Merge branch 'master' into fileChooserRefactor

* master: define xjc input/ouput dir (subsequent builds will be faster) (JabRef#1628) Consistent file name casing (and other localization improvements) (JabRef#1629) Builds are now stored via build-upload.jabref.org Some enhancements and cleanups related to dates (JabRef#1575) changes should be tested manually Cleanup FindFile and asssociated tests (JabRef#1596) More field names and a method (JabRef#1627) Moved, removed, and used String constants (JabRef#1618) Updated preview entries (JabRef#1606) Improved LaTeX to Unicode/HTML formatters to output more sensible values for unknown commands (JabRef#1622) Fixed JabRef#636 by using DOICheck and DOIStrip in export filters (JabRef#1624) Converted a few getField to getFieldOptional (JabRef#1625)
Siedlerchr · Jul 26, 2016 · d83ec67 · d83ec67
2 parents d1dc7bf + 653c8a9
commit d83ec67
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diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
@@ -3,3 +3,4 @@
 - [ ] Change in CHANGELOG.md described
 - [ ] Tests created for changes
 - [ ] Screenshots added (for bigger UI changes)
+- [ ] Manually tested changed features in running JabRef
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -26,8 +26,11 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 ### Fixed
 - Fixed [#1264](https://github.com/JabRef/jabref/issues/1264): S with caron does not render correctly
 - LaTeX to Unicode converter now handles combining accents
+- Fixed [#636](https://github.com/JabRef/jabref/issues/636): DOI in export filters
 - Fixed [#1527](https://github.com/JabRef/jabref/issues/1527): 'Get BibTeX data from DOI' Removes Marking
 - Fixed [#1592](https://github.com/JabRef/jabref/issues/1592): LibreOffice: wrong numbers in citation labels
+- Fixed [#1321](https://github.com/JabRef/jabref/issues/1321): LaTeX commands in fields not displayed in the list of references
+- Date fields in the BibLatex standard are now always formatted in the correct way, independent of the preferences
 
 ### Removed
 - It is not longer possible to choose to convert HTML sub- and superscripts to equations

diff --git a/medline.gradle b/medline.gradle
@@ -1,18 +1,22 @@
-
 configurations {
- xjc
-} 
+    xjc
+}
 
 dependencies {
- xjc group: 'com.sun.xml.bind', name: 'jaxb-xjc', version: '2.2.4-1'
+    xjc 'com.sun.xml.bind:jaxb-xjc:2.2.4-1'
 }
 
-task xjc () << { 
- ant.taskdef(name: 'xjc', classname: 'com.sun.tools.xjc.XJCTask', classpath: configurations.xjc.asPath)
-
- ant.xjc(destdir: 'src/main/gen/', package: 'net.sf.jabref.importer.fileformat.medline'){
-  schema(dir: 'src/main/resources/xjc/medline', includes: 'medline.xsd')
-  }
+task xjc {
+    inputs.dir "src/main/resources/xjc/medline/"
+    outputs.dir "src/main/gen/net/sf/jabref/importer/fileformat/medline"
+
+    ant.taskdef(name: 'xjc', classname: 'com.sun.tools.xjc.XJCTask', classpath: configurations.xjc.asPath)
+
+    doLast {
+        ant.xjc(destdir: 'src/main/gen/', package: 'net.sf.jabref.importer.fileformat.medline') {
+            schema(dir: 'src/main/resources/xjc/medline', includes: 'medline.xsd')
+        }
+    }
 }
 
-tasks. compileJava.dependsOn xjc
+tasks.compileJava.dependsOn xjc
diff --git a/scripts/upload-to-builds.jabref.org.sh b/scripts/upload-to-builds.jabref.org.sh
@@ -33,4 +33,4 @@ command="${command}exit\n"
 
 # now $command is complete
 
-echo -e "$command" | sftp -P 9922 builds_jabref_org@builds.jabref.org
+echo -e "$command" | sftp -P 9922 builds_jabref_org@build-upload.jabref.org
diff --git a/src/main/java/net/sf/jabref/BibDatabaseContext.java b/src/main/java/net/sf/jabref/BibDatabaseContext.java
@@ -6,14 +6,15 @@
 import java.util.Objects;
 import java.util.Optional;
 
+import net.sf.jabref.logic.layout.format.FileLinkPreferences;
 import net.sf.jabref.model.database.BibDatabase;
 import net.sf.jabref.model.database.BibDatabaseMode;
 import net.sf.jabref.model.database.BibDatabaseModeDetection;
 import net.sf.jabref.model.entry.FieldName;
 import net.sf.jabref.preferences.JabRefPreferences;
 
