Merge remote-tracking branch 'upstream/master' into fixlookupfulltext

* upstream/master: fix bug where main file directory is not set correctly (#5215) Use UTF-8 as default encoding for files (#5213) fix: missing separator for unchanged diff words fix: use UTF-8 as default encoding for files ~ resolves #5133 Minor improvements to TexParser Fix lookup entry types in enums (#5209)
JabRef · Aug 24, 2019 · 4ef1460 · 4ef1460
2 parents 33fb6c5 + dd0f304
commit 4ef1460
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Showing 17 changed files with 108 additions and 35 deletions.
diff --git a/src/main/java/org/jabref/gui/entryeditor/LatexCitationsTabViewModel.java b/src/main/java/org/jabref/gui/entryeditor/LatexCitationsTabViewModel.java
@@ -77,6 +77,7 @@ public void init(BibEntry entry) {
 
         currentEntry = entry;
         Optional<String> citeKey = entry.getCiteKeyOptional();
+
         if (citeKey.isPresent()) {
             startSearch(citeKey.get());
         } else {

diff --git a/src/main/java/org/jabref/gui/mergeentries/DiffHighlighting.java b/src/main/java/org/jabref/gui/mergeentries/DiffHighlighting.java
@@ -22,7 +22,7 @@ private DiffHighlighting() {
 
     public static List<Text> generateDiffHighlighting(String baseString, String modifiedString, String separator) {
         List<String> stringList = Arrays.asList(baseString.split(separator));
-        List<Text> result = stringList.stream().map(DiffHighlighting::forUnchanged).collect(Collectors.toList());
+        List<Text> result = stringList.stream().map(text -> forUnchanged(text + separator)).collect(Collectors.toList());
         List<AbstractDelta<String>> deltaList;
         try {
             deltaList = DiffUtils.diff(stringList, Arrays.asList(modifiedString.split(separator))).getDeltas();

diff --git a/src/main/java/org/jabref/gui/preferences/FileTabViewModel.java b/src/main/java/org/jabref/gui/preferences/FileTabViewModel.java
@@ -77,6 +77,7 @@ public FileTabViewModel(DialogService dialogService, JabRefPreferences preferenc
         );
     }
 
+    @Override
     public void setValues() {
         openLastStartupProperty.setValue(preferences.getBoolean(JabRefPreferences.OPEN_LAST_EDITED));
         backupOldFileProperty.setValue(preferences.getBoolean(JabRefPreferences.BACKUP));
@@ -88,7 +89,7 @@ public void setValues() {
         selectedNewLineSeparatorProperty.setValue(preferences.getNewLineSeparator());
         alwaysReformatBibProperty.setValue(preferences.getBoolean(JabRefPreferences.REFORMAT_FILE_ON_SAVE_AND_EXPORT));
 
-        mainFileDirProperty.setValue(preferences.getAsOptional(StandardField.FILE + FilePreferences.DIR_SUFFIX).orElse(""));
+        mainFileDirProperty.setValue(preferences.getAsOptional(StandardField.FILE.getName() + FilePreferences.DIR_SUFFIX).orElse(""));
         useBibLocationAsPrimaryProperty.setValue(preferences.getBoolean(JabRefPreferences.BIB_LOC_AS_PRIMARY_DIR));
         if (preferences.getBoolean(JabRefPreferences.AUTOLINK_USE_REG_EXP_SEARCH_KEY)) { // Flipped around
             autolinkUseRegexProperty.setValue(true);
@@ -104,6 +105,7 @@ public void setValues() {
         autosaveLocalLibraries.setValue(preferences.getBoolean(JabRefPreferences.LOCAL_AUTO_SAVE));
     }
 
+    @Override
     public void storeSettings() {
         preferences.putBoolean(JabRefPreferences.OPEN_LAST_EDITED, openLastStartupProperty.getValue());
         preferences.putBoolean(JabRefPreferences.BACKUP, backupOldFileProperty.getValue());
@@ -119,7 +121,7 @@ public void storeSettings() {
         preferences.setNewLineSeparator(selectedNewLineSeparatorProperty.getValue());
         preferences.putBoolean(JabRefPreferences.REFORMAT_FILE_ON_SAVE_AND_EXPORT, alwaysReformatBibProperty.getValue());
 
