Fix parser exception when loading tex-groups with non-existing file (#4839)

tobiasdiez · web-flow · commit 47772fd8ceff · 2019-04-02T23:33:56.000+02:00
* Fix #4735. Catch file not found exception and handle non existing aux files gracefully. * Fix build * Fix checkstyle
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -74,6 +74,7 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - We fixed an issue where selecting a group messed up the focus of the main table / entry editor. https://github.com/JabRef/jabref/issues/3367
 - We fixed an issue where composite author names were sorted incorrectly. https://github.com/JabRef/jabref/issues/2828
 - We fixed an issue where commands followed by `-` didn't work. [#3805](https://github.com/JabRef/jabref/issues/3805)
+- We fixed an issue where a non-existing aux file in a group made it impossible to open the library. [#4735](https://github.com/JabRef/jabref/issues/4735)
 - We fixed an issue where some journal names were wrongly marked as abbreviated. [#4115](https://github.com/JabRef/jabref/issues/4115)
 - We fixed an issue where the custom file column were sorted incorrectly. https://github.com/JabRef/jabref/issues/3119
 - We fixed an issues where the entry losses focus when a field is edited and at the same time used for sorting. https://github.com/JabRef/jabref/issues/3373
diff --git a/src/main/java/org/jabref/gui/groups/GroupDialog.java b/src/main/java/org/jabref/gui/groups/GroupDialog.java
@@ -335,7 +335,7 @@ groupName, getContext(),
                                     autoGroupPersonsField.getText().trim());
                         }
                     } else if (texRadioButton.isSelected()) {
-                        resultingGroup = new TexGroup(groupName, getContext(),
+                        resultingGroup = TexGroup.create(groupName, getContext(),
                                                       Paths.get(texGroupFilePath.getText().trim()), new DefaultAuxParser(new BibDatabase()), Globals.getFileUpdateMonitor(), basePanel.getBibDatabaseContext().getMetaData());
                     }
 
@@ -466,7 +466,7 @@ private VBox createOptionsTexGroup() {
         texGroupBrowseButton.setOnAction((ActionEvent e) -> openBrowseDialog());
         texGroupHBox.getChildren().add(texGroupFilePath);
         texGroupHBox.getChildren().add(texGroupBrowseButton);
-        texGroupHBox.setHgrow(texGroupFilePath, Priority.ALWAYS);
+        HBox.setHgrow(texGroupFilePath, Priority.ALWAYS);
         texPanel.getChildren().add(texGroupHBox);
         return texPanel;
     }
diff --git a/src/main/java/org/jabref/logic/auxparser/DefaultAuxParser.java b/src/main/java/org/jabref/logic/auxparser/DefaultAuxParser.java
@@ -77,7 +77,7 @@ private AuxParserResult parseAuxFile(Path auxFile) {
                     matchNestedAux(auxFile, result, fileList, line);
                 }
             } catch (FileNotFoundException e) {
-                LOGGER.info("Cannot locate input file", e);
+                LOGGER.warn("Cannot locate input file", e);
             } catch (IOException e) {
                 LOGGER.warn("Problem opening file", e);
             }
diff --git a/src/main/java/org/jabref/logic/importer/util/GroupsParser.java b/src/main/java/org/jabref/logic/importer/util/GroupsParser.java
@@ -28,11 +28,15 @@
 import org.jabref.model.strings.StringUtil;
 import org.jabref.model.util.FileUpdateMonitor;
 
+import org.slf4j.LoggerFactory;
+
 /**
  * Converts string representation of groups to a parsed {@link GroupTreeNode}.
  */
 public class GroupsParser {
 
+    private static final org.slf4j.Logger LOGGER = LoggerFactory.getLogger(GroupsParser.class);
+
     private GroupsParser() {
     }
 
