Add doi-to-bibtex to examples and JabKit

.github/workflows/tests-code.yml

@@ -462,6 +462,7 @@ jobs:
         run: |
           echo "cache_key=jbang-$(date +%F)" >> $GITHUB_OUTPUT
       - name: Use cache
+        if: steps.changed-jablib-files.outputs.any_changed != 'true'
         uses: actions/cache@v4
         with:
           path: ~/.jbang
@@ -515,6 +516,7 @@ jobs:
         with:
           files: |
             .jbang/*.java
+            jabkit/src/main/java/**/*.java
             jablib/src/main/java/**/*.java
             jablib-examples/**/*.java
           files_ignore: |
@@ -546,7 +548,16 @@ jobs:
           # We modify the JBang scripts directly to avoid issues with relative paths
           for f in ${{ steps.changed-jablib-files.outputs.all_changed_files }}; do
             case "$f" in
-              jablib-examples/*) continue ;; # skip scripts
+              jablib-examples/*)
+                # skip scripts
+                continue
+                ;;
+              jabkit/*)
+                # only JabKit needs its modified sources
+                if [ "${{ matrix.script }}" != ".jbang/JabKitLauncher.java" ]; then
+                  continue
+                fi
+                ;;
             esac
             echo "//SOURCES ../$f" >> "${{ matrix.script }}"
           done

CHANGELOG.md

@@ -13,6 +13,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 
 - We added "IEEE" as another option for parsing plain text citations. [#14233](github.com/JabRef/jabref/pull/14233)
 - We added automatic date-based groups that create year/month/day subgroups from an entry’s date fields. [#10822](https://github.com/JabRef/jabref/issues/10822)
+- We added `doi-to-bibtex` to `JabKit`. [#14244](https://github.com/JabRef/jabref/pull/14244)
 
 ### Changed
 

jabkit/src/main/java/org/jabref/JabKit.java

@@ -32,6 +32,7 @@
 import org.jabref.logic.util.Directories;
 import org.jabref.logic.util.strings.StringUtil;
 import org.jabref.model.entry.BibEntryTypesManager;
+import org.jabref.model.entry.identifier.DOI;
 import org.jabref.model.util.DummyFileUpdateMonitor;
 import org.jabref.model.util.FileUpdateMonitor;
 
@@ -72,7 +73,8 @@ public static void main(String[] args) {
             Injector.setModelOrService(BibEntryTypesManager.class, entryTypesManager);
 
             ArgumentProcessor argumentProcessor = new ArgumentProcessor(preferences, entryTypesManager);
-            CommandLine commandLine = new CommandLine(argumentProcessor);
+            CommandLine commandLine = new CommandLine(argumentProcessor)
+                    .registerConverter(DOI.class, DOI::new);
             String usageHeader = BuildInfo.JABREF_BANNER.formatted(buildInfo.version) + "\n" + JABKIT_BRAND;
             commandLine.getCommandSpec().usageMessage().header(usageHeader);
             applyUsageFooters(commandLine,

jabkit/src/main/java/org/jabref/cli/ArgumentProcessor.java

@@ -43,6 +43,7 @@
                 CheckConsistency.class,
                 CheckIntegrity.class,
                 Convert.class,
+                DoiToBibtex.class,
                 Fetch.class,
                 GenerateBibFromAux.class,
                 GenerateCitationKeys.class,

jabkit/src/main/java/org/jabref/cli/DoiToBibtex.java

@@ -0,0 +1,68 @@
+package org.jabref.cli;
+
+import java.io.IOException;
+import java.io.OutputStreamWriter;
+import java.nio.charset.StandardCharsets;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Optional;
+import java.util.concurrent.Callable;
+
+import org.jabref.logic.exporter.BibDatabaseWriter;
+import org.jabref.logic.importer.FetcherException;
+import org.jabref.logic.importer.fetcher.CrossRef;
+import org.jabref.model.database.BibDatabase;
+import org.jabref.model.database.BibDatabaseContext;
+import org.jabref.model.entry.BibEntry;
+import org.jabref.model.entry.identifier.DOI;
+
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import picocli.CommandLine;
+import picocli.CommandLine.Command;
+import picocli.CommandLine.Parameters;
+
+@Command(name = "doi-to-bibtex", description = "Converts a DOI to BibTeX")
+public class DoiToBibtex implements Callable<Integer> {
+
+    private static final Logger LOGGER = LoggerFactory.getLogger(DoiToBibtex.class);
+
+    @CommandLine.ParentCommand
+    private ArgumentProcessor argumentProcessor;
+
+    @Parameters(paramLabel = "DOI", description = "one or more DOIs to fetch", arity = "1..*")
+    private DOI[] dois;
+
+    @Override
+    public Integer call() {
+        var fetcher = new CrossRef();
+        List<BibEntry> entries = new ArrayList<>(dois.length);
+
+        for (DOI doi : dois) {
+            Optional<BibEntry> entry;
+            try {
+                entry = fetcher.performSearchById(doi.asString());
+            } catch (FetcherException e) {
+                LOGGER.error("Could not fetch DOI from BibTeX", e);
+                continue;
+            }
+
+            if (entry.isEmpty()) {
+                LOGGER.error("Could not fetch DOI from BibTeX");
+                continue;
+            }
+
+            entries.add(entry.get());
+        }
+
+        try (var writer = new OutputStreamWriter(System.out, StandardCharsets.UTF_8)) {
+            var context = new BibDatabaseContext(new BibDatabase(entries));
+            var bibWriter = new BibDatabaseWriter(writer, context, argumentProcessor.cliPreferences);
+            bibWriter.writeDatabase(context);
+        } catch (IOException e) {
+            LOGGER.error("Could not write BibTeX", e);
+            return 1;
+        }
+        return 0;
+    }
+}