 /**
- * Represents everything related to a .bib file.
+ * Represents everything related to a BIB file.
  * <p>
  * The entries are stored in BibDatabase, the other data in MetaData and the options relevant for this file in Defaults.
  */
@@ -116,7 +117,7 @@ public boolean isBiblatexMode() {
      * 1. metadata user-specific directory
      * 2. metadata general directory
      * 3. preferences directory
-     * 4. bib file directory
+     * 4. BIB file directory
      *
      * @param fieldName The field type
      * @return The default directory for this field type.
@@ -137,12 +138,12 @@ public List<String> getFileDirectory(String fieldName) {
         }
 
         // 3. preferences directory
-        String dir = Globals.prefs.get(fieldName + Globals.DIR_SUFFIX); // FILE_DIR
+        String dir = Globals.prefs.get(fieldName + FileLinkPreferences.DIR_SUFFIX); // FILE_DIR
         if (dir != null) {
             fileDirs.add(dir);
         }
 
-        // 4. bib file directory
+        // 4. BIB file directory
         if (getDatabaseFile() != null) {
             String parentDir = getDatabaseFile().getParent();
             // Check if we should add it as primary file dir (first in the list) or not:
@@ -159,7 +160,7 @@ public List<String> getFileDirectory(String fieldName) {
     private String getFileDirectoryPath(String directoryName) {
         String dir = directoryName;
         // If this directory is relative, we try to interpret it as relative to
-        // the file path of this bib file:
+        // the file path of this BIB file:
         if (!new File(dir).isAbsolute() && (getDatabaseFile() != null)) {
             String relDir;
             if (".".equals(dir)) {

diff --git a/src/main/java/net/sf/jabref/Globals.java b/src/main/java/net/sf/jabref/Globals.java
@@ -31,30 +31,14 @@
 
 public class Globals {
 
-    public static final String DIR_SUFFIX = "Directory";
-
     // JabRef version info
     public static final BuildInfo BUILD_INFO = new BuildInfo();
-    // Signature written at the top of the .bib file.
-    public static final String SIGNATURE = "This file was created with JabRef";
-    public static final String ENCODING_PREFIX = "Encoding: ";
-    // Character separating field names that are to be used in sequence as
-    // fallbacks for a single column (e.g. "author/editor" to use editor where
-    // author is not set):
-    public static final String COL_DEFINITION_FIELD_SEPARATOR = "/";
-    // Newlines
-    // will be overridden in initialization due to feature #857 @ JabRef.java
-    public static String NEWLINE = System.lineSeparator();
-
     // Remote listener
     public static final RemoteListenerServerLifecycle REMOTE_LISTENER = new RemoteListenerServerLifecycle();
 
     public static final ImportFormatReader IMPORT_FORMAT_READER = new ImportFormatReader();
 
 
-    // Non-letters which are used to denote accents in LaTeX-commands, e.g., in {\"{a}}
-    public static final String SPECIAL_COMMAND_CHARS = "\"`^~'=.|";
-
     // In the main program, this field is initialized in JabRef.java
     // Each test case initializes this field if required
     public static JabRefPreferences prefs;

diff --git a/src/main/java/net/sf/jabref/JabRefMain.java b/src/main/java/net/sf/jabref/JabRefMain.java
@@ -30,6 +30,7 @@
 import net.sf.jabref.logic.net.ProxyRegisterer;
 import net.sf.jabref.logic.remote.RemotePreferences;
 import net.sf.jabref.logic.remote.client.RemoteListenerClient;
+import net.sf.jabref.logic.util.OS;
 import net.sf.jabref.model.entry.InternalBibtexFields;
 import net.sf.jabref.preferences.JabRefPreferences;
 
@@ -92,7 +93,7 @@ private static void start(String[] args) {
 
         // override used newline character with the one stored in the preferences
         // The preferences return the system newline character sequence as default
-        Globals.NEWLINE = Globals.prefs.get(JabRefPreferences.NEWLINE);
+        OS.NEWLINE = Globals.prefs.get(JabRefPreferences.NEWLINE);
 
