Restructure code and try-out GROBID for extraction

pom.xml

@@ -18,6 +18,12 @@
 
 
 	<dependencies>
+		<dependency>
+			<groupId>com.google.inject</groupId>
+			<artifactId>guice</artifactId>
+			<version>7.0.0</version>
+		</dependency>
+
 		<dependency>
 			<groupId>pl.edu.icm</groupId>
 			<artifactId>cermine</artifactId>

src/main/java/com/cerca/App.java

@@ -2,6 +2,8 @@
 
 import com.cerca.controller.MainController;
 import com.cerca.view.MainView;
+import com.google.inject.Guice;
+import com.google.inject.Injector;
 import javafx.application.Application;
 import javafx.scene.Scene;
 import javafx.stage.Stage;
@@ -10,13 +12,13 @@
 public class App extends Application {
     @Override
     public void start(Stage stage) {
+        Injector injector = Guice.createInjector(new AppModule());
+
         // Initialize MVC Components
-        MainView view = new MainView();
-        new MainController(view); 
-
+        MainView view = injector.getInstance(MainView.class);
+        injector.getInstance(MainController.class);
 
         var iconStream = getClass().getResourceAsStream("/images/app_icon.png");
-
 
         if (iconStream != null) {
             Image icon = new Image(iconStream);

src/main/java/com/cerca/AppModule.java

@@ -0,0 +1,25 @@
+package com.cerca;
+
+import com.cerca.service.ConfigService;
+import com.cerca.service.extraction.*;
+import com.google.inject.AbstractModule;
+import com.google.inject.Provides;
+import com.google.inject.Singleton;
+import com.google.inject.name.Named;
+
+/**
+ * Dependency Injection Container
+ */
+public class AppModule extends AbstractModule {
+    @Override
+    protected void configure() {
+        bind(PdfExtractor.class).to(CerminePdfExtractor.class).in(Singleton.class);
+        bind(TextExtractor.class).to(GrobidTextExtractor.class).in(Singleton.class);
+    }
+
+    @Provides
+    @Named("USER_EMAIL")
+    public String provideUserEmail(ConfigService configService) {
+        return configService.getProperty("USER_EMAIL");
+    }
+}

src/main/java/com/cerca/controller/MainController.java

@@ -11,18 +11,19 @@
 import java.util.concurrent.CompletionException;
 
 import com.cerca.model.ReferenceItem;
-import com.cerca.service.CermineService;
+import com.cerca.service.extraction.*;
 import com.cerca.service.ConfigService;
-import com.cerca.service.CrossrefService;
-import com.cerca.service.CsvService;
+import com.cerca.service.lookup.CrossrefService;
+import com.cerca.service.report.CsvService;
 import com.cerca.service.LogService;
-import com.cerca.service.OpenAlexService;
-import com.cerca.service.ReportService;
-import com.cerca.service.SemanticScholarService;
-import com.cerca.service.ZenodoService;
-import com.cerca.utils.ReferenceParser;
+import com.cerca.service.lookup.OpenAlexService;
+import com.cerca.service.report.ReportService;
+import com.cerca.service.lookup.SemanticScholarService;
+import com.cerca.service.lookup.ZenodoService;
 import com.cerca.view.MainView;
 
+import com.google.inject.Inject;
+import com.google.inject.Singleton;
 import javafx.application.Platform;
 import javafx.collections.FXCollections;
 import javafx.collections.ObservableList;
@@ -48,11 +49,13 @@
  * @author Lidiany Cerqueira
  * 
  */
+@Singleton
 public class MainController {
 
 	private final MainView view;
 	private final ObservableList<ReferenceItem> data;
-	private final CermineService cermineService;
+	private final PdfExtractor pdfExtractor;
+	private final TextExtractor textExtractor;
 	private final CrossrefService crossrefService;
 	private final CsvService csvService;
 	private final ReportService reportService;
@@ -63,22 +66,32 @@ public class MainController {
 	private final OpenAlexService openAlexService;
 	private final ConfigService configService;
 
-	public MainController(MainView view) {
+	@Inject
+	public MainController(MainView view,
+						  LogService logService,
+						  ConfigService configService,
+						  PdfExtractor pdfExtractor,
+						  TextExtractor textExtractor,
+						  CrossrefService crossrefService,
+						  OpenAlexService openAlexService,
+						  ZenodoService zenodoService,
+						  SemanticScholarService semScholarService,
+						  CsvService csvService,
+						  ReportService reportService) {
 		this.view = view;
 		this.data = FXCollections.observableArrayList();
-		this.cermineService = new CermineService();
-		this.csvService = new CsvService();
-		this.reportService = new ReportService();
-		this.logService = new LogService();
-		this.crossrefService = new CrossrefService(logService);
-		this.zenodoService = new ZenodoService(logService);
-		this.openAlexService = new OpenAlexService(logService);
-
-		this.semScholarService = new SemanticScholarService(logService);
-		this.configService = new ConfigService(logService);
-		this.semScholarService.setApiKey(configService.getProperty("SEMANTIC_SCHOLAR_API_KEY"));
-		this.crossrefService.setEmail(configService.getProperty("USER_EMAIL"));
-		this.openAlexService.setEmail(configService.getProperty("USER_EMAIL"));
+		this.pdfExtractor = pdfExtractor;
+		this.textExtractor = textExtractor;
+		this.csvService = csvService;
+		this.reportService = reportService;
+		this.logService = logService;
+		this.crossrefService = crossrefService;
+		this.zenodoService = zenodoService;
+		this.openAlexService = openAlexService;
+
+		this.semScholarService = semScholarService;
+		this.configService = configService;
+
 		view.getTable().setItems(data);
 
 		setupDragAndDrop();
@@ -135,7 +148,7 @@ private void processPdf(File file) {
 
 		CompletableFuture.supplyAsync(() -> {
 			try {
-				return cermineService.extractReferences(file);
+				return pdfExtractor.extractReferences(file);
 			} catch (Exception e) {
 
 				throw new CompletionException(e);
@@ -415,9 +428,9 @@ private void loadManualReferences(String text) {
 			if (line.trim().length() < 5)
 				continue;
 
-			ReferenceParser.ParsedData parsedData = ReferenceParser.parse(line);
+			ParsedData parsedData = textExtractor.parse(line);
 
-			ReferenceItem item = new ReferenceItem(idCounter++, "WAITING", parsedData.authors, parsedData.title, line,
+			ReferenceItem item = new ReferenceItem(idCounter++, "WAITING", parsedData.authors(), parsedData.title(), line,
 					"");
 
 			data.add(item);
@@ -428,7 +441,7 @@ private void loadManualReferences(String text) {
 	}
 
 	public void openSettingsDialog() {
-		String currentKey = this.semScholarService.getApiKey();
+		String currentKey = configService.getProperty("SEMANTIC_SCHOLAR_API_KEY");
 
 		Dialog<String> dialog = new Dialog<>();
 		dialog.setTitle("CERCA Settings");
@@ -487,7 +500,6 @@ public void openSettingsDialog() {
 
 		result.ifPresent(newKey -> {
 			configService.setProperty("SEMANTIC_SCHOLAR_API_KEY", newKey);
-			this.semScholarService.setApiKey(newKey);
 			logService.log("INFO", "API Key updated successfully!");
 		});
 	}

src/main/java/com/cerca/service/ConfigService.java

@@ -1,19 +1,23 @@
 package com.cerca.service;
 
-import java.io.File;
+import com.google.inject.Inject;
+import com.google.inject.Singleton;
+
 import java.io.InputStream;
 import java.io.OutputStream;
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.nio.file.Paths;
 import java.util.Properties;
 
+@Singleton
 public class ConfigService {
 
 	private static final Path CONFIG_FILE = Paths.get("config.properties");
     private final LogService logger;
     private Properties properties;
-
+
+    @Inject
     public ConfigService(LogService logger) {
         this.logger = logger;
         this.properties = new Properties();

src/main/java/com/cerca/service/LogService.java

@@ -1,6 +1,8 @@
 package com.cerca.service;
 
 
+import com.google.inject.Singleton;
+
 import java.io.IOException;
 import java.nio.file.Files;
 import java.nio.file.Path;
@@ -14,6 +16,7 @@
  *
  * @author Lidiany Cerqueira
  */
+@Singleton
 public class LogService {
 
     private static final Path LOG_FILE = Paths.get("cerca_audit.log");

src/main/java/com/cerca/service/CermineService.java → src/main/java/com/cerca/service/extraction/CerminePdfExtractor.java

@@ -1,4 +1,4 @@
-package com.cerca.service;
+package com.cerca.service.extraction;
 
 import com.cerca.model.ReferenceItem;
 import pl.edu.icm.cermine.ContentExtractor;
@@ -23,7 +23,7 @@
  * Privacy note: PDF files are processed locally.
  * @author Lidiany Cerqueira
  */
-public class CermineService {
+public class CerminePdfExtractor implements PdfExtractor {
 
     public List<ReferenceItem> extractReferences(File pdfFile) throws Exception {
         List<ReferenceItem> results = new ArrayList<>();

src/main/java/com/cerca/utils/ReferenceParser.java → src/main/java/com/cerca/service/extraction/CermineTextExtractor.java

@@ -1,7 +1,7 @@
 /**
  * @author Lidiany Cerqueira
  */
-package com.cerca.utils;
+package com.cerca.service.extraction;
 
 import pl.edu.icm.cermine.bibref.CRFBibReferenceParser;
 import pl.edu.icm.cermine.bibref.model.BibEntry;
@@ -10,29 +10,20 @@
 
 import java.util.List;
 
-public class ReferenceParser {
+public class CermineTextExtractor implements TextExtractor {
 
-    private static CRFBibReferenceParser parser;
+    private CRFBibReferenceParser parser;
 
-    static {
+    public CermineTextExtractor() {
         try {
-            parser = CRFBibReferenceParser.getInstance();
+            this.parser = CRFBibReferenceParser.getInstance();
         } catch (AnalysisException e) {
             System.err.println("CERMINE Model Error: " + e.getMessage());
-        }
-    }
-
-    public static class ParsedData {
-        public String authors;
-        public String title;
-
-        public ParsedData(String authors, String title) {
-            this.authors = authors;
-            this.title = title;
-        }
+        };
     }
 
-    public static ParsedData parse(String rawReference) {
+    @Override
+    public ParsedData parse(String rawReference) {
         if (rawReference == null || rawReference.trim().isEmpty()) {
             return new ParsedData("Unknown", "Unknown");
         }

src/main/java/com/cerca/service/extraction/GrobidTextExtractor.java

@@ -0,0 +1,96 @@
+package com.cerca.service.extraction;
+
+import org.w3c.dom.Document;
+import org.w3c.dom.NodeList;
+import org.xml.sax.InputSource;
+
+import javax.xml.parsers.DocumentBuilderFactory;
+import javax.xml.xpath.XPathConstants;
+import javax.xml.xpath.XPathFactory;
+import java.io.IOException;
+import java.io.StringReader;
+import java.net.URI;
+import java.net.URLEncoder;
+import java.net.http.HttpClient;
+import java.net.http.HttpRequest;
+import java.net.http.HttpResponse;
+import java.nio.charset.StandardCharsets;
+import java.util.ArrayList;
+import java.util.List;
+
+/**
+ * Call GROBID to extract a reference from a citation.
+ * <p>
+ * To run GROBID in a Docker container, call
+ * <code>docker run --rm -p 8070:8070 grobid/grobid:0.8.2-full</code>.
+ */
+public class GrobidTextExtractor implements TextExtractor {
+    private static final String GROBID_URL = "http://localhost:8070";
+
+    private final HttpClient httpClient;
+
+    public GrobidTextExtractor() {
+        this.httpClient = HttpClient.newHttpClient();
+    }
+
+    @Override
+    public ParsedData parse(String rawReference) {
+        try {
+            String responseXml = callGrobid(rawReference);
+            return parseTei(responseXml, rawReference);
+        } catch (Exception e) {
+            throw new RuntimeException("Failed to parse reference with GROBID", e);
+        }
+    }
+
+    private String callGrobid(String citation) throws IOException, InterruptedException {
+        String body = "citations=" + URLEncoder.encode(citation, StandardCharsets.UTF_8);
+
+        HttpRequest request = HttpRequest.newBuilder()
+                .uri(URI.create(GROBID_URL + "/api/processCitation"))
+                .header("Content-Type", "application/x-www-form-urlencoded")
+                .POST(HttpRequest.BodyPublishers.ofString(body))
+                .build();
+
+        HttpResponse<String> response =
+                httpClient.send(request, HttpResponse.BodyHandlers.ofString());
+
+        if (response.statusCode() != 200) {
+            throw new RuntimeException("GROBID returned status " + response.statusCode());
+        }
+
+        return response.body();
+    }
+
+    private ParsedData parseTei(String xml, String rawReference) throws Exception {
+        DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
+        factory.setNamespaceAware(false);
+
+        Document doc = factory.newDocumentBuilder()
+                .parse(new InputSource(new StringReader(xml)));
+
+        var xpath = XPathFactory.newInstance().newXPath();
+
+        // --- Authors ---
+        NodeList surnameNodes = (NodeList) xpath.evaluate("//author/persName/surname", doc, XPathConstants.NODESET);
+
+        List<String> authors = new ArrayList<>();
+        for (int i = 0; i < surnameNodes.getLength(); i++) {
+            authors.add(surnameNodes.item(i).getTextContent().trim());
+        }
+
+        String authorsJoined = String.join(", ", authors);
+
+        // --- Title (analytic preferred) ---
+        String title = xpath.evaluate("//analytic/title/text()", doc).trim();
+
+        if (title.isEmpty()) {
+            title = xpath.evaluate("//monogr/title/text()", doc).trim();
+        }
+
+        // --- DOI ---
+        String doi = xpath.evaluate("//idno[@type='DOI']/text()", doc).trim();
+
+        return new ParsedData(authorsJoined, title);
+    }
+}

src/main/java/com/cerca/service/extraction/ParsedData.java

@@ -0,0 +1,4 @@
+package com.cerca.service.extraction;
+
+public record ParsedData (String authors, String title) {
+}