Merge remote-tracking branch 'upstream/main' into tinylog

* upstream/main: Fix xmp import (#8311) New Crowdin updates (#8308) Fix file-filter in XMP Export (#8307) New Crowdin updates (#8306) Bump h2-mvstore from 1.4.200 to 2.0.202 (#8302) Remove bytebuddy (#8300) Bump postgresql from 42.2.24 to 42.3.1 (#8301) Update Gradle Wrapper from 7.3 to 7.3.1. (#8299) Apply search string to open library when keep search string is selected (#8294)
JabRef · Dec 10, 2021 · 6fc081a · 6fc081a
2 parents c061b88 + 74a4edb
commit 6fc081a
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -73,6 +73,8 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - We fixed an issue where right-clicking on a tab and selecting close will close the focused tab even if it is not the tab we right-clicked [#8193](https://github.com/JabRef/jabref/pull/8193)
 - We fixed an issue where selecting a citation style in the preferences would sometimes produce an exception [#7860](https://github.com/JabRef/jabref/issues/7860)
 - We fixed an issue where an exception would occur when clicking on a DOI link in the preview pane [#7706](https://github.com/JabRef/jabref/issues/7706)
+- We fixed an issue where XMP and embedded BibTeX export would not work [#8278](https://github.com/JabRef/jabref/issues/8278)
+- We fixed an issue where the XMP and embedded BibTeX import of a file containing multiple schemas failed [#8278](https://github.com/JabRef/jabref/issues/8278)
 
 ### Removed
 

diff --git a/build.gradle b/build.gradle
@@ -121,7 +121,7 @@ dependencies {
     implementation 'org.apache.pdfbox:xmpbox:2.0.24'
 
     implementation group: 'org.apache.commons', name: 'commons-csv', version: '1.9.0'
-    implementation 'com.h2database:h2-mvstore:1.4.200'
+    implementation 'com.h2database:h2-mvstore:2.0.202'
 
     implementation group: 'org.apache.tika', name: 'tika-core', version: '2.1.0'
 
@@ -149,7 +149,7 @@ dependencies {
 
     implementation group: 'org.mariadb.jdbc', name: 'mariadb-java-client', version: '2.7.4'
 
-    implementation 'org.postgresql:postgresql:42.2.24'
+    implementation 'org.postgresql:postgresql:42.3.1'
 
     implementation ('com.oracle.ojdbc:ojdbc10:19.3.0.0') {
         // causing module issues
@@ -207,7 +207,6 @@ dependencies {
     testImplementation 'org.junit.jupiter:junit-jupiter:5.8.1'
     testImplementation 'org.junit.platform:junit-platform-launcher:1.8.1'
 
-    testImplementation 'net.bytebuddy:byte-buddy-parent:1.12.2'
     testRuntimeOnly group: 'org.apache.logging.log4j', name: 'log4j-core', version: '3.0.0-SNAPSHOT'
     testRuntimeOnly group: 'org.apache.logging.log4j', name: 'log4j-jul', version: '3.0.0-SNAPSHOT'
     testImplementation 'org.mockito:mockito-core:4.1.0'

diff --git a/buildSrc/build.gradle b/buildSrc/build.gradle
@@ -6,9 +6,9 @@ repositories {
 }
 
 dependencies {
-    implementation 'com.h2database:h2-mvstore:1.4.200'
-    implementation 'org.apache.commons:commons-csv:1.8'
-    implementation 'org.slf4j:slf4j-api:2.0.0-alpha1'
+    implementation 'com.h2database:h2-mvstore:2.0.202'
+    implementation 'org.apache.commons:commons-csv:1.9.0'
+    implementation 'org.slf4j:slf4j-api:2.0.0-alpha5'
 }
 
 sourceSets{

diff --git a/gradle/wrapper/gradle-wrapper.properties b/gradle/wrapper/gradle-wrapper.properties
@@ -1,5 +1,6 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-7.3-bin.zip
+distributionSha256Sum=9afb3ca688fc12c761a0e9e4321e4d24e977a4a8916c8a768b1fe05ddb4d6b66
+distributionUrl=https\://services.gradle.org/distributions/gradle-7.3.1-bin.zip
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists
diff --git a/gradlew b/gradlew
@@ -1,7 +1,7 @@
 #!/bin/sh
 