-        preferences.put(StandardField.FILE + FilePreferences.DIR_SUFFIX, mainFileDirProperty.getValue());
+        preferences.put(StandardField.FILE.getName() + FilePreferences.DIR_SUFFIX, mainFileDirProperty.getValue());
         preferences.putBoolean(JabRefPreferences.BIB_LOC_AS_PRIMARY_DIR, useBibLocationAsPrimaryProperty.getValue());
         preferences.putBoolean(JabRefPreferences.AUTOLINK_USE_REG_EXP_SEARCH_KEY, autolinkUseRegexProperty.getValue());
         preferences.putBoolean(JabRefPreferences.AUTOLINK_EXACT_KEY_ONLY, autolinkFileExactBibtexProperty.getValue());
@@ -133,6 +135,7 @@ ValidationStatus mainFileDirValidationStatus() {
         return mainFileDirValidator.getValidationStatus();
     }
 
+    @Override
     public boolean validateSettings() {
         ValidationStatus status = mainFileDirValidationStatus();
         if (!status.isValid()) {

diff --git a/src/main/java/org/jabref/logic/journals/AbbreviationParser.java b/src/main/java/org/jabref/logic/journals/AbbreviationParser.java
@@ -4,7 +4,6 @@
 import java.io.File;
 import java.io.FileInputStream;
 import java.io.FileNotFoundException;
-import java.io.FileReader;
 import java.io.IOException;
 import java.io.InputStreamReader;
 import java.io.Reader;
@@ -39,7 +38,8 @@ public void readJournalListFromResource(String resourceFileName) {
     }
 
     public void readJournalListFromFile(File file) throws FileNotFoundException {
-        try (FileReader reader = new FileReader(Objects.requireNonNull(file))) {
+        try (FileInputStream stream = new FileInputStream(Objects.requireNonNull(file));
+             InputStreamReader reader = new InputStreamReader(stream, Objects.requireNonNull(StandardCharsets.UTF_8))) {
             readJournalList(reader);
         } catch (FileNotFoundException e) {
             throw e;

diff --git a/src/main/java/org/jabref/logic/journals/JournalAbbreviationLoader.java b/src/main/java/org/jabref/logic/journals/JournalAbbreviationLoader.java
@@ -11,7 +11,6 @@
 import org.slf4j.LoggerFactory;
 
 public class JournalAbbreviationLoader {
-
     private static final Logger LOGGER = LoggerFactory.getLogger(JournalAbbreviationLoader.class);
 
     // journal initialization

diff --git a/src/main/java/org/jabref/logic/texparser/DefaultTexParser.java b/src/main/java/org/jabref/logic/texparser/DefaultTexParser.java
@@ -2,6 +2,7 @@
 
 import java.io.IOException;
 import java.io.LineNumberReader;
+import java.io.Reader;
 import java.io.UncheckedIOException;
 import java.nio.channels.ClosedChannelException;
 import java.nio.file.Files;
@@ -27,8 +28,8 @@ public class DefaultTexParser implements TexParser {
     private static final String TEX_EXT = ".tex";
 
     /**
-     * It is allowed to add new cite commands for pattern matching.
-     * Some valid examples: "citep", "[cC]ite", and "[cC]ite(author|title|year|t|p)?".
+     * It is allowed to add new cite commands for pattern matching. Some valid examples: "citep", "[cC]ite", and
+     * "[cC]ite(author|title|year|t|p)?".
      */
     private static final String[] CITE_COMMANDS = {
             "[cC]ite(alt|alp|author|authorfull|date|num|p|t|text|title|url|year|yearpar)?",
@@ -76,7 +77,9 @@ public TexParserResult parse(List<Path> texFiles) {
                 continue;
             }
 
