From ea5d56e4a7a8bcb25c2bb00dc3651c807bc9739e Mon Sep 17 00:00:00 2001
From: Stefan <st155160@stud.uni-stuttgart.de>
Date: Sun, 18 Feb 2018 04:48:56 +0100
Subject: [PATCH 01/40] Fixed unicode string

---
 scripts/syncLang.py | 55 ++++++++++++++++++++++++++++++++++++++++-----
 1 file changed, 50 insertions(+), 5 deletions(-)

diff --git a/scripts/syncLang.py b/scripts/syncLang.py
index 150d1bbc662..a0359f18bc8 100644
--- a/scripts/syncLang.py
+++ b/scripts/syncLang.py
@@ -14,7 +14,47 @@
 URL_BASE = "https://github.com/JabRef/jabref/tree/master/src/main/resources/l10n/"
 
 
+try:
+    # Just to make sure not to break anything, in case py3.x is not supported.
+    import pathlib
+    
+    class PathFinder:
+        """
+        This class is designed to automatically locate this script's path within the repository.
+        Once it found it's location it can easily provide paths to other important directories and files.
+        
+        requires Python 3.4 or higher
+        """
+        
+        
+        @staticmethod
+        def getScriptLocation():
+            """
+            :return the path this script is currently located as pathlib.Path object.
+            """
+            return pathlib.Path(__file__)
+        
+        @staticmethod
+        def getJabRefMainDirectory():
+            """
+            Searches the script's path backwards until it finds the matching base directory.
+            :return the path to JabRef's base directory as pathlib.Path object.
+            """
+            scriptLocation = PathFinder.getScriptLocation()
+            for parent in scriptLocation.parents:
+                if parent.name == 'jabref':
+                    return parent
+    
+    # Important paths of the JabRef repository
+    JABREF_BASE_DIRECTORY = PathFinder.getJabRefMainDirectory()
+    JABREF_SOURCE_DIRECTORY = JABREF_BASE_DIRECTORY / 'src'
+    JABREF_SCRIPTS_DIRECTORY = JABREF_BASE_DIRECTORY / 'scripts'
+    JABREF_LOCALIZATION_DIRECTORY = JABREF_SOURCE_DIRECTORY / 'main/resources/l10n'
+except:
+    logging.info("Unable to use PathFinder class.")
+    
 class Git:
+
     def get_current_branch(self):
         """
         :return: the current git branch
@@ -36,6 +76,7 @@ def __call_command(self, command):
 
 
 class Keys:
+
     def __init__(self, lines):
         self.lines = lines
 
@@ -50,7 +91,7 @@ def duplicates(self):
             if key:
                 if key in keys_checked:
                     duplicates.append(u"{key}={value}".format(key=key, value=value))
-                    translation_in_list = "u{key}={value}".format(key=key, value=keys_checked[key])
+                    translation_in_list = u"{key}={value}".format(key=key, value=keys_checked[key])
                     if translation_in_list not in duplicates:
                         duplicates.append(translation_in_list)
                 else:
@@ -152,6 +193,7 @@ def __extract_key_and_value(line):
 
 
 class SyncLang:
+
     def __init__(self, extended, out_file='status.md'):
         """
         :param extended: boolean: if the keys with problems should be printed
@@ -258,7 +300,7 @@ def __all_jabref_properties(self):
         :return: list of strings: all the JabRef_*.preferences files with the english at the beginning
         """
         jabref_property_files = sorted(self.__other_jabref_properties())
-        jabref_property_files.insert(0, os.path.join(RES_DIR, "JabRef_en.properties"))
+        jabref_property_files.insert(0, self.main_jabref_preferences)
         return jabref_property_files
 
     def __other_jabref_properties(self):
@@ -315,7 +357,7 @@ def __update_properties(self, main_property_file, other_property_files):
                 key = main_keys.key_from_line(line)
                 if key is not None:
                     # Do not write empty keys
-                    if keys[key] !=  "":
+                    if keys[key] != "":
                         other_lines_to_write.append(u"{key}={value}\n".format(key=key, value=keys[key]))
                 else:
                     other_lines_to_write.append(line)
@@ -433,8 +475,7 @@ def _percentage(whole, part):
         logging.info('Current status written to ' + self.markdown_output)
 
 
-if '__main__' == __name__:
-
+def main():
     if len(sys.argv) == 2 and sys.argv[1] == "markdown":
         SyncLang(extended=False, out_file='status.md').status_create_markdown()
 
@@ -464,3 +505,7 @@ def _percentage(whole, part):
             [-e | --extended]:
                 if the translations keys which create problems should be printed
     """)
+
+
+if '__main__' == __name__:
+    main()

From ba7d87d2415c54992952b89cdc4673194a5ee929 Mon Sep 17 00:00:00 2001
From: Stefan <st155160@stud.uni-stuttgart.de>
Date: Sun, 18 Feb 2018 05:55:53 +0100
Subject: [PATCH 02/40] Fixed logical issue within merging process

---
 scripts/syncLang.py | 16 +++++++++-------
 1 file changed, 9 insertions(+), 7 deletions(-)

diff --git a/scripts/syncLang.py b/scripts/syncLang.py
index a0359f18bc8..33305f9c01b 100644
--- a/scripts/syncLang.py
+++ b/scripts/syncLang.py
@@ -111,15 +111,15 @@ def fix_duplicates(self):
             if key:
                 if key in keys:
                     if not keys[key]:
-                        fixed.append("{key}={value}".format(key=key, value=keys[key]))
+                        fixed.append(u"{key}={value}".format(key=key, value=keys[key]))
                         keys[key] = value
                     elif not value:
-                        fixed.append("{key}={value}".format(key=key, value=value))
+                        fixed.append(u"{key}={value}".format(key=key, value=value))
                     elif keys[key] == value:
-                        fixed.append("{key}={value}".format(key=key, value=value))
+                        fixed.append(u"{key}={value}".format(key=key, value=value))
                     elif keys[key] != value:
-                        not_fixed.append("{key}={value}".format(key=key, value=value))
-                        not_fixed.append("{key}={value}".format(key=key, value=keys[key]))
+                        not_fixed.append(u"{key}={value}".format(key=key, value=value))
+                        not_fixed.append(u"{key}={value}".format(key=key, value=keys[key]))
                 else:
                     keys[key] = value
 
