Support for exporting to YAML format

CHANGELOG.md

@@ -15,6 +15,7 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - We added a query parser and mapping layer to enable conversion of queries formulated in simplified lucene syntax by the user into api queries. [#6799](https://github.com/JabRef/jabref/pull/6799)
 - We added some basic functionality to customise the look of JabRef by importing a css theme file. [#5790](https://github.com/JabRef/jabref/issues/5790)
 - We added connection check function in network preference setting [#6560](https://github.com/JabRef/jabref/issues/6560)
+- We added support for exporting to YAML. [#6974](https://github.com/JabRef/jabref/issues/6974)
 - We added a DOI format and organization check to detect [American Physical Society](https://journals.aps.org/) journals to copy the article ID
 to the page field for cases where the page numbers are missing. [#7019](https://github.com/JabRef/jabref/issues/7019)
 - We added a new fetcher to enable users to search jstor.org [#6627](https://github.com/JabRef/jabref/issues/6627)
@@ -56,6 +57,7 @@ inserting new citations in a OpenOffic/LibreOffice document. [#6957](https://git
 - We fixed an issue with the python script used by browser plugins that failed to locate JabRef if not installed in its default location. [#6963](https://github.com/JabRef/jabref/pull/6963/files)
 - We fixed an issue where spaces and newlines in an isbn would generate an exception. [#6456](https://github.com/JabRef/jabref/issues/6456)
 - We fixed an issue where identity column header had incorrect foreground color in the Dark theme. [#6796](https://github.com/JabRef/jabref/issues/6796)
+- We fixed an issue where the RIS exporter added extra blank lines.[#7007](https://github.com/JabRef/jabref/pull/7007/files)
 - We fixed an issue where clicking on Collapse All button in the Search for Unlinked Local Files expanded the directory structure erroneously [#6848](https://github.com/JabRef/jabref/issues/6848)
 - We fixed an issue, when pulling changes from shared database via shortcut caused creation a new new tech report [6867](https://github.com/JabRef/jabref/issues/6867)
 - We fixed an issue where the JabRef GUI does not highlight the "All entries" group on start-up [#6691](https://github.com/JabRef/jabref/issues/6691)

src/main/java/org/jabref/logic/exporter/BlankLineBehaviour.java

@@ -0,0 +1,9 @@
+package org.jabref.logic.exporter;
+
+/**
+ * This enum represents the behaviour for blank lines in {@link TemplateExporter}
+ */
+public enum BlankLineBehaviour {
+ KEEP_BLANKS,
+ DELETE_BLANKS
+}

src/main/java/org/jabref/logic/exporter/ExporterFactory.java

@@ -49,8 +49,9 @@ public static ExporterFactory create(List<TemplateExporter> customFormats,
  exporters.add(new TemplateExporter("ISO 690", "iso690txt", "iso690", "iso690txt", StandardFileType.TXT, layoutPreferences, savePreferences));
  exporters.add(new TemplateExporter("Endnote", "endnote", "EndNote", "endnote", StandardFileType.TXT, layoutPreferences, savePreferences));
  exporters.add(new TemplateExporter("OpenOffice/LibreOffice CSV", "oocsv", "openoffice-csv", "openoffice", StandardFileType.CSV, layoutPreferences, savePreferences));
- exporters.add(new TemplateExporter("RIS", "ris", "ris", "ris", StandardFileType.RIS, layoutPreferences, savePreferences).withEncoding(StandardCharsets.UTF_8));
+ exporters.add(new TemplateExporter("RIS", "ris", "ris", "ris", StandardFileType.RIS, layoutPreferences, savePreferences, BlankLineBehaviour.DELETE_BLANKS).withEncoding(StandardCharsets.UTF_8));
  exporters.add(new TemplateExporter("MIS Quarterly", "misq", "misq", "misq", StandardFileType.RTF, layoutPreferences, savePreferences));
+ exporters.add(new TemplateExporter("CSL YAML", "yaml", "yaml", null, StandardFileType.YAML, layoutPreferences, savePreferences, BlankLineBehaviour.DELETE_BLANKS));
  exporters.add(new BibTeXMLExporter());
  exporters.add(new OpenOfficeDocumentCreator());
  exporters.add(new OpenDocumentSpreadsheetCreator());

src/main/java/org/jabref/logic/exporter/TemplateExporter.java

@@ -14,12 +14,12 @@
 import java.util.List;
 import java.util.Map;
 import java.util.Objects;
-import java.util.regex.Pattern;
 
 import org.jabref.logic.layout.Layout;
 import org.jabref.logic.layout.LayoutFormatterPreferences;
 import org.jabref.logic.layout.LayoutHelper;
 import org.jabref.logic.util.FileType;
+import org.jabref.logic.util.OS;
 import org.jabref.logic.util.StandardFileType;
 import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.entry.BibEntry;
@@ -33,15 +33,8 @@
  */
 public class TemplateExporter extends Exporter {
 
