Improve error handling on GROBID server connection issues

CHANGELOG.md

@@ -37,6 +37,7 @@ inserting new citations in a OpenOffic/LibreOffice document. [#6957](https://git
 - We improved the duplicate detection when identifiers like DOI or arxiv are semantiaclly the same, but just syntactically differ (e.g. with or without http(s):// prefix). [#6707](https://github.com/JabRef/jabref/issues/6707)
 - We changed in the group interface "Generate groups from keywords in a BibTeX field" by "Generate groups from keywords in the following field". [#6983](https://github.com/JabRef/jabref/issues/6983)
 - We changed the name of a group type from "Searching for keywords" to "Searching for a keyword". [6995](https://github.com/JabRef/jabref/pull/6995)
+- We changed connect timeouts for server requests to 30 seconds in general and 5 seconds for GROBID server (special) and improved user notifications on connection issues. [7026](https://github.com/JabRef/jabref/pull/7026)
 
 ### Fixed
 

src/main/java/org/jabref/gui/bibtexextractor/BibtexExtractorViewModel.java

@@ -15,15 +15,21 @@
 import org.jabref.gui.externalfiletype.ExternalFileTypes;
 import org.jabref.gui.util.BackgroundTask;
 import org.jabref.gui.util.TaskExecutor;
+import org.jabref.logic.importer.FetcherException;
 import org.jabref.logic.importer.fetcher.GrobidCitationFetcher;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.entry.BibEntry;
 import org.jabref.model.util.FileUpdateMonitor;
 import org.jabref.preferences.JabRefPreferences;
 
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
 public class BibtexExtractorViewModel {
 
+    private static final Logger LOGGER = LoggerFactory.getLogger(BibtexExtractorViewModel.class);
+
     private final StringProperty inputTextProperty = new SimpleStringProperty("");
     private DialogService dialogService;
     private GrobidCitationFetcher currentCitationfetcher;
@@ -58,6 +64,15 @@ public StringProperty inputTextProperty() {
     public void startParsing() {
         BackgroundTask.wrap(() -> currentCitationfetcher.performSearch(inputTextProperty.getValue()))
                       .onRunning(() -> dialogService.notify(Localization.lang("Your text is being parsed...")))
+                      .onFailure((e) -> {
+                          if (e instanceof FetcherException) {
+                              String msg = Localization.lang("There are connection issues with a JabRef server. Detailed information: %0.",
+                                      e.getMessage());
+                              dialogService.notify(msg);
+                          } else {
+                              LOGGER.warn("Missing exception handling.", e);
+                          }
+                      })
                       .onSuccess(parsedEntries -> {
                           dialogService.notify(Localization.lang("%0 entries were parsed from your query.", String.valueOf(parsedEntries.size())));
                           importHandler.importEntries(parsedEntries);

src/main/java/org/jabref/logic/importer/fetcher/GrobidCitationFetcher.java

@@ -1,11 +1,13 @@
 package org.jabref.logic.importer.fetcher;
 
 import java.io.IOException;
+import java.net.SocketTimeoutException;
 import java.util.Arrays;
 import java.util.List;
 import java.util.Optional;
 import java.util.stream.Collectors;
 
+import org.jabref.logic.importer.FetcherException;
 import org.jabref.logic.importer.ImportFormatPreferences;
 import org.jabref.logic.importer.ParseException;
 import org.jabref.logic.importer.SearchBasedFetcher;
@@ -20,13 +22,18 @@
 public class GrobidCitationFetcher implements SearchBasedFetcher {
 
     private static final Logger LOGGER = LoggerFactory.getLogger(GrobidCitationFetcher.class);
+
     private static final String GROBID_URL = "http://grobid.jabref.org:8070";
     private ImportFormatPreferences importFormatPreferences;
     private GrobidService grobidService;
 
     public GrobidCitationFetcher(ImportFormatPreferences importFormatPreferences) {
+        this(importFormatPreferences, new GrobidService(GROBID_URL));
+    }
+
+    GrobidCitationFetcher(ImportFormatPreferences importFormatPreferences, GrobidService grobidService) {
         this.importFormatPreferences = importFormatPreferences;
-        this.grobidService = new GrobidService(GROBID_URL);
+        this.grobidService = grobidService;
     }
 
     /**
@@ -38,9 +45,14 @@ public GrobidCitationFetcher(ImportFormatPreferences importFormatPreferences) {
     private Optional<String> parseUsingGrobid(String plainText) {
         try {
             return Optional.of(grobidService.processCitation(plainText, GrobidService.ConsolidateCitations.WITH_METADATA));
+        } catch (SocketTimeoutException e) {
+            String msg = "Connection timed out.";
+            LOGGER.debug(msg, e);
+            throw new RuntimeException(msg, e);
         } catch (IOException e) {
-            LOGGER.debug("Could not process citation", e);
-            return Optional.empty();
+            String msg = "Could not process citation. " + e.getMessage();
+            LOGGER.debug(msg, e);
+            throw new RuntimeException(msg, e);
         }
     }
 
