From 72cd809a8d711dfc00b861c5266f8e25e0130294 Mon Sep 17 00:00:00 2001
From: Siedlerchr <siedlerkiller@gmail.com>
Date: Mon, 25 Jan 2021 20:52:35 +0100
Subject: [PATCH 1/5] Fix File Filter and some layout issues

Fixes part of #7383
---
 .../externalfiles/FileExtensionViewModel.java |  2 +-
 .../externalfiles/UnlinkedFilesCrawler.java   |  2 +-
 .../externalfiles/UnlinkedFilesDialog.fxml    | 10 +--
 .../externalfiles/UnlinkedPDFFileFilter.java  |  8 +-
 .../java/org/jabref/logic/util/FileType.java  |  2 +
 .../jabref/logic/util/StandardFileType.java   | 78 ++++++++++---------
 .../jabref/logic/util/UnknownFileType.java    |  5 ++
 .../logic/util/io/DatabaseFileLookup.java     |  6 +-
 8 files changed, 66 insertions(+), 47 deletions(-)

diff --git a/src/main/java/org/jabref/gui/externalfiles/FileExtensionViewModel.java b/src/main/java/org/jabref/gui/externalfiles/FileExtensionViewModel.java
index f1f51862c30..121517bf5bc 100644
--- a/src/main/java/org/jabref/gui/externalfiles/FileExtensionViewModel.java
+++ b/src/main/java/org/jabref/gui/externalfiles/FileExtensionViewModel.java
@@ -19,7 +19,7 @@ public class FileExtensionViewModel {
     private final ExternalFileTypes externalFileTypes;
 
     FileExtensionViewModel(FileType fileType, ExternalFileTypes externalFileTypes) {
-        this.description = Localization.lang("%0 file", fileType.toString());
+        this.description = Localization.lang("%0 file", fileType.getName());
         this.extensions = fileType.getExtensionsWithDot();
         this.externalFileTypes = externalFileTypes;
     }
diff --git a/src/main/java/org/jabref/gui/externalfiles/UnlinkedFilesCrawler.java b/src/main/java/org/jabref/gui/externalfiles/UnlinkedFilesCrawler.java
index 60d89246e1b..4b29a57204f 100644
--- a/src/main/java/org/jabref/gui/externalfiles/UnlinkedFilesCrawler.java
+++ b/src/main/java/org/jabref/gui/externalfiles/UnlinkedFilesCrawler.java
@@ -74,7 +74,7 @@ private FileNodeViewModel searchDirectory(Path directory, UnlinkedPDFFileFilter
         Map<Boolean, List<Path>> fileListPartition;
 
         try (Stream<Path> filesStream = StreamSupport.stream(Files.newDirectoryStream(directory, fileFilter).spliterator(), false)) {
-            fileListPartition = filesStream.collect(Collectors.partitioningBy(path -> path.toFile().isDirectory()));
+            fileListPartition = filesStream.collect(Collectors.partitioningBy(Files::isDirectory));
         } catch (IOException e) {
             LOGGER.error(String.format("%s while searching files: %s", e.getClass().getName(), e.getMessage()));
             return parent;
diff --git a/src/main/java/org/jabref/gui/externalfiles/UnlinkedFilesDialog.fxml b/src/main/java/org/jabref/gui/externalfiles/UnlinkedFilesDialog.fxml
index 0d3246da39d..479158b6a41 100644
--- a/src/main/java/org/jabref/gui/externalfiles/UnlinkedFilesDialog.fxml
+++ b/src/main/java/org/jabref/gui/externalfiles/UnlinkedFilesDialog.fxml
@@ -50,9 +50,9 @@
                     </tooltip>
                 </Button>
 
