Merge pull request #12 from guenesaydin/grobid-request-server-async

Grobid request server async

build.gradle

@@ -115,7 +115,7 @@ dependencies {
 
     compile group: 'org.apache.tika', name: 'tika-core', version: '1.22'
 
-    compile 'org.apache.httpcomponents:httpclient:4.5.10'
+    compile group: 'org.apache.httpcomponents', name: 'httpclient', version: '4.5.10'
     compile group: 'commons-io', name: 'commons-io', version: '2.6'
 
     // required for reading write-protected PDFs - see https://github.com/JabRef/jabref/pull/942#issuecomment-209252635

src/main/java/org/jabref/gui/entrybyplaintext/EntryByPlainTextViewModel.java

@@ -1,12 +1,17 @@
 package org.jabref.gui.entrybyplaintext;
 
 import java.util.HashMap;
+import java.util.List;
 import java.util.Map;
+import java.util.Optional;
+
+import javafx.application.Platform;
 import javafx.beans.property.SimpleStringProperty;
 import javafx.beans.property.StringProperty;
 
 
 import org.jabref.Globals;
+import org.jabref.JabRefExecutorService;
 import org.jabref.JabRefGUI;
 import org.jabref.logic.plaintextparser.ParserPipeline;
 import org.jabref.model.Defaults;
@@ -22,7 +27,7 @@ public class EntryByPlainTextViewModel {
   private final BibDatabaseContext bibDatabaseContext;
   private boolean directAdd;
   private final BibDatabaseContext newDatabaseContext;
-
+  private List<BibEntry> extractedEntries;
 
 
   public EntryByPlainTextViewModel(BibDatabaseContext bibDatabaseContext){
@@ -40,13 +45,18 @@ public StringProperty inputTextProperty(){
 
   public void startParsing(boolean directAdd){
     this.directAdd = directAdd;
-    executeParse();
+    this.extractedEntries = null;
+    JabRefExecutorService.INSTANCE.execute(() -> {
+        this.extractedEntries = ParserPipeline.parsePlainRefCit(inputText.getValue());
+        Platform.runLater(this::executeParse);
+    });
   }
 
   public void executeParse(){
-      if(ParserPipeline.parsePlainRefCit(inputText.getValue()).isPresent()){
-          BibEntry bibEntry = ParserPipeline.parsePlainRefCit(inputText.getValue()).get();
-          parsingSuccess(bibEntry);
+      if(extractedEntries.size() > 0){
+          for (BibEntry bibEntry: extractedEntries) {
+              parsingSuccess(bibEntry);
+          }
       } else{
           parsingFail(inputText.getValue());
       }

src/main/java/org/jabref/gui/preferences/AdvancedTab.fxml

@@ -45,6 +45,8 @@
             <RowConstraints minHeight="10.0" vgrow="SOMETIMES"/>
             <RowConstraints minHeight="10.0" vgrow="SOMETIMES"/>
             <RowConstraints minHeight="10.0" vgrow="SOMETIMES"/>
+            <RowConstraints minHeight="10.0" vgrow="SOMETIMES"/>
+            <RowConstraints minHeight="10.0" vgrow="SOMETIMES"/>
         </rowConstraints>
         <CheckBox fx:id="proxyUse" text="%Use custom proxy configuration" GridPane.columnSpan="3"
                   GridPane.rowIndex="0"/>
@@ -61,5 +63,9 @@
                              GridPane.rowIndex="5"/>
         <Label fx:id="proxyAttentionLabel" styleClass="warning-message"
                text="%Attention: Password is stored in plain text!" GridPane.columnIndex="2" GridPane.rowIndex="5"/>
+        <CheckBox fx:id="customGrobidServer" text="%Use custom GROBID server" GridPane.columnSpan="3"
+                  GridPane.rowIndex="6"/>
+        <Label fx:id="grobidServerAddressLabel" text="%Server Address" GridPane.rowIndex="7"/>
+        <TextField fx:id="grobidServerAddress" prefWidth="200.0" GridPane.columnIndex="1" GridPane.rowIndex="7"/>
     </GridPane>
 </fx:root>

src/main/java/org/jabref/gui/preferences/AdvancedTabView.java

@@ -44,6 +44,9 @@ public class AdvancedTabView extends AbstractPreferenceTabView<AdvancedTabViewMo
     @FXML private Label proxyPasswordLabel;
     @FXML private CustomPasswordField proxyPassword;
     @FXML private Label proxyAttentionLabel;
+    @FXML private CheckBox customGrobidServer;
+    @FXML private Label grobidServerAddressLabel;
+    @FXML private TextField grobidServerAddress;
 