@@ -347,9 +347,11 @@ def __update_properties(self, main_property_file, other_property_files):
             num_keys_obsolete = len(keys_obsolete)
 
             for missing_key in keys_missing:
+                logging.debug("Adding missing Key: " + missing_key)
                 keys[missing_key] = ""
 
             for obsolete_key in keys_obsolete:
+                logging.debug("Deleting obsolete Key: " + obsolete_key)
                 del keys[obsolete_key]
 
             other_lines_to_write = []
@@ -357,8 +359,8 @@ def __update_properties(self, main_property_file, other_property_files):
                 key = main_keys.key_from_line(line)
                 if key is not None:
                     # Do not write empty keys
-                    if keys[key] != "":
-                        other_lines_to_write.append(u"{key}={value}\n".format(key=key, value=keys[key]))
+                    #if keys[key] != "":
+                    other_lines_to_write.append(u"{key}={value}\n".format(key=key, value=keys[key]))
                 else:
                     other_lines_to_write.append(line)
 

From 254449fea3e712ece044322c7a73adc547014cba Mon Sep 17 00:00:00 2001
From: Stefan <st155160@stud.uni-stuttgart.de>
Date: Sun, 18 Feb 2018 13:22:44 +0100
Subject: [PATCH 03/40] Added format_key_and_value method

---
 scripts/syncLang.py | 25 ++++++++++++++-----------
 1 file changed, 14 insertions(+), 11 deletions(-)

diff --git a/scripts/syncLang.py b/scripts/syncLang.py
index 33305f9c01b..11c870460e8 100644
--- a/scripts/syncLang.py
+++ b/scripts/syncLang.py
@@ -13,7 +13,6 @@
 RES_DIR = "src/main/resources/l10n"
 URL_BASE = "https://github.com/JabRef/jabref/tree/master/src/main/resources/l10n/"
 
-
 try:
     # Just to make sure not to break anything, in case py3.x is not supported.
     import pathlib
@@ -26,7 +25,6 @@ class PathFinder:
         requires Python 3.4 or higher
         """
         
-        
         @staticmethod
         def getScriptLocation():
             """
@@ -52,6 +50,7 @@ def getJabRefMainDirectory():
     JABREF_LOCALIZATION_DIRECTORY = JABREF_SOURCE_DIRECTORY / 'main/resources/l10n'
 except:
     logging.info("Unable to use PathFinder class.")
+
     
 class Git:
 
@@ -90,8 +89,8 @@ def duplicates(self):
             key, value = self.__extract_key_and_value(line=line)
             if key:
                 if key in keys_checked:
-                    duplicates.append(u"{key}={value}".format(key=key, value=value))
-                    translation_in_list = u"{key}={value}".format(key=key, value=keys_checked[key])
+                    duplicates.append(self.format_key_and_value(key=key, value=value))
+                    translation_in_list = self.format_key_and_value(key=key, value=keys_checked[key])
                     if translation_in_list not in duplicates:
                         duplicates.append(translation_in_list)
                 else:
@@ -111,15 +110,15 @@ def fix_duplicates(self):
             if key:
                 if key in keys:
                     if not keys[key]:
-                        fixed.append(u"{key}={value}".format(key=key, value=keys[key]))
+                        fixed.append(self.format_key_and_value(key=key, value=keys[key]))
                         keys[key] = value
                     elif not value:
-                        fixed.append(u"{key}={value}".format(key=key, value=value))
+                        fixed.append(self.format_key_and_value(key=key, value=value))
                     elif keys[key] == value:
-                        fixed.append(u"{key}={value}".format(key=key, value=value))
+                        fixed.append(self.format_key_and_value(key=key, value=value))
                     elif keys[key] != value:
-                        not_fixed.append(u"{key}={value}".format(key=key, value=value))
-                        not_fixed.append(u"{key}={value}".format(key=key, value=keys[key]))
+                        not_fixed.append(self.format_key_and_value(key=key, value=value))
+                        not_fixed.append(self.format_key_and_value(key=key, value=keys[key]))
                 else:
                     keys[key] = value
 
@@ -190,6 +189,10 @@ def __extract_key_and_value(line):
             if index_key_end > 0:
                 return line[0:index_key_end].strip(), line[index_key_end + 1:].strip()
         return None, None
+    
+    @staticmethod
+    def format_key_and_value(key, value):
+        return u"{key}={value}".format(key=key, value=value)
 
 
 class SyncLang:
@@ -359,8 +362,8 @@ def __update_properties(self, main_property_file, other_property_files):
                 key = main_keys.key_from_line(line)
                 if key is not None:
                     # Do not write empty keys
-                    #if keys[key] != "":
-                    other_lines_to_write.append(u"{key}={value}\n".format(key=key, value=keys[key]))
+                    # if keys[key] != "":
+                    other_lines_to_write.append(Keys.format_key_and_value(key=key, value=keys[key]))
                 else:
                     other_lines_to_write.append(line)
 

From b00bfdd6ce8b3373fa58f6757edee04f79426fe0 Mon Sep 17 00:00:00 2001
From: Stefan <st155160@stud.uni-stuttgart.de>
Date: Sun, 18 Feb 2018 13:40:13 +0100
Subject: [PATCH 04/40] Added new line for new properties

---
 scripts/syncLang.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/syncLang.py b/scripts/syncLang.py
index 11c870460e8..c9fa5dc70d6 100644
--- a/scripts/syncLang.py
+++ b/scripts/syncLang.py
@@ -363,7 +363,7 @@ def __update_properties(self, main_property_file, other_property_files):
                 if key is not None:
                     # Do not write empty keys
                     # if keys[key] != "":
-                    other_lines_to_write.append(Keys.format_key_and_value(key=key, value=keys[key]))
+                    other_lines_to_write.append(Keys.format_key_and_value(key=key, value=keys[key]) + "\n")
                 else:
                     other_lines_to_write.append(line)
 

From 7a7f33f27a6e38737869b5756df1dfa4d8f26ee3 Mon Sep 17 00:00:00 2001
From: Stefan <st155160@stud.uni-stuttgart.de>
Date: Sun, 18 Feb 2018 15:40:47 +0100
Subject: [PATCH 05/40] Renamed method and moved Path variables into PathFinder
 class

---
 scripts/syncLang.py | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/scripts/syncLang.py b/scripts/syncLang.py
index c9fa5dc70d6..52a5fdf062f 100644
--- a/scripts/syncLang.py
+++ b/scripts/syncLang.py
@@ -33,7 +33,7 @@ def getScriptLocation():
             return pathlib.Path(__file__)
         
         @staticmethod
-        def getJabRefMainDirectory():
+        def getJabRefBaseDirectory():
             """
             Searches the script's path backwards until it finds the matching base directory.
             :return the path to JabRef's base directory as pathlib.Path object.
@@ -43,11 +43,11 @@ def getJabRefMainDirectory():
                 if parent.name == 'jabref':
                     return parent
     