@@ -123,9 +127,18 @@ private static AbstractGroup texGroupFromString(String string, FileUpdateMonitor
         GroupHierarchyType context = GroupHierarchyType.getByNumberOrDefault(Integer.parseInt(tok.nextToken()));
         try {
             Path path = Paths.get(tok.nextToken());
-            TexGroup newGroup = new TexGroup(name, context, path, new DefaultAuxParser(new BibDatabase()), fileMonitor, metaData);
-            addGroupDetails(tok, newGroup);
-            return newGroup;
+            try {
+                TexGroup newGroup = TexGroup.create(name, context, path, new DefaultAuxParser(new BibDatabase()), fileMonitor, metaData);
+                addGroupDetails(tok, newGroup);
+                return newGroup;
+            } catch (IOException ex) {
+                // Problem accessing file -> create without file monitoring
+                LOGGER.warn("Could not access file " + path + ". The group " + name + " will not reflect changes to the aux file.", ex);
+
+                TexGroup newGroup = TexGroup.createWithoutFileMonitoring(name, context, path, new DefaultAuxParser(new BibDatabase()), fileMonitor, metaData);
+                addGroupDetails(tok, newGroup);
+                return newGroup;
+            }
         } catch (InvalidPathException | IOException ex) {
             throw new ParseException(ex);
         }
diff --git a/src/main/java/org/jabref/model/groups/TexGroup.java b/src/main/java/org/jabref/model/groups/TexGroup.java
@@ -30,20 +30,29 @@ public class TexGroup extends AbstractGroup implements FileUpdateListener {
     private final MetaData metaData;
     private String user;
 
-    public TexGroup(String name, GroupHierarchyType context, Path filePath, AuxParser auxParser, FileUpdateMonitor fileMonitor, MetaData metaData, String user) throws IOException {
+    TexGroup(String name, GroupHierarchyType context, Path filePath, AuxParser auxParser, FileUpdateMonitor fileMonitor, MetaData metaData, String user) {
         super(name, context);
         this.metaData = metaData;
         this.user = user;
         this.filePath = expandPath(Objects.requireNonNull(filePath));
         this.auxParser = auxParser;
         this.fileMonitor = fileMonitor;
-        fileMonitor.addListenerForFile(this.filePath, this);
     }
 
-    public TexGroup(String name, GroupHierarchyType context, Path filePath, AuxParser auxParser, FileUpdateMonitor fileMonitor, MetaData metaData) throws IOException {
+    TexGroup(String name, GroupHierarchyType context, Path filePath, AuxParser auxParser, FileUpdateMonitor fileMonitor, MetaData metaData) throws IOException {
         this(name, context, filePath, auxParser, fileMonitor, metaData, System.getProperty("user.name") + '-' + InetAddress.getLocalHost().getHostName());
     }
 
+    public static TexGroup create(String name, GroupHierarchyType context, Path filePath, AuxParser auxParser, FileUpdateMonitor fileMonitor, MetaData metaData) throws IOException {
+        TexGroup group = new TexGroup(name, context, filePath, auxParser, fileMonitor, metaData);
+        fileMonitor.addListenerForFile(filePath, group);
+        return group;
+    }
+
+    public static TexGroup createWithoutFileMonitoring(String name, GroupHierarchyType context, Path filePath, AuxParser auxParser, FileUpdateMonitor fileMonitor, MetaData metaData) throws IOException {
+        return new TexGroup(name, context, filePath, auxParser, fileMonitor, metaData);
+    }
+    
     @Override
     public boolean contains(BibEntry entry) {
         if (keysUsedInAux == null) {
@@ -124,7 +133,7 @@ private List<Path> getFileDirectoriesAsPaths() {
         List<Path> fileDirs = new ArrayList<>();
 
         metaData.getLaTexFileDirectory(user)
-                .ifPresent(laTexFileDirectory -> fileDirs.add(laTexFileDirectory));
+                .ifPresent(fileDirs::add);
 
         return fileDirs;
     }
diff --git a/src/test/java/org/jabref/logic/exporter/GroupSerializerTest.java b/src/test/java/org/jabref/logic/exporter/GroupSerializerTest.java
@@ -30,31 +30,31 @@
 
 import static org.junit.jupiter.api.Assertions.assertEquals;
 