-            try (LineNumberReader lineNumberReader = new LineNumberReader(new CharsetDetector().setText(Files.readAllBytes(file)).detect().getReader())) {
+            try (
+                    Reader reader = new CharsetDetector().setText(Files.readAllBytes(file)).detect().getReader();
+                    LineNumberReader lineNumberReader = new LineNumberReader(reader)) {
                 for (String line = lineNumberReader.readLine(); line != null; line = lineNumberReader.readLine()) {
                     // Skip comments and blank lines.
                     if (line.trim().isEmpty() || line.trim().charAt(0) == '%') {
@@ -86,15 +89,19 @@ public TexParserResult parse(List<Path> texFiles) {
                     matchNestedFile(file, texFiles, referencedFiles, line);
                 }
             } catch (ClosedChannelException e) {
-                LOGGER.error("Parsing has been interrupted");
-                return null;
+                // User changed the underlying LaTeX file
+                // We ignore this error and just continue with parsing
+                LOGGER.info("Parsing has been interrupted");
             } catch (IOException | UncheckedIOException e) {
-                LOGGER.error("Error while parsing file {}", file, e);
+                // Some weired error during reading
+                // We ignore this error and just continue with parsing
+                LOGGER.info("Error while parsing file {}", file, e);
             }
         }
 
         // Parse all files referenced by TEX files, recursively.
         if (!referencedFiles.isEmpty()) {
+            // modifies class variable texParserResult
             parse(referencedFiles);
         }
 

diff --git a/src/main/java/org/jabref/model/entry/types/EntryType.java b/src/main/java/org/jabref/model/entry/types/EntryType.java
@@ -10,4 +10,5 @@ public interface EntryType {
     String getName();
 
     String getDisplayName();
+
 }
diff --git a/src/main/java/org/jabref/model/entry/types/EntryTypeFactory.java b/src/main/java/org/jabref/model/entry/types/EntryTypeFactory.java
@@ -1,7 +1,12 @@
 package org.jabref.model.entry.types;
 
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+import java.util.Locale;
+import java.util.Objects;
+
 import org.jabref.model.entry.BibEntryType;
-import org.jabref.model.util.OptionalUtil;
 
 public class EntryTypeFactory {
 
@@ -22,10 +27,10 @@ public static boolean isEqualNameAndFieldBased(BibEntryType type1, BibEntryType
         } else if ((type1 == null) || (type2 == null)) {
             return false;
         } else {
-            return type1.getType().equals(type2.getType())
-                    && type1.getRequiredFields().equals(type2.getRequiredFields())
-                    && type1.getOptionalFields().equals(type2.getOptionalFields())
-                    && type1.getSecondaryOptionalFields().equals(type2.getSecondaryOptionalFields());
+            return Objects.equals(type1.getType(), type2.getType())
+                   && Objects.equals(type1.getRequiredFields(), type2.getRequiredFields())
+                   && Objects.equals(type1.getOptionalFields(), type2.getOptionalFields())
+                   && Objects.equals(type1.getSecondaryOptionalFields(), type2.getSecondaryOptionalFields());
         }
     }
 
@@ -42,6 +47,10 @@ private static boolean isBiblatex(EntryType type) {
     }
 
     public static EntryType parse(String typeName) {
-        return OptionalUtil.orElse(StandardEntryType.fromName(typeName), new UnknownEntryType(typeName));
+
+        List<EntryType> types = new ArrayList<>(Arrays.<EntryType> asList(StandardEntryType.values()));
+        types.addAll(Arrays.<EntryType> asList(IEEETranEntryType.values()));
+
+        return types.stream().filter(type -> type.getName().equals(typeName.toLowerCase(Locale.ENGLISH))).findFirst().orElse(new UnknownEntryType(typeName));
     }
 }
diff --git a/src/main/java/org/jabref/model/entry/types/StandardEntryType.java b/src/main/java/org/jabref/model/entry/types/StandardEntryType.java
@@ -1,8 +1,6 @@
 package org.jabref.model.entry.types;
 
-import java.util.Arrays;
 import java.util.Locale;
-import java.util.Optional;
 
 public enum StandardEntryType implements EntryType {
     // BibTeX
@@ -44,12 +42,6 @@ public enum StandardEntryType implements EntryType {
         this.displayName = displayName;
     }
 
