Merge branch 'master' of github.com:JabRef/jabref

* 'master' of github.com:JabRef/jabref:
  Allow spaces in DOIs
  Remove irrelevant log messages during XMP reading
  Adapt log4j configuration for cleaner junit tests #3511
  Eclipse Django style #3655
  Better code style for chained methods
  Update build.gradle
  Update build.gradle
  cleanup and refactoring in DuplicateCheck class
  code review fixes - consider pages of the same book separately in duplications detection process; add more tests
  differentiate inbooks with the same author and title, but different chapter
  Remove deprecated static BibtexParser.parse method
  Use stream in matcher (#3696)
  Add some BibtexNameFomatter comments
  Add exception for Jacoco
  Set jacoco toolVersion earlier
  set jacoco version globally

build.gradle

@@ -175,6 +175,10 @@ dependencies {
     checkstyle 'com.puppycrawl.tools:checkstyle:8.8'
 }
 
+jacoco {
+    toolVersion = '0.8.0'
+}
+
 dependencyUpdates {
     outputFormatter = "json"
 }
@@ -227,7 +231,16 @@ dependencyUpdates.resolutionStrategy = {
                 selection.reject("http://dev.mysql.com/downloads/connector/j/ lists the version 5.* as last stable version.")
             }
         }
-
+        withModule("org.jacoco.agent") { ComponentSelection selection ->
+            if (selection.candidate.version.equals("0.8.0")) {
+                selection.reject("As a native plugin we cannot control the actual version of jacoco. This dependency should be hidden.")
+            }
+        }
+        withModule("org.jacoco.ant") { ComponentSelection selection ->
+            if (selection.candidate.version.equals("0.8.0")) {
+                selection.reject("As a native plugin we cannot control the actual version of jacoco. This dependency should be hidden.")
+            }
+        }
     }
 }
 
@@ -391,7 +404,6 @@ afterEvaluate {
     def junitPlatformTest = tasks.junitPlatformTest
 
     jacoco {
-        toolVersion = '0.8.0'
         applyTo(junitPlatformTest)
     }
 

config/IntelliJ Code Style.xml

@@ -31,6 +31,7 @@
     <option name="KEEP_BLANK_LINES_IN_DECLARATIONS" value="1" />
     <option name="KEEP_BLANK_LINES_IN_CODE" value="1" />
     <option name="KEEP_BLANK_LINES_BEFORE_RBRACE" value="0" />
+    <option name="ALIGN_MULTILINE_CHAINED_METHODS" value="true" />
     <arrangement>
       <rules>
         <section>

eclipse.gradle

@@ -154,7 +154,7 @@ tasks.eclipse.doFirst {
         org.eclipse.jdt.core.formatter.alignment_for_parameters_in_constructor_declaration=16
         org.eclipse.jdt.core.formatter.alignment_for_parameters_in_method_declaration=16
         org.eclipse.jdt.core.formatter.alignment_for_resources_in_try=88
-        org.eclipse.jdt.core.formatter.alignment_for_selector_in_method_invocation=16
+        org.eclipse.jdt.core.formatter.alignment_for_selector_in_method_invocation=80
         org.eclipse.jdt.core.formatter.alignment_for_superclass_in_type_declaration=16
         org.eclipse.jdt.core.formatter.alignment_for_superinterfaces_in_enum_declaration=0
         org.eclipse.jdt.core.formatter.alignment_for_superinterfaces_in_type_declaration=16

src/main/java/org/jabref/gui/EntryTypeDialog.java

@@ -288,6 +288,7 @@ protected Optional<BibEntry> doInBackground() throws Exception {
                 generateButton.setText(Localization.lang("Searching..."));
             });
             searchID = idTextField.getText().trim();
+            searchID = searchID.replaceAll(" ", "");
             fetcher = WebFetchers.getIdBasedFetchers(Globals.prefs.getImportFormatPreferences()).get(comboBox.getSelectedIndex());
             if (!searchID.isEmpty()) {
                 try {

src/main/java/org/jabref/logic/bst/BibtexNameFormatter.java

@@ -29,6 +29,15 @@ public class BibtexNameFormatter {
     private BibtexNameFormatter() {
     }
 
+    /**
+     * Formats the nth author of the author name list by a given format string
+     *
+     * @param authorsNameList The string from an author field
+     * @param whichName index of the list, starting with 1
+     * @param formatString TODO
+     * @param warn collects the warnings, may-be-null
+     * @return
+     */
     public static String formatName(String authorsNameList, int whichName, String formatString, Warn warn) {
         AuthorList al = AuthorList.parse(authorsNameList);
 
@@ -40,11 +49,7 @@ public static String formatName(String authorsNameList, int whichName, String fo
     }
 