-public class GroupSerializerTest {
+class GroupSerializerTest {
 
     private GroupSerializer groupSerializer;
 
     @BeforeEach
-    public void setUp() throws Exception {
+    void setUp() throws Exception {
         groupSerializer = new GroupSerializer();
     }
 
     @Test
-    public void serializeSingleAllEntriesGroup() {
+    void serializeSingleAllEntriesGroup() {
         AllEntriesGroup group = new AllEntriesGroup("");
         List<String> serialization = groupSerializer.serializeTree(GroupTreeNode.fromGroup(group));
         assertEquals(Collections.singletonList("0 AllEntriesGroup:"), serialization);
     }
 
     @Test
-    public void serializeSingleExplicitGroup() {
+    void serializeSingleExplicitGroup() {
         ExplicitGroup group = new ExplicitGroup("myExplicitGroup", GroupHierarchyType.INDEPENDENT, ',');
         List<String> serialization = groupSerializer.serializeTree(GroupTreeNode.fromGroup(group));
         assertEquals(Collections.singletonList("0 StaticGroup:myExplicitGroup;0;1;;;;"), serialization);
     }
 
     @Test
-    public void serializeSingleExplicitGroupWithIconAndDescription() {
+    void serializeSingleExplicitGroupWithIconAndDescription() {
         ExplicitGroup group = new ExplicitGroup("myExplicitGroup", GroupHierarchyType.INDEPENDENT, ',');
         group.setIconName("test icon");
         group.setExpanded(true);
@@ -66,63 +66,63 @@ public void serializeSingleExplicitGroupWithIconAndDescription() {
 
     @Test
     // For https://github.com/JabRef/jabref/issues/1681
-    public void serializeSingleExplicitGroupWithEscapedSlash() {
+    void serializeSingleExplicitGroupWithEscapedSlash() {
         ExplicitGroup group = new ExplicitGroup("B{\\\"{o}}hmer", GroupHierarchyType.INDEPENDENT, ',');
         List<String> serialization = groupSerializer.serializeTree(GroupTreeNode.fromGroup(group));
         assertEquals(Collections.singletonList("0 StaticGroup:B{\\\\\"{o}}hmer;0;1;;;;"), serialization);
     }
 
     @Test
-    public void serializeSingleSimpleKeywordGroup() {
+    void serializeSingleSimpleKeywordGroup() {
         WordKeywordGroup group = new WordKeywordGroup("name", GroupHierarchyType.INDEPENDENT, "keywords", "test", false, ',', false);
         List<String> serialization = groupSerializer.serializeTree(GroupTreeNode.fromGroup(group));
         assertEquals(Collections.singletonList("0 KeywordGroup:name;0;keywords;test;0;0;1;;;;"), serialization);
     }
 
     @Test
-    public void serializeSingleRegexKeywordGroup() {
+    void serializeSingleRegexKeywordGroup() {
         KeywordGroup group = new RegexKeywordGroup("myExplicitGroup", GroupHierarchyType.REFINING, "author", "asdf", false);
         List<String> serialization = groupSerializer.serializeTree(GroupTreeNode.fromGroup(group));
         assertEquals(Collections.singletonList("0 KeywordGroup:myExplicitGroup;1;author;asdf;0;1;1;;;;"), serialization);
     }
 
     @Test
-    public void serializeSingleSearchGroup() {
+    void serializeSingleSearchGroup() {
         SearchGroup group = new SearchGroup("myExplicitGroup", GroupHierarchyType.INDEPENDENT, "author=harrer", true, true);
         List<String> serialization = groupSerializer.serializeTree(GroupTreeNode.fromGroup(group));
         assertEquals(Collections.singletonList("0 SearchGroup:myExplicitGroup;0;author=harrer;1;1;1;;;;"), serialization);
     }
 