         // Process arguments
         ArgumentProcessor argumentProcessor = new ArgumentProcessor(args, ArgumentProcessor.Mode.INITIAL_START);

diff --git a/src/main/java/net/sf/jabref/MetaData.java b/src/main/java/net/sf/jabref/MetaData.java
@@ -38,6 +38,8 @@
 import net.sf.jabref.logic.l10n.Localization;
 import net.sf.jabref.logic.labelpattern.AbstractLabelPattern;
 import net.sf.jabref.logic.labelpattern.DatabaseLabelPattern;
+import net.sf.jabref.logic.layout.format.FileLinkPreferences;
+import net.sf.jabref.logic.util.OS;
 import net.sf.jabref.logic.util.strings.StringUtil;
 import net.sf.jabref.model.database.BibDatabaseMode;
 import net.sf.jabref.model.entry.FieldName;
@@ -58,7 +60,7 @@ public class MetaData implements Iterable<String> {
     private static final String DATABASE_TYPE = "databaseType";
 
     private static final String GROUPSTREE = "groupstree";
-    private static final String FILE_DIRECTORY = FieldName.FILE + Globals.DIR_SUFFIX;
+    private static final String FILE_DIRECTORY = FieldName.FILE + FileLinkPreferences.DIR_SUFFIX;
     public static final String SELECTOR_META_PREFIX = "selector_";
     private static final String PROTECTED_FLAG_META = "protectedFlag";
 
@@ -364,7 +366,7 @@ public Map<String, String> getAsStringMap() {
 
                 //in case of save actions, add an additional newline after the enabled flag
                 if (metaItem.getKey().equals(SAVE_ACTIONS) && ("enabled".equals(dataItem) || "disabled".equals(dataItem))) {
-                    stringBuilder.append(Globals.NEWLINE);
+                    stringBuilder.append(OS.NEWLINE);
                 }
             }
 
@@ -379,12 +381,12 @@ public Map<String, String> getAsStringMap() {
         // (which is always the AllEntriesGroup).
         if ((groupsRoot != null) && (groupsRoot.getNumberOfChildren() > 0)) {
             StringBuilder stringBuilder = new StringBuilder();
-            stringBuilder.append(Globals.NEWLINE);
+            stringBuilder.append(OS.NEWLINE);
 
             for (String groupNode : groupsRoot.getTreeAsString()) {
                 stringBuilder.append(StringUtil.quote(groupNode, ";", '\\'));
                 stringBuilder.append(";");
-                stringBuilder.append(Globals.NEWLINE);
+                stringBuilder.append(OS.NEWLINE);
             }
             serializedMetaData.put(GROUPSTREE, stringBuilder.toString());
         }

diff --git a/src/main/java/net/sf/jabref/cli/ArgumentProcessor.java b/src/main/java/net/sf/jabref/cli/ArgumentProcessor.java
@@ -232,7 +232,7 @@ private List<ParserResult> importAndOpenFiles() {
         if (!cli.isBlank() && (cli.getLeftOver().length > 0)) {
             for (String aLeftOver : cli.getLeftOver()) {
                 // Leftover arguments that have a "bib" extension are interpreted as
-                // bib files to open. Other files, and files that could not be opened
+                // BIB files to open. Other files, and files that could not be opened
                 // as bib, we try to import instead.
                 boolean bibExtension = aLeftOver.toLowerCase(Locale.ENGLISH).endsWith("bib");
                 ParserResult pr = null;
@@ -294,7 +294,7 @@ private boolean generateAux(List<ParserResult> loaded, String[] data) {
                     SaveSession session = databaseWriter.saveDatabase(new BibDatabaseContext(newBase, defaults),
                             prefs);
 
-                    // Show just a warning message if encoding didn't work for all characters:
+                    // Show just a warning message if encoding did not work for all characters:
                     if (!session.getWriter().couldEncodeAll()) {
                         System.err.println(Localization.lang("Warning") + ": "
                                 + Localization.lang(
@@ -336,7 +336,7 @@ private void exportFile(List<ParserResult> loaded, String[] data) {
                         SaveSession session = databaseWriter.saveDatabase(
                                 new BibDatabaseContext(pr.getDatabase(), pr.getMetaData(), defaults), prefs);
 
-                        // Show just a warning message if encoding didn't work for all characters:
+                        // Show just a warning message if encoding did not work for all characters:
                         if (!session.getWriter().couldEncodeAll()) {
                             System.err.println(Localization.lang("Warning") + ": "
                                     + Localization.lang(
@@ -438,7 +438,7 @@ private void regenerateBibtexKeys(List<ParserResult> loaded) {
                     LabelPatternUtil.makeLabel(metaData, database, entry, Globals.prefs);
                 }
             } else {
-                LOGGER.info(Localization.lang("No meta data present in bibfile. Cannot regenerate BibTeX keys"));
+                LOGGER.info(Localization.lang("No meta data present in BIB_file. Cannot regenerate BibTeX keys"));
             }
         }
     }
@@ -483,7 +483,7 @@ private Optional<ParserResult> fetch(String fetchCommand) {
         }
 