+ private static final String BLANK_LINE_PATTERN = "\\r\\n|\\n";
  private static final String LAYOUT_PREFIX = "/resource/layout/";
-
- /**
- * A regular expression that matches blank lines
- *
- * ?m activates "multimode", which makes ^ match line starts/ends.
- * \\s simply marks any whitespace character
- */
- private static final Pattern BLANK_LINE_MATCHER = Pattern.compile("(?m)^\\s");
  private static final String LAYOUT_EXTENSION = ".layout";
  private static final String FORMATTERS_EXTENSION = ".formatters";
  private static final String BEGIN_INFIX = ".begin";
@@ -55,11 +48,10 @@ public class TemplateExporter extends Exporter {
  private final SavePreferences savePreferences;
  private Charset encoding; // If this value is set, it will be used to override the default encoding for the getCurrentBasePanel.
  private boolean customExport;
- private boolean deleteBlankLines;
+ private BlankLineBehaviour blankLineBehaviour;
 
  /**
- * Initialize another export format based on templates stored in dir with
- * layoutFile lfFilename.
+ * Initialize another export format based on templates stored in dir with layoutFile lfFilename.
  *
  * @param displayName Name to display to the user.
  * @param consoleName Name to call this format in the console.
@@ -72,8 +64,7 @@ public TemplateExporter(String displayName, String consoleName, String lfFileNam
  }
 
  /**
- * Initialize another export format based on templates stored in dir with
- * layoutFile lfFilename.
+ * Initialize another export format based on templates stored in dir with layoutFile lfFilename.
  *
  * @param name to display to the user and to call this format in the console.
  * @param lfFileName Name of the main layout file.
@@ -87,8 +78,7 @@ public TemplateExporter(String name, String lfFileName, String extension, Layout
  }
 
  /**
- * Initialize another export format based on templates stored in dir with
- * layoutFile lfFilename.
+ * Initialize another export format based on templates stored in dir with layoutFile lfFilename.
  *
  * @param displayName Name to display to the user.
  * @param consoleName Name to call this format in the console.
@@ -112,27 +102,36 @@ public TemplateExporter(String displayName, String consoleName, String lfFileNam
  }
 
  /**
- * Initialize another export format based on templates stored in dir with
- * layoutFile lfFilename.
- * The display name is automatically derived from the FileType
+ * Initialize another export format based on templates stored in dir with layoutFile lfFilename.
  *
+ * @param displayName Name to display to the user.
  * @param consoleName Name to call this format in the console.
  * @param lfFileName Name of the main layout file.
  * @param directory Directory in which to find the layout file.
  * @param extension Should contain the . (for instance .txt).
  * @param layoutPreferences Preferences for layout
  * @param savePreferences Preferences for saving
- * @param deleteBlankLines If blank lines should be remove (default: false)
+ * @param blankLineBehaviour how to behave regarding blank lines.
  */
- public TemplateExporter(String consoleName, String lfFileName, String directory, StandardFileType extension, LayoutFormatterPreferences layoutPreferences, SavePreferences savePreferences, boolean deleteBlankLines) {
- this(consoleName, consoleName, lfFileName, directory, extension, layoutPreferences, savePreferences);
- this.deleteBlankLines = deleteBlankLines;
+ public TemplateExporter(String displayName, String consoleName, String lfFileName, String directory, FileType extension,
+ LayoutFormatterPreferences layoutPreferences, SavePreferences savePreferences,
+ BlankLineBehaviour blankLineBehaviour) {
+ super(consoleName, displayName, extension);
+ if (Objects.requireNonNull(lfFileName).endsWith(LAYOUT_EXTENSION)) {
+ this.lfFileName = lfFileName.substring(0, lfFileName.length() - LAYOUT_EXTENSION.length());
+ } else {
+ this.lfFileName = lfFileName;
+ }
+ this.directory = directory;
+ this.layoutPreferences = layoutPreferences;
+ this.savePreferences = savePreferences;
+ this.blankLineBehaviour = blankLineBehaviour;
  }
 
  /**
- * Indicate whether this is a custom export. A custom export looks for its
- * layout files using a normal file path, while a built-in export looks in
- * the classpath.
+ * Indicate whether this is a custom export.
+ * A custom export looks for its layout files using a normal file path,
+ * while a built-in export looks in the classpath.
  *
  * @param custom true to indicate a custom export format.
  */
@@ -141,8 +140,7 @@ public void setCustomExport(boolean custom) {
  }
 