 #
-# Copyright © 2015-2021 the original authors.
+# Copyright © 2015-2021 the original authors.
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
@@ -32,10 +32,10 @@
 #       Busybox and similar reduced shells will NOT work, because this script
 #       requires all of these POSIX shell features:
 #         * functions;
-#         * expansions «$var», «${var}», «${var:-default}», «${var+SET}»,
-#           «${var#prefix}», «${var%suffix}», and «$( cmd )»;
-#         * compound commands having a testable exit status, especially «case»;
-#         * various built-in commands including «command», «set», and «ulimit».
+#         * expansions «$var», «${var}», «${var:-default}», «${var+SET}»,
+#           «${var#prefix}», «${var%suffix}», and «$( cmd )»;
+#         * compound commands having a testable exit status, especially «case»;
+#         * various built-in commands including «command», «set», and «ulimit».
 #
 #   Important for patching:
 #

diff --git a/src/main/java/org/jabref/gui/JabRefFrame.java b/src/main/java/org/jabref/gui/JabRefFrame.java
@@ -634,7 +634,12 @@ public void init() {
             stateManager.setSelectedEntries(libraryTab.getSelectedEntries());
 
             // Update active search query when switching between databases
-            stateManager.activeSearchQueryProperty().set(libraryTab.getCurrentSearchQuery());
+            if (prefs.getSearchPreferences().shouldKeepSearchString() && libraryTab.getCurrentSearchQuery().isEmpty() && stateManager.activeSearchQueryProperty().get().isPresent()) {
+                // apply search query also when opening a new library and keep search string is activated
+               libraryTab.setCurrentSearchQuery(stateManager.activeSearchQueryProperty().get());
+            } else {
+                stateManager.activeSearchQueryProperty().set(libraryTab.getCurrentSearchQuery());
+            }
 
             // Update search autocompleter with information for the correct database:
             libraryTab.updateSearchManager();

diff --git a/src/main/java/org/jabref/gui/actions/StandardActions.java b/src/main/java/org/jabref/gui/actions/StandardActions.java
@@ -88,7 +88,7 @@ public enum StandardActions implements Action {
 
     PARSE_LATEX(Localization.lang("Search for citations in LaTeX files..."), IconTheme.JabRefIcons.LATEX_CITATIONS),
     NEW_SUB_LIBRARY_FROM_AUX(Localization.lang("New sublibrary based on AUX file") + "...", Localization.lang("New BibTeX sublibrary") + Localization.lang("This feature generates a new library based on which entries are needed in an existing LaTeX document."), IconTheme.JabRefIcons.NEW),
-    WRITE_METADATA_TO_PDF(Localization.lang("Write XMP metadata to PDFs"), Localization.lang("Will write XMP metadata to the PDFs linked from selected entries."), KeyBinding.WRITE_XMP),
+    WRITE_METADATA_TO_PDF(Localization.lang("Write metadata to PDF files"), Localization.lang("Will write metadata to the PDFs linked from selected entries."), KeyBinding.WRITE_METADATA_TO_PDF),
     START_NEW_STUDY(Localization.lang("Start new systematic literature review")),
     SEARCH_FOR_EXISTING_STUDY(Localization.lang("Perform search for existing systematic literature review")),
     OPEN_DATABASE_FOLDER(Localization.lang("Reveal in file explorer")),

diff --git a/src/main/java/org/jabref/gui/exporter/WriteMetadataToPdfAction.java b/src/main/java/org/jabref/gui/exporter/WriteMetadataToPdfAction.java
@@ -30,7 +30,6 @@
 import org.jabref.logic.bibtex.FieldWriterPreferences;
 import org.jabref.logic.exporter.EmbeddedBibFilePdfExporter;
 import org.jabref.logic.l10n.Localization;
-import org.jabref.logic.util.StandardFileType;
 import org.jabref.logic.util.io.FileUtil;
 import org.jabref.logic.xmp.XmpPreferences;
 import org.jabref.logic.xmp.XmpUtilWriter;
@@ -133,7 +132,7 @@ private void writeMetadata() {
                                     .map(file -> file.findIn(stateManager.getActiveDatabase().get(), filePreferences))
                                     .filter(Optional::isPresent)
                                     .map(Optional::get)
-                                    .filter(path -> StandardFileType.PDF.getExtensions().contains(FileUtil.getFileExtension(path)))
+                                    .filter(path -> FileUtil.isPDFFile(path))
                                     .collect(Collectors.toList());
 