-    # Important paths of the JabRef repository
-    JABREF_BASE_DIRECTORY = PathFinder.getJabRefMainDirectory()
-    JABREF_SOURCE_DIRECTORY = JABREF_BASE_DIRECTORY / 'src'
-    JABREF_SCRIPTS_DIRECTORY = JABREF_BASE_DIRECTORY / 'scripts'
-    JABREF_LOCALIZATION_DIRECTORY = JABREF_SOURCE_DIRECTORY / 'main/resources/l10n'
+        # Important paths of the JabRef repository
+        JABREF_BASE_DIRECTORY = self.getJabRefBaseDirectory()
+        JABREF_SOURCE_DIRECTORY = JABREF_BASE_DIRECTORY / 'src'
+        JABREF_SCRIPTS_DIRECTORY = JABREF_BASE_DIRECTORY / 'scripts'
+        JABREF_LOCALIZATION_DIRECTORY = JABREF_SOURCE_DIRECTORY / 'main/resources/l10n'
 except:
     logging.info("Unable to use PathFinder class.")
 

From 759ea5d4436ac3fb3321453a2aaca97630dc5cf0 Mon Sep 17 00:00:00 2001
From: Stefan <st155160@stud.uni-stuttgart.de>
Date: Mon, 19 Feb 2018 12:44:27 +0100
Subject: [PATCH 06/40] Removed empty line, except statement is now catching
 ImportErrors

---
 scripts/syncLang.py | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/scripts/syncLang.py b/scripts/syncLang.py
index 52a5fdf062f..817dcfbed08 100644
--- a/scripts/syncLang.py
+++ b/scripts/syncLang.py
@@ -16,7 +16,6 @@
 try:
     # Just to make sure not to break anything, in case py3.x is not supported.
     import pathlib
-    
     class PathFinder:
         """
         This class is designed to automatically locate this script's path within the repository.
@@ -48,7 +47,7 @@ def getJabRefBaseDirectory():
         JABREF_SOURCE_DIRECTORY = JABREF_BASE_DIRECTORY / 'src'
         JABREF_SCRIPTS_DIRECTORY = JABREF_BASE_DIRECTORY / 'scripts'
         JABREF_LOCALIZATION_DIRECTORY = JABREF_SOURCE_DIRECTORY / 'main/resources/l10n'
-except:
+except ImportError:
     logging.info("Unable to use PathFinder class.")
 
     

From f5752453b825c1fe4763130c736c469fcb33fa31 Mon Sep 17 00:00:00 2001
From: Stefan <st155160@stud.uni-stuttgart.de>
Date: Mon, 19 Feb 2018 22:15:55 +0100
Subject: [PATCH 07/40] Ignoring empty keys again, new keys are added in
 english by default.

---
 scripts/syncLang.py | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/scripts/syncLang.py b/scripts/syncLang.py
index 817dcfbed08..fb612e494a9 100644
--- a/scripts/syncLang.py
+++ b/scripts/syncLang.py
@@ -315,6 +315,7 @@ def __other_jabref_properties(self):
     def __update_properties(self, main_property_file, other_property_files):
         main_lines = self.__read_file_as_lines(filename=main_property_file)
         main_keys = Keys(main_lines)
+        main_keys_dict = main_keys.translations_as_dict()
 
         main_duplicates = main_keys.duplicates()
         num_main_duplicates = len(main_duplicates)
@@ -350,7 +351,8 @@ def __update_properties(self, main_property_file, other_property_files):
 
             for missing_key in keys_missing:
                 logging.debug("Adding missing Key: " + missing_key)
-                keys[missing_key] = ""
+                # Missing keys are added with english translation by default.
+                keys[missing_key] = main_keys_dict[missing_key]
 
             for obsolete_key in keys_obsolete:
                 logging.debug("Deleting obsolete Key: " + obsolete_key)
@@ -361,8 +363,8 @@ def __update_properties(self, main_property_file, other_property_files):
                 key = main_keys.key_from_line(line)
                 if key is not None:
                     # Do not write empty keys
-                    # if keys[key] != "":
-                    other_lines_to_write.append(Keys.format_key_and_value(key=key, value=keys[key]) + "\n")
+                    if keys[key] != "":
+                        other_lines_to_write.append(Keys.format_key_and_value(key=key, value=keys[key]) + "\n")
                 else:
                     other_lines_to_write.append(line)
 

From 19edb0fb0bf68745f4d37a7d546e61ee54645fc7 Mon Sep 17 00:00:00 2001
From: Stefan <st155160@stud.uni-stuttgart.de>
Date: Mon, 19 Feb 2018 22:19:46 +0100
Subject: [PATCH 08/40] Removed debug messages

---
 scripts/syncLang.py | 2 --
 1 file changed, 2 deletions(-)

diff --git a/scripts/syncLang.py b/scripts/syncLang.py
index fb612e494a9..a4903490d5d 100644
--- a/scripts/syncLang.py
+++ b/scripts/syncLang.py
@@ -350,12 +350,10 @@ def __update_properties(self, main_property_file, other_property_files):
             num_keys_obsolete = len(keys_obsolete)
 
             for missing_key in keys_missing:
-                logging.debug("Adding missing Key: " + missing_key)
                 # Missing keys are added with english translation by default.
                 keys[missing_key] = main_keys_dict[missing_key]
 
             for obsolete_key in keys_obsolete:
-                logging.debug("Deleting obsolete Key: " + obsolete_key)
                 del keys[obsolete_key]
 
             other_lines_to_write = []

From 011501dde1559b92cc82262612719741b56ddc00 Mon Sep 17 00:00:00 2001
From: Stefan <st155160@stud.uni-stuttgart.de>
Date: Mon, 19 Feb 2018 22:35:36 +0100
Subject: [PATCH 09/40] Had to kick out the Path variables of the class again.
 :/

---
 scripts/syncLang.py | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/scripts/syncLang.py b/scripts/syncLang.py
index a4903490d5d..3f303c4ca34 100644
--- a/scripts/syncLang.py
+++ b/scripts/syncLang.py
@@ -42,11 +42,11 @@ def getJabRefBaseDirectory():
                 if parent.name == 'jabref':
                     return parent
     
-        # Important paths of the JabRef repository
-        JABREF_BASE_DIRECTORY = self.getJabRefBaseDirectory()
-        JABREF_SOURCE_DIRECTORY = JABREF_BASE_DIRECTORY / 'src'
-        JABREF_SCRIPTS_DIRECTORY = JABREF_BASE_DIRECTORY / 'scripts'
-        JABREF_LOCALIZATION_DIRECTORY = JABREF_SOURCE_DIRECTORY / 'main/resources/l10n'
+    # Important paths, files and directories of the JabRef repository
+    JABREF_BASE_DIRECTORY = PathFinder.getJabRefBaseDirectory()
+    JABREF_SOURCE_DIRECTORY = JABREF_BASE_DIRECTORY / 'src'
+    JABREF_SCRIPTS_DIRECTORY = JABREF_BASE_DIRECTORY / 'scripts'
+    JABREF_LOCALIZATION_DIRECTORY = JABREF_SOURCE_DIRECTORY / 'main/resources/l10n'
 except ImportError:
     logging.info("Unable to use PathFinder class.")
 