     /**
-     *
-     * @param author
-     * @param format
-     * @param warn may-be-null
-     * @return
+     * @param warn collects the warnings, may-be-null
      */
     public static String formatName(Author author, String format, Warn warn) {
 

src/main/java/org/jabref/logic/importer/fileformat/BibtexParser.java

@@ -78,19 +78,6 @@ public BibtexParser(ImportFormatPreferences importFormatPreferences, FileUpdateM
         metaDataParser = new MetaDataParser(fileMonitor);
     }
 
-    /**
-     * Shortcut usage to create a Parser and read the input.
-     *
-     * @param in the Reader to read from
-     * @param fileMonitor
-     * @throws IOException
-     * @deprecated inline this method
-     */
-    @Deprecated
-    public static ParserResult parse(Reader in, ImportFormatPreferences importFormatPreferences, FileUpdateMonitor fileMonitor) throws IOException {
-        return new BibtexParser(importFormatPreferences, fileMonitor).parse(in);
-    }
-
     /**
      * Parses BibtexEntries from the given string and returns one entry found (or null if none found)
      * <p>

src/main/java/org/jabref/logic/remote/client/RemoteListenerClient.java

@@ -35,8 +35,8 @@ public static boolean sendToActiveJabRefInstance(String[] args, int remoteServer
 
                 if (!Protocol.IDENTIFIER.equals(identifier)) {
                     String port = String.valueOf(remoteServerPort);
-                    String error = Localization.lang("Cannot use port %0 for remote operation; another application may be using it. Try specifying another port.", port);
-                    System.out.println(error);
+                    String errorMessage = Localization.lang("Cannot use port %0 for remote operation; another application may be using it. Try specifying another port.", port);
+                    LOGGER.error(errorMessage);
                     return false;
                 }
                 protocol.sendMessage(String.join("\n", args));

src/main/java/org/jabref/logic/xmp/XMPUtil.java

@@ -1033,7 +1033,7 @@ public static boolean hasMetadata(Path path, XMPPreferences xmpPreferences) {
         try (InputStream inputStream = Files.newInputStream(path, StandardOpenOption.READ)) {
             return hasMetadata(inputStream, xmpPreferences);
         } catch (IOException e) {
-            LOGGER.error("XMP reading failed", e);
+            // happens if no metadata is found, no reason to log the exception
             return false;
         }
     }
@@ -1056,7 +1056,7 @@ public static boolean hasMetadata(InputStream inputStream, XMPPreferences xmpPre
             LOGGER.info("Encryption not supported by XMPUtil");
             return false;
         } catch (IOException e) {
-            LOGGER.error("XMP reading failed", e);
+            // happens if no metadata is found, no reason to log the exception
             return false;
         }
     }

src/main/java/org/jabref/model/search/matchers/AndMatcher.java

@@ -1,26 +1,15 @@
 package org.jabref.model.search.matchers;
 
 import org.jabref.model.entry.BibEntry;
-import org.jabref.model.search.SearchMatcher;
 
 /**
- * Subclass of MatcherSet that ANDs or ORs between its rules, returning 0 or
- * 1.
+ * A set of matchers that returns true if all matcher match the given entry.
  */
 public class AndMatcher extends MatcherSet {
 
     @Override
-    public boolean isMatch(BibEntry bibEntry) {
-        int score = 0;
-
-        // We let each rule add a maximum of 1 to the score.
-        for (SearchMatcher rule : matchers) {
-            if (rule.isMatch(bibEntry)) {
-                score++;
-            }
-        }
-
-        // Then an AND rule demands that score == number of rules
-        return score == matchers.size();
+    public boolean isMatch(BibEntry entry) {
+        return matchers.stream()
+                       .allMatch(rule -> rule.isMatch(entry));
     }
 }

src/main/java/org/jabref/model/search/matchers/OrMatcher.java

@@ -1,26 +1,15 @@
 package org.jabref.model.search.matchers;
 
 import org.jabref.model.entry.BibEntry;
-import org.jabref.model.search.SearchMatcher;
 
 /**
- * Subclass of MatcherSet that ANDs or ORs between its rules, returning 0 or
- * 1.
+ * A set of matchers that returns true if any matcher matches the given entry.
  */
 public class OrMatcher extends MatcherSet {
 
     @Override
-    public boolean isMatch(BibEntry bibEntry) {
-        int score = 0;
-
-        // We let each rule add a maximum of 1 to the score.
-        for (SearchMatcher rule : matchers) {
-            if (rule.isMatch(bibEntry)) {
-                score++;
-            }
-        }
-
-        // OR rule demands score > 0.
-        return score > 0;
+    public boolean isMatch(BibEntry entry) {
+        return matchers.stream()
+                       .anyMatch(rule -> rule.isMatch(entry));
     }
 }

src/test/java/org/jabref/logic/bibtex/DuplicateCheckTest.java

@@ -16,6 +16,8 @@ public class DuplicateCheckTest {
 
     private BibEntry simpleArticle;
     private BibEntry unrelatedArticle;
+    private BibEntry simpleInbook;
+    private BibEntry simpleIncollection;
 
     @Before
     public void setUp() {
@@ -27,6 +29,19 @@ public void setUp() {
                 .withField(FieldName.AUTHOR, "Completely Different")
                 .withField(FieldName.TITLE, "Holy Moly Uffdada und Trallalla")
                 .withField(FieldName.YEAR, "1992");
+        simpleInbook = new BibEntry(BibtexEntryTypes.INBOOK.getName())
+                .withField(FieldName.TITLE, "Alice in Wonderland")
+                .withField(FieldName.AUTHOR, "Charles Lutwidge Dodgson")
+                .withField(FieldName.CHAPTER, "Chapter One – Down the Rabbit Hole")
+                .withField(FieldName.LANGUAGE, "English")
+                .withField(FieldName.PUBLISHER, "Macmillan")
+                .withField(FieldName.YEAR, "1865");
+        simpleIncollection = new BibEntry(BibtexEntryTypes.INCOLLECTION.getName())
+                .withField(FieldName.TITLE, "Innovation and Intellectual Property Rights")
+                .withField(FieldName.AUTHOR, "Ove Grandstrand")
+                .withField(FieldName.BOOKTITLE, "The Oxford Handbook of Innovation")
+                .withField(FieldName.PUBLISHER, "Oxford University Press")
+                .withField(FieldName.YEAR, "2004");
     }
 
     @Test
@@ -142,6 +157,51 @@ public void twoEntriesWithSameDoiButDifferentTypesAreDuplicates() {
         assertTrue(DuplicateCheck.isDuplicate(simpleArticle, duplicateWithDifferentType, BibDatabaseMode.BIBTEX));
     }
 
+    @Test
+    public void twoInbooksWithDifferentChaptersAreNotDuplicates() {
+        twoEntriesWithDifferentSpecificFieldsAreNotDuplicates(simpleInbook, FieldName.CHAPTER,
+                "Chapter One – Down the Rabbit Hole",
+                "Chapter Two – The Pool of Tears");
+    }
+
+    @Test
+    public void twoInbooksWithDifferentPagesAreNotDuplicates() {
+        twoEntriesWithDifferentSpecificFieldsAreNotDuplicates(simpleInbook, FieldName.PAGES, "1-20", "21-40");
+    }
+
+    @Test
+    public void twoIncollectionsWithDifferentChaptersAreNotDuplicates() {
+        twoEntriesWithDifferentSpecificFieldsAreNotDuplicates(simpleIncollection, FieldName.CHAPTER, "10", "9");
+    }
+
+    @Test
+    public void twoIncollectionsWithDifferentPagesAreNotDuplicates() {
+        twoEntriesWithDifferentSpecificFieldsAreNotDuplicates(simpleIncollection, FieldName.PAGES, "1-20", "21-40");
+    }
+
+    private void twoEntriesWithDifferentSpecificFieldsAreNotDuplicates(final BibEntry cloneable,
+                                                                       final String fieldType,
+                                                                       final String firstValue,
+                                                                       final String secondValue) {
+        final BibEntry entry1 = (BibEntry) cloneable.clone();
+        entry1.setField(fieldType, firstValue);
+
+        final BibEntry entry2 = (BibEntry) cloneable.clone();
+        entry2.setField(fieldType, secondValue);
+
+        assertFalse(DuplicateCheck.isDuplicate(entry1, entry2, BibDatabaseMode.BIBTEX));
+    }
+
+    @Test
+    public void inbookWithoutChapterCouldBeDuplicateOfInbookWithChapter() {
+        final BibEntry inbook1 = (BibEntry) simpleInbook.clone();
+        final BibEntry inbook2 = (BibEntry) simpleInbook.clone();
+        inbook2.setField(FieldName.CHAPTER, "");
+
+        assertTrue(DuplicateCheck.isDuplicate(inbook1, inbook2, BibDatabaseMode.BIBTEX));
+        assertTrue(DuplicateCheck.isDuplicate(inbook2, inbook1, BibDatabaseMode.BIBTEX));
+    }
+
     @Test
     public void twoBooksWithDifferentEditionsAreNotDuplicates() {
         BibEntry editionOne = new BibEntry(BibtexEntryTypes.BOOK.getName());