-    public static Optional<StandardEntryType> fromName(String name) {
-        return Arrays.stream(StandardEntryType.values())
-                     .filter(field -> field.getName().equalsIgnoreCase(name))
-                     .findAny();
-    }
-
     @Override
     public String getName() {
         return displayName.toLowerCase(Locale.ENGLISH);

diff --git a/src/main/java/org/jabref/model/entry/types/UnknownEntryType.java b/src/main/java/org/jabref/model/entry/types/UnknownEntryType.java
@@ -34,7 +34,7 @@ public boolean equals(Object o) {
         if (this == o) {
             return true;
         }
-        if (o == null || getClass() != o.getClass()) {
+        if ((o == null) || (getClass() != o.getClass())) {
             return false;
         }
         UnknownEntryType that = (UnknownEntryType) o;

diff --git a/src/main/java/org/jabref/model/texparser/TexParserResult.java b/src/main/java/org/jabref/model/texparser/TexParserResult.java
@@ -17,6 +17,8 @@ public class TexParserResult {
 
     private final List<Path> fileList;
     private final List<Path> nestedFiles;
+
+    // BibTeXKey --> set of citations
     private final Multimap<String, Citation> citations;
 
     public TexParserResult() {

diff --git a/src/main/java/org/jabref/preferences/JabRefPreferences.java b/src/main/java/org/jabref/preferences/JabRefPreferences.java
@@ -896,6 +896,7 @@ private static void insertDefaultCleanupPreset(Map<String, Object> storage) {
         storage.put(CLEANUP_FORMATTERS, convertListToString(Cleanups.DEFAULT_SAVE_ACTIONS.getAsStringList(OS.NEWLINE)));
     }
 
+    @Override
     public EntryEditorPreferences getEntryEditorPreferences() {
         return new EntryEditorPreferences(getEntryEditorTabList(),
                                           getLatexFieldFormatterPreferences(),
@@ -1589,7 +1590,7 @@ private NameFormatterPreferences getNameFormatterPreferences() {
 
     public FileLinkPreferences getFileLinkPreferences() {
         return new FileLinkPreferences(
-                Collections.singletonList(get(StandardField.FILE + FilePreferences.DIR_SUFFIX)),
+                                       Collections.singletonList(get(StandardField.FILE.getName() + FilePreferences.DIR_SUFFIX)),
                                        fileDirForDatabase);
     }
 
@@ -2034,6 +2035,7 @@ public Map<String, SortType> getMainTableColumnSortTypes() {
         return map;
     }
 
+    @Override
     public FileDragDropPreferenceType getEntryEditorFileLinkPreference() {
         return FileDragDropPreferenceType.valueOf(get(ENTRY_EDITOR_DRAG_DROP_PREFERENCE_TYPE));
     }

diff --git a/src/test/java/org/jabref/logic/texparser/DefaultTexParserTest.java b/src/test/java/org/jabref/logic/texparser/DefaultTexParserTest.java
@@ -70,7 +70,46 @@ public void testTwoCitationsSameLine() {
     }
 
     @Test
-    public void testFileEncoding() throws URISyntaxException {
+    public void testFileEncodingUtf8() throws URISyntaxException {
+        Path texFile = Paths.get(DefaultTexParserTest.class.getResource("utf-8.tex").toURI());
+
+        TexParserResult parserResult = new DefaultTexParser().parse(texFile);
+        TexParserResult expectedParserResult = new TexParserResult();
+
+        expectedParserResult.getFileList().add(texFile);
+        expectedParserResult.addKey("anykey", texFile, 1, 32, 45, "Danach wir anschließend mittels \\cite{anykey}.");
+
+        assertEquals(expectedParserResult, parserResult);
+    }
+
+    @Test
+    public void testFileEncodingIso88591() throws URISyntaxException {
+        Path texFile = Paths.get(DefaultTexParserTest.class.getResource("iso-8859-1.tex").toURI());
+
+        TexParserResult parserResult = new DefaultTexParser().parse(texFile);
+        TexParserResult expectedParserResult = new TexParserResult();
+
+        expectedParserResult.getFileList().add(texFile);
+        expectedParserResult.addKey("anykey", texFile, 1, 32, 45, "Danach wir anschließend mittels \\cite{anykey}.");
+
+        assertEquals(expectedParserResult, parserResult);
+    }
+
+    @Test
+    public void testFileEncodingIso885915() throws URISyntaxException {
+        Path texFile = Paths.get(DefaultTexParserTest.class.getResource("iso-8859-15.tex").toURI());
+
+        TexParserResult parserResult = new DefaultTexParser().parse(texFile);
+        TexParserResult expectedParserResult = new TexParserResult();
+
+        expectedParserResult.getFileList().add(texFile);
+        expectedParserResult.addKey("anykey", texFile, 1, 32, 45, "Danach wir anschließend mittels \\cite{anykey}.");
+
+        assertEquals(expectedParserResult, parserResult);
+    }
+
+    @Test
+    public void testFileEncodingForThreeFiles() throws URISyntaxException {
         Path texFile = Paths.get(DefaultTexParserTest.class.getResource("utf-8.tex").toURI());
         Path texFile2 = Paths.get(DefaultTexParserTest.class.getResource("iso-8859-1.tex").toURI());
         Path texFile3 = Paths.get(DefaultTexParserTest.class.getResource("iso-8859-15.tex").toURI());
@@ -79,9 +118,9 @@ public void testFileEncoding() throws URISyntaxException {
         TexParserResult expectedParserResult = new TexParserResult();
 