-                <Label text="%File extension:" GridPane.columnIndex="0" GridPane.rowIndex="1"/>
+                <Label text="%File type:" GridPane.columnIndex="0" GridPane.rowIndex="1"/>
                 <ComboBox fx:id="fileTypeCombo" maxWidth="Infinity" GridPane.columnIndex="1" GridPane.rowIndex="1"/>
-                <Button fx:id="scanButton" onAction="#scanFiles" text="%Scan directory"
+                <Button fx:id="scanButton" onAction="#scanFiles" text="%Search"
                         GridPane.columnIndex="2" GridPane.rowIndex="1">
                     <tooltip>
                         <Tooltip text="%Searches the selected directory for unlinked files."/>
@@ -68,14 +68,14 @@
                             </ScrollPane>
                         </TitledPane>
                         <TitledPane fx:id="resultPane" text="%Import result" disable="true">
-                            <TableView fx:id="importResultTable">
+                            <TableView fx:id="importResultTable" styleClass="unlinkedFilesResultTable">
                                 <columns>
                                     <TableColumn fx:id="colStatus" prefWidth="100.0" text="%Status"/>
-                                    <TableColumn fx:id="colMessage" prefWidth="300.0" text="%Message"/>
                                     <TableColumn fx:id="colFile" prefWidth="500.0" text="%File"/>
+                                    <TableColumn fx:id="colMessage" prefWidth="300.0" text="%Message"/>
                                 </columns>
                                 <columnResizePolicy>
-                                    <TableView fx:constant="CONSTRAINED_RESIZE_POLICY"/>
+                                    <TableView fx:constant="UNCONSTRAINED_RESIZE_POLICY"/>
                                 </columnResizePolicy>
                             </TableView>
                         </TitledPane>
diff --git a/src/main/java/org/jabref/gui/externalfiles/UnlinkedPDFFileFilter.java b/src/main/java/org/jabref/gui/externalfiles/UnlinkedPDFFileFilter.java
index 1d235d7fbf3..0cdb7263263 100644
--- a/src/main/java/org/jabref/gui/externalfiles/UnlinkedPDFFileFilter.java
+++ b/src/main/java/org/jabref/gui/externalfiles/UnlinkedPDFFileFilter.java
@@ -4,6 +4,7 @@
 import java.io.IOException;
 import java.nio.file.DirectoryStream;
 import java.nio.file.DirectoryStream.Filter;
+import java.nio.file.Files;
 import java.nio.file.Path;
 
 import org.jabref.logic.util.io.DatabaseFileLookup;
@@ -31,6 +32,11 @@ public UnlinkedPDFFileFilter(DirectoryStream.Filter<Path> fileFilter, BibDatabas
 
     @Override
     public boolean accept(Path pathname) throws IOException {
-        return fileFilter.accept(pathname) && !lookup.lookupDatabase(pathname.toFile());
+
+        if (Files.isDirectory(pathname)) {
+            return true;
+        } else {
+            return fileFilter.accept(pathname) && !lookup.lookupDatabase(pathname);
+        }
     }
 }
diff --git a/src/main/java/org/jabref/logic/util/FileType.java b/src/main/java/org/jabref/logic/util/FileType.java
index e39d5ba90fb..7e4ba2199ec 100644
--- a/src/main/java/org/jabref/logic/util/FileType.java
+++ b/src/main/java/org/jabref/logic/util/FileType.java
@@ -15,4 +15,6 @@ default List<String> getExtensionsWithDot() {
     }
 
     List<String> getExtensions();
+
+    String getName();
 }
diff --git a/src/main/java/org/jabref/logic/util/StandardFileType.java b/src/main/java/org/jabref/logic/util/StandardFileType.java
index 3ad3d1d7e3b..c899ae5a60d 100644
--- a/src/main/java/org/jabref/logic/util/StandardFileType.java
+++ b/src/main/java/org/jabref/logic/util/StandardFileType.java
@@ -10,45 +10,46 @@
  */
 public enum StandardFileType implements FileType {
 
