Add doi-to-bibtex to examples and JabKit

.github/workflows/tests-code.yml

@@ -469,6 +469,7 @@ 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
@@ -522,6 +523,7 @@ jobs:
         with:
           files: |
             .jbang/*.java
+            jabkit/src/main/java/**/*.java
             jablib/src/main/java/**/*.java
             jablib-examples/**/*.java
           files_ignore: |
@@ -553,7 +555,16 @@ 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

@@ -13,9 +13,11 @@ 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`: `--porcelain` does not output any logs to the console anymore. [#14244](https://github.com/JabRef/jabref/pull/14244)
 - <kbd>Ctrl</kbd> + <kbd>Shift</kbd> + <kbd>L</kbd> now opens the terminal in the active library directory. [#14130](https://github.com/JabRef/jabref/issues/14130)
 
 ### Fixed

jabkit/build.gradle.kts

@@ -68,6 +68,9 @@ application {
 
     // Also passed to launcher by java-module-packaging plugin
     applicationDefaultJvmArgs = listOf(
+        // JEP 158: Disable all java util logging
+        "-Xlog:disable",
+
         // Enable JEP 450: Compact Object Headers
         "-XX:+UnlockExperimentalVMOptions", "-XX:+UseCompactObjectHeaders",
 

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

@@ -7,7 +7,6 @@
 import java.nio.file.Path;
 import java.util.Arrays;
 import java.util.List;
-import java.util.Map;
 import java.util.Set;
 import java.util.stream.Collectors;
 
@@ -58,6 +57,8 @@ public class JabKit {
 
     private static final String JABKIT_BRAND = "JabKit - command line toolkit for JabRef";
 
+    /// Note: To test with gradle, use jabkit -> Tasks -> application -> run
+    ///       Use `--args="..."` as parameters to "Run"
     public static void main(String[] args) {
         initLogging(args);
 
@@ -143,11 +144,10 @@ public static void initLogging(String[] args) {
 
         // We must configure logging as soon as possible, which is why we cannot wait for the usual
         // argument parsing workflow to parse logging options e.g. --debug or --porcelain
+        boolean isPorcelain = Arrays.stream(args).anyMatch("--porcelain"::equalsIgnoreCase);
         Level logLevel;
         if (Arrays.stream(args).anyMatch("--debug"::equalsIgnoreCase)) {
             logLevel = Level.DEBUG;
-        } else if (Arrays.stream(args).anyMatch("--porcelain"::equalsIgnoreCase)) {
-            logLevel = Level.ERROR;
         } else {
             logLevel = Level.INFO;
         }
@@ -163,18 +163,23 @@ public static void initLogging(String[] args) {
             return;
         }
 
+        String fileWriterName;
+        if (isPorcelain) {
+            fileWriterName = "writer";
+        } else {
+            fileWriterName = "writerFile";
+        }
+
         // The "Shared File Writer" is explained at
         // https://tinylog.org/v2/configuration/#shared-file-writer
-        Map<String, String> configuration = Map.of(
-                "level", logLevel.name().toLowerCase(),
-                "writerFile", "rolling file",
-                "writerFile.logLevel", logLevel == Level.DEBUG ? "debug" : "info",
-                // We need to manually join the path, because ".resolve" does not work on Windows, because ":" is not allowed in file names on Windows
-                "writerFile.file", directory + File.separator + "log_{date:yyyy-MM-dd_HH-mm-ss}.txt",
-                "writerFile.charset", "UTF-8",
-                "writerFile.policies", "startup",
-                "writerFile.backups", "30");
-        configuration.forEach(Configuration::set);
+        Configuration.set("level", logLevel.name().toLowerCase());
+        Configuration.set(fileWriterName, "rolling file");
+        Configuration.set("%s.logLevel".formatted(fileWriterName), logLevel == Level.DEBUG ? "debug" : "info");
+        // We need to manually join the path, because ".resolve" does not work on Windows, because ":" is not allowed in file names on Windows
+        Configuration.set("%s.file".formatted(fileWriterName), directory + File.separator + "log_{date:yyyy-MM-dd_HH-mm-ss}.txt");
+        Configuration.set("%s.charset".formatted(fileWriterName), "UTF-8");
+        Configuration.set("%s.policies".formatted(fileWriterName), "startup");
+        Configuration.set("%s.backups".formatted(fileWriterName), "30");
 
         LOGGER = LoggerFactory.getLogger(JabKit.class);
     }

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 +1,87 @@
+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.logic.l10n.Localization;
+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;
+
+    @CommandLine.Mixin
+    private ArgumentProcessor.SharedOptions sharedOptions = new ArgumentProcessor.SharedOptions();
+
+    @Parameters(paramLabel = "DOI", description = "one or more DOIs to fetch", arity = "1..*")
+    private String[] dois;
+
+    @Override
+    public Integer call() {
+        CrossRef fetcher = new CrossRef();
+        List<BibEntry> entries = new ArrayList<>(dois.length);
+
+        for (String doiString : dois) {
+            Optional<DOI> doiParsed = DOI.parse(doiString);
+            if (doiParsed.isEmpty()) {
+                LOGGER.warn("Skipped DOI {}, because it is not a valid DOI string", doiString);
+                System.out.println(Localization.lang("DOI %0 is invalid", doiString));
+                System.err.println();
+                continue;
+            }
+            Optional<BibEntry> entry;
+            try {
+                entry = fetcher.performSearchById(doiParsed.get().asString());
+            } catch (FetcherException e) {
+                LOGGER.error("Could not fetch BibTeX based on DOI", e);
+                System.err.print(Localization.lang("No data was found for the identifier"));
+                System.err.println(" - " + doiString);
+                System.err.println(e.getLocalizedMessage());
+                System.err.println();
+                continue;
+            }
+
+            if (entry.isEmpty()) {
+                LOGGER.error("Could not fetch BibTeX based on DOI - entry is empty");
+                System.err.print(Localization.lang("No data was found for the identifier"));
+                System.err.println(" - " + doiString);
+                System.err.println();
+                continue;
+            }
+
+            entries.add(entry.get());
+        }
+
+        try (OutputStreamWriter writer = new OutputStreamWriter(System.out, StandardCharsets.UTF_8)) {
+            BibDatabaseContext context = new BibDatabaseContext(new BibDatabase(entries));
+            BibDatabaseWriter bibWriter = new BibDatabaseWriter(writer, context, argumentProcessor.cliPreferences);
+            bibWriter.writeDatabase(context);
+        } catch (IOException e) {
+            LOGGER.error("Could not write BibTeX", e);
+            System.err.println(Localization.lang("Unable to write to %0.", "stdout"));
+            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();
         }

jablib/src/main/resources/l10n/JabRef_en.properties

@@ -1450,6 +1450,7 @@ No\ problems\ found.=No problems found.
 Print\ entry\ preview=Print entry preview
 
 Invalid\ DOI\:\ '%0'.=Invalid DOI: '%0'.
+DOI\ %0\ is\ invalid=DOI %0 is invalid
 Same\ DOI\ used\ in\ multiple\ entries=Same DOI used in multiple entries
 should\ start\ with\ a\ name=should start with a name
 should\ end\ with\ a\ name=should end with a name
@@ -1974,7 +1975,6 @@ Update\ with\ bibliographic\ information\ from\ the\ web=Update with bibliograph
 
 Could\ not\ find\ any\ bibliographic\ information.=Could not find any bibliographic information.
 Citation\ key\ deviates\ from\ generated\ key=Citation key deviates from generated key
-DOI\ %0\ is\ invalid=DOI %0 is invalid
 
 Select\ all\ customized\ types\ to\ be\ stored\ in\ local\ preferences\:=Select all customized types to be stored in local preferences\:
 Different\ customization,\ current\ settings\ will\ be\ overwritten=Different customization, current settings will be overwritten