Removed BIB file directory from search when preferences has option unchecked

CHANGELOG.md

@@ -43,6 +43,7 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 
 ### Fixed
 
+- We fixed to only search file links in the BIB file location directory when preferences has corresponding checkbox checked. [#5891](https://github.com/JabRef/jabref/issues/5891)
 - We fixed wrong button order (Apply and Cancel) in ManageProtectedTermsDialog.
 - We fixed an issue with incompatible characters at BibTeX key [#6257](https://github.com/JabRef/jabref/issues/6257)
 - We fixed an issue where dash (`-`) was reported as illegal BibTeX key [#6295](https://github.com/JabRef/jabref/issues/6295)

src/main/java/org/jabref/gui/preferences/FileTab.fxml

@@ -43,7 +43,7 @@
         <TextField fx:id="mainFileDir" HBox.hgrow="ALWAYS"/>
         <Button onAction="#mainFileDirBrowse" text="%Browse"/>
     </HBox>
-    <CheckBox fx:id="useBibLocationAsPrimary" text="%Use the BIB file location as primary file directory">
+    <CheckBox fx:id="useBibLocationAsPrimary" text="%Search and store files relative to library file location">
         <tooltip>
             <Tooltip
                     text="%When downloading files, or moving linked files to the file directory, prefer the BIB file location rather than the file directory set above"/>

src/main/java/org/jabref/model/database/BibDatabaseContext.java

@@ -144,8 +144,6 @@ public List<Path> getFileDirectoriesAsPaths(FilePreferences preferences) {
             // Check if we should add it as primary file dir (first in the list) or not:
             if (preferences.isBibLocationAsPrimary()) {
                 fileDirs.add(0, parentPath);
-            } else {
-                fileDirs.add(parentPath);
             }
         });
 

src/main/resources/l10n/JabRef_en.properties

@@ -1096,7 +1096,7 @@ Web\ search=Web search
 Style\ selection=Style selection
 No\ valid\ style\ file\ defined=No valid style file defined
 Choose\ pattern=Choose pattern
-Use\ the\ BIB\ file\ location\ as\ primary\ file\ directory=Use the BIB file location as primary file directory
+Search\ and\ store\ files\ relative\ to\ library\ file\ location=Search and store files relative to library file location
 Could\ not\ run\ the\ gnuclient/emacsclient\ program.\ Make\ sure\ you\ have\ the\ emacsclient/gnuclient\ program\ installed\ and\ available\ in\ the\ PATH.=Could not run the gnuclient/emacsclient program. Make sure you have the emacsclient/gnuclient program installed and available in the PATH.
 You\ must\ select\ either\ a\ valid\ style\ file,\ or\ use\ one\ of\ the\ default\ styles.=You must select either a valid style file, or use one of the default styles.
 

src/main/resources/l10n/JabRef_ru.properties

@@ -2168,7 +2168,7 @@ This\ entry\ type\ is\ intended\ for\ sources\ such\ as\ web\ sites\ which\ are\
 A\ single-volume\ work\ of\ reference\ such\ as\ an\ encyclopedia\ or\ a\ dictionary.=Неделимая работа или ссылка, как энциклопедия или словарь.
 A\ technical\ report,\ research\ report,\ or\ white\ paper\ published\ by\ a\ university\ or\ some\ other\ institution.=Технический отчет, исследовательский отчет, или белая книга, выпущенная институтом или другим учреждением.
 An\ entry\ set\ is\ a\ group\ of\ entries\ which\ are\ cited\ as\ a\ single\ reference\ and\ listed\ as\ a\ single\ item\ in\ the\ bibliography.=Набор записей представляет собой группу записей, которые приводятся в виде единой ссылки и перечислены в виде одного элемента в библиографии.
-Supplemental\ material\ in\ a\ "Book".\ This\ type\ is\ provided\ for\ elements\ such\ as\ prefaces,\ introductions,\ forewords,\ afterwords,\ etc.\ which\ often\ have\ a\ generic\ title\ only.=Дополнительный материал в "Книге" предназначен для таких элементов, как предисловия, введения, послесловия и т.д. 
+Supplemental\ material\ in\ a\ "Book".\ This\ type\ is\ provided\ for\ elements\ such\ as\ prefaces,\ introductions,\ forewords,\ afterwords,\ etc.\ which\ often\ have\ a\ generic\ title\ only.=Дополнительный материал в "Книге" предназначен для таких элементов, как предисловия, введения, послесловия и т.д.
 Supplemental\ material\ in\ a\ "Collection".=Дополнительные материалы в "Коллекции".
 Supplemental\ material\ in\ a\ "Periodical".\ This\ type\ may\ be\ useful\ when\ referring\ to\ items\ such\ as\ regular\ columns,\ obituaries,\ letters\ to\ the\ editor,\ etc.\ which\ only\ have\ a\ generic\ title.=Дополнительные материалы в "Периодическом издании". Этот тип может быть полезен при обращении к таким элементам, как обычные колонки, некрологи, письма к редактору и т.д., которые имеют только общее название.
 A\ thesis\ written\ for\ an\ educational\ institution\ to\ satisfy\ the\ requirements\ for\ a\ degree.=Тезис, написанный для учебного заведения с целью удовлетворения требований к степени.