From e864d2cdca6e8fe867ee695d3ccb427d4fd5c691 Mon Sep 17 00:00:00 2001
From: Stefan <st155160@stud.uni-stuttgart.de>
Date: Tue, 20 Feb 2018 01:59:38 +0100
Subject: [PATCH 10/40] Improved method names

---
 scripts/syncLang.py | 33 +++++++++++++++------------------
 1 file changed, 15 insertions(+), 18 deletions(-)

diff --git a/scripts/syncLang.py b/scripts/syncLang.py
index 3f303c4ca34..adbc7f7f616 100644
--- a/scripts/syncLang.py
+++ b/scripts/syncLang.py
@@ -78,7 +78,7 @@ class Keys:
     def __init__(self, lines):
         self.lines = lines
 
-    def duplicates(self):
+    def find_duplicates(self):
         """
         return: list of unicode strings
         """
@@ -220,7 +220,7 @@ def __print_status_menu_properties(self):
     def __print_status_jabref_properties(self):
         self.__check_properties(main_property_file=self.main_jabref_preferences, property_files=self.__all_jabref_properties())
 
-    def update(self):
+    def update_properties(self):
         """
         updates all the localization files
         fixing unambiguous duplicates, removing obsolete keys, adding missing keys, and sorting them
@@ -236,19 +236,19 @@ def __update_jabref_properties(self):
         self.__update_properties(main_property_file=self.main_jabref_preferences, other_property_files=self.__other_jabref_properties())
 
     def __check_properties(self, main_property_file, property_files):
-        main_lines = self.__read_file_as_lines(filename=main_property_file)
+        main_lines = self.__read_lines_from_file(filename=main_property_file)
         main_keys = Keys(main_lines)
 
         # the main property file gets compared to itself, but that is OK
         for file in property_files:
             filename = self.__format_filename(filepath=file)
-            lines = self.__read_file_as_lines(file)
+            lines = self.__read_lines_from_file(file)
             keys1 = Keys(main_lines)
             keys = keys1.keys_from_lines()
 
             keys_missing = self.__missing_keys(main_keys.keys_from_lines(), keys)
             keys_obsolete = self.__missing_keys(keys, main_keys.keys_from_lines())
-            keys_duplicate = Keys(lines).duplicates()
+            keys_duplicate = Keys(lines).find_duplicates()
             keys_not_translated = Keys(lines=lines).empty_keys()
 
             num_keys = len(keys)
@@ -313,11 +313,11 @@ def __other_jabref_properties(self):
         return [os.path.join(RES_DIR, file) for file in jabref_property_files]
 
     def __update_properties(self, main_property_file, other_property_files):
-        main_lines = self.__read_file_as_lines(filename=main_property_file)
+        main_lines = self.__read_lines_from_file(filename=main_property_file)
         main_keys = Keys(main_lines)
         main_keys_dict = main_keys.translations_as_dict()
 
-        main_duplicates = main_keys.duplicates()
+        main_duplicates = main_keys.find_duplicates()
         num_main_duplicates = len(main_duplicates)
         if num_main_duplicates != 0:
             logging.error("There are {num_duplicates} duplicates in {file}, please fix them manually".format(num_duplicates=num_main_duplicates,
@@ -329,7 +329,7 @@ def __update_properties(self, main_property_file, other_property_files):
 
         for other_property_file in other_property_files:
             filename = self.__format_filename(filepath=other_property_file)
-            lines = self.__read_file_as_lines(filename=other_property_file)
+            lines = self.__read_lines_from_file(filename=other_property_file)
             keys, not_fixed, fixed = Keys(lines).fix_duplicates()
 
             num_keys = len(keys)
@@ -408,13 +408,13 @@ def __write_file(filename, content):
         """
         writes the lines to the file in `UTF-8`
         :param filename: string
-        :param content: list of unicode unicode: the lines to write
+        :param content: list of unicode strings: the lines to write
         """
         with codecs.open(filename, 'w', encoding="UTF-8") as f:
             f.writelines(content)
 
     @staticmethod
-    def __read_file_as_lines(filename):
+    def __read_lines_from_file(filename):
         """
         :param filename: string
         :param encoding: string: the encoding of the file to read (standard: `UTF-8`)
@@ -423,7 +423,8 @@ def __read_file_as_lines(filename):
         with codecs.open(filename, 'r', encoding="UTF-8") as file:
             return [u"{}\n".format(line.strip()) for line in file.readlines()]
 
-    def __missing_keys(self, first_list, second_list):
+    @staticmethod
+    def __missing_keys(first_list, second_list):
         """
         Finds all keys in the first list that are not present in the second list
 
@@ -431,11 +432,7 @@ def __missing_keys(self, first_list, second_list):
         :param second_list: list of unicode strings
         :return: list of unicode strings
         """
-        missing = []
-        for key in first_list:
-            if key not in second_list:
-                missing.append(key)
-        return missing
+        return list(set(first_list).difference(second_list))
 
     def status_create_markdown(self):
         """
@@ -447,7 +444,7 @@ def _write_properties(output_file, property_files):
             output_file.write("| ------------- | ---- | --------------- | ------------------- | ------------ |\n")
 
             for file in property_files:
-                lines = self.__read_file_as_lines(file)
+                lines = self.__read_lines_from_file(file)
                 keys = Keys(lines)
                 num_keys = len(keys.translations_as_dict())
                 num_keys_missing_value = len(keys.empty_keys())
@@ -484,7 +481,7 @@ def main():
         SyncLang(extended=False, out_file='status.md').status_create_markdown()
 
     elif (len(sys.argv) == 2 or len(sys.argv) == 3) and sys.argv[1] == "update":
-        SyncLang(extended=len(sys.argv) == 3 and (sys.argv[2] == "-e" or sys.argv[2] == "--extended")).update()
+        SyncLang(extended=len(sys.argv) == 3 and (sys.argv[2] == "-e" or sys.argv[2] == "--extended")).update_properties()
 
     elif (len(sys.argv) == 2 or len(sys.argv) == 3) and sys.argv[1] == "status":
         SyncLang(extended=len(sys.argv) == 3 and (sys.argv[2] == "-e" or sys.argv[2] == "--extended")).status()