             Platform.runLater(() -> optionsDialog.getProgressArea()

diff --git a/src/main/java/org/jabref/gui/keyboard/KeyBinding.java b/src/main/java/org/jabref/gui/keyboard/KeyBinding.java
@@ -106,7 +106,7 @@ public enum KeyBinding {
     UNABBREVIATE("Unabbreviate", Localization.lang("Unabbreviate"), "ctrl+alt+shift+A", KeyBindingCategory.TOOLS),
     UNDO("Undo", Localization.lang("Undo"), "ctrl+Z", KeyBindingCategory.EDIT),
     WEB_SEARCH("Web search", Localization.lang("Web search"), "alt+4", KeyBindingCategory.SEARCH),
-    WRITE_XMP("Write XMP", Localization.lang("Write XMP"), "F6", KeyBindingCategory.TOOLS),
+    WRITE_METADATA_TO_PDF("Write metadata to PDF files", Localization.lang("Write metadata to PDF files"), "F6", KeyBindingCategory.TOOLS),
     CLEAR_SEARCH("Clear search", Localization.lang("Clear search"), "ESCAPE", KeyBindingCategory.SEARCH),
     CLEAR_READ_STATUS("Clear read status", Localization.lang("Clear read status"), "", KeyBindingCategory.EDIT),
     READ("Set read status to read", Localization.lang("Set read status to read"), "", KeyBindingCategory.EDIT),

diff --git a/src/main/java/org/jabref/gui/search/GlobalSearchResultDialog.java b/src/main/java/org/jabref/gui/search/GlobalSearchResultDialog.java
@@ -16,6 +16,7 @@
 import org.jabref.gui.maintable.columns.SpecialFieldColumn;
 import org.jabref.gui.preview.PreviewViewer;
 import org.jabref.gui.util.BaseDialog;
+import org.jabref.logic.l10n.Localization;
 import org.jabref.preferences.PreferencesService;
 
 import com.airhacks.afterburner.views.ViewLoader;
@@ -39,6 +40,7 @@ public GlobalSearchResultDialog(ExternalFileTypes externalFileTypes, UndoManager
         this.undoManager = undoManager;
         this.externalFileTypes = externalFileTypes;
 
+        setTitle(Localization.lang("Search results from open libraries"));
         ViewLoader.view(this)
                   .load()
                   .setAsDialogPane(this);

diff --git a/src/main/java/org/jabref/logic/exporter/EmbeddedBibFilePdfExporter.java b/src/main/java/org/jabref/logic/exporter/EmbeddedBibFilePdfExporter.java
@@ -64,7 +64,7 @@ public void export(BibDatabaseContext databaseContext, Path file, Charset encodi
     }
 
     private void embedBibTex(String bibTeX, Path file, Charset encoding) throws IOException {
-        if (!Files.exists(file) || !StandardFileType.PDF.getExtensions().contains(FileUtil.getFileExtension(file).orElse(""))) {
+        if (!Files.exists(file) || !FileUtil.isPDFFile(file)) {
             return;
         }
         try (PDDocument document = PDDocument.load(file.toFile())) {
@@ -80,7 +80,15 @@ private void embedBibTex(String bibTeX, Path file, Charset encoding) throws IOEx
                 document.getDocumentCatalog().setNames(nameDictionary);
             } else {
                 efTree = nameDictionary.getEmbeddedFiles();
+                if (efTree == null) {
+                    efTree = new PDEmbeddedFilesNameTreeNode();
+                    nameDictionary.setEmbeddedFiles(efTree);
+                }
                 names = efTree.getNames();
+                if (names == null) {
+                    names = new HashMap<>();
+                    efTree.setNames(names);
+                }
             }
 
             if (efTree != null) {

diff --git a/src/main/java/org/jabref/logic/importer/fileformat/PdfEmbeddedBibFileImporter.java b/src/main/java/org/jabref/logic/importer/fileformat/PdfEmbeddedBibFileImporter.java
@@ -90,9 +90,11 @@ private List<BibEntry> getEmbeddedBibFileEntries(PDDocument document) throws IOE
                     allParsedEntries.addAll(extractAndParseFiles(names));
                 } else {
                     List<PDNameTreeNode<PDComplexFileSpecification>> kids = efTree.getKids();
-                    for (PDNameTreeNode<PDComplexFileSpecification> node : kids) {
-                        names = node.getNames();
-                        allParsedEntries.addAll(extractAndParseFiles(names));
+                    if (kids != null) {
+                        for (PDNameTreeNode<PDComplexFileSpecification> node : kids) {
+                            names = node.getNames();
+                            allParsedEntries.addAll(extractAndParseFiles(names));
+                        }
                     }
                 }
             }

diff --git a/src/main/java/org/jabref/logic/journals/AbbreviationFormat.java b/src/main/java/org/jabref/logic/journals/AbbreviationFormat.java
@@ -12,11 +12,12 @@ private AbbreviationFormat() {
     }
 
