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

* upstream/master: Fix Some Codacy Code Convention Issues (#4904) Bump ridl from 6.2.2 to 6.2.3 (#4903) Bump juh from 6.2.2 to 6.2.3 (#4902) Bump jurt from 6.2.2 to 6.2.3 (#4901) Bump unoil from 6.2.2 to 6.2.3 (#4900) Bump richtextfx from 0.9.3 to 0.10.0 (#4899) Store column widths as integer (#4896) Improve full text search for several files (#4855)
JabRef · Apr 20, 2019 · 6342c8f · 6342c8f
2 parents b2971ed + 1c11575
commit 6342c8f
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Showing 8 changed files with 101 additions and 76 deletions.
diff --git a/build.gradle b/build.gradle
@@ -101,10 +101,10 @@ dependencies {
 
     compile 'commons-cli:commons-cli:1.4'
 
-    compile "org.libreoffice:juh:6.2.2"
-    compile "org.libreoffice:jurt:6.2.2"
-    compile "org.libreoffice:ridl:6.2.2"
-    compile "org.libreoffice:unoil:6.2.2"
+    compile "org.libreoffice:juh:6.2.3"
+    compile "org.libreoffice:jurt:6.2.3"
+    compile "org.libreoffice:ridl:6.2.3"
+    compile "org.libreoffice:unoil:6.2.3"
 
     compile 'io.github.java-diff-utils:java-diff-utils:4.0'
     compile 'info.debatty:java-string-similarity:1.2.1'
@@ -130,7 +130,7 @@ dependencies {
     compile 'de.saxsys:mvvmfx:1.8.0'
     compile 'org.fxmisc.easybind:easybind:1.0.3'
     compile 'org.fxmisc.flowless:flowless:0.6.1'
-    compile 'org.fxmisc.richtext:richtextfx:0.9.3'
+    compile 'org.fxmisc.richtext:richtextfx:0.10.0'
     compile 'com.sibvisions.external.jvxfx:dndtabpane:0.1'
     compile 'javax.inject:javax.inject:1'
     compile 'com.jfoenix:jfoenix:8.0.8'

diff --git a/src/main/java/org/jabref/gui/externalfiles/FindFullTextAction.java b/src/main/java/org/jabref/gui/externalfiles/FindFullTextAction.java
@@ -1,19 +1,24 @@
 package org.jabref.gui.externalfiles;
 
+import java.net.MalformedURLException;
 import java.net.URL;
 import java.nio.file.Path;
 import java.util.Map;
 import java.util.Optional;
 import java.util.concurrent.ConcurrentHashMap;
 
+import javafx.concurrent.Task;
+
 import org.jabref.Globals;
 import org.jabref.gui.BasePanel;
 import org.jabref.gui.DialogService;
 import org.jabref.gui.actions.SimpleCommand;
 import org.jabref.gui.fieldeditors.LinkedFileViewModel;
+import org.jabref.gui.fieldeditors.LinkedFilesEditorViewModel;
 import org.jabref.gui.util.BackgroundTask;
 import org.jabref.logic.importer.FulltextFetchers;
 import org.jabref.logic.l10n.Localization;
+import org.jabref.logic.net.URLDownload;
 import org.jabref.model.entry.BibEntry;
 import org.jabref.model.entry.LinkedFile;
 import org.jabref.preferences.JabRefPreferences;
@@ -63,18 +68,29 @@ public void execute() {
                 return;
             }
         }
-        BackgroundTask.wrap(this::findFullTexts)
-                      .onSuccess(this::downloadFullTexts)
-                      .executeWith(Globals.TASK_EXECUTOR);
-    }
 
-    private Map<Optional<URL>, BibEntry> findFullTexts() {
-        Map<Optional<URL>, BibEntry> downloads = new ConcurrentHashMap<>();
-        for (BibEntry entry : basePanel.getSelectedEntries()) {
-            FulltextFetchers fetchers = new FulltextFetchers(Globals.prefs.getImportFormatPreferences());
-            downloads.put(fetchers.findFullTextPDF(entry), entry);
-        }
-        return downloads;
+        Task<Map<Optional<URL>, BibEntry>> findFullTextsTask = new Task<Map<Optional<URL>, BibEntry>>() {
+            @Override
+            protected Map<Optional<URL>, BibEntry> call() {
+                Map<Optional<URL>, BibEntry> downloads = new ConcurrentHashMap<>();
+                int count = 0;
+                for (BibEntry entry : basePanel.getSelectedEntries()) {
+                    FulltextFetchers fetchers = new FulltextFetchers(Globals.prefs.getImportFormatPreferences());
+                    downloads.put(fetchers.findFullTextPDF(entry), entry);
+                    updateProgress(++count, basePanel.getSelectedEntries().size());
+                }
+                return downloads;
+            }
+        };
+
+        findFullTextsTask.setOnSucceeded(value -> downloadFullTexts(findFullTextsTask.getValue()));
+
+        dialogService.showProgressDialogAndWait(
+                Localization.lang("Look up full text documents"),
+                Localization.lang("Looking for full text document..."),
+                findFullTextsTask);
+
+        Globals.TASK_EXECUTOR.execute(findFullTextsTask);
     }
 