From d940de0fcb1f4bf96a21e1bf166d56a7432a8e52 Mon Sep 17 00:00:00 2001
From: Stefan <st155160@stud.uni-stuttgart.de>
Date: Tue, 20 Feb 2018 21:03:36 +0100
Subject: [PATCH 11/40] Reworked command-line interface

---
 scripts/syncLang.py | 72 +++++++++++++++++++++++++--------------------
 1 file changed, 40 insertions(+), 32 deletions(-)

diff --git a/scripts/syncLang.py b/scripts/syncLang.py
index adbc7f7f616..65e75e6a7d5 100644
--- a/scripts/syncLang.py
+++ b/scripts/syncLang.py
@@ -1,6 +1,7 @@
 # coding=utf-8
 from __future__ import division
 
+import argparse # Requires Python 2.7, should be safe to use with jython.
 import codecs
 import datetime
 import logging
@@ -42,11 +43,15 @@ def getJabRefBaseDirectory():
                 if parent.name == 'jabref':
                     return parent
     
-    # Important paths, files and directories of the JabRef repository
+    # Important directories of the JabRef repository
     JABREF_BASE_DIRECTORY = PathFinder.getJabRefBaseDirectory()
     JABREF_SOURCE_DIRECTORY = JABREF_BASE_DIRECTORY / 'src'
     JABREF_SCRIPTS_DIRECTORY = JABREF_BASE_DIRECTORY / 'scripts'
     JABREF_LOCALIZATION_DIRECTORY = JABREF_SOURCE_DIRECTORY / 'main/resources/l10n'
+    
+    # Important files
+    JABREF_MAIN_LOCALIZATION_FILE = JABREF_LOCALIZATION_DIRECTORY / 'JabRef_en.properties'
+    JABREF_MAIN_MENU_LOCALIZATION_FILE = JABREF_LOCALIZATION_DIRECTORY / 'Menu_en.properties'
 except ImportError:
     logging.info("Unable to use PathFinder class.")
 
@@ -196,7 +201,7 @@ def format_key_and_value(key, value):
 
 class SyncLang:
 
-    def __init__(self, extended, out_file='status.md'):
+    def __init__(self, extended):
         """
         :param extended: boolean: if the keys with problems should be printed
 
@@ -204,7 +209,6 @@ def __init__(self, extended, out_file='status.md'):
         self.extended = extended
         self.main_jabref_preferences = os.path.join(RES_DIR, "JabRef_en.properties")
         self.main_menu_preferences = os.path.join(RES_DIR, "Menu_en.properties")
-        self.markdown_output = out_file
 
     def status(self):
         """
@@ -350,7 +354,7 @@ def __update_properties(self, main_property_file, other_property_files):
             num_keys_obsolete = len(keys_obsolete)
 
             for missing_key in keys_missing:
-                # Missing keys are added with english translation by default.
+                # Missing keys are added with main translation by default.
                 keys[missing_key] = main_keys_dict[missing_key]
 
             for obsolete_key in keys_obsolete:
@@ -434,7 +438,7 @@ def __missing_keys(first_list, second_list):
         """
         return list(set(first_list).difference(second_list))
 
-    def status_create_markdown(self):
+    def status_create_markdown(self, markdown_file='status.md'):
         """
         Creates a markdown file of the current status.
         """
@@ -465,7 +469,7 @@ def _percentage(whole, part):
                 return 0
             return int(part / whole * 100.0)
 
-        with codecs.open(self.markdown_output, "w", encoding="UTF-8") as status_file:
+        with codecs.open(markdown_file, "w", encoding="UTF-8") as status_file:
             status_file.write('### Localization files status (' + datetime.datetime.now().strftime(
                 "%Y-%m-%d %H:%M") + ' - Branch `' + Git().get_current_branch() + '` `' + Git().get_current_hash_short() + '`)\n\n')
             status_file.write('Note: To get the current status from your local repository, run `python ./scripts/syncLang.py markdown`\n')
@@ -473,39 +477,43 @@ def _percentage(whole, part):
             _write_properties(status_file, self.__all_menu_properties())
             _write_properties(status_file, self.__all_jabref_properties())
 
-        logging.info('Current status written to ' + self.markdown_output)
+        logging.info('Current status written to ' + markdown_file)
 
 
 def main():
-    if len(sys.argv) == 2 and sys.argv[1] == "markdown":
-        SyncLang(extended=False, out_file='status.md').status_create_markdown()
-
-    elif (len(sys.argv) == 2 or len(sys.argv) == 3) and sys.argv[1] == "update":
-        SyncLang(extended=len(sys.argv) == 3 and (sys.argv[2] == "-e" or sys.argv[2] == "--extended")).update_properties()
-
-    elif (len(sys.argv) == 2 or len(sys.argv) == 3) and sys.argv[1] == "status":
-        SyncLang(extended=len(sys.argv) == 3 and (sys.argv[2] == "-e" or sys.argv[2] == "--extended")).status()
-
-    else:
-        logging.info("""This program must be run from the JabRef base directory.
     
-    Usage: syncLang.py {markdown, status [-e | --extended], update [-e | --extended]}
-    Option can be one of the following:
+    def markdown(args):
+        SyncLang(extended=False).status_create_markdown()
+    def status(args):
+        SyncLang(extended=args.extended).status()
+    def update(args):
+        SyncLang(extended=args.extended).update_properties()
+    
+    
+    parser = argparse.ArgumentParser(add_help=True)
+    parser.description = "This script is used to synchronize the keys of different *.properties files."
+    
+    
+    shared_arguments = argparse.ArgumentParser(add_help=False)
+    extended_argument = shared_arguments.add_argument("-e", "--extended", help="Prints extended information about the process to the terminal", required=False, action='store_true', default=False)
+    
+    subcommands = parser.add_subparsers(title="Subcommands", description="Provide different options for the user")
+    
+    # markdown parser
+    markdown_parser = subcommands.add_parser("markdown", description="Creates a markdown file of the current status")
+    markdown_parser.set_defaults(func=markdown)
+    # TODO add argument to pass a file name for the markdown file
     