     public static CSVFormat getCSVFormat() {
-        return CSVFormat.DEFAULT
-                .withIgnoreEmptyLines(true)
-                .withDelimiter(DELIMITER)
-                .withEscape(ESCAPE)
-                .withQuote(QUOTE)
-                .withTrim();
+        return CSVFormat.DEFAULT.builder()
+                .setIgnoreEmptyLines(true)
+                .setDelimiter(DELIMITER)
+                .setEscape(ESCAPE)
+                .setQuote(QUOTE)
+                .setTrim(true)
+                .build();
     }
 }
diff --git a/src/main/java/org/jabref/logic/xmp/XmpUtilReader.java b/src/main/java/org/jabref/logic/xmp/XmpUtilReader.java
@@ -17,9 +17,13 @@
 import org.apache.pdfbox.pdmodel.common.PDMetadata;
 import org.apache.xmpbox.XMPMetadata;
 import org.apache.xmpbox.schema.DublinCoreSchema;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 public class XmpUtilReader {
 
+    private static final Logger LOGGER = LoggerFactory.getLogger(XmpUtilReader.class);
+
     private static final String START_TAG = "<rdf:Description";
     private static final String END_TAG = "</rdf:Description>";
 
@@ -120,7 +124,7 @@ private static List<XMPMetadata> getXmpMetadata(PDDocument document) throws IOEx
         int startDescriptionSection = xmp.indexOf(START_TAG);
         int endDescriptionSection = xmp.lastIndexOf(END_TAG) + END_TAG.length();
 
-        if (startDescriptionSection < 0 || startDescriptionSection > endDescriptionSection || endDescriptionSection == END_TAG.length() - 1) {
+        if ((startDescriptionSection < 0) || (startDescriptionSection > endDescriptionSection) || (endDescriptionSection == (END_TAG.length() - 1))) {
             return metaList;
         }
 
@@ -134,7 +138,11 @@ private static List<XMPMetadata> getXmpMetadata(PDDocument document) throws IOEx
         for (String s : descriptionsArray) {
             // END_TAG is appended, because of the split operation above
             String xmpMetaString = start + s + END_TAG + end;
-            metaList.add(XmpUtilShared.parseXmpMetadata(new ByteArrayInputStream(xmpMetaString.getBytes())));
+            try {
+                metaList.add(XmpUtilShared.parseXmpMetadata(new ByteArrayInputStream(xmpMetaString.getBytes())));
+            } catch (IOException ex) {
+                LOGGER.error("Problem parsing XMP schema. Continuing with other schemas.", ex);
+            }
         }
         return metaList;
     }

diff --git a/src/main/resources/journals/journalList.mv b/src/main/resources/journals/journalList.mv
diff --git a/src/main/resources/l10n/JabRef_da.properties b/src/main/resources/l10n/JabRef_da.properties
@@ -247,8 +247,6 @@ Edit\ file\ type=Rediger filtype
 
 Edit\ group=Rediger gruppe
 
-
-Edit\ preamble=Rediger præambel
 Edit\ strings=Rediger tekststrenge
 
 empty\ library=tom library
@@ -605,8 +603,6 @@ Replace\ string=Erstat streng
 
 Required\ fields=Obligatoriske felter
 
-Reset\ all=Nulstil alle
-
 Resolve\ strings\ for\ all\ fields\ except=Slå strenge op for alle felter undtagen
 Resolve\ strings\ for\ standard\ BibTeX\ fields\ only=Slå kun strenge op for standard BibTeX-felter
 
@@ -627,13 +623,10 @@ Save\ before\ closing=Gem før libraryn lukkes
 
 Save\ library=Gem library
 Save\ library\ as...=Gem library som ...
-
-Saved\ selected\ to\ '%0'.=Gemte valgte i '%0'.
-
 Saving=Gemmer
 Saving\ all\ libraries...=Gemmer alle libraryr...
-
 Saving\ library=Gemmer library
+Saved\ selected\ to\ '%0'.=Gemte valgte i '%0'.
 
 Search=Søg
 
@@ -692,7 +685,6 @@ Special\ name\ formatters=Specielle navneformateringer
 
 Statically\ group\ entries\ by\ manual\ assignment=Grupper poster statisk ved manuel tildeling
 
-Strings\ for\ library=Strenge for library
 
 
 Switches\ between\ full\ and\ abbreviated\ journal\ name\ if\ the\ journal\ name\ is\ known.=Skifter mellem fuldt og forkortet tidsskriftsnavn hvis navnet er kendt.