Removed BibTeX file type and included HTML and Markdown types

CHANGELOG.md

@@ -45,6 +45,9 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - We fixed an issue where a message about changed metadata would occur on saving although nothing changed. [#9159](https://github.com/JabRef/jabref/issues/9159)
 - When adding or editing a subgroup it is placed w.r.t. to alphabetical ordering rather than at the end. [koppor#577](https://github.com/koppor/jabref/issues/577)
 - We modified the Directory of Open Access Books (DOAB) fetcher so that it will now also fetch the ISBN when possible. [#8708](https://github.com/JabRef/jabref/issues/8708)
+- We modified the "Delete file" dialog and add the full file path to the dialog text. The file path in the title was changed to file name only. [koppor#534](https://github.com/koppor/jabref/issues/534)
+- Download from URL now automatically fills with URL from clipboard. [koppor#535](https://github.com/koppor/jabref/issues/535)
+- We added HTML and Markdown files to Find Unlinked Files and removed BibTex. Markdown was added as a StandardFileType and StandardExternalFileType [koppor#547](https://github.com/koppor/jabref/issues/547)
 
 ### Fixed
 
@@ -768,10 +771,10 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - We fixed an issue where some importers used the field `pubstatus` instead of the standard BibTeX field `pubstate`.
 - We changed the latex command removal for docbook exporter. [#3838](https://github.com/JabRef/jabref/issues/3838)
 - We changed the location of some fields in the entry editor (you might need to reset your preferences for these changes to come into effect)
-  - Journal/Year/Month in biblatex mode -> Deprecated (if filled)
-  - DOI/URL: General -> Optional
-  - Internal fields like ranking, read status and priority: Other -> General
-  - Moreover, empty deprecated fields are no longer shown
+    - Journal/Year/Month in biblatex mode -> Deprecated (if filled)
+    - DOI/URL: General -> Optional
+    - Internal fields like ranking, read status and priority: Other -> General
+    - Moreover, empty deprecated fields are no longer shown
 - Added server timezone parameter when connecting to a shared database.
 - We updated the dialog for setting up general fields.
 - URL field formatting is updated. All whitespace chars, located at the beginning/ending of the URL, are trimmed automatically
@@ -903,12 +906,12 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - We removed the coloring of cells in the main table according to whether the field is optional/required.
 - We removed the feature to find and resolve duplicate BibTeX keys (as this use case is already covered by the integrity check).
 - We removed a few commands from the right-click menu that are not needed often and thus don't need to be placed that prominently:
-  - Print entry preview: available through entry preview
-  - All commands related to marking: marking is not yet reimplemented
-  - Set/clear/append/rename fields: available through Edit menu
-  - Manage keywords: available through the Edit menu
-  - Copy linked files to folder: available through File menu
-  - Add/move/remove from group: removed completely (functionality still available through group interface)
+    - Print entry preview: available through entry preview
+    - All commands related to marking: marking is not yet reimplemented
+    - Set/clear/append/rename fields: available through Edit menu
+    - Manage keywords: available through the Edit menu
+    - Copy linked files to folder: available through File menu
+    - Add/move/remove from group: removed completely (functionality still available through group interface)
 - We removed the option to change the column widths in the preferences dialog. [#4546](https://github.com/JabRef/jabref/issues/4546)
 
 ## Older versions

src/main/java/org/jabref/gui/externalfiles/UnlinkedFilesDialogViewModel.java

@@ -1,52 +1,36 @@
 package org.jabref.gui.externalfiles;
 
-import java.io.BufferedWriter;
-import java.io.IOException;
-import java.nio.charset.StandardCharsets;
-import java.nio.file.DirectoryStream.Filter;
-import java.nio.file.Files;
-import java.nio.file.Path;
-import java.nio.file.StandardOpenOption;
-import java.util.List;
-import java.util.Optional;
-import java.util.function.Predicate;
-import java.util.stream.Collectors;
-
-import javax.swing.undo.UndoManager;
-
-import javafx.beans.property.BooleanProperty;
-import javafx.beans.property.DoubleProperty;
-import javafx.beans.property.ObjectProperty;
-import javafx.beans.property.SimpleBooleanProperty;
-import javafx.beans.property.SimpleDoubleProperty;
-import javafx.beans.property.SimpleListProperty;
-import javafx.beans.property.SimpleObjectProperty;
-import javafx.beans.property.SimpleStringProperty;
-import javafx.beans.property.StringProperty;
+import de.saxsys.mvvmfx.utils.validation.FunctionBasedValidator;
+import de.saxsys.mvvmfx.utils.validation.ValidationMessage;
+import de.saxsys.mvvmfx.utils.validation.ValidationStatus;
+import javafx.beans.property.*;
 import javafx.collections.FXCollections;
 import javafx.collections.ObservableList;
 import javafx.scene.control.ProgressIndicator;
 import javafx.scene.control.TreeItem;
-
 import org.jabref.gui.DialogService;
 import org.jabref.gui.StateManager;
-import org.jabref.gui.util.BackgroundTask;
-import org.jabref.gui.util.DirectoryDialogConfiguration;
-import org.jabref.gui.util.FileDialogConfiguration;
-import org.jabref.gui.util.FileNodeViewModel;
-import org.jabref.gui.util.TaskExecutor;
+import org.jabref.gui.util.*;
 import org.jabref.logic.importer.ImportFormatReader;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.logic.util.StandardFileType;
 import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.util.FileUpdateMonitor;
 import org.jabref.preferences.PreferencesService;
-
-import de.saxsys.mvvmfx.utils.validation.FunctionBasedValidator;
-import de.saxsys.mvvmfx.utils.validation.ValidationMessage;
-import de.saxsys.mvvmfx.utils.validation.ValidationStatus;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
+import javax.swing.undo.UndoManager;
+import java.io.BufferedWriter;
+import java.io.IOException;
+import java.nio.charset.StandardCharsets;
+import java.nio.file.DirectoryStream.Filter;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.StandardOpenOption;
+import java.util.List;
+import java.util.Optional;
+import java.util.function.Predicate;
+import java.util.stream.Collectors;
 