@@ -54,20 +66,28 @@ private Optional<BibEntry> parseBibToBibEntry(String bibtexString) {
     }
 
     @Override
-    public List<BibEntry> performSearch(String query) {
-        return Arrays
-                .stream(query.split("\\r\\r+|\\n\\n+|\\r\\n(\\r\\n)+"))
-                .map(String::trim)
-                .filter(str -> !str.isBlank())
-                .map(reference -> parseUsingGrobid(reference))
-                .flatMap(Optional::stream)
-                .map(reference -> parseBibToBibEntry(reference))
-                .flatMap(Optional::stream)
-                .collect(Collectors.toList());
+    public List<BibEntry> performSearch(String query) throws FetcherException {
+        List<BibEntry> bibEntries = null;
+        try {
+            bibEntries = Arrays
+                    .stream(query.split("\\r\\r+|\\n\\n+|\\r\\n(\\r\\n)+"))
+                    .map(String::trim)
+                    .filter(str -> !str.isBlank())
+                    .map(this::parseUsingGrobid)
+                    .flatMap(Optional::stream)
+                    .map(this::parseBibToBibEntry)
+                    .flatMap(Optional::stream)
+                    .collect(Collectors.toList());
+        } catch (RuntimeException e) {
+            // un-wrap the wrapped exceptions
+            throw new FetcherException(e.getMessage(), e.getCause());
+        }
+        return bibEntries;
     }
 
     @Override
     public String getName() {
         return "GROBID";
     }
+
 }

src/main/java/org/jabref/logic/importer/util/GrobidService.java

@@ -3,6 +3,7 @@
 import java.io.IOException;
 import java.net.URLEncoder;
 import java.nio.charset.StandardCharsets;
+import java.time.Duration;
 
 import org.jabref.logic.net.URLDownload;
 
@@ -47,6 +48,7 @@ public String processCitation(String rawCitation, ConsolidateCitations consolida
         rawCitation = URLEncoder.encode(rawCitation, StandardCharsets.UTF_8);
         URLDownload urlDownload = new URLDownload(grobidServerURL
                 + "/api/processCitation");
+        urlDownload.setConnectTimeout(Duration.ofSeconds(5));
         urlDownload.addHeader("Accept", MediaTypes.APPLICATION_BIBTEX);
         urlDownload.setPostData("citations=" + rawCitation + "&consolidateCitations=" + consolidateCitations);
         String httpResponse = urlDownload.asString();

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

@@ -26,6 +26,7 @@
 import java.nio.file.StandardCopyOption;
 import java.security.SecureRandom;
 import java.security.cert.X509Certificate;
+import java.time.Duration;
 import java.util.Collections;
 import java.util.HashMap;
 import java.util.List;
@@ -62,11 +63,13 @@
 public class URLDownload {
 
     public static final String USER_AGENT = "Mozilla/5.0 (Windows NT 10.0; Win64; x64; rv:79.0) Gecko/20100101 Firefox/79.0";
-
     private static final Logger LOGGER = LoggerFactory.getLogger(URLDownload.class);
+    private static final Duration DEFAULT_CONNECT_TIMEOUT = Duration.ofSeconds(30);
+
     private final URL source;
     private final Map<String, String> parameters = new HashMap<>();
     private String postData = "";
+    private Duration connectTimeout = DEFAULT_CONNECT_TIMEOUT;
 
     /**
      * @param source the URL to download from
@@ -316,6 +319,7 @@ private void copy(InputStream in, Writer out, Charset encoding) throws IOExcepti
 
     private URLConnection openConnection() throws IOException {
         URLConnection connection = this.source.openConnection();
+        connection.setConnectTimeout((int) connectTimeout.toMillis());
         for (Entry<String, String> entry : this.parameters.entrySet()) {
             connection.setRequestProperty(entry.getKey(), entry.getValue());
         }
@@ -346,4 +350,14 @@ private URLConnection openConnection() throws IOException {
 
         return connection;
     }
+
+    public void setConnectTimeout(Duration connectTimeout) {
+        if (connectTimeout != null) {
+            this.connectTimeout = connectTimeout;
+        }
+    }
+
+    public Duration getConnectTimeout() {
+        return connectTimeout;
+    }
 }

src/main/resources/l10n/JabRef_de.properties

@@ -1637,6 +1637,7 @@ User=Benutzer
 Connect=Verbinden
 Connection\ error=Verbindungsfehler
 Connection\ to\ %0\ server\ established.=Verbindung zum %0 Server hergestellt.
+There\ are\ connection\ issues\ with\ a\ JabRef\ server.\ Detailed\ information\:\ %0.=Es gibt Verbindungsprobleme mit einem JabRef Server. Detailinformation: %0.
 Required\ field\ "%0"\ is\ empty.=Erforederliches Feld "%0" ist leer.
 %0\ driver\ not\ available.=%0-Treiber nicht verfügbar.
 The\ connection\ to\ the\ server\ has\ been\ terminated.=Verbindung zum Server wurde abgebrochen.