-    BIBTEXML("bibx", "xml"),
-    ENDNOTE("ref", "enw"),
-    ISI("isi", "txt"),
-    MEDLINE("nbib", "xml"),
-    MEDLINE_PLAIN("nbib", "txt"),
-    PUBMED("fcgi"),
-    SILVER_PLATTER("dat", "txt"),
-
-    AUX("aux"),
-    BIBTEX_DB("bib"),
-    CITATION_STYLE("csl"),
-    CLASS("class"),
-    CSV("csv"),
-    HTML("html", "htm"),
-    JAR("jar"),
-    JAVA_KEYSTORE("jks"),
-    JSTYLE("jstyle"),
-    LAYOUT("layout"),
-    ODS("ods"),
-    PDF("pdf"),
-    RIS("ris"),
-    TERMS("terms"),
-    TXT("txt"),
-    RDF("rdf"),
-    RTF("rtf"),
-    SXC("sxc"),
-    TEX("tex"),
-    XML("xml"),
-    JSON("json"),
-    XMP("xmp"),
-    ZIP("zip"),
-    CSS("css"),
-    YAML("yaml"),
-    ANY_FILE("*");
+    BIBTEXML("BibTeXML", "bibx", "xml"),
+    ENDNOTE("Endnote", "ref", "enw"),
+    ISI("Isi", "isi", "txt"),
+    MEDLINE("Medline", "nbib", "xml"),
+    MEDLINE_PLAIN("Medline Plain", "nbib", "txt"),
+    PUBMED("Pubmed", "fcgi"),
+    SILVER_PLATTER("SilverPlatter", "dat", "txt"),
+    AUX("Aux file", "aux"),
+    BIBTEX_DB("Bibtex library", "bib"),
+    CITATION_STYLE("Citation Style", "csl"),
+    CLASS("Class file", "class"),
+    CSV("CSV", "csv"),
+    HTML("HTML", "html", "htm"),
+    JAR("JAR", "jar"),
+    JAVA_KEYSTORE("Java Keystore", "jks"),
+    JSTYLE("LibreOffice layout style", "jstyle"),
+    LAYOUT("Custom Exporter format", "layout"),
+    ODS("OpenOffice Calc", "ods"),
+    PDF("PDF", "pdf"),
+    RIS("RIS", "ris"),
+    TERMS("Protected terms", "terms"),
+    TXT("Plain Text", "txt"),
+    RDF("RDF", "rdf"),
+    RTF("RTF", "rtf"),
+    SXC("Open Office Calc 1.x", "sxc"),
+    TEX("LaTeX", "tex"),
+    XML("XML", "xml"),
+    JSON("JSON", "json"),
+    XMP("XMP", "xmp"),
+    ZIP("Zip Archive", "zip"),
+    CSS("CSS Styleshet", "css"),
+    YAML("YAML Markup", "yaml"),
+    ANY_FILE("All files", "*");
 
     private final List<String> extensions;
+    private final String name;
 
-    StandardFileType(String... extensions) {
+    StandardFileType(String name, String... extensions) {
         this.extensions = Arrays.asList(extensions);
+        this.name = name;
     }
 
     @Override
@@ -56,12 +57,17 @@ public List<String> getExtensions() {
         return extensions;
     }
 
+    @Override
+    public String getName() {
+        return this.name;
+    }
+
     public static FileType fromExtensions(String... extensions) {
         var exts = Arrays.asList(extensions);
 
         return OptionalUtil.orElse(Arrays.stream(StandardFileType.values())
                                          .filter(field -> field.getExtensions().stream().anyMatch(elem -> exts.contains(elem)))
                                          .findAny(),
-                new UnknownFileType(extensions));
+                                   new UnknownFileType(extensions));
     }
 }
diff --git a/src/main/java/org/jabref/logic/util/UnknownFileType.java b/src/main/java/org/jabref/logic/util/UnknownFileType.java
index e057caa3974..a2b7453d261 100644
--- a/src/main/java/org/jabref/logic/util/UnknownFileType.java
+++ b/src/main/java/org/jabref/logic/util/UnknownFileType.java
@@ -43,4 +43,9 @@ public boolean equals(Object o) {
     public int hashCode() {
         return Objects.hash(extensions);
     }
+
+    @Override
+    public String getName() {
+        return "Unknown File Type" + extensions.toString();
+    }
 }
diff --git a/src/main/java/org/jabref/logic/util/io/DatabaseFileLookup.java b/src/main/java/org/jabref/logic/util/io/DatabaseFileLookup.java
index 839a6432a71..11c076820ce 100644
--- a/src/main/java/org/jabref/logic/util/io/DatabaseFileLookup.java
+++ b/src/main/java/org/jabref/logic/util/io/DatabaseFileLookup.java
@@ -48,12 +48,12 @@ public DatabaseFileLookup(BibDatabaseContext databaseContext, FilePreferences fi
      * <br>
      * For the matching, the absolute file paths will be used.
      *
-     * @param file A {@link File} Object.
+     * @param pathname A {@link File} Object.
      * @return <code>true</code>, if the file Object is stored in at least one
      * entry in the database, otherwise <code>false</code>.
      */
-    public boolean lookupDatabase(File file) {
-        return fileCache.contains(file.toPath());
+    public boolean lookupDatabase(Path pathname) {
+        return fileCache.contains(pathname);
     }
 