     private void downloadFullTexts(Map<Optional<URL>, BibEntry> downloads) {
@@ -92,7 +108,7 @@ private void downloadFullTexts(Map<Optional<URL>, BibEntry> downloads) {
                     return;
                 }
                 //Download and link full text
-                addLinkedFileFromURL(result.get(), entry);
+                addLinkedFileFromURL(result.get(), entry, dir.get());
 
             } else {
                 dialogService.notify(Localization.lang("No full text document found for entry %0.",
@@ -103,12 +119,13 @@ private void downloadFullTexts(Map<Optional<URL>, BibEntry> downloads) {
 
     /**
      * This method attaches a linked file from a URL (if not already linked) to an entry using the key and value pair
-     * from the findFullTexts map
+     * from the findFullTexts map and then downloads the file into the given targetDirectory
      *
      * @param url   the url "key"
      * @param entry the entry "value"
+     * @param targetDirectory the target directory for the downloaded file
      */
-    private void addLinkedFileFromURL(URL url, BibEntry entry) {
+    private void addLinkedFileFromURL(URL url, BibEntry entry, Path targetDirectory) {
         LinkedFile newLinkedFile = new LinkedFile(url, "");
 
         if (!entry.getFiles().contains(newLinkedFile)) {
@@ -121,12 +138,21 @@ private void addLinkedFileFromURL(URL url, BibEntry entry) {
                     dialogService,
                     JabRefPreferences.getInstance());
 
-            onlineFile.download();
-
-            entry.addFile(onlineFile.getFile());
-
-            dialogService.notify(Localization.lang("Finished downloading full text document for entry %0.",
-                    entry.getCiteKeyOptional().orElse(Localization.lang("undefined"))));
+            try {
+                URLDownload urlDownload = new URLDownload(newLinkedFile.getLink());
+                BackgroundTask<Path> downloadTask = onlineFile.prepareDownloadTask(targetDirectory, urlDownload);
+                downloadTask.onSuccess(destination -> {
+                    LinkedFile downloadedFile = LinkedFilesEditorViewModel.fromFile(
+                            destination,
+                            basePanel.getBibDatabaseContext().getFileDirectoriesAsPaths(JabRefPreferences.getInstance().getFilePreferences()));
+                    entry.addFile(downloadedFile);
+                    dialogService.notify(Localization.lang("Finished downloading full text document for entry %0.",
+                            entry.getCiteKeyOptional().orElse(Localization.lang("undefined"))));
+                });
+                Globals.TASK_EXECUTOR.execute(downloadTask);
+            } catch (MalformedURLException exception) {
+                dialogService.showErrorDialogAndWait(Localization.lang("Invalid URL"), exception);
+            }
         } else {
             dialogService.notify(Localization.lang("Full text document for entry %0 already linked.",
                     entry.getCiteKeyOptional().orElse(Localization.lang("undefined"))));

diff --git a/src/main/java/org/jabref/gui/fieldeditors/LinkedFileViewModel.java b/src/main/java/org/jabref/gui/fieldeditors/LinkedFileViewModel.java
@@ -394,7 +394,6 @@ public void download() {
         if (!linkedFile.isOnlineLink()) {
             throw new UnsupportedOperationException("In order to download the file it has to be an online link");
         }
-
         try {
             Optional<Path> targetDirectory = databaseContext.getFirstExistingFileDir(filePreferences);
             if (!targetDirectory.isPresent()) {
@@ -403,30 +402,34 @@ public void download() {
             }
 