src/main/resources/l10n/JabRef_en.properties

@@ -1631,6 +1631,7 @@ User=User
 Connect=Connect
 Connection\ error=Connection error
 Connection\ to\ %0\ server\ established.=Connection to %0 server established.
+There\ are\ connection\ issues\ with\ a\ JabRef\ server.\ Detailed\ information\:\ %0.=There are connection issues with a JabRef server. Detailed information: %0.
 Required\ field\ "%0"\ is\ empty.=Required field "%0" is empty.
 %0\ driver\ not\ available.=%0 driver not available.
 The\ connection\ to\ the\ server\ has\ been\ terminated.=The connection to the server has been terminated.

src/test/java/org/jabref/logic/importer/fetcher/GrobidCitationFetcherTest.java

@@ -1,10 +1,13 @@
 package org.jabref.logic.importer.fetcher;
 
+import java.io.IOException;
 import java.util.Collections;
 import java.util.List;
 import java.util.stream.Stream;
 
+import org.jabref.logic.importer.FetcherException;
 import org.jabref.logic.importer.ImportFormatPreferences;
+import org.jabref.logic.importer.util.GrobidService;
 import org.jabref.model.entry.BibEntry;
 import org.jabref.model.entry.field.StandardField;
 import org.jabref.model.entry.types.StandardEntryType;
@@ -17,7 +20,11 @@
 import org.mockito.Answers;
 
 import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertThrows;
+import static org.mockito.ArgumentMatchers.any;
+import static org.mockito.ArgumentMatchers.anyString;
 import static org.mockito.Mockito.mock;
+import static org.mockito.Mockito.when;
 
 @FetcherTest
 public class GrobidCitationFetcherTest {
@@ -76,28 +83,38 @@ public static Stream<Arguments> provideInvalidInput() {
 
     @ParameterizedTest(name = "{0}")
     @MethodSource("provideExamplesForCorrectResultTest")
-    public void grobidPerformSearchCorrectResultTest(String testName, BibEntry expectedBibEntry, String searchQuery) {
+    public void grobidPerformSearchCorrectResultTest(String testName, BibEntry expectedBibEntry, String searchQuery) throws FetcherException {
         List<BibEntry> entries = grobidCitationFetcher.performSearch(searchQuery);
         assertEquals(List.of(expectedBibEntry), entries);
     }
 
     @Test
-    public void grobidPerformSearchCorrectlySplitsStringTest() {
+    public void grobidPerformSearchCorrectlySplitsStringTest() throws FetcherException {
         List<BibEntry> entries = grobidCitationFetcher.performSearch(example1 + "\n\n" + example2 + "\r\n\r\n" + example3 + "\r\r" + example4);
         assertEquals(List.of(example1AsBibEntry, example2AsBibEntry, example3AsBibEntry, example4AsBibEntry), entries);
     }
 
     @Test
-    public void grobidPerformSearchWithEmptyStringsTest() {
+    public void grobidPerformSearchWithEmptyStringsTest() throws FetcherException {
         List<BibEntry> entries = grobidCitationFetcher.performSearch("   \n   ");
         assertEquals(Collections.emptyList(), entries);
     }
 
     @ParameterizedTest
     @MethodSource("provideInvalidInput")
-    public void grobidPerformSearchWithInvalidDataTest(String invalidInput) {
+    public void grobidPerformSearchWithInvalidDataTest(String invalidInput) throws FetcherException {
         List<BibEntry> entries = grobidCitationFetcher.performSearch(invalidInput);
         assertEquals(Collections.emptyList(), entries);
     }
 
+    @Test
+    public void performSearchThrowsExceptionInCaseOfConnectionIssues() throws IOException {
+        GrobidService grobidServiceMock = mock(GrobidService.class);
+        when(grobidServiceMock.processCitation(anyString(), any())).thenThrow(new IOException("Any IO Exception"));
+        grobidCitationFetcher = new GrobidCitationFetcher(importFormatPreferences, grobidServiceMock);
+
+        assertThrows(FetcherException.class, () -> {
+            grobidCitationFetcher.performSearch("any text");
+        }, "performSearch should throw an FetcherException, when there are underlying IOException.");
+    }
 }

src/test/java/org/jabref/logic/net/URLDownloadTest.java

@@ -109,4 +109,12 @@ public void testCheckConnectionFail() throws MalformedURLException {
         assertThrows(UnirestException.class, nonsense::canBeReached);
     }
 
+    @Test
+    public void connectTimeoutIsNeverNull() throws MalformedURLException {
+        URLDownload urlDownload = new URLDownload(new URL("http://www.example.com"));
+        assertNotNull(urlDownload.getConnectTimeout(), "there's a non-null default by the constructor");
+
+        urlDownload.setConnectTimeout(null);
+        assertNotNull(urlDownload.getConnectTimeout(), "no null value can be set");
+    }
 }