     private String proxyPasswordText = "";
     private int proxyPasswordCaretPosition = 0;
@@ -109,6 +112,12 @@ public void initialize() {
             validationVisualizer.initVisualization(viewModel.proxyUsernameValidationStatus(), proxyUsername);
             validationVisualizer.initVisualization(viewModel.proxyPasswordValidationStatus(), proxyPassword);
         });
+
+        customGrobidServer.selectedProperty().bindBidirectional(viewModel.useCustomGrobidServer());
+        customGrobidServer.selectedProperty().addListener(((observable, oldValue, newValue) -> grobidServerReset(newValue)));
+        grobidServerAddress.textProperty().bindBidirectional(viewModel.customGrobidServer());
+        grobidServerAddress.disableProperty().bind(viewModel.useCustomGrobidServer().not());
+        grobidServerAddressLabel.disableProperty().bind(viewModel.useCustomGrobidServer().not());
     }
 
     private void proxyPasswordReveal(MouseEvent event) {
@@ -127,4 +136,10 @@ private void proxyPasswordMask(MouseEvent event) {
             proxyPasswordCaretPosition = 0;
         }
     }
+
+    private void grobidServerReset(boolean newObservedValue) {
+      if (!newObservedValue) {
+        grobidServerAddress.setText((String) preferences.defaults.get(JabRefPreferences.CUSTOM_GROBID_SERVER));
+      }
+    }
 }

src/main/java/org/jabref/gui/preferences/AdvancedTabViewModel.java

@@ -38,6 +38,8 @@ public class AdvancedTabViewModel implements PreferenceTabViewModel {
     private final BooleanProperty proxyUseAuthenticationProperty = new SimpleBooleanProperty();
     private final StringProperty proxyUsernameProperty = new SimpleStringProperty("");
     private final StringProperty proxyPasswordProperty = new SimpleStringProperty("");
+    private final BooleanProperty customGrobidServerProperty = new SimpleBooleanProperty();
+    private final StringProperty grobidServerProperty = new SimpleStringProperty("");
 
     private FunctionBasedValidator remotePortValidator;
     private FunctionBasedValidator proxyHostnameValidator;
@@ -121,6 +123,9 @@ public void setValues() {
         proxyUseAuthenticationProperty.setValue(proxyPreferences.isUseAuthentication());
         proxyUsernameProperty.setValue(proxyPreferences.getUsername());
         proxyPasswordProperty.setValue(proxyPreferences.getPassword());
+
+        customGrobidServerProperty.setValue(preferences.getBoolean(JabRefPreferences.USE_CUSTOM_GROBID_SERVER));
+        grobidServerProperty.setValue(preferences.get(JabRefPreferences.CUSTOM_GROBID_SERVER));
     }
 
     public void storeSettings() {
@@ -137,6 +142,9 @@ public void storeSettings() {
         preferences.putBoolean(JabRefPreferences.USE_UNIT_FORMATTER_ON_SEARCH, useUnitFormatterProperty.getValue());
 
         storeProxySettings();
+
+        preferences.putBoolean(JabRefPreferences.USE_CUSTOM_GROBID_SERVER, customGrobidServerProperty.getValue());
+        preferences.put(JabRefPreferences.CUSTOM_GROBID_SERVER, grobidServerProperty.getValue());
     }
 
     private void storeRemoteSettings() {
@@ -248,4 +256,8 @@ public boolean validateSettings() {
     public StringProperty proxyUsernameProperty() { return proxyUsernameProperty; }
 
     public StringProperty proxyPasswordProperty() { return proxyPasswordProperty; }
+
+    public BooleanProperty useCustomGrobidServer() { return customGrobidServerProperty; }
+
+    public StringProperty customGrobidServer() { return grobidServerProperty; }
 }

src/main/java/org/jabref/logic/net/GrobidClient.java

@@ -0,0 +1,42 @@
+package org.jabref.logic.net;
+
+import org.apache.commons.io.IOUtils;
+import org.apache.http.HttpEntity;
+import org.jabref.Globals;
+import org.jabref.preferences.JabRefPreferences;
+
+import java.io.IOException;
+import java.io.InputStream;
+import java.nio.charset.StandardCharsets;
+import java.util.Map;
+
+/**
+ * Implements an API to a GROBID server, as described at
+ * https://grobid.readthedocs.io/en/latest/Grobid-service/#grobid-web-services
+ *
+ * The methods are structured to match the GROBID server api.
+ * Each method corresponds to a GROBID service request. Only the ones already used are already implemented.
+ */
+public class GrobidClient {
+
+    public static String processCitation(String rawCitation, int consolidateCitations) throws GrobidClientException {
+        try {
+            if (consolidateCitations < 0 || consolidateCitations > 2) {
+                throw new GrobidClientException("");
+            }
+            HttpEntity httpResponse = HttpPostService.sendPostAndWait(
+                    Globals.prefs.get(JabRefPreferences.CUSTOM_GROBID_SERVER),
+                    "/api/processCitation",
+                    Map.of("citations", rawCitation, "consolidateCitations", String.valueOf(consolidateCitations))
+                    ).getEntity();
+            if (httpResponse == null) {
+                throw new GrobidClientException("The GROBID server response does not contain anything.");
+            }
+            InputStream serverResponseAsStream = httpResponse.getContent();
+            return IOUtils.toString(serverResponseAsStream, StandardCharsets.UTF_8);
+        } catch (HttpPostServiceException | IOException e) {
+            throw new GrobidClientException();
+        }
+    }
+
+}