             URLDownload urlDownload = new URLDownload(linkedFile.getLink());
-            BackgroundTask<Path> downloadTask = BackgroundTask
-                    .wrap(() -> {
-                        Optional<ExternalFileType> suggestedType = inferFileType(urlDownload);
-                        String suggestedTypeName = suggestedType.map(ExternalFileType::getName).orElse("");
-                        linkedFile.setFileType(suggestedTypeName);
-
-                        String suggestedName = linkedFileHandler.getSuggestedFileName();
-                        return targetDirectory.get().resolve(suggestedName);
-                    })
-                    .then(destination -> new FileDownloadTask(urlDownload.getSource(), destination))
-                    .onSuccess(destination -> {
-                        LinkedFile newLinkedFile = LinkedFilesEditorViewModel.fromFile(destination, databaseContext.getFileDirectoriesAsPaths(filePreferences));
-                        linkedFile.setLink(newLinkedFile.getLink());
-                        linkedFile.setFileType(newLinkedFile.getFileType());
-                    })
-                    .onFailure(exception -> dialogService.showErrorDialogAndWait("Download failed", exception));
-
+            BackgroundTask<Path> downloadTask = prepareDownloadTask(targetDirectory.get(), urlDownload);
+            downloadTask.onSuccess(destination -> {
+                LinkedFile newLinkedFile = LinkedFilesEditorViewModel.fromFile(destination, databaseContext.getFileDirectoriesAsPaths(filePreferences));
+                linkedFile.setLink(newLinkedFile.getLink());
+                linkedFile.setFileType(newLinkedFile.getFileType());
+            });
             downloadProgress.bind(downloadTask.workDonePercentageProperty());
             taskExecutor.execute(downloadTask);
         } catch (MalformedURLException exception) {
             dialogService.showErrorDialogAndWait(Localization.lang("Invalid URL"), exception);
         }
     }
 
+    public BackgroundTask<Path> prepareDownloadTask(Path targetDirectory, URLDownload urlDownload) {
+        BackgroundTask<Path> downloadTask = BackgroundTask
+                .wrap(() -> {
+                    Optional<ExternalFileType> suggestedType = inferFileType(urlDownload);
+                    String suggestedTypeName = suggestedType.map(ExternalFileType::getName).orElse("");
+                    linkedFile.setFileType(suggestedTypeName);
+
+                    String suggestedName = linkedFileHandler.getSuggestedFileName();
+                    return targetDirectory.resolve(suggestedName);
+                })
+                .then(destination -> new FileDownloadTask(urlDownload.getSource(), destination))
+                .onFailure(exception -> dialogService.showErrorDialogAndWait("Download failed", exception));
+        return downloadTask;
+    }
+
     private Optional<ExternalFileType> inferFileType(URLDownload urlDownload) {
         Optional<ExternalFileType> suggestedType = inferFileTypeFromMimeType(urlDownload);
 

diff --git a/src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesDialogView.java b/src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesDialogView.java
@@ -72,7 +72,7 @@ private void initialize() {
 
         generalFileDirectory.textProperty().bindBidirectional(viewModel.generalFileDirectoryPropertyProperty());
         userSpecificFileDirectory.textProperty().bindBidirectional(viewModel.userSpecificFileDirectoryProperty());
-        laTexFileDirectory.textProperty().bindBidirectional(viewModel.LaTexFileDirectoryProperty());
+        laTexFileDirectory.textProperty().bindBidirectional(viewModel.laTexFileDirectoryProperty());
 
         encoding.itemsProperty().bind(viewModel.encodingsProperty());
         encoding.valueProperty().bindBidirectional(viewModel.selectedEncodingProperty());
@@ -142,7 +142,7 @@ private void storeSettings() {
             metaData.setUserFileDirectory(preferencesService.getUser(), text);
         }
 
-        text = viewModel.LaTexFileDirectoryProperty().getValue();
+        text = viewModel.laTexFileDirectoryProperty().getValue();
         if (text.isEmpty()) {
             metaData.clearLaTexFileDirectory(preferencesService.getUser());
         } else {
@@ -180,7 +180,7 @@ private void storeSettings() {
 
         boolean changed = saveOrderConfigChanged || encodingChanged
                           || viewModel.generalFileDirChanged() || viewModel.userFileDirChanged()
-                          || viewModel.protectedValueChanged() || saveActionsChanged || viewModel.LaTexFileDirChanged();
+                          || viewModel.protectedValueChanged() || saveActionsChanged || viewModel.laTexFileDirChanged();
         // ... if so, mark base changed. Prevent the Undo button from removing
         // change marking:
         if (changed) {

diff --git a/src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesDialogViewModel.java b/src/main/java/org/jabref/gui/libraryproperties/LibraryPropertiesDialogViewModel.java
@@ -80,7 +80,7 @@ public StringProperty userSpecificFileDirectoryProperty() {
         return this.userSpecificFileDirectoryProperty;
     }
 
-    public StringProperty LaTexFileDirectoryProperty() {
+    public StringProperty laTexFileDirectoryProperty() {
         return this.laTexFileDirectoryProperty;
     }
 
@@ -116,7 +116,7 @@ public boolean userFileDirChanged() {
         return !oldUserSpecificFileDir.equals(userSpecificFileDirectoryProperty.getValue());
     }
 
-    public boolean LaTexFileDirChanged() {
+    public boolean laTexFileDirChanged() {
         return !oldLaTexFileDir.equals(laTexFileDirectoryProperty.getValue());
     }
 

diff --git a/src/main/java/org/jabref/gui/maintable/PersistenceVisualStateTable.java b/src/main/java/org/jabref/gui/maintable/PersistenceVisualStateTable.java
@@ -61,12 +61,12 @@ private void updateColumnPreferences() {
                 NormalTableColumn normalColumn = (NormalTableColumn) column;
 
                 columnNames.add(normalColumn.getColumnName());
-                columnsWidths.add(String.valueOf(normalColumn.getWidth()));
+                columnsWidths.add(String.valueOf(Double.valueOf(normalColumn.getWidth()).intValue()));
             }
         }
 