jablib-examples/doi_to_bibtex.java

@@ -0,0 +1,34 @@
+///usr/bin/env jbang "$0" "$@" ; exit $?
+
+import org.jabref.logic.exporter.BibWriter;
+import org.jabref.logic.exporter.BibDatabaseWriter;
+import org.jabref.logic.importer.fetcher.CrossRef;
+import org.jabref.logic.preferences.JabRefCliPreferences;
+import org.jabref.model.database.BibDatabase;
+import org.jabref.model.database.BibDatabaseContext;
+
+import org.tinylog.Logger;
+
+//DESCRIPTION Converts a DOI to BibTeX
+
+//JAVA 25+
+//RUNTIME_OPTIONS --enable-native-access=ALL-UNNAMED
+//FILES tinylog.properties=tinylog.properties
+
+//DEPS org.jabref:jablib:6.0-SNAPSHOT
+//REPOS mavencentral,mavencentralsnapshots=https://central.sonatype.com/repository/maven-snapshots/,s01oss=https://s01.oss.sonatype.org/content/repositories/snapshots/,oss=https://oss.sonatype.org/content/repositories,jitpack=https://jitpack.io,oss2=https://oss.sonatype.org/content/groups/public,ossrh=https://oss.sonatype.org/content/repositories/snapshots,raw=https://raw.githubusercontent.com/JabRef/jabref/refs/heads/main/jablib/lib/
+
+void main() throws Exception {
+    var preferences = JabRefCliPreferences.getInstance();
+
+    // All `IdParserFetcher<DOI>` can do. In JabRef, there is currently only one implemented
+
+    var fetcher = new CrossRef();
+    var entry = fetcher.performSearchById("10.47397/tb/44-3/tb138kopp-jabref").get(); // will throw an exception if not found
+
+    try (var writer = new OutputStreamWriter(System.out, StandardCharsets.UTF_8)) {
+        var context = new BibDatabaseContext(new BibDatabase(List.of(entry)));
+        var bibWriter = new BibDatabaseWriter(writer, context, preferences);
+        bibWriter.writeDatabase(context);
+    }
+}

jablib/src/main/java/org/jabref/logic/exporter/BibDatabaseWriter.java

@@ -32,7 +32,7 @@
 import org.jabref.logic.cleanup.FieldFormatterCleanups;
 import org.jabref.logic.cleanup.NormalizeWhitespacesCleanup;
 import org.jabref.logic.formatter.bibtexfields.TrimWhitespaceFormatter;
-import org.jabref.logic.preferences.JabRefCliPreferences;
+import org.jabref.logic.preferences.CliPreferences;
 import org.jabref.logic.util.strings.StringUtil;
 import org.jabref.model.FieldChange;
 import org.jabref.model.database.BibDatabase;
@@ -95,7 +95,7 @@ public BibDatabaseWriter(@NonNull BibWriter bibWriter,
     /// @param  preferences - used to read all the preferences
     public BibDatabaseWriter(@NonNull Writer writer,
                              @NonNull BibDatabaseContext bibDatabaseContext,
-                             @NonNull JabRefCliPreferences preferences) {
+                             @NonNull CliPreferences preferences) {
         this(new BibWriter(writer, bibDatabaseContext.getDatabase().getNewLineSeparator()),
                 preferences.getSelfContainedExportConfiguration(),
                 preferences.getFieldPreferences(),

jablib/src/main/java/org/jabref/logic/importer/plaincitation/PlainCitationParser.java

@@ -2,7 +2,6 @@
 
 import java.util.List;
 import java.util.Optional;
-import java.util.stream.Collectors;
 
 import org.jabref.logic.importer.FetcherException;
 import org.jabref.model.entry.BibEntry;
@@ -19,7 +18,7 @@ default List<BibEntry> parseMultiplePlainCitations(String text) throws FetcherEx
             return CitationSplitter.splitCitations(text)
                                    .map(Unchecked.function(this::parsePlainCitation))
                                    .flatMap(Optional::stream)
-                                   .collect(Collectors.toList());
+                                   .toList();
         } catch (UncheckedException e) {
             throw (FetcherException) e.getCause();
         }