src/test/java/org/jabref/gui/externalfiles/AutoSetFileLinksUtilTest.java

@@ -30,24 +30,31 @@ public class AutoSetFileLinksUtilTest {
     private final BibDatabaseContext databaseContext = mock(BibDatabaseContext.class);
     private final ExternalFileTypes externalFileTypes = mock(ExternalFileTypes.class);
     private final BibEntry entry = new BibEntry(StandardEntryType.Article);
+    private Path path = null;
 
     @BeforeEach
     public void setUp(@TempDir Path folder) throws Exception {
-        Path path = folder.resolve("CiteKey.pdf");
+        path = folder.resolve("CiteKey.pdf");
         Files.createFile(path);
         entry.setCiteKey("CiteKey");
-        when(databaseContext.getFileDirectoriesAsPaths(any())).thenReturn(Collections.singletonList(path.getParent()));
         when(externalFileTypes.getExternalFileTypeSelection()).thenReturn(new TreeSet<>(ExternalFileTypes.getDefaultExternalFileTypes()));
     }
 
     @Test
-    public void test() throws Exception {
+    public void testFindAssociatedNotLinkedFilesSuccess() throws Exception {
         // Due to mocking the externalFileType class, the file extension will not be found
-
+        when(databaseContext.getFileDirectoriesAsPaths(any())).thenReturn(Collections.singletonList(path.getParent()));
         List<LinkedFile> expected = Collections.singletonList(new LinkedFile("", "CiteKey.pdf", ""));
-
         AutoSetFileLinksUtil util = new AutoSetFileLinksUtil(databaseContext, fileDirPrefs, autoLinkPrefs, externalFileTypes);
         List<LinkedFile> actual = util.findAssociatedNotLinkedFiles(entry);
         assertEquals(expected, actual);
     }
+
+    @Test
+    public void testFindAssociatedNotLinkedFilesForEmptySearchDir() throws Exception {
+        when(fileDirPrefs.isBibLocationAsPrimary()).thenReturn(false);
+        AutoSetFileLinksUtil util = new AutoSetFileLinksUtil(databaseContext, fileDirPrefs, autoLinkPrefs, externalFileTypes);
+        List<LinkedFile> actual = util.findAssociatedNotLinkedFiles(entry);
+        assertEquals(Collections.emptyList(), actual);
+    }
 }

src/test/java/org/jabref/logic/cleanup/MoveFilesCleanupTest.java

@@ -4,8 +4,11 @@
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.util.Arrays;
+import java.util.Collections;
+import java.util.List;
 import java.util.Optional;
 
+import org.jabref.model.FieldChange;
 import org.jabref.model.database.BibDatabase;
 import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.entry.BibEntry;
@@ -32,6 +35,7 @@ class MoveFilesCleanupTest {
     private MoveFilesCleanup cleanup;
     private BibEntry entry;
     private FilePreferences filePreferences;
+    private BibDatabaseContext databaseContext;
 
     @BeforeEach
     void setUp(@TempDir Path bibFolder) throws IOException {
@@ -47,7 +51,7 @@ void setUp(@TempDir Path bibFolder) throws IOException {
 
         MetaData metaData = new MetaData();
         metaData.setDefaultFileDirectory(defaultFileFolder.toAbsolutePath().toString());
-        BibDatabaseContext databaseContext = new BibDatabaseContext(new BibDatabase(), metaData);
+        databaseContext = new BibDatabaseContext(new BibDatabase(), metaData);
         Files.createFile(bibFolder.resolve("test.bib"));
         databaseContext.setDatabasePath(bibFolder.resolve("test.bib"));
 
@@ -119,4 +123,12 @@ void movesFileWithSubdirectoryPattern() throws Exception {
         assertFalse(Files.exists(fileBefore));
         assertTrue(Files.exists(fileAfter));
     }
+
+    @Test
+    void movesFileWithNoDirectory() throws Exception {
+        databaseContext.setMetaData(new MetaData());
+        when(filePreferences.getFileDirPattern()).thenReturn("");
+        List<FieldChange> changes = cleanup.cleanup(entry);
+        assertEquals(Collections.emptyList(), changes);
+    }
 }

src/test/java/org/jabref/logic/integrity/IntegrityCheckTest.java

@@ -36,6 +36,7 @@
 import static org.junit.jupiter.api.Assertions.assertNotEquals;
 import static org.mockito.ArgumentMatchers.any;
 import static org.mockito.Mockito.mock;
+import static org.mockito.Mockito.when;
 
 /**
  * This class tests the Integrity Checker as a whole.
@@ -177,8 +178,10 @@ private void assertWrong(BibDatabaseContext context) {
     }
 
     private void assertCorrect(BibDatabaseContext context) {
+        FilePreferences filePreferencesMock = mock(FilePreferences.class);
+        when(filePreferencesMock.isBibLocationAsPrimary()).thenReturn(true);
         List<IntegrityMessage> messages = new IntegrityCheck(context,
-                mock(FilePreferences.class),
+                filePreferencesMock,
                 createBibtexKeyPatternPreferences(),
                 JournalAbbreviationLoader.loadBuiltInRepository(), false
         ).check();