     private List<Path> parseFileField(BibEntry entry) {

From 2685814fb381605d864a700a343b98bdf0652e83 Mon Sep 17 00:00:00 2001
From: Siedlerchr <siedlerkiller@gmail.com>
Date: Mon, 25 Jan 2021 21:08:28 +0100
Subject: [PATCH 2/5] better min width

---
 src/main/java/org/jabref/gui/Base.css                       | 2 +-
 .../org/jabref/gui/externalfiles/UnlinkedFilesDialog.fxml   | 6 +++---
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/src/main/java/org/jabref/gui/Base.css b/src/main/java/org/jabref/gui/Base.css
index bf6f8fb5612..ffe7cd3f04f 100644
--- a/src/main/java/org/jabref/gui/Base.css
+++ b/src/main/java/org/jabref/gui/Base.css
@@ -1217,6 +1217,6 @@ TextFlow * {
 
 }
 
-.mainTable-header{
+.mainTable-header {
     -fx-fill: -fx-mid-text-color;
 }
diff --git a/src/main/java/org/jabref/gui/externalfiles/UnlinkedFilesDialog.fxml b/src/main/java/org/jabref/gui/externalfiles/UnlinkedFilesDialog.fxml
index 479158b6a41..987db814aee 100644
--- a/src/main/java/org/jabref/gui/externalfiles/UnlinkedFilesDialog.fxml
+++ b/src/main/java/org/jabref/gui/externalfiles/UnlinkedFilesDialog.fxml
@@ -34,14 +34,14 @@
                 <ColumnConstraints hgrow="SOMETIMES"/>
             </columnConstraints>
             <rowConstraints>
-                <RowConstraints minHeight="10.0" vgrow="SOMETIMES"/>
-                <RowConstraints minHeight="10.0" vgrow="SOMETIMES"/>
+                <RowConstraints minHeight="20.0" vgrow="SOMETIMES"/>
+                <RowConstraints minHeight="20.0" vgrow="SOMETIMES"/>
             </rowConstraints>
                 <Label text="%Start directory:" GridPane.columnIndex="0" GridPane.rowIndex="0"/>
                 <TextField fx:id="directoryPathField" GridPane.columnIndex="1" GridPane.rowIndex="0"/>
                 <Button onAction="#browseFileDirectory" styleClass="icon-button,narrow"
                         GridPane.columnIndex="2" GridPane.rowIndex="0"
-                        prefHeight="20.0" prefWidth="20.0">
+                        minWidth="20.0" minHeight="20.0" prefHeight="20.0" prefWidth="20.0">
                     <graphic>
                         <JabRefIconView glyph="OPEN"/>
                     </graphic>

From ad087bb292200ff3eaa6c5a1f23a58854a8017c7 Mon Sep 17 00:00:00 2001
From: Siedlerchr <siedlerkiller@gmail.com>
Date: Mon, 25 Jan 2021 21:15:35 +0100
Subject: [PATCH 3/5] Any file instead of all