-        status [-e | --extended]:
-            prints the current status to the terminal
-            [-e | --extended]:
-                if the translations keys which create problems should be printed
+    # status parser
+    status_parser = subcommands.add_parser("status", description="Prints the current status to the terminal", parents=[shared_arguments])
+    status_parser.set_defaults(func=status)
     
-        markdown:
-            Creates a markdown file of the current status and opens it
+    # update parser
+    update_parser = subcommands.add_parser("update", description="Compares all the localization files against the English one and fixes unambiguous duplicates, removes obsolete keys, adds missing keys, and sorts them", parents=[shared_arguments])
+    update_parser.set_defaults(func=update)
     
-        update [-e | --extended]:
-            compares all the localization files against the English one and fixes unambiguous duplicates,
-            removes obsolete keys, adds missing keys, and sorts them
-            [-e | --extended]:
-                if the translations keys which create problems should be printed
-    """)
+    parsed_args = parser.parse_args()
+    parsed_args.func(parsed_args)
 
 
 if '__main__' == __name__:

From c5eecef7ed48f5e04ab5d41b3a62f966656b14ef Mon Sep 17 00:00:00 2001
From: Stefan <st155160@stud.uni-stuttgart.de>
Date: Wed, 21 Feb 2018 03:18:27 +0100
Subject: [PATCH 12/40] Reworked logging functionality, added new command-line
 options

---
 scripts/syncLang.py | 189 ++++++++++++++++++++++++++++++++++----------
 1 file changed, 148 insertions(+), 41 deletions(-)

diff --git a/scripts/syncLang.py b/scripts/syncLang.py
index 65e75e6a7d5..733c6a340ba 100644
--- a/scripts/syncLang.py
+++ b/scripts/syncLang.py
@@ -1,7 +1,7 @@
 # coding=utf-8
 from __future__ import division
 
-import argparse # Requires Python 2.7, should be safe to use with jython.
+import argparse  # Requires Python 2.7, should be safe to use with jython.
 import codecs
 import datetime
 import logging
@@ -17,6 +17,7 @@
 try:
     # Just to make sure not to break anything, in case py3.x is not supported.
     import pathlib
+
     class PathFinder:
         """
         This class is designed to automatically locate this script's path within the repository.
@@ -201,14 +202,52 @@ def format_key_and_value(key, value):
 
 class SyncLang:
 
-    def __init__(self, extended):
+    def __init__(self, extended_logging=False):
         """
         :param extended: boolean: if the keys with problems should be printed
 
         """
-        self.extended = extended
+        self.extended_logging = extended_logging
         self.main_jabref_preferences = os.path.join(RES_DIR, "JabRef_en.properties")
         self.main_menu_preferences = os.path.join(RES_DIR, "Menu_en.properties")
+        
+    def set_extended_logging_enabled(self, value):
+        self.extended_logging = bool(value)
+        
+    def print_missing_keys_for_file(self, file_name):
+        file_status = self.__get_status_for_file(file_name)
+        if file_status:
+            keys_missing, _, _, _ = file_status
+            
+            if len(keys_missing) > 0:
+                logging.info("Printing missing keys for file: " + file_name)
+                self.__print_keys(keys_missing)
+            else:
+                logging.info("No missing keys found for file:" + file_name)
+    
+    def print_obsolete_keys_for_file(self, file_name):
+        file_status = self.__get_status_for_file(file_name)
+        if file_status:
+            _, keys_obsolete, _, _ = file_status
+            
+            if len(keys_obsolete) > 0:
+                
+                logging.info("Printing obsolete keys for file: " + file_name)
+                self.__print_keys(keys_obsolete)
+            else:
+                logging.info("No obsolete keys found for file: " + file_name)
+
+    def print_duplicate_keys_for_file(self, file_name):
+        file_status = self.__get_status_for_file(file_name)
+        if file_status:
+            _, _, keys_duplicate, _ = file_status
+            
+            if len(keys_duplicate) > 0:
+                
+                logging.info("Printing duplicate keys for file: " + file_name)
+                self.__print_keys(keys_duplicate)
+            else:
+                logging.info("No duplicate keys found for file: " + file_name)
 
     def status(self):
         """
@@ -219,10 +258,10 @@ def status(self):
         self.__print_status_menu_properties()
 
     def __print_status_menu_properties(self):
-        self.__check_properties(main_property_file=self.main_menu_preferences, property_files=self.__all_menu_properties())
+        self.__compare_properties(main_property_file=self.main_menu_preferences, property_files=self.__all_menu_properties())
 
     def __print_status_jabref_properties(self):
-        self.__check_properties(main_property_file=self.main_jabref_preferences, property_files=self.__all_jabref_properties())
+        self.__compare_properties(main_property_file=self.main_jabref_preferences, property_files=self.__all_jabref_properties())
 
     def update_properties(self):
         """
@@ -238,8 +277,37 @@ def __update_menu_properties(self):
 
     def __update_jabref_properties(self):
         self.__update_properties(main_property_file=self.main_jabref_preferences, other_property_files=self.__other_jabref_properties())
+        
+    def __get_main_file(self, file_name):
+        
+        file = os.path.join(RES_DIR, file_name)
+        
+        if file in self.__all_jabref_properties():
+            return self.main_jabref_preferences
+        elif file in self.__all_menu_properties():
+            return self.main_menu_preferences
+        
+    def __get_status_for_file(self, file_name):
+        main_file = self.__get_main_file(file_name)
+        if main_file:
+            main_lines = self.__read_lines_from_file(filename=main_file)
+            main_keys = Keys(main_lines)
+            
+            file = os.path.join(RES_DIR, file_name)
+            lines = self.__read_lines_from_file(file)
+            keys1 = Keys(lines)
+            keys = keys1.keys_from_lines()
 
-    def __check_properties(self, main_property_file, property_files):
+            keys_missing = self.__missing_keys(main_keys.keys_from_lines(), keys)
+            keys_obsolete = self.__missing_keys(keys, main_keys.keys_from_lines())
+            keys_duplicates = keys1.find_duplicates()
+            keys_not_translated = keys1.empty_keys()
+            
+            return (keys_missing, keys_obsolete, keys_duplicates, keys_not_translated)
+        else:
+            logging.debug("Unable to find main file for: " + file_name)
+
+    def __compare_properties(self, main_property_file, property_files):
         main_lines = self.__read_lines_from_file(filename=main_property_file)
         main_keys = Keys(main_lines)
 