     @Test
-    public void serializeSingleSearchGroupWithRegex() {
+    void serializeSingleSearchGroupWithRegex() {
         SearchGroup group = new SearchGroup("myExplicitGroup", GroupHierarchyType.INCLUDING, "author=\"harrer\"", true, false);
         List<String> serialization = groupSerializer.serializeTree(GroupTreeNode.fromGroup(group));
         assertEquals(Collections.singletonList("0 SearchGroup:myExplicitGroup;2;author=\"harrer\";1;0;1;;;;"), serialization);
     }
 
     @Test
-    public void serializeSingleAutomaticKeywordGroup() {
+    void serializeSingleAutomaticKeywordGroup() {
         AutomaticGroup group = new AutomaticKeywordGroup("myAutomaticGroup", GroupHierarchyType.INDEPENDENT, "keywords", ',', '>');
         List<String> serialization = groupSerializer.serializeTree(GroupTreeNode.fromGroup(group));
         assertEquals(Collections.singletonList("0 AutomaticKeywordGroup:myAutomaticGroup;0;keywords;,;>;1;;;;"), serialization);
     }
 
     @Test
-    public void serializeSingleAutomaticPersonGroup() {
+    void serializeSingleAutomaticPersonGroup() {
         AutomaticPersonsGroup group = new AutomaticPersonsGroup("myAutomaticGroup", GroupHierarchyType.INDEPENDENT, "authors");
         List<String> serialization = groupSerializer.serializeTree(GroupTreeNode.fromGroup(group));
         assertEquals(Collections.singletonList("0 AutomaticPersonsGroup:myAutomaticGroup;0;authors;1;;;;"), serialization);
     }
 
     @Test
-    public void serializeSingleTexGroup() throws Exception {
-        TexGroup group = new TexGroup("myTexGroup", GroupHierarchyType.INDEPENDENT, Paths.get("path", "To", "File"), new DefaultAuxParser(new BibDatabase()), new DummyFileUpdateMonitor(), new MetaData());
+    void serializeSingleTexGroup() throws Exception {
+        TexGroup group = TexGroup.createWithoutFileMonitoring("myTexGroup", GroupHierarchyType.INDEPENDENT, Paths.get("path", "To", "File"), new DefaultAuxParser(new BibDatabase()), new DummyFileUpdateMonitor(), new MetaData());
         List<String> serialization = groupSerializer.serializeTree(GroupTreeNode.fromGroup(group));
         assertEquals(Collections.singletonList("0 TexGroup:myTexGroup;0;path/To/File;1;;;;"), serialization);
     }
 
     @Test
-    public void getTreeAsStringInSimpleTree() throws Exception {
+    void getTreeAsStringInSimpleTree() throws Exception {
         GroupTreeNode root = GroupTreeNodeTest.getRoot();
         GroupTreeNodeTest.getNodeInSimpleTree(root);
 
@@ -136,7 +136,7 @@ public void getTreeAsStringInSimpleTree() throws Exception {
     }
 
     @Test
-    public void getTreeAsStringInComplexTree() throws Exception {
+    void getTreeAsStringInComplexTree() throws Exception {
         GroupTreeNode root = GroupTreeNodeTest.getRoot();
         GroupTreeNodeTest.getNodeInComplexTree(root);
 
diff --git a/src/test/java/org/jabref/logic/importer/util/GroupsParserTest.java b/src/test/java/org/jabref/logic/importer/util/GroupsParserTest.java
@@ -27,46 +27,46 @@
 import static org.junit.jupiter.api.Assertions.assertEquals;
 import static org.junit.jupiter.api.Assertions.assertThrows;
 
-public class GroupsParserTest {
+class GroupsParserTest {
     private FileUpdateMonitor fileMonitor;
     private MetaData metaData;
 