         expectedParserResult.getFileList().addAll(Arrays.asList(texFile, texFile2, texFile3));
-        expectedParserResult.addKey("anschließend", texFile, 1, 11, 30, "Danach wir \\cite{anschließend} mittels.");
-        expectedParserResult.addKey("Lässt", texFile2, 1, 4, 16, "Man \\cite{Lässt} auf verweisen.");
-        expectedParserResult.addKey("Läste", texFile3, 1, 13, 25, "Man einfache \\cite{Läste}.");
+        expectedParserResult.addKey("anykey", texFile, 1, 32, 45, "Danach wir anschließend mittels \\cite{anykey}.");
+        expectedParserResult.addKey("anykey", texFile2, 1, 32, 45, "Danach wir anschließend mittels \\cite{anykey}.");
+        expectedParserResult.addKey("anykey", texFile3, 1, 32, 45, "Danach wir anschließend mittels \\cite{anykey}.");
 
         assertEquals(expectedParserResult, parserResult);
     }

diff --git a/src/test/java/org/jabref/model/entry/EntryTypeFactoryTest.java b/src/test/java/org/jabref/model/entry/EntryTypeFactoryTest.java
@@ -0,0 +1,18 @@
+package org.jabref.model.entry;
+
+import org.jabref.model.entry.types.EntryType;
+import org.jabref.model.entry.types.EntryTypeFactory;
+import org.jabref.model.entry.types.IEEETranEntryType;
+
+import org.junit.jupiter.api.Test;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+
+public class EntryTypeFactoryTest {
+
+    @Test
+    public void testParseEntryTypePatent() {
+        EntryType patent = IEEETranEntryType.Patent;
+        assertEquals(patent, EntryTypeFactory.parse("patent"));
+    }
+}
diff --git a/src/test/resources/org/jabref/logic/texparser/iso-8859-1.tex b/src/test/resources/org/jabref/logic/texparser/iso-8859-1.tex
@@ -1 +1 @@
-Man \cite{Lässt} auf verweisen.
+Danach wir anschließend mittels \cite{anykey}.
diff --git a/src/test/resources/org/jabref/logic/texparser/iso-8859-15.tex b/src/test/resources/org/jabref/logic/texparser/iso-8859-15.tex
@@ -1 +1 @@
-Man einfache \cite{L�ste}.
+Danach wir anschließend mittels \cite{anykey}.
diff --git a/src/test/resources/org/jabref/logic/texparser/utf-8.tex b/src/test/resources/org/jabref/logic/texparser/utf-8.tex
@@ -1 +1 @@
-Danach wir \cite{anschließend} mittels.
+Danach wir anschließend mittels \cite{anykey}.
Original file line number	Diff line number	Diff line change
Expand Up		@@ -10,4 +10,5 @@ public interface EntryType {
		String getName();

		String getDisplayName();

		}
Original file line number	Diff line number	Diff line change
		@@ -1 +1 @@
		Man \cite{Lässt} auf verweisen.
		Danach wir anschließend mittels \cite{anykey}.
Original file line number	Diff line number	Diff line change
		@@ -1 +1 @@
		Man einfache \cite{L�ste}.
		Danach wir anschließend mittels \cite{anykey}.
Original file line number	Diff line number	Diff line change
		@@ -1 +1 @@
		Danach wir \cite{anschließend} mittels.
		Danach wir anschließend mittels \cite{anykey}.