-        if (columnNames.size() == columnsWidths.size() &&
-                columnNames.size() == preferences.getStringList(JabRefPreferences.COLUMN_NAMES).size()) {
+        if ((columnNames.size() == columnsWidths.size()) &&
+                (columnNames.size() == preferences.getStringList(JabRefPreferences.COLUMN_NAMES).size())) {
             preferences.putStringList(JabRefPreferences.COLUMN_NAMES, columnNames);
             preferences.putStringList(JabRefPreferences.COLUMN_WIDTHS, columnsWidths);
         }

diff --git a/src/main/java/org/jabref/gui/preferences/TableColumnsTab.java b/src/main/java/org/jabref/gui/preferences/TableColumnsTab.java
@@ -502,7 +502,7 @@ public void storeSettings() {
 
             for (TableRow tr : data) {
                 names.add(tr.getName().toLowerCase(Locale.ROOT));
-                widths.add(String.valueOf(tr.getLength()));
+                widths.add(String.valueOf(Double.valueOf(tr.getLength()).intValue()));
             }
 
             // Finally, we store the new preferences.
@@ -522,14 +522,14 @@ private void updateOrderAction() {
         final HashMap<String, Integer> map = new HashMap<>();
 
         // first element (#) not inside data
-            /*
-            for (TableColumn<BibEntry, ?> column : panel.getMainTable().getColumns()) {
-                String name = column.getText();
-                if ((name != null) && !name.isEmpty()) {
-                    map.put(name.toLowerCase(Locale.ROOT), i);
-                }
+        /*
+        for (TableColumn<BibEntry, ?> column : panel.getMainTable().getColumns()) {
+            String name = column.getText();
+            if ((name != null) && !name.isEmpty()) {
+                map.put(name.toLowerCase(Locale.ROOT), i);
             }
-            */
+        }
+        */
         data.sort((o1, o2) -> {
             Integer n1 = map.get(o1.getName());
             Integer n2 = map.get(o2.getName());

diff --git a/src/main/java/org/jabref/logic/auxparser/DefaultAuxParser.java b/src/main/java/org/jabref/logic/auxparser/DefaultAuxParser.java
@@ -24,16 +24,13 @@
 /**
  * LaTeX Aux to BibTeX Parser
  * <p>
- * Extracts a subset of BibTeX entries from a BibDatabase that are included in an AUX file.
- * Also supports nested AUX files (latex \\include).
+ * Extracts a subset of BibTeX entries from a BibDatabase that are included in an AUX file. Also supports nested AUX
+ * files (latex \\include).
  *
- * There exists no specification of the AUX file.
- * Every package, class or document can write to the AUX file.
- * The AUX file consists of LaTeX macros and is read at the \begin{document} and again at the \end{document}.
+ * There exists no specification of the AUX file. Every package, class or document can write to the AUX file. The AUX
+ * file consists of LaTeX macros and is read at the \begin{document} and again at the \end{document}.
  *
- * BibTeX citation: \citation{x,y,z}
- * Biblatex citation: \abx@aux@cite{x,y,z}
- * Nested AUX files: \@input{x}
+ * BibTeX citation: \citation{x,y,z} Biblatex citation: \abx@aux@cite{x,y,z} Nested AUX files: \@input{x}
  */
 public class DefaultAuxParser implements AuxParser {
     private static final Logger LOGGER = LoggerFactory.getLogger(DefaultAuxParser.class);
@@ -128,15 +125,14 @@ private void matchCitation(AuxParserResult result, String line) {
      */
     private void resolveTags(AuxParserResult result) {
         for (String key : result.getUniqueKeys()) {
-            Optional<BibEntry> entry = masterDatabase.getEntryByKey(key);
-
-            if (result.getGeneratedBibDatabase().getEntryByKey(key).isPresent()) {
-                // do nothing, key has already been processed
-            } else if (entry.isPresent()) {
-                insertEntry(entry.get(), result);
-                resolveCrossReferences(entry.get(), result);
-            } else {
-                result.getUnresolvedKeys().add(key);
+            if (!result.getGeneratedBibDatabase().getEntryByKey(key).isPresent()) {
+                Optional<BibEntry> entry = masterDatabase.getEntryByKey(key);
+                if (entry.isPresent()) {
+                    insertEntry(entry.get(), result);
+                    resolveCrossReferences(entry.get(), result);
+                } else {
+                    result.getUnresolvedKeys().add(key);
+                }
             }
         }