         String query = split[1];
-        System.out.println(Localization.lang("Running Query '%0' with fetcher '%1'.", query, engine) + " "
+        System.out.println(Localization.lang("Running query '%0' with fetcher '%1'.", query, engine) + " "
                 + Localization.lang("Please wait..."));
         Collection<BibEntry> result = new ImportInspectionCommandLine().query(query, fetcher);
 

diff --git a/src/main/java/net/sf/jabref/cli/JabRefCLI.java b/src/main/java/net/sf/jabref/cli/JabRefCLI.java
@@ -198,7 +198,7 @@ private Options getOptions() {
 
         options.addOption(Option.builder("a").
                 longOpt("aux").
-                desc(String.format("%s: %s[.aux],%s[.bib]", Localization.lang("Subdatabase from aux"),
+                desc(String.format("%s: %s[.aux],%s[.bib]", Localization.lang("Subdatabase from AUX"),
                         Localization.lang("file"),
                         Localization.lang("new"))).
                 hasArg().
@@ -214,7 +214,7 @@ private Options getOptions() {
 
         options.addOption(Option.builder("f").
                 longOpt("fetch").
-                desc(Localization.lang("Run Fetcher, e.g. \"--fetch=Medline:cancer\"")).
+                desc(Localization.lang("Run fetcher, e.g. \"--fetch=Medline:cancer\"")).
                 hasArg().
                 argName("FILE").
                 build());

diff --git a/src/main/java/net/sf/jabref/external/AutoSetLinks.java b/src/main/java/net/sf/jabref/external/AutoSetLinks.java
@@ -40,7 +40,7 @@ public class AutoSetLinks {
      * @param entries  the entries for which links should be set
      * @param databaseContext the database for which links are set
      */
-    public static void autoSetLinks(Collection<BibEntry> entries, BibDatabaseContext databaseContext) {
+    public static void autoSetLinks(List<BibEntry> entries, BibDatabaseContext databaseContext) {
         autoSetLinks(entries, null, null, null, databaseContext, null, null);
     }
 
@@ -69,7 +69,9 @@ public static void autoSetLinks(Collection<BibEntry> entries, BibDatabaseContext
      *                         parameter can be null, which means that no progress update will be shown.
      * @return the thread performing the automatically setting
      */
-    public static Runnable autoSetLinks(final Collection<BibEntry> entries, final NamedCompound ce, final Set<BibEntry> changedEntries, final FileListTableModel singleTableModel, final BibDatabaseContext databaseContext, final ActionListener callback, final JDialog diag) {
+    public static Runnable autoSetLinks(final List<BibEntry> entries, final NamedCompound ce,
+            final Set<BibEntry> changedEntries, final FileListTableModel singleTableModel,
+            final BibDatabaseContext databaseContext, final ActionListener callback, final JDialog diag) {
         final Collection<ExternalFileType> types = ExternalFileTypes.getInstance().getExternalFileTypeSelection();
         if (diag != null) {
             final JProgressBar prog = new JProgressBar(JProgressBar.HORIZONTAL, 0, types.size() - 1);
@@ -94,7 +96,7 @@ public void run() {
                 dirs.addAll(dirsS.stream().map(File::new).collect(Collectors.toList()));
 
                 // determine extensions
-                Collection<String> extensions = new ArrayList<>();
+                List<String> extensions = new ArrayList<>();
                 for (final ExternalFileType type : types) {
                     extensions.add(type.getExtension());
                 }
@@ -105,7 +107,8 @@ public void run() {
                     String regExp = Globals.prefs.get(JabRefPreferences.REG_EXP_SEARCH_EXPRESSION_KEY);
                     result = RegExpFileSearch.findFilesForSet(entries, extensions, dirs, regExp);
                 } else {
-                    result = FileUtil.findAssociatedFiles(entries, extensions, dirs, Globals.prefs);
+                    boolean autoLinkExactKeyOnly = Globals.prefs.getBoolean(JabRefPreferences.AUTOLINK_EXACT_KEY_ONLY);
+                    result = FileUtil.findAssociatedFiles(entries, extensions, dirs, autoLinkExactKeyOnly);
                 }
 
                 boolean foundAny = false;
@@ -210,7 +213,8 @@ public void run() {
      *                         parameter can be null, which means that no progress update will be shown.
      * @return the runnable able to perform the automatically setting
      */
-    public static Runnable autoSetLinks(final BibEntry entry, final FileListTableModel singleTableModel, final BibDatabaseContext databaseContext, final ActionListener callback, final JDialog diag) {
+    public static Runnable autoSetLinks(final BibEntry entry, final FileListTableModel singleTableModel,
+            final BibDatabaseContext databaseContext, final ActionListener callback, final JDialog diag) {
         return autoSetLinks(Collections.singletonList(entry), null, null, singleTableModel, databaseContext, callback,
                 diag);
     }

