Merge remote-tracking branch 'upstream/main' into fixSavingFileLockNe…

…tworkShare * upstream/main: Infer DOI from ArXiv identifier (#10449) Add TexShop Icon (#10447) Fix PDF export (#10361) # Conflicts: # CHANGELOG.md
JabRef · Oct 6, 2023 · bb27bba · bb27bba
2 parents 3d672c0 + 3f53201
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -26,6 +26,8 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - The export formats `listrefs`, `tablerefs`, `tablerefsabsbib`, now use the ISO date format in the footer [#10383](https://github.com/JabRef/jabref/pull/10383).
 - When searching for an identifier in the "Web search", the title of the search window is now "Identifier-based Web Search". [#10391](https://github.com/JabRef/jabref/pull/10391)
 - The ampersand checker now skips verbatim fields (`file`, `url`, ...). [#10419](https://github.com/JabRef/jabref/pull/10419)
+- If no existing document is selected for exporting "XMP annotated pdf" JabRef will now create a new PDF file with a sample text and the metadata. [#10102](https://github.com/JabRef/jabref/issues/10102)
+- We modified the DOI cleanup to infer the DOI from an ArXiV ID if it's present. [10426](https://github.com/JabRef/jabref/issues/10426)
 
 ### Fixed
 
@@ -39,6 +41,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - Biblatex's `journaltitle` is now also respected for showing the journal information. [#10397](https://github.com/JabRef/jabref/issues/10397)
 - JabRef does not hang anymore when exporting via CLI. [#10380](https://github.com/JabRef/jabref/issues/10380)
 - We fixed an issue where it was not possible to save a library on a network share under macOS due to an exception when acquiring a file lock [#10452](https://github.com/JabRef/jabref/issues/10452)
+- We fixed an issue where exporting "XMP annotated pdf" without selecting an existing document would produce an exception. [#10102](https://github.com/JabRef/jabref/issues/10102)
 
 ### Removed
 

diff --git a/src/main/java/org/jabref/gui/icon/IconTheme.java b/src/main/java/org/jabref/gui/icon/IconTheme.java
@@ -277,6 +277,7 @@ public enum JabRefIcons implements JabRefIcon {
         APPLICATION_VIM(JabRefMaterialDesignIcon.VIM),
         APPLICATION_WINEDT(JabRefMaterialDesignIcon.WINEDT),
         APPLICATION_SUBLIMETEXT(JabRefMaterialDesignIcon.SUBLIME_TEXT),
+        APPLICATION_TEXSHOP(JabRefMaterialDesignIcon.TEXSHOP),
         KEY_BINDINGS(MaterialDesignK.KEYBOARD),
         FIND_DUPLICATES(MaterialDesignC.CODE_EQUAL),
         CONNECT_DB(MaterialDesignC.CLOUD_UPLOAD),
@@ -351,7 +352,6 @@ public enum JabRefIcons implements JabRefIcon {
         ACCEPT_LEFT(MaterialDesignS.SUBDIRECTORY_ARROW_LEFT),
         ACCEPT_RIGHT(MaterialDesignS.SUBDIRECTORY_ARROW_RIGHT),
         MERGE_GROUPS(MaterialDesignS.SOURCE_MERGE);
-
         private final JabRefIcon icon;
 
         JabRefIcons(Ikon... icons) {

diff --git a/src/main/java/org/jabref/gui/icon/JabRefMaterialDesignIcon.java b/src/main/java/org/jabref/gui/icon/JabRefMaterialDesignIcon.java
@@ -30,7 +30,8 @@ public enum JabRefMaterialDesignIcon implements Ikon {
     SET_ALL("jab-setall", '\ue90c'),
     VSCODE("jab-vsvode", '\ue90d'),
     CANCEL("jab-cancel", '\ue90e'),
-    SUBLIME_TEXT("jab-sublime-text", '\ue90f');
+    SUBLIME_TEXT("jab-sublime-text", '\ue90f'),
+    TEXSHOP("jab-texshop", '\ue910');
 
     private String description;
     private int code;

diff --git a/src/main/java/org/jabref/gui/push/PushToTexShop.java b/src/main/java/org/jabref/gui/push/PushToTexShop.java
@@ -34,7 +34,7 @@ public String getDisplayName() {
 
     @Override
     public JabRefIcon getApplicationIcon() {
-        return IconTheme.JabRefIcons.APPLICATION_GENERIC;
+        return IconTheme.JabRefIcons.APPLICATION_TEXSHOP;
     }
 
     @Override

diff --git a/src/main/java/org/jabref/logic/cleanup/DoiCleanup.java b/src/main/java/org/jabref/logic/cleanup/DoiCleanup.java
@@ -13,17 +13,19 @@
 import org.jabref.model.entry.field.Field;
 import org.jabref.model.entry.field.StandardField;
 import org.jabref.model.entry.field.UnknownField;
+import org.jabref.model.entry.identifier.ArXivIdentifier;
 import org.jabref.model.entry.identifier.DOI;
 
 /**
- * Formats the DOI (e.g. removes http part) and also moves DOIs from note, url or ee field to the doi field.
+ * Formats the DOI (e.g. removes http part) and also infers DOIs from the note, url, eprint or ee fields.
  */
 public class DoiCleanup implements CleanupJob {
 
     /**
      * Fields to check for DOIs.
      */
-    private static final List<Field> FIELDS = Arrays.asList(StandardField.NOTE, StandardField.URL, new UnknownField("ee"));
+    private static final List<Field> FIELDS = Arrays.asList(StandardField.NOTE, StandardField.URL, StandardField.EPRINT,
+            new UnknownField("ee"));
 
     @Override
     public List<FieldChange> cleanup(BibEntry entry) {
@@ -57,14 +59,25 @@ public List<FieldChange> cleanup(BibEntry entry) {
         } else {
             // As the Doi field is empty we now check if note, url, or ee field contains a Doi
             for (Field field : FIELDS) {
-                Optional<DOI> doi = entry.getField(field).flatMap(DOI::parse);
+                Optional<String> fieldContentOpt = entry.getField(field);
+
+                Optional<DOI> doi = fieldContentOpt.flatMap(DOI::parse);
 
                 if (doi.isPresent()) {
                     // Update Doi
                     Optional<FieldChange> change = entry.setField(StandardField.DOI, doi.get().getDOI());
                     change.ifPresent(changes::add);
                     removeFieldValue(entry, field, changes);
                 }
+
+                if (StandardField.EPRINT == field) {
+                    fieldContentOpt.flatMap(ArXivIdentifier::parse)
+                                   .flatMap(ArXivIdentifier::inferDOI)
+                                   .ifPresent(inferredDoi -> {
+                                       Optional<FieldChange> change = entry.setField(StandardField.DOI, inferredDoi.getDOI());
+                                       change.ifPresent(changes::add);
+                                   });
+                }
             }
         }
         return changes;

diff --git a/src/main/java/org/jabref/logic/exporter/XmpPdfExporter.java b/src/main/java/org/jabref/logic/exporter/XmpPdfExporter.java
@@ -1,5 +1,7 @@
 package org.jabref.logic.exporter;
 
+import java.io.IOException;
+import java.nio.file.Files;
 import java.nio.file.Path;
 import java.util.List;
 import java.util.Objects;
@@ -11,6 +13,12 @@
 import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.entry.BibEntry;
 
+import org.apache.pdfbox.pdmodel.PDDocument;
+import org.apache.pdfbox.pdmodel.PDPage;
+import org.apache.pdfbox.pdmodel.PDPageContentStream;
+import org.apache.pdfbox.pdmodel.font.PDType1Font;
+import org.apache.pdfbox.pdmodel.font.Standard14Fonts;
+
 public class XmpPdfExporter extends Exporter {
 
     private final XmpPreferences xmpPreferences;
@@ -26,7 +34,24 @@ public void export(BibDatabaseContext databaseContext, Path pdfFile, List<BibEnt
         Objects.requireNonNull(pdfFile);
         Objects.requireNonNull(entries);
 
-        if (pdfFile.toString().endsWith(".pdf")) {
+        Path filePath = pdfFile.toAbsolutePath();
+
+        if (!Files.exists(filePath)) {
+            try (PDDocument document = new PDDocument()) {
+                PDPage page = new PDPage();
+                document.addPage(page);
+
+                try (PDPageContentStream contentStream = new PDPageContentStream(document, page)) {
+                    contentStream.beginText();
+                    contentStream.newLineAtOffset(25, 500);
+                    contentStream.setFont(new PDType1Font(Standard14Fonts.FontName.HELVETICA), 12);
+                    contentStream.showText("This PDF was created by JabRef. It demonstrates the embedding of XMP data in PDF files. Please open the file metadata view of your PDF viewer to see the attached files. Note that the normal usage is to embed the BibTeX data in an existing PDF.");
+                    contentStream.endText();
+                }
+                document.save(filePath.toString());
+            } catch (IOException e) {
+                throw new Exception("Error creating PDF", e);
+            }
             new XmpUtilWriter(xmpPreferences).writeXmp(pdfFile, entries, databaseContext.getDatabase());
         }
     }

diff --git a/src/main/java/org/jabref/model/entry/identifier/ArXivIdentifier.java b/src/main/java/org/jabref/model/entry/identifier/ArXivIdentifier.java
@@ -9,10 +9,14 @@
 
 import org.jabref.model.strings.StringUtil;
 
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
 /**
  * Identifier for the arXiv. See https://arxiv.org/help/arxiv_identifier
  */
 public class ArXivIdentifier extends EprintIdentifier {
+    private static final Logger LOGGER = LoggerFactory.getLogger(ArXivIdentifier.class);
 
     private static final String ARXIV_PREFIX = "http(s)?://arxiv.org/(abs|pdf)/|arxiv|arXiv";
     private final String identifier;
@@ -71,6 +75,22 @@ public Optional<String> getClassification() {
         }
     }
 
+    /**
+     * ArXiV articles are assigned DOIs automatically, which starts with a DOI prefix '10.48550/' followed by the ArXiV
+     * ID (replacing the colon with a period).
+     *<p>
+     * For more information:
+     * <a href="https://blog.arxiv.org/2022/02/17/new-arxiv-articles-are-now-automatically-assigned-dois/">
+     *     new-arxiv-articles-are-now-automatically-assigned-dois</a>
+     * */
+    public Optional<DOI> inferDOI() {
+        if (StringUtil.isBlank(identifier)) {
+            return Optional.empty();
+        }
+
+        return DOI.parse("10.48550/arxiv." + identifier);
+    }
+
     @Override
     public String toString() {
         return "ArXivIdentifier{" +

diff --git a/src/main/resources/fonts/JabRefMaterialDesign.ttf b/src/main/resources/fonts/JabRefMaterialDesign.ttf
diff --git a/src/test/java/org/jabref/logic/exporter/XmpPdfExporterTest.java b/src/test/java/org/jabref/logic/exporter/XmpPdfExporterTest.java
@@ -7,9 +7,15 @@
 import java.util.stream.Stream;
 
 import javafx.beans.property.SimpleObjectProperty;
+import javafx.collections.FXCollections;
 
+import org.jabref.logic.cleanup.FieldFormatterCleanup;
+import org.jabref.logic.formatter.bibtexfields.NormalizeNamesFormatter;
+import org.jabref.logic.importer.ImportFormatPreferences;
+import org.jabref.logic.importer.fileformat.PdfXmpImporter;
 import org.jabref.logic.journals.JournalAbbreviationRepository;
 import org.jabref.logic.xmp.XmpPreferences;
+import org.jabref.logic.xmp.XmpUtilWriter;
 import org.jabref.model.database.BibDatabase;
 import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.entry.BibEntry;
@@ -21,12 +27,18 @@
 
 import org.apache.pdfbox.pdmodel.PDDocument;
 import org.apache.pdfbox.pdmodel.PDPage;
+import org.apache.pdfbox.pdmodel.PDPageContentStream;
+import org.apache.pdfbox.pdmodel.font.PDType1Font;
+import org.apache.pdfbox.pdmodel.font.Standard14Fonts;
+import org.junit.jupiter.api.AfterEach;
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.io.TempDir;
 import org.junit.jupiter.params.ParameterizedTest;
 import org.junit.jupiter.params.provider.Arguments;
 import org.junit.jupiter.params.provider.MethodSource;
+import org.mockito.Answers;
 
+import static org.junit.jupiter.api.Assertions.assertEquals;
 import static org.junit.jupiter.api.Assertions.assertFalse;
 import static org.junit.jupiter.api.Assertions.assertTrue;
 import static org.mockito.Mockito.mock;
@@ -41,6 +53,8 @@ class XmpPdfExporterTest {
     private static BibEntry vapnik2000 = new BibEntry(StandardEntryType.Article);
 
     private XmpPdfExporter exporter;
+    private PdfXmpImporter importer;
+    private XmpPreferences xmpPreferences;
 
     private BibDatabaseContext databaseContext;
     private JournalAbbreviationRepository abbreviationRepository;
@@ -84,7 +98,7 @@ private static void initBibEntries() throws IOException {
         vapnik2000.setCitationKey("vapnik2000");
         vapnik2000.setField(StandardField.TITLE, "The Nature of Statistical Learning Theory");
         vapnik2000.setField(StandardField.PUBLISHER, "Springer Science + Business Media");
-        vapnik2000.setField(StandardField.AUTHOR, "Vladimir N. Vapnik");
+        vapnik2000.setField(StandardField.AUTHOR, "Vapnik, Vladimir N.");
         vapnik2000.setField(StandardField.DOI, "10.1007/978-1-4757-3264-1");
         vapnik2000.setField(StandardField.OWNER, "Ich");
     }
@@ -99,9 +113,13 @@ void setUp() throws IOException {
         when(filePreferences.getUserAndHost()).thenReturn(tempDir.toAbsolutePath().toString());
         when(filePreferences.shouldStoreFilesRelativeToBibFile()).thenReturn(false);
 
-        XmpPreferences xmpPreferences = new XmpPreferences(false, Collections.emptySet(), new SimpleObjectProperty<>(','));
+        xmpPreferences = new XmpPreferences(false, Collections.emptySet(), new SimpleObjectProperty<>(','));
         exporter = new XmpPdfExporter(xmpPreferences);
 
+        ImportFormatPreferences importFormatPreferences = mock(ImportFormatPreferences.class, Answers.RETURNS_DEEP_STUBS);
+        when(importFormatPreferences.fieldPreferences().getNonWrappableFields()).thenReturn(FXCollections.emptyObservableList());
+        importer = new PdfXmpImporter(xmpPreferences);
+
         databaseContext = new BibDatabaseContext();
         BibDatabase dataBase = databaseContext.getDatabase();
 
@@ -111,6 +129,17 @@ void setUp() throws IOException {
         dataBase.insertEntry(vapnik2000);
     }
 
+    @AfterEach
+    void reset() throws IOException {
+        List<BibEntry> expectedEntries = databaseContext.getEntries();
+        for (BibEntry entry : expectedEntries) {
+            entry.clearField(StandardField.FILE);
+        }
+        LinkedFile linkedFile = createDefaultLinkedFile("existing.pdf", tempDir);
+        olly2018.setFiles(List.of(linkedFile));
+        toral2006.setFiles(List.of(new LinkedFile("non-existing", "path/to/nowhere.pdf", "PDF")));
+    }
+
     @ParameterizedTest
     @MethodSource("provideBibEntriesWithValidPdfFileLinks")
     void successfulExportToAllFilesOfEntry(BibEntry bibEntryWithValidPdfFileLink) throws Exception {
@@ -143,6 +172,39 @@ void unsuccessfulExportToFileByPath(Path path) throws Exception {
         assertFalse(exporter.exportToFileByPath(databaseContext, filePreferences, path, abbreviationRepository));
     }
 
+    @ParameterizedTest
+    @MethodSource("providePathToNewPDFs")
+    public void testRoundtripExportImport(Path path) throws Exception {
+        try (PDDocument document = new PDDocument()) {
+            PDPage page = new PDPage();
+            document.addPage(page);
+
+            try (PDPageContentStream contentStream = new PDPageContentStream(document, page)) {
+                contentStream.beginText();
+                contentStream.newLineAtOffset(25, 500);
+                contentStream.setFont(new PDType1Font(Standard14Fonts.FontName.HELVETICA), 12);
+                contentStream.showText("This PDF was created by JabRef. It demonstrates the embedding of XMP data in PDF files. Please open the file metadata view of your PDF viewer to see the attached files. Note that the normal usage is to embed the BibTeX data in an existing PDF.");
+                contentStream.endText();
+            }
+            document.save(path.toString());
+        }
+        new XmpUtilWriter(xmpPreferences).writeXmp(path, databaseContext.getEntries(), databaseContext.getDatabase());
+
+        List<BibEntry> importedEntries = importer.importDatabase(path).getDatabase().getEntries();
+        importedEntries.forEach(bibEntry -> new FieldFormatterCleanup(StandardField.AUTHOR, new NormalizeNamesFormatter()).cleanup(bibEntry));
+
+        List<BibEntry> expectedEntries = databaseContext.getEntries();
+        for (BibEntry entry : expectedEntries) {
+            entry.clearField(StandardField.FILE);
+            entry.addFile(createDefaultLinkedFile("original.pdf", tempDir));
+        }
+        assertEquals(expectedEntries, importedEntries);
+    }
+
+    public static Stream<Arguments> providePathToNewPDFs() {
+        return Stream.of(Arguments.of(tempDir.resolve("original.pdf").toAbsolutePath()));
+    }
+
     public static Stream<Arguments> providePathsToValidPDFs() {
         return Stream.of(Arguments.of(tempDir.resolve("existing.pdf").toAbsolutePath()));
     }
@@ -156,12 +218,16 @@ public static Stream<Arguments> providePathsToInvalidPDFs() throws IOException {
     }
 
     private static LinkedFile createDefaultLinkedFile(String fileName, Path tempDir) throws IOException {
+        return createDefaultLinkedFile("", fileName, tempDir);
+    }
+
+    private static LinkedFile createDefaultLinkedFile(String description, String fileName, Path tempDir) throws IOException {
         Path pdfFile = tempDir.resolve(fileName);
         try (PDDocument pdf = new PDDocument()) {
             pdf.addPage(new PDPage());
             pdf.save(pdfFile.toAbsolutePath().toString());
         }
 
-        return new LinkedFile("A linked pdf", pdfFile, "PDF");
+        return new LinkedFile("", pdfFile, "PDF");
     }
 }