  /**
- * Set an encoding which will be used in preference to the default value
- * obtained from the basepanel.
+ * Set an encoding which will be used in preference to the default value obtained from the basepanel.
  *
  * @param encoding The name of the encoding to use.
  */
@@ -152,11 +150,9 @@ public TemplateExporter withEncoding(Charset encoding) {
  }
 
  /**
- * This method should return a reader from which the given layout file can
- * be read.
+ * This method should return a reader from which the given layout file can be read.
  * <p>
- * Subclasses of TemplateExporter are free to override and provide their own
- * implementation.
+ * Subclasses of TemplateExporter are free to override and provide their own implementation.
  *
  * @param filename the filename
  * @return a newly created reader
@@ -277,9 +273,13 @@ public void export(final BibDatabaseContext databaseContext, final Path file,
 
  // Write the entry
  if (layout != null) {
- if (deleteBlankLines) {
- String withoutBlankLines = BLANK_LINE_MATCHER.matcher(layout.doLayout(entry, databaseContext.getDatabase())).replaceAll("");
- ps.write(withoutBlankLines);
+ if (blankLineBehaviour == BlankLineBehaviour.DELETE_BLANKS) {
+ String[] lines = layout.doLayout(entry, databaseContext.getDatabase()).split(BLANK_LINE_PATTERN);
+ for (String line : lines) {
+ if (!line.isBlank() && !line.isEmpty()) {
+ ps.write(line + OS.NEWLINE);
+ }
+ }
  } else {
  ps.write(layout.doLayout(entry, databaseContext.getDatabase()));
  }
@@ -316,9 +316,8 @@ public void export(final BibDatabaseContext databaseContext, final Path file,
  }
 
  /**
- * See if there is a name formatter file bundled with this export format. If so, read
- * all the name formatters so they can be used by the filter layouts.
- *
+ * See if there is a name formatter file bundled with this export format.
+ * If so, read all the name formatters so they can be used by the filter layouts.
  */
  private void readFormatterFile() {
  File formatterFile = new File(lfFileName + FORMATTERS_EXTENSION);

src/main/java/org/jabref/logic/layout/LayoutEntry.java

@@ -32,6 +32,7 @@
 import org.jabref.logic.layout.format.AuthorNatBib;
 import org.jabref.logic.layout.format.AuthorOrgSci;
 import org.jabref.logic.layout.format.Authors;
+import org.jabref.logic.layout.format.CSLType;
 import org.jabref.logic.layout.format.CompositeFormat;
 import org.jabref.logic.layout.format.CreateBibORDFAuthors;
 import org.jabref.logic.layout.format.CreateDocBook4Authors;
@@ -539,6 +540,8 @@ private LayoutFormatter getLayoutFormatterByName(String name) {
  return new WrapFileLinks(prefs.getFileLinkPreferences());
  case "Markdown":
  return new MarkdownFormatter();
+ case "CSLType":
+ return new CSLType();
  default:
  return null;
  }

src/main/java/org/jabref/logic/layout/format/CSLType.java

@@ -0,0 +1,21 @@
+package org.jabref.logic.layout.format;
+
+import org.jabref.logic.layout.LayoutFormatter;
+import org.jabref.model.entry.types.StandardEntryType;
+
+public class CSLType implements LayoutFormatter {
+
+ @Override
+ public String format(String value) {
+ return switch (StandardEntryType.valueOf(value)) {
+ case Article -> "article";
+ case Book -> "book";
+ case Conference -> "paper-conference";
+ case Report, TechReport -> "report";
+ case Thesis, MastersThesis, PhdThesis -> "thesis";
+ case WWW, Online -> "webpage";
+
+ default -> "no-type";
+ };
+ }
+}

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

@@ -41,7 +41,8 @@ public enum StandardFileType implements FileType {
  JSON("json"),
  XMP("xmp"),
  ZIP("zip"),
- CSS("css");
+ CSS("css"),
+ YAML("yaml");
 
  private final List<String> extensions;
 

src/main/resources/resource/layout/yaml.begin.layout

@@ -0,0 +1,2 @@
+---
+references:

src/main/resources/resource/layout/yaml.end.layout

@@ -0,0 +1 @@
+---

src/main/resources/resource/layout/yaml.layout

@@ -0,0 +1,14 @@
+- id: \citationkey
+\begin{entrytype} type: \format[CSLType]{\entrytype}\end{entrytype}
+\begin{author}
+ author:
+ - literal: "\author"
+\end{author}
+\begin{title} title: "\title"\end{title}
+\begin{shorttitle} title-short: "\shorttitle"\end{shorttitle}
+\begin{date} issued: \date\end{date}
+\begin{url} url: \url\end{url}
+\begin{doi} doi: \doi\end{doi}
+\begin{volume} volume: \volume\end{volume}
+\begin{number} number: \number\end{number}
+\begin{urldate} accessed: \urldate\end{urldate}

src/test/java/org/jabref/logic/exporter/YamlExporterTest.java

@@ -0,0 +1,108 @@
+package org.jabref.logic.exporter;
+
+import java.nio.charset.Charset;
+import java.nio.charset.StandardCharsets;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.List;
+
+import org.jabref.logic.layout.LayoutFormatterPreferences;
+import org.jabref.logic.xmp.XmpPreferences;
+import org.jabref.model.database.BibDatabaseContext;
+import org.jabref.model.entry.BibEntry;
+import org.jabref.model.entry.field.StandardField;
+import org.jabref.model.entry.types.StandardEntryType;
+
+import org.junit.jupiter.api.BeforeAll;
+import org.junit.jupiter.api.Test;
+import org.junit.jupiter.api.io.TempDir;
+import org.mockito.Answers;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.mockito.Mockito.mock;
+
+public class YamlExporterTest {
+
+ private static Charset charset;
+ private static Exporter yamlExporter;
+ private static BibDatabaseContext databaseContext;
+
+ @BeforeAll
+ static void setUp() {
+ List<TemplateExporter> customFormats = new ArrayList<>();
+ LayoutFormatterPreferences layoutPreferences = mock(LayoutFormatterPreferences.class, Answers.RETURNS_DEEP_STUBS);
+ SavePreferences savePreferences = mock(SavePreferences.class);
+ XmpPreferences xmpPreferences = mock(XmpPreferences.class);
+ ExporterFactory exporterFactory = ExporterFactory.create(customFormats, layoutPreferences, savePreferences, xmpPreferences);
+
+ databaseContext = new BibDatabaseContext();
+ charset = StandardCharsets.UTF_8;
+ yamlExporter = exporterFactory.getExporterByName("yaml").get();
+ }
+
+ @Test
+ public final void exportForNoEntriesWritesNothing(@TempDir Path tempFile) throws Exception {
+ Path file = tempFile.resolve("ThisIsARandomlyNamedFile");
+ Files.createFile(file);
+ yamlExporter.export(databaseContext, tempFile, charset, Collections.emptyList());
+ assertEquals(Collections.emptyList(), Files.readAllLines(file));
+ }
+
+ @Test
+ public final void exportsCorrectContent(@TempDir Path tempFile) throws Exception {
+ BibEntry entry = new BibEntry(StandardEntryType.Article)
+ .withCitationKey("test")
+ .withField(StandardField.AUTHOR, "Test Author")
+ .withField(StandardField.TITLE, "Test Title")
+ .withField(StandardField.URL, "http://example.com")
+ .withField(StandardField.DATE, "2020-10-14");
+
+ Path file = tempFile.resolve("RandomFileName");
+ Files.createFile(file);
+ yamlExporter.export(databaseContext, file, charset, Collections.singletonList(entry));
+
+ List<String> expected = List.of(
+ "---",
+ "references:",
+ "- id: test",
+ " type: article",
+ " author:",
+ " - literal: \"Test Author\"",
+ " title: \"Test Title\"",
+ " issued: 2020-10-14",
+ " url: http://example.com",
+ "---");
+
+ assertEquals(expected, Files.readAllLines(file));
+ }
+
+ @Test
+ public final void formatsContentCorrect(@TempDir Path tempFile) throws Exception {
+ BibEntry entry = new BibEntry(StandardEntryType.Misc)
+ .withCitationKey("test")
+ .withField(StandardField.AUTHOR, "Test Author")
+ .withField(StandardField.TITLE, "Test Title")
+ .withField(StandardField.URL, "http://example.com")
+ .withField(StandardField.DATE, "2020-10-14");
+
+ Path file = tempFile.resolve("RandomFileName");
+ Files.createFile(file);
+ yamlExporter.export(databaseContext, file, charset, Collections.singletonList(entry));
+
+ List<String> expected = List.of(
+ "---",
+ "references:",
+ "- id: test",
+ " type: no-type",
+ " author:",
+ " - literal: \"Test Author\"",
+ " title: \"Test Title\"",
+ " issued: 2020-10-14",
+ " url: http://example.com",
+ "---");
+
+ assertEquals(expected, Files.readAllLines(file));
+ }
+}