     @BeforeEach
-    public void setUp() throws Exception {
+    void setUp() throws Exception {
         fileMonitor = new DummyFileUpdateMonitor();
         metaData = new MetaData();
     }
 
     @Test
     // For https://github.com/JabRef/jabref/issues/1681
-    public void fromStringParsesExplicitGroupWithEscapedCharacterInName() throws Exception {
+    void fromStringParsesExplicitGroupWithEscapedCharacterInName() throws Exception {
         ExplicitGroup expected = new ExplicitGroup("B{\\\"{o}}hmer", GroupHierarchyType.INDEPENDENT, ',');
         AbstractGroup parsed = GroupsParser.fromString("ExplicitGroup:B{\\\\\"{o}}hmer;0;", ',', fileMonitor, metaData);
 
         assertEquals(expected, parsed);
     }
 
     @Test
-    public void keywordDelimiterThatNeedsToBeEscaped() throws Exception {
+    void keywordDelimiterThatNeedsToBeEscaped() throws Exception {
         AutomaticGroup expected = new AutomaticKeywordGroup("group1", GroupHierarchyType.INDEPENDENT, "keywords", ';', '>');
         AbstractGroup parsed = GroupsParser.fromString("AutomaticKeywordGroup:group1;0;keywords;\\;;>;1;;;;;", ';', fileMonitor, metaData);
         assertEquals(expected, parsed);
     }
 
     @Test
-    public void hierarchicalDelimiterThatNeedsToBeEscaped() throws Exception {
+    void hierarchicalDelimiterThatNeedsToBeEscaped() throws Exception {
         AutomaticGroup expected = new AutomaticKeywordGroup("group1", GroupHierarchyType.INDEPENDENT, "keywords", ',', ';');
         AbstractGroup parsed = GroupsParser.fromString("AutomaticKeywordGroup:group1;0;keywords;,;\\;;1;;;;;", ';', fileMonitor, metaData);
         assertEquals(expected, parsed);
     }
 
     @Test
-    public void fromStringThrowsParseExceptionForNotEscapedGroupName() throws Exception {
+    void fromStringThrowsParseExceptionForNotEscapedGroupName() throws Exception {
         assertThrows(ParseException.class, () -> GroupsParser.fromString("ExplicitGroup:slit\\\\;0\\;mertsch_slit2_2007\\;;", ',', fileMonitor, metaData));
     }
 
     @Test
-    public void testImportSubGroups() throws Exception {
+    void testImportSubGroups() throws Exception {
 
         List<String> orderedData = Arrays.asList("0 AllEntriesGroup:", "1 ExplicitGroup:1;0;",
                 "2 ExplicitGroup:2;0;", "0 ExplicitGroup:3;0;");
@@ -93,7 +93,7 @@ public void testImportSubGroups() throws Exception {
     }
 
     @Test
-    public void fromStringParsesExplicitGroupWithIconAndDescription() throws Exception {
+    void fromStringParsesExplicitGroupWithIconAndDescription() throws Exception {
         ExplicitGroup expected = new ExplicitGroup("myExplicitGroup", GroupHierarchyType.INDEPENDENT, ',');
         expected.setIconName("test icon");
         expected.setExpanded(true);
@@ -105,28 +105,28 @@ public void fromStringParsesExplicitGroupWithIconAndDescription() throws Excepti
     }
 
     @Test
-    public void fromStringParsesAutomaticKeywordGroup() throws Exception {
+    void fromStringParsesAutomaticKeywordGroup() throws Exception {
         AutomaticGroup expected = new AutomaticKeywordGroup("myAutomaticGroup", GroupHierarchyType.INDEPENDENT, "keywords", ',', '>');
         AbstractGroup parsed = GroupsParser.fromString("AutomaticKeywordGroup:myAutomaticGroup;0;keywords;,;>;1;;;;", ',', fileMonitor, metaData);
         assertEquals(expected, parsed);
     }
 