@@ -247,19 +315,19 @@ def __check_properties(self, main_property_file, property_files):
         for file in property_files:
             filename = self.__format_filename(filepath=file)
             lines = self.__read_lines_from_file(file)
-            keys1 = Keys(main_lines)
+            keys1 = Keys(lines)
             keys = keys1.keys_from_lines()
 
             keys_missing = self.__missing_keys(main_keys.keys_from_lines(), keys)
             keys_obsolete = self.__missing_keys(keys, main_keys.keys_from_lines())
-            keys_duplicate = Keys(lines).find_duplicates()
-            keys_not_translated = Keys(lines=lines).empty_keys()
+            keys_duplicates = keys1.find_duplicates()
+            keys_not_translated = keys1.empty_keys()
 
             num_keys = len(keys)
             num_keys_missing = len(keys_missing)
             num_keys_not_translated = len(keys_not_translated)
             num_keys_obsolete = len(keys_obsolete)
-            num_keys_duplicate = len(keys_duplicate)
+            num_keys_duplicate = len(keys_duplicates)
             num_keys_translated = num_keys - num_keys_not_translated
 
             log = logging.error if num_keys_missing != 0 or num_keys_not_translated != 0 or num_keys_obsolete != 0 or num_keys_duplicate != 0 else logging.info
@@ -268,23 +336,23 @@ def __check_properties(self, main_property_file, property_files):
 
             log = logging.error if num_keys_not_translated != 0 else logging.info
             log("\t{} not translated keys".format(num_keys_not_translated))
-            if self.extended and num_keys_not_translated != 0:
-                logging.info("\t\t{}".format(", ".join(keys_not_translated)))
+            if self.extended_logging and num_keys_not_translated != 0:
+                self.__print_keys(keys_not_translated)
 
             log = logging.error if num_keys_missing != 0 else logging.info
             log("\t{} missing keys".format(num_keys_missing))
-            if self.extended and num_keys_missing != 0:
-                logging.info("\t\t{}".format(", ".join(keys_missing)))
+            if self.extended_logging and num_keys_missing != 0:
+                self.__print_keys(keys_missing)
 
             log = logging.error if num_keys_obsolete != 0 else logging.info
             log("\t{} obsolete keys".format(num_keys_obsolete))
-            if self.extended and num_keys_obsolete != 0:
-                logging.info("\t\t{}".format(", ".join(keys_obsolete)))
+            if self.extended_logging and num_keys_obsolete != 0:
+                self.__print_keys(keysobsolete)
 
             log = logging.error if num_keys_duplicate != 0 else logging.info
             log("\t{} duplicates".format(num_keys_duplicate))
-            if self.extended and num_keys_duplicate != 0:
-                logging.info("\t\t{}".format(", ".join(keys_duplicate)))
+            if self.extended_logging and num_keys_duplicate != 0:
+                self.__print_keys(keys_duplicates)
 
     def __all_menu_properties(self):
         """
@@ -303,7 +371,7 @@ def __other_menu_properties(self):
 
     def __all_jabref_properties(self):
         """
-        :return: list of strings: all the JabRef_*.preferences files with the english at the beginning
+        :return: list of strings: all the JabRef_*.preferences file paths with the english at the beginning
         """
         jabref_property_files = sorted(self.__other_jabref_properties())
         jabref_property_files.insert(0, self.main_jabref_preferences)
@@ -311,7 +379,7 @@ def __all_jabref_properties(self):
 
     def __other_jabref_properties(self):
         """
-        :return: list of strings: all the JabRef_*.preferences files without the english one
+        :return: list of strings: all the JabRef_*.preferences file paths without the english one
         """
         jabref_property_files = [s for s in os.listdir(RES_DIR) if (s.startswith('JabRef_') and not (s.startswith('JabRef_en')))]
         return [os.path.join(RES_DIR, file) for file in jabref_property_files]
@@ -327,8 +395,8 @@ def __update_properties(self, main_property_file, other_property_files):
             logging.error("There are {num_duplicates} duplicates in {file}, please fix them manually".format(num_duplicates=num_main_duplicates,
                                                                                                              file=self.__format_filename(
                                                                                                                  filepath=main_property_file)))
-            if self.extended:
-                logging.info("\t{}".format(", ".join(main_duplicates)))
+            if self.extended_logging:
+                self.__print_keys(main_duplicates)
             return
 
         for other_property_file in other_property_files:
@@ -343,8 +411,8 @@ def __update_properties(self, main_property_file, other_property_files):
             if num_not_fixed != 0:
                 logging.error("There are {num_not_fixed_duplicates} ambiguous duplicates in {file}, please fix them manually".format(
                     num_not_fixed_duplicates=num_not_fixed, file=filename))
-                if self.extended:
-                    logging.error("\t{}".format(", ".join(not_fixed)))
+                if self.extended_logging:
+                    self.__print_keys(not_fixed)
                 continue
 
             keys_missing = self.__missing_keys(main_keys.keys_from_lines(), keys)
@@ -381,18 +449,18 @@ def __update_properties(self, main_property_file, other_property_files):
             logging.info("Processing file '{file}' with {num_keys} Keys".format(file=filename, num_keys=num_keys))
             if num_fixed != 0:
                 logging.info("\tfixed {} unambiguous duplicates".format(num_fixed))
-                if self.extended:
-                    logging.info("\t\t{}".format(", ".join(fixed)))
+                if self.extended_logging:
+                    self.__print_keys(fixed)
 
             if num_keys_missing != 0:
                 logging.info("\tadded {} missing keys".format(num_keys_missing))
-                if self.extended:
-                    logging.info("\t\t{}".format(", ".join(keys_missing)))
+                if self.extended_logging:
+                    self.__print_keys(keys_missing)
 
             if num_keys_obsolete != 0:
                 logging.info("\tdeleted {} obsolete keys".format(num_keys_obsolete))
-                if self.extended:
-                    logging.info("\t\t{}".format(", ".join(keys_obsolete)))
+                if self.extended_logging:
+                    self.__print_keys(keys_obsolete)
 
             if sorted_lines:
                 logging.info("\thas been sorted successfully")
@@ -403,7 +471,7 @@ def __format_filename(filepath):
         removes the res_dir path
 
         :param filepath: string
-        :return: string
+        :return: pure file name of this file path (including file extension e.g. *.txt)
         """
         return filepath.replace("{}\\".format(RES_DIR), "")
 
@@ -437,6 +505,11 @@ def __missing_keys(first_list, second_list):
         :return: list of unicode strings
         """
         return list(set(first_list).difference(second_list))
+    
+    @staticmethod
+    def __print_keys(keys, logger=logging.info):
+        for key in keys:
+            logger("\t{}\n".format(key))
 
     def status_create_markdown(self, markdown_file='status.md'):
         """
@@ -482,18 +555,35 @@ def _percentage(whole, part):
 
 def main():
     