src/main/java/org/jabref/logic/net/GrobidClientException.java

@@ -0,0 +1,30 @@
+package org.jabref.logic.net;
+
+import org.jabref.JabRefException;
+
+public class GrobidClientException extends JabRefException {
+
+    public GrobidClientException() {
+        super("An error occurred while processing your query.");
+    }
+
+    public GrobidClientException(String message) {
+        super(message);
+    }
+
+    public static GrobidClientException getNewGrobidClientExceptionByCode(int httpCode) {
+        switch(httpCode) {
+            case 204:
+                return new GrobidClientException("The GROBID service could not extract any Information from this String.");
+            case 400:
+                return new GrobidClientException("The generated Request was wrong.");
+            case 500:
+                return new GrobidClientException("An internal GROBID service error occured.");
+            case 503:
+                return new GrobidClientException("There are too many requests at a time, please try again later.");
+            default:
+                return new GrobidClientException("An error occured processing your GROBID request.");
+        }
+    }
+
+}

src/main/java/org/jabref/logic/net/HttpPostService.java

@@ -4,55 +4,40 @@
 import org.apache.http.client.HttpClient;
 import org.apache.http.client.entity.UrlEncodedFormEntity;
 import org.apache.http.client.methods.HttpPost;
-//import org.apache.http.concurrent.FutureCallback;
+import org.apache.http.concurrent.FutureCallback;
 import org.apache.http.impl.client.HttpClients;
-//import org.apache.http.impl.nio.client.HttpAsyncClients;
 import org.apache.http.message.BasicNameValuePair;
-//import org.apache.http.nio.client.HttpAsyncClient;
 
 import java.io.IOException;
 import java.io.UnsupportedEncodingException;
-import java.net.URI;
-import java.net.URISyntaxException;
 import java.util.ArrayList;
 import java.util.List;
 import java.util.Map;
-//import java.util.concurrent.Future;
+import java.util.concurrent.Future;
+
 
 /**
  * Makes it easy to send http post requests
  * HttpClients are reused.
  */
 public class HttpPostService {
 
-    private static final HttpClient httpClient = HttpClients.createDefault();
-    //private static final HttpAsyncClient httpAsyncClient = HttpAsyncClients.createDefault();
-    private URI url;
-
-    public HttpPostService(String url) throws URISyntaxException {
-        this(new URI(url));
-    }
-
-    public HttpPostService(URI url) {
-        this.url = url;
-    }
+    private static final HttpClient HTTP_CLIENT = HttpClients.createSystem();
 
-    public HttpResponse sendPostAndWait(Map<String, String> params) throws IOException {
-        return httpClient.execute(prepareHttpPost(params));
+    public static HttpResponse sendPostAndWait(String url, String subUrl, Map<String, String> params) throws HttpPostServiceException {
+        try {
+            return HTTP_CLIENT.execute(prepareHttpPost(url, subUrl, params));
+        } catch (IOException e) {
+            throw new HttpPostServiceException();
+        }
     }
 
-    /* sadly this does not work due to gradle compile errors
-    public Future<HttpResponse> sendPost(Map<String, String> params,
-                                         FutureCallback<HttpResponse> httpResponseHandler) throws IOException {
-        return httpAsyncClient.execute(prepareHttpPost(params), httpResponseHandler);
+    public static HttpResponse sendPostAndWait(String url, Map<String, String> params) throws HttpPostServiceException {
+        return sendPostAndWait(url, "", params);
     }
 
-    public Future<HttpResponse> sendPost(Map<String, String> params) throws IOException {
-        return httpAsyncClient.execute(prepareHttpPost(params), null);
-    }*/
-
-    private HttpPost prepareHttpPost(Map<String, String> params) throws UnsupportedEncodingException {
-        HttpPost httpPost = new HttpPost(url);
+    private static HttpPost prepareHttpPost(String url, String urlSubPath, Map<String, String> params) throws UnsupportedEncodingException {
+        HttpPost httpPost = new HttpPost(url + urlSubPath);
         List<BasicNameValuePair> parameterList = new ArrayList<>();
         for (Map.Entry<String, String> e: params.entrySet()) {
             parameterList.add(new BasicNameValuePair(e.getKey(), e.getValue()));
@@ -61,4 +46,9 @@ private HttpPost prepareHttpPost(Map<String, String> params) throws UnsupportedE
         return httpPost;
     }
 
+    private static HttpPost prepareHttpPost(String url, Map<String, String> params) throws UnsupportedEncodingException {
+      return prepareHttpPost(url, "", params);
+    }
+
+
 }

src/main/java/org/jabref/logic/net/HttpPostServiceException.java

@@ -0,0 +1,15 @@
+package org.jabref.logic.net;
+
+import org.jabref.JabRefException;
+
+public class HttpPostServiceException extends JabRefException {
+
+  public HttpPostServiceException() {
+    super("An error occurred connecting to the external http server.");
+  }
+
+  public HttpPostServiceException(String message) {
+    super(message);
+  }
+
+}