     @Test
-    public void fromStringParsesAutomaticPersonGroup() throws Exception {
+    void fromStringParsesAutomaticPersonGroup() throws Exception {
         AutomaticPersonsGroup expected = new AutomaticPersonsGroup("myAutomaticGroup", GroupHierarchyType.INDEPENDENT, "authors");
         AbstractGroup parsed = GroupsParser.fromString("AutomaticPersonsGroup:myAutomaticGroup;0;authors;1;;;;", ',', fileMonitor, metaData);
         assertEquals(expected, parsed);
     }
 
     @Test
-    public void fromStringParsesTexGroup() throws Exception {
-        TexGroup expected = new TexGroup("myTexGroup", GroupHierarchyType.INDEPENDENT, Paths.get("path", "To", "File"), new DefaultAuxParser(new BibDatabase()), fileMonitor, metaData);
+    void fromStringParsesTexGroup() throws Exception {
+        TexGroup expected = TexGroup.createWithoutFileMonitoring("myTexGroup", GroupHierarchyType.INDEPENDENT, Paths.get("path", "To", "File"), new DefaultAuxParser(new BibDatabase()), fileMonitor, metaData);
         AbstractGroup parsed = GroupsParser.fromString("TexGroup:myTexGroup;0;path/To/File;1;;;;", ',', fileMonitor, metaData);
         assertEquals(expected, parsed);
     }
 
     @Test
-    public void fromStringUnknownGroupThrowsException() throws Exception {
+    void fromStringUnknownGroupThrowsException() throws Exception {
         assertThrows(ParseException.class, () -> GroupsParser.fromString("0 UnknownGroup:myUnknownGroup;0;;1;;;;", ',', fileMonitor, metaData));
     }
 }

Original file line number	Diff line number	Diff line change
`@@ -335,7 +335,7 @@ groupName, getContext(),`
`335`	`335`	`autoGroupPersonsField.getText().trim());`
`336`	`336`	`}`
`337`	`337`	`} else if (texRadioButton.isSelected()) {`
`338`		`- resultingGroup = new TexGroup(groupName, getContext(),`
	`338`	`+ resultingGroup = TexGroup.create(groupName, getContext(),`
`339`	`339`	`Paths.get(texGroupFilePath.getText().trim()), new DefaultAuxParser(new BibDatabase()), Globals.getFileUpdateMonitor(), basePanel.getBibDatabaseContext().getMetaData());`
`340`	`340`	`}`
`341`	`341`
`@@ -466,7 +466,7 @@ private VBox createOptionsTexGroup() {`
`466`	`466`	`texGroupBrowseButton.setOnAction((ActionEvent e) -> openBrowseDialog());`
`467`	`467`	`texGroupHBox.getChildren().add(texGroupFilePath);`
`468`	`468`	`texGroupHBox.getChildren().add(texGroupBrowseButton);`
`469`		`- texGroupHBox.setHgrow(texGroupFilePath, Priority.ALWAYS);`
	`469`	`+ HBox.setHgrow(texGroupFilePath, Priority.ALWAYS);`
`470`	`470`	`texPanel.getChildren().add(texGroupHBox);`
`471`	`471`	`return texPanel;`
`472`	`472`	`}`
Original file line number	Diff line number	Diff line change
`@@ -77,7 +77,7 @@ private AuxParserResult parseAuxFile(Path auxFile) {`
`77`	`77`	`matchNestedAux(auxFile, result, fileList, line);`
`78`	`78`	`}`
`79`	`79`	`} catch (FileNotFoundException e) {`
`80`		`- LOGGER.info("Cannot locate input file", e);`
	`80`	`+ LOGGER.warn("Cannot locate input file", e);`
`81`	`81`	`} catch (IOException e) {`
`82`	`82`	`LOGGER.warn("Problem opening file", e);`
`83`	`83`	`}`