-    def markdown(args):
-        SyncLang(extended=False).status_create_markdown()
-    def status(args):
-        SyncLang(extended=args.extended).status()
-    def update(args):
-        SyncLang(extended=args.extended).update_properties()
+    syncer = SyncLang()
     
+    def markdown_command(args):
+        syncer.set_extended_logging_enabled(False)
+        syncer.status_create_markdown()
+
+    def status_command(args):
+        syncer.set_extended_logging_enabled(args.extended)
+        syncer.status()
+
+    def update_command(args):
+        syncer.set_extended_logging_enabled(args.extended)
+        syncer.update_properties()
+
+    def print_missing(args):
+        file_name = args.f
+        syncer.print_missing_keys_for_file(file_name)
+
+    def print_obsolete(args):
+        file_name = args.f
+        syncer.print_obsolete_keys_for_file(file_name)
+
+    def print_duplicates(args):
+        file_name = args.f
+        syncer.print_duplicate_keys_for_file(file_name)
     
     parser = argparse.ArgumentParser(add_help=True)
     parser.description = "This script is used to synchronize the keys of different *.properties files."
     
-    
     shared_arguments = argparse.ArgumentParser(add_help=False)
     extended_argument = shared_arguments.add_argument("-e", "--extended", help="Prints extended information about the process to the terminal", required=False, action='store_true', default=False)
     
@@ -501,16 +591,33 @@ def update(args):
     
     # markdown parser
     markdown_parser = subcommands.add_parser("markdown", description="Creates a markdown file of the current status")
-    markdown_parser.set_defaults(func=markdown)
+    markdown_parser.set_defaults(func=markdown_command)
     # TODO add argument to pass a file name for the markdown file
     
     # status parser
     status_parser = subcommands.add_parser("status", description="Prints the current status to the terminal", parents=[shared_arguments])
-    status_parser.set_defaults(func=status)
+    status_parser.set_defaults(func=status_command)
     
     # update parser
     update_parser = subcommands.add_parser("update", description="Compares all the localization files against the English one and fixes unambiguous duplicates, removes obsolete keys, adds missing keys, and sorts them", parents=[shared_arguments])
-    update_parser.set_defaults(func=update)
+    update_parser.set_defaults(func=update_command)
+    
+    # print parser
+    print_parser = subcommands.add_parser("print", description="Prints specific status info to the console")
+    
+    shared_print_arguments = argparse.ArgumentParser(add_help=False)
+    file_argument = shared_print_arguments.add_argument("-f", "-file", help="Specifies a file for the command to run with", required=True, action='store')
+    
+    print_options = print_parser.add_subparsers(title="Print Options", description="Different options for printing")
+    
+    missing_parser = print_options.add_parser("missing", description="Prints all missing keys", parents=[shared_print_arguments])
+    missing_parser.set_defaults(func=print_missing)
+    
+    obsolete_parser = print_options.add_parser("obsolete", description="Prints all obsolete keys", parents=[shared_print_arguments])
+    obsolete_parser.set_defaults(func=print_obsolete)
+    
+    duplicates_parser = print_options.add_parser("duplicates", description="Prints all duplicate keys", parents=[shared_print_arguments])
+    duplicates_parser.set_defaults(func=print_duplicates)
     
     parsed_args = parser.parse_args()
     parsed_args.func(parsed_args)

From 35b7f8330fb2694afbfc7f5e2be056276d415b3a Mon Sep 17 00:00:00 2001
From: Stefan <st155160@stud.uni-stuttgart.de>
Date: Wed, 21 Feb 2018 03:33:51 +0100
Subject: [PATCH 13/40] =?UTF-8?q?small=20fix=20on=20=C2=B4getJabRefBaseDir?=
 =?UTF-8?q?ectory=C2=B4=20method?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 scripts/syncLang.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/scripts/syncLang.py b/scripts/syncLang.py
index 733c6a340ba..09d6403ca39 100644
--- a/scripts/syncLang.py
+++ b/scripts/syncLang.py
@@ -39,6 +39,9 @@ def getJabRefBaseDirectory():
             Searches the script's path backwards until it finds the matching base directory.
             :return the path to JabRef's base directory as pathlib.Path object.
             """
+            if pathlib.Path.cwd().name == 'jabref':
+                return pathlib.Path.cwd
+            
             scriptLocation = PathFinder.getScriptLocation()
             for parent in scriptLocation.parents:
                 if parent.name == 'jabref':

From ded149b0b1da11a6c92ae9e9212206da8436b82b Mon Sep 17 00:00:00 2001
From: Stefan <st155160@stud.uni-stuttgart.de>
Date: Wed, 21 Feb 2018 03:34:32 +0100
Subject: [PATCH 14/40] forgot brackets...

---
 scripts/syncLang.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/syncLang.py b/scripts/syncLang.py
index 09d6403ca39..338a504ed74 100644
--- a/scripts/syncLang.py
+++ b/scripts/syncLang.py
@@ -40,7 +40,7 @@ def getJabRefBaseDirectory():
             :return the path to JabRef's base directory as pathlib.Path object.
             """
             if pathlib.Path.cwd().name == 'jabref':
-                return pathlib.Path.cwd
+                return pathlib.Path.cwd()
             
             scriptLocation = PathFinder.getScriptLocation()
             for parent in scriptLocation.parents:

From 1379dad815880963bfaf1149498cda43ecd9412e Mon Sep 17 00:00:00 2001
From: Stefan <st155160@stud.uni-stuttgart.de>
Date: Wed, 21 Feb 2018 03:47:58 +0100
Subject: [PATCH 15/40] =?UTF-8?q?Removed=20=C2=B4getScriptLocation=C2=B4?=
 =?UTF-8?q?=20method?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 scripts/syncLang.py | 16 +++++-----------
 1 file changed, 5 insertions(+), 11 deletions(-)

diff --git a/scripts/syncLang.py b/scripts/syncLang.py
index 338a504ed74..0a679231f1a 100644
--- a/scripts/syncLang.py
+++ b/scripts/syncLang.py
@@ -26,26 +26,20 @@ class PathFinder:
         requires Python 3.4 or higher
         """
         
-        @staticmethod
-        def getScriptLocation():
-            """
-            :return the path this script is currently located as pathlib.Path object.
-            """
-            return pathlib.Path(__file__)
-        
         @staticmethod
         def getJabRefBaseDirectory():
             """
             Searