;
 import org.jabref.preferences.JabRefPreferences;
 import org.jabref.preferences.PreviewPreferences;
 
@@ -489,16 +489,10 @@ public void run() {
 
                 // generate the new cite keys for each entry
                 final NamedCompound ce = new NamedCompound(Localization.lang("Autogenerate BibTeX keys"));
-                AbstractBibtexKeyPattern citeKeyPattern = bibDatabaseContext.getMetaData()
-                        .getCiteKeyPattern(Globals.prefs.getBibtexKeyPatternPreferences().getKeyPattern());
+                BibtexKeyGenerator keyGenerator = new BibtexKeyGenerator(bibDatabaseContext, Globals.prefs.getBibtexKeyPatternPreferences());
                 for (BibEntry entry : entries) {
-                    String oldCiteKey = entry.getCiteKeyOptional().orElse("");
-                    BibtexKeyPatternUtil.makeAndSetLabel(citeKeyPattern, bibDatabaseContext.getDatabase(),
-                            entry, Globals.prefs.getBibtexKeyPatternPreferences());
-                    String newCiteKey = entry.getCiteKeyOptional().orElse("");
-                    if (!oldCiteKey.equals(newCiteKey)) {
-                        ce.addEdit(new UndoableKeyChange(entry, oldCiteKey, newCiteKey));
-                    }
+                    Optional<FieldChange> change = keyGenerator.generateAndSetKey(entry);
+                    change.ifPresent(fieldChange -> ce.addEdit(new UndoableKeyChange(fieldChange)));
                 }
                 ce.end();
 
@@ -1754,15 +1748,12 @@ public void autoGenerateKeysBeforeSaving() {
         if (Globals.prefs.getBoolean(JabRefPreferences.GENERATE_KEYS_BEFORE_SAVING)) {
             NamedCompound ce = new NamedCompound(Localization.lang("Autogenerate BibTeX keys"));
 
+            BibtexKeyGenerator keyGenerator = new BibtexKeyGenerator(bibDatabaseContext, Globals.prefs.getBibtexKeyPatternPreferences());
             for (BibEntry bes : bibDatabaseContext.getDatabase().getEntries()) {
                 Optional<String> oldKey = bes.getCiteKeyOptional();
-                if (!(oldKey.isPresent()) || oldKey.get().isEmpty()) {
-                    BibtexKeyPatternUtil.makeAndSetLabel(bibDatabaseContext.getMetaData()
-                            .getCiteKeyPattern(Globals.prefs.getBibtexKeyPatternPreferences().getKeyPattern()),
-                            bibDatabaseContext.getDatabase(),
-                            bes, Globals.prefs.getBibtexKeyPatternPreferences());
-                    bes.getCiteKeyOptional().ifPresent(
-                            newKey -> ce.addEdit(new UndoableKeyChange(bes, oldKey.orElse(""), newKey)));
+                if (StringUtil.isBlank(oldKey)) {
+                    Optional<FieldChange> change = keyGenerator.generateAndSetKey(bes);
+                    change.ifPresent(fieldChange -> ce.addEdit(new UndoableKeyChange(fieldChange)));
                 }
             }
 
@@ -2230,8 +2221,8 @@ public SaveSelectedAction(SavePreferences.DatabaseSaveType saveType) {
         @Override
         public void action() throws SaveException {
             FileDialogConfiguration fileDialogConfiguration = new FileDialogConfiguration.Builder()
-                    .withDefaultExtension(FileExtensions.BIBTEX_DB)
-                    .addExtensionFilter(FileExtensions.BIBTEX_DB)
+                    .withDefaultExtension(FileType.BIBTEX_DB)
+                    .addExtensionFilter(FileType.BIBTEX_DB)
                     .withInitialDirectory(Globals.prefs.get(JabRefPreferences.WORKING_DIRECTORY)).build();
 
             DialogService ds = new FXDialogService();