Feat: Implement a basic Zotero picker compatible CAYW endpoint

CHANGELOG.md

@@ -15,6 +15,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - We distribute arm64 images for Linux. [#10842](https://github.com/JabRef/jabref/issues/10842)
 - We added the field `monthfiled` to the default list of fields to resolve BibTeX-Strings for [#13375](https://github.com/JabRef/jabref/issues/13375)
 - We added a new ID based fetcher for [EuropePMC](https://europepmc.org/). [#13389](https://github.com/JabRef/jabref/pull/13389)
+- We added an initial [cite as you write](https://retorque.re/zotero-better-bibtex/citing/cayw/) endpoint. [#13187](https://github.com/JabRef/jabref/issues/13187)  
 
 ### Changed
 

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

@@ -91,6 +91,8 @@ Application=Application
 
 Application\ to\ push\ entries\ to=Application to push entries to
 
+%0\ |\ Cite\ As\ You\ Write=%0 | Cite As You Write
+
 Apply=Apply
 
 Assign\ the\ original\ group's\ entries\ to\ this\ group?=Assign the original group's entries to this group?

jabsrv-cli/src/main/java/org/jabref/http/server/cli/ServerCli.java

@@ -29,7 +29,7 @@ public class ServerCli implements Callable<Void> {
     private String host = "localhost";
 
     @CommandLine.Option(names = {"-p", "--port"}, description = "the port")
-    private Integer port = 6050;
+    private Integer port = 23119;
 
     /**
      * Starts an http server serving the last files opened in JabRef<br>

jabsrv/src/main/java/module-info.java

@@ -4,6 +4,8 @@
     exports org.jabref.http.dto to com.google.gson, org.glassfish.hk2.locator;
 
     opens org.jabref.http.server to org.glassfish.hk2.utilities, org.glassfish.hk2.locator;
+    exports org.jabref.http.server.cayw;
+    opens org.jabref.http.server.cayw to org.glassfish.hk2.locator, org.glassfish.hk2.utilities;
 
     // For ServiceLocatorUtilities.createAndPopulateServiceLocator()
     requires org.glassfish.hk2.locator;

jabsrv/src/main/java/org/jabref/http/server/Server.java

@@ -9,6 +9,7 @@
 
 import org.jabref.http.dto.GlobalExceptionMapper;
 import org.jabref.http.dto.GsonFactory;
+import org.jabref.http.server.cayw.CAYWResource;
 import org.jabref.http.server.services.FilesToServe;
 import org.jabref.logic.os.OS;
 
@@ -55,6 +56,7 @@ private HttpServer startServer(ServiceLocator serviceLocator, URI uri) {
         resourceConfig.register(RootResource.class);
         resourceConfig.register(LibrariesResource.class);
         resourceConfig.register(LibraryResource.class);
+        resourceConfig.register(CAYWResource.class);
         resourceConfig.register(CORSFilter.class);
         resourceConfig.register(GlobalExceptionMapper.class);
 