 public class UnlinkedFilesDialogViewModel {
 
@@ -102,7 +86,8 @@ public UnlinkedFilesDialogViewModel(DialogService dialogService,
 
         this.fileFilterList = FXCollections.observableArrayList(
                 new FileExtensionViewModel(StandardFileType.ANY_FILE, preferences.getFilePreferences()),
-                new FileExtensionViewModel(StandardFileType.BIBTEX_DB, preferences.getFilePreferences()),
+                new FileExtensionViewModel(StandardFileType.HTML, preferences.getFilePreferences()),
+                new FileExtensionViewModel(StandardFileType.MARKDOWN, preferences.getFilePreferences()),
                 new FileExtensionViewModel(StandardFileType.PDF, preferences.getFilePreferences()));
 
         this.dateFilterList = FXCollections.observableArrayList(DateRange.values());

src/main/java/org/jabref/gui/externalfiletype/StandardExternalFileType.java

@@ -28,8 +28,8 @@ public enum StandardExternalFileType implements ExternalFileType {
     TIFF(Localization.lang("%0 image", "TIFF"), "tiff", "image/tiff", "gimp", "picture", IconTheme.JabRefIcons.PICTURE),
     URL("URL", "html", "text/html", "firefox", "www", IconTheme.JabRefIcons.WWW),
     MHT("MHT", "mht", "multipart/related", "firefox", "www", IconTheme.JabRefIcons.WWW),
-    ePUB("ePUB", "epub", "application/epub+zip", "firefox", "www", IconTheme.JabRefIcons.WWW);
-
+    ePUB("ePUB", "epub", "application/epub+zip", "firefox", "www", IconTheme.JabRefIcons.WWW),
+    MARKDOWN("Markdown", "md", "application/x-latex", "emacs", "emacs", IconTheme.JabRefIcons.FILE_TEXT);
     private final String name;
     private final String extension;
     private final String mimeType;

src/main/java/org/jabref/logic/util/StandardFileType.java

@@ -1,10 +1,9 @@
 package org.jabref.logic.util;
 
+import org.jabref.model.util.OptionalUtil;
 import java.util.Arrays;
 import java.util.List;
 
-import org.jabref.model.util.OptionalUtil;
-
 /**
  * @implNote Enter the extensions in lowercase without a dot! The dot is added implicitly.
  */
@@ -45,7 +44,9 @@ public enum StandardFileType implements FileType {
     CFF("CFF", "cff"),
     ANY_FILE("Any", "*"),
     CER("SSL Certificate", "cer"),
-    CITAVI("Citavi", "ctv6bak", "ctv5bak");
+    CITAVI("Citavi", "ctv6bak", "ctv5bak"),
+    MARKDOWN("Markdown", "md");
+    ;
 
 
 

src/main/java/org/jabref/logic/util/io/FileUtil.java

@@ -1,36 +1,21 @@
 package org.jabref.logic.util.io;
 
-import java.io.File;
-import java.io.IOException;
-import java.io.UncheckedIOException;
-import java.nio.file.CopyOption;
-import java.nio.file.FileSystems;
-import java.nio.file.Files;
-import java.nio.file.Path;
-import java.nio.file.StandardCopyOption;
-import java.nio.file.StandardOpenOption;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collections;
-import java.util.List;
-import java.util.Locale;
-import java.util.Objects;
-import java.util.Optional;
-import java.util.Stack;
-import java.util.Vector;
-import java.util.regex.Pattern;
-import java.util.stream.Collectors;
-import java.util.stream.Stream;
-
 import org.jabref.logic.citationkeypattern.BracketedPattern;
 import org.jabref.model.database.BibDatabase;
 import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.entry.BibEntry;
 import org.jabref.model.util.FileHelper;
 import org.jabref.model.util.OptionalUtil;
-
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
+import java.io.File;
+import java.io.IOException;
+import java.io.UncheckedIOException;
+import java.nio.file.*;
+import java.util.*;
+import java.util.regex.Pattern;
+import java.util.stream.Collectors;
+import java.util.stream.Stream;
 
 /**
  * The idea of this class is to add general functionality that could possibly even in the
@@ -380,15 +365,26 @@ public static boolean isBibFile(Path file) {
     }
 
     /**
-     * Test if the file is a bib file by simply checking the extension to be ".bib"
+     * Test if the file is a pdf file by simply checking the extension to be ".pdf"
      *
      * @param file The file to check
-     * @return True if file extension is ".bib", false otherwise
+     * @return True if file extension is ".pdf", false otherwise
      */
     public static boolean isPDFFile(Path file) {
         return getFileExtension(file).filter("pdf"::equals).isPresent();
     }
 
+    /**
+     * Test if the file is a html file by simply checking the extension to be ".html"
+     *
+     * @param file The file to check
+     * @return True if file extension is ".html", false otherwise
+     */
+    public static boolean isHTMLFile(Path file) {
+        return getFileExtension(file).filter("html"::equals).isPresent();
+    }
+
+
     /**
      * @return Path of current panel database directory or the standard working directory in case the database was not saved yet
      */