---
 src/main/java/org/jabref/logic/util/StandardFileType.java | 2 +-
 src/main/resources/l10n/JabRef_en.properties              | 1 -
 2 files changed, 1 insertion(+), 2 deletions(-)

diff --git a/src/main/java/org/jabref/logic/util/StandardFileType.java b/src/main/java/org/jabref/logic/util/StandardFileType.java
index c899ae5a60d..7a9d5d08c48 100644
--- a/src/main/java/org/jabref/logic/util/StandardFileType.java
+++ b/src/main/java/org/jabref/logic/util/StandardFileType.java
@@ -42,7 +42,7 @@ public enum StandardFileType implements FileType {
     ZIP("Zip Archive", "zip"),
     CSS("CSS Styleshet", "css"),
     YAML("YAML Markup", "yaml"),
-    ANY_FILE("All files", "*");
+    ANY_FILE("Any", "*");
 
     private final List<String> extensions;
     private final String name;
diff --git a/src/main/resources/l10n/JabRef_en.properties b/src/main/resources/l10n/JabRef_en.properties
index 8cfb645b5fb..3e41ffec464 100644
--- a/src/main/resources/l10n/JabRef_en.properties
+++ b/src/main/resources/l10n/JabRef_en.properties
@@ -1107,7 +1107,6 @@ Unable\ to\ clear\ preferences.=Unable to clear preferences.
 Unselect\ all=Unselect all
 Expand\ all=Expand all
 Collapse\ all=Collapse all
-Scan\ directory=Scan directory
 Searches\ the\ selected\ directory\ for\ unlinked\ files.=Searches the selected directory for unlinked files.
 Starts\ the\ import\ of\ BibTeX\ entries.=Starts the import of BibTeX entries.
 Start\ directory\:=Start directory:

From 3ed8d3e23349e2023ab20e829f0c00a678ebdf4b Mon Sep 17 00:00:00 2001
From: Siedlerchr <siedlerkiller@gmail.com>
Date: Fri, 29 Jan 2021 17:47:46 +0100
Subject: [PATCH 4/5] remove style class

---
 .../java/org/jabref/gui/externalfiles/UnlinkedFilesDialog.fxml  | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/main/java/org/jabref/gui/externalfiles/UnlinkedFilesDialog.fxml b/src/main/java/org/jabref/gui/externalfiles/UnlinkedFilesDialog.fxml
index 987db814aee..bea10fcc9c3 100644
--- a/src/main/java/org/jabref/gui/externalfiles/UnlinkedFilesDialog.fxml
+++ b/src/main/java/org/jabref/gui/externalfiles/UnlinkedFilesDialog.fxml
@@ -68,7 +68,7 @@
                             </ScrollPane>
                         </TitledPane>
                         <TitledPane fx:id="resultPane" text="%Import result" disable="true">
-                            <TableView fx:id="importResultTable" styleClass="unlinkedFilesResultTable">
+                            <TableView fx:id="importResultTable">
                                 <columns>
                                     <TableColumn fx:id="colStatus" prefWidth="100.0" text="%Status"/>
                                     <TableColumn fx:id="colFile" prefWidth="500.0" text="%File"/>

From 399bce59a20877db4b192da335a361e3d69bcf2f Mon Sep 17 00:00:00 2001
From: Carl Christian Snethlage <50491877+calixtus@users.noreply.github.com>
Date: Fri, 29 Jan 2021 18:20:33 +0100
Subject: [PATCH 5/5] l10n

---
 src/main/resources/l10n/JabRef_en.properties | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/main/resources/l10n/JabRef_en.properties b/src/main/resources/l10n/JabRef_en.properties
index 3e41ffec464..e343995123a 100644
--- a/src/main/resources/l10n/JabRef_en.properties
+++ b/src/main/resources/l10n/JabRef_en.properties
@@ -1110,6 +1110,7 @@ Collapse\ all=Collapse all
 Searches\ the\ selected\ directory\ for\ unlinked\ files.=Searches the selected directory for unlinked files.
 Starts\ the\ import\ of\ BibTeX\ entries.=Starts the import of BibTeX entries.
 Start\ directory\:=Start directory:
+File\ type\:=File type:
 Currently\ unlinked\ files=Currently unlinked files
 Import\ result=Import result
 Searching\ file\ system...=Searching file system...