jabsrv/src/main/java/org/jabref/http/server/cayw/CAYWResource.java

@@ -0,0 +1,191 @@
+package org.jabref.http.server.cayw;
+
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.nio.charset.StandardCharsets;
+import java.nio.file.Files;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Optional;
+import java.util.concurrent.CompletableFuture;
+import java.util.concurrent.CountDownLatch;
+import java.util.concurrent.ExecutionException;
+
+import javafx.application.Platform;
+
+import org.jabref.http.server.cayw.gui.CAYWEntry;
+import org.jabref.http.server.cayw.gui.SearchDialog;
+import org.jabref.logic.importer.fileformat.BibtexImporter;
+import org.jabref.logic.preferences.CliPreferences;
+import org.jabref.logic.preferences.JabRefCliPreferences;
+import org.jabref.model.database.BibDatabase;
+import org.jabref.model.database.BibDatabaseContext;
+import org.jabref.model.entry.BibEntry;
+import org.jabref.model.entry.field.StandardField;
+import org.jabref.model.util.DummyFileUpdateMonitor;
+
+import com.google.gson.Gson;
+import jakarta.inject.Inject;
+import jakarta.ws.rs.DefaultValue;
+import jakarta.ws.rs.GET;
+import jakarta.ws.rs.Path;
+import jakarta.ws.rs.Produces;
+import jakarta.ws.rs.QueryParam;
+import jakarta.ws.rs.core.MediaType;
+import jakarta.ws.rs.core.Response;
+import org.jspecify.annotations.Nullable;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+@Path("better-bibtex/cayw")
+public class CAYWResource {
+    public static final Logger LOGGER = LoggerFactory.getLogger(CAYWResource.class);
+    private static final String CHOCOLATEBIB_PATH = "/Chocolate.bib";
+    private static boolean initialized = false;
+
+    @Inject
+    private CliPreferences preferences;
+
+    @Inject
+    private Gson gson;
+
+    @GET
+    @Produces(MediaType.TEXT_PLAIN)
+    public Response getCitation(
+            @QueryParam("probe") String probe,
+            @QueryParam("format") @DefaultValue("latex") String format,
+            @QueryParam("clipboard") String clipboard,
+            @QueryParam("minimize") String minimize,
+            @QueryParam("texstudio") String texstudio,
+            @QueryParam("selected") String selected,
+            @QueryParam("select") String select,
+            @QueryParam("librarypath") String libraryPath
+    ) throws IOException, ExecutionException, InterruptedException {
+        if (probe != null && !probe.isEmpty()) {
+            return Response.ok("ready").build();
+        }
+
+        BibDatabaseContext databaseContext = getBibDatabaseContext(libraryPath);
+
+        /* unused until DatabaseSearcher is fixed
+        PostgreServer postgreServer = new PostgreServer();
+        IndexManager.clearOldSearchIndices();
+        searcher = new DatabaseSearcher(
+                databaseContext,
+                new CurrentThreadTaskExecutor(),
+                preferences,
+                postgreServer);
+          */
+
+        List<CAYWEntry<BibEntry>> entries = databaseContext.getEntries()
+                                 .stream()
+                                 .map(this::createCAYWEntry)
+                                 .toList();
+
+        initializeGUI();
+
+        CompletableFuture<List<BibEntry>> future = new CompletableFuture<>();
+        Platform.runLater(() -> {
+                SearchDialog<BibEntry> dialog = new SearchDialog<>();
+                // TODO: Using the DatabaseSearcher directly here results in a lot of exceptions being thrown, so we use an alternative for now until we have a nice way of using the DatabaseSearcher class.
+                //       searchDialog.set(new SearchDialog<>(s -> searcher.getMatches(new SearchQuery(s)), entries));
+            List<BibEntry> results = dialog.show(searchQuery ->
+                    entries.stream()
+                           .filter(bibEntryCAYWEntry -> matches(bibEntryCAYWEntry, searchQuery))
+                           .map(CAYWEntry::getValue)
+                           .toList(),
+                    entries);
+
+                future.complete(results);
+        });
+
+        List<String> citationKeys = future.get().stream()
+                .map(BibEntry::getCitationKey)
+                .filter(Optional::isPresent)
+                .map(Optional::get)
+                .toList();
+
+        if (citationKeys.isEmpty()) {
+            return Response.noContent().build();
+        }
+
+        return Response.ok(gson.toJson(citationKeys)).build();
+    }
+
+    private BibDatabaseContext getBibDatabaseContext(String libraryPath) throws IOException {
+        InputStream libraryStream;
+        if (libraryPath != null && !libraryPath.isEmpty()) {
+            java.nio.file.Path path = java.nio.file.Path.of(libraryPath);
+            if (!Files.exists(path)) {
+                LOGGER.error("Library path does not exist, using the default chocolate.bib: {}", libraryPath);
+                libraryStream = getChocolateBibAsStream();
+            } else {
+                libraryStream = Files.newInputStream(path);
+            }
+        } else {
+            // Use the latest opened library as the default library
+            final List<java.nio.file.Path> lastOpenedLibraries = new ArrayList<>(JabRefCliPreferences.getInstance().getLastFilesOpenedPreferences().getLastFilesOpened());
+            if (lastOpenedLibraries.isEmpty()) {
+                LOGGER.warn("No library path provided and no last opened libraries found, using the default chocolate.bib.");
+                libraryStream = getChocolateBibAsStream();
+            } else {
+                java.nio.file.Path lastOpenedLibrary = lastOpenedLibraries.getFirst();
+                if (!Files.exists(lastOpenedLibrary)) {
+                    LOGGER.error("Last opened library does not exist, using the default chocolate.bib: {}", lastOpenedLibrary);
+                    libraryStream = getChocolateBibAsStream();
+                } else {
+                    libraryStream = Files.newInputStream(lastOpenedLibrary);
+                }
+            }
+        }
+
+        BibtexImporter bibtexImporter = new BibtexImporter(preferences.getImportFormatPreferences(), new DummyFileUpdateMonitor());
+        BibDatabaseContext databaseContext;
+        try (BufferedReader reader = new BufferedReader(new InputStreamReader(libraryStream, StandardCharsets.UTF_8))) {
+            databaseContext = bibtexImporter.importDatabase(reader).getDatabaseContext();
+        }
+        return databaseContext;
+    }
+
+    private synchronized void initializeGUI() {
+        // TODO: Implement a better way to handle the window popup since this is a bit hacky.
+        if (!initialized) {
+            CountDownLatch latch = new CountDownLatch(1);
+            Platform.startup(() -> {
+                Platform.setImplicitExit(false);
+                initialized = true;
+                latch.countDown();
+            });
+            try {
+                latch.await();
+            } catch (InterruptedException e) {
+                Thread.currentThread().interrupt();
+                throw new RuntimeException("JavaFX initialization interrupted", e);
+            }
+        }
+    }
+
+    /// @return a stream to the `Chocolate.bib` file in the classpath (is null only if the file was moved or there are issues with the classpath)
+    private @Nullable InputStream getChocolateBibAsStream() {
+        return BibDatabase.class.getResourceAsStream(CHOCOLATEBIB_PATH);
+    }
+
+    private CAYWEntry<BibEntry> createCAYWEntry(BibEntry entry) {
+        String label = entry.getCitationKey().orElse("");
+        String shortLabel = label;
+        String description = entry.getField(StandardField.TITLE).orElse(entry.getAuthorTitleYear());
+        return new CAYWEntry<>(entry, label, shortLabel, description);
+    }
+
+    private boolean matches(CAYWEntry<BibEntry> entry, String searchText) {
+        if (searchText == null || searchText.isEmpty()) {
+            return true;
+        }
+        String lowerSearchText = searchText.toLowerCase();
+        return entry.getLabel().toLowerCase().contains(lowerSearchText) ||
+                entry.getDescription().toLowerCase().contains(lowerSearchText) ||
+                entry.getShortLabel().toLowerCase().contains(lowerSearchText);
+    }
+}

jabsrv/src/main/java/org/jabref/http/server/cayw/gui/CAYWEntry.java

@@ -0,0 +1,51 @@
+package org.jabref.http.server.cayw.gui;
+
+import javafx.event.ActionEvent;
+import javafx.event.EventHandler;
+
+public class CAYWEntry<T> {
+
+    private final T value;
+
+    // Used on the buttons ("chips")
+    private final String shortLabel;
+
+    // Used in the list
+    private final String label;
+
+    // Used when hovering and used as bases on the second line
+    private final String description;
+
+    private EventHandler<ActionEvent> onClick;
+
+    public CAYWEntry(T value, String label, String shortLabel, String description) {
+        this.value = value;
+        this.label = label;
+        this.shortLabel = shortLabel;
+        this.description = description;
+    }
+
+    public T getValue() {
+        return value;
+    }
+
+    public String getLabel() {
+        return label;
+    }
+
+    public String getShortLabel() {
+        return shortLabel;
+    }
+
+    public String getDescription() {
+        return description;
+    }
+
+    public EventHandler<ActionEvent> getOnClick() {
+        return onClick;
+    }
+
+    public void setOnClick(EventHandler<ActionEvent> onClick) {
+        this.onClick = onClick;
+    }
+}