diff --git a/src/main/java/net/sf/jabref/external/DownloadExternalFile.java b/src/main/java/net/sf/jabref/external/DownloadExternalFile.java
@@ -151,7 +151,7 @@ public void download(URL url, final DownloadCallback callback) throws IOExceptio
         if (suggestedType.isPresent()) {
             suffix = suggestedType.get().getExtension();
         } else {
-            // If we didn't find a file type from the MIME type, try based on extension:
+            // If we did not find a file type from the MIME type, try based on extension:
             suffix = getSuffix(res);
             if (suffix == null) {
                 suffix = "";
@@ -200,10 +200,10 @@ public void download(URL url, final DownloadCallback callback) throws IOExceptio
             if (directory == null) {
                 dirPrefix = null;
             } else {
-                if (directory.endsWith(System.getProperty("file.separator"))) {
+                if (directory.endsWith(OS.FILE_SEPARATOR)) {
                     dirPrefix = directory;
                 } else {
-                    dirPrefix = directory + System.getProperty("file.separator");
+                    dirPrefix = directory + OS.FILE_SEPARATOR;
                 }
             }
 
@@ -249,7 +249,7 @@ public void download(URL url, final DownloadCallback callback) throws IOExceptio
     private File expandFilename(String directory, String link) {
         File toFile = new File(link);
         // If this is a relative link, we should perhaps append the directory:
-        String dirPrefix = directory + System.getProperty("file.separator");
+        String dirPrefix = directory + OS.FILE_SEPARATOR;
         if (!toFile.isAbsolute()) {
             toFile = new File(dirPrefix + link);
         }

diff --git a/src/main/java/net/sf/jabref/external/DroppedFileHandler.java b/src/main/java/net/sf/jabref/external/DroppedFileHandler.java
@@ -40,6 +40,7 @@
 import net.sf.jabref.gui.undo.UndoableFieldChange;
 import net.sf.jabref.gui.undo.UndoableInsertEntry;
 import net.sf.jabref.logic.l10n.Localization;
+import net.sf.jabref.logic.util.OS;
 import net.sf.jabref.logic.util.io.FileUtil;
 import net.sf.jabref.logic.xmp.XMPUtil;
 import net.sf.jabref.model.database.BibDatabase;
@@ -478,7 +479,7 @@ private boolean doMove(String fileName, String destFilename,
             LOGGER.warn("Cannot determine destination directory or destination directory does not exist");
             return false;
         }
-        File toFile = new File(dirs.get(found) + System.getProperty("file.separator") + destFilename);
+        File toFile = new File(dirs.get(found) + OS.FILE_SEPARATOR + destFilename);
         if (toFile.exists()) {
             int answer = JOptionPane.showConfirmDialog(frame,
                     Localization.lang("'%0' exists. Overwrite file?", toFile.getAbsolutePath()),
@@ -530,7 +531,7 @@ private boolean doCopy(String fileName, String toFile, NamedCompound edits) {
         }
         String destinationFileName = new File(toFile).getName();
 
-        File destFile = new File(dirs.get(found) + System.getProperty("file.separator") + destinationFileName);
+        File destFile = new File(dirs.get(found) + OS.FILE_SEPARATOR + destinationFileName);
         if (destFile.equals(new File(fileName))) {
             // File is already in the correct position. Don't override!
             return true;

diff --git a/src/main/java/net/sf/jabref/external/ExternalFileTypes.java b/src/main/java/net/sf/jabref/external/ExternalFileTypes.java
@@ -1,7 +1,6 @@
 package net.sf.jabref.external;
 
 import java.util.ArrayList;
-import java.util.Collection;
 import java.util.List;
 import java.util.Optional;
 import java.util.Set;
@@ -104,7 +103,7 @@ public static List<ExternalFileType> getDefaultExternalFileTypes() {
         return list;
     }
 
-    public Collection<ExternalFileType> getExternalFileTypeSelection() {
+    public Set<ExternalFileType> getExternalFileTypeSelection() {
         return externalFileTypes;
     }
Original file line number	Diff line number	Diff line change
Expand Up		@@ -33,4 +33,4 @@ command="${command}exit\n"

		# now $command is complete

		echo -e "$command" \| sftp -P 9922 builds_jabref_org@builds.jabref.org
		echo -e "$command" \| sftp -P 9922 builds_jabref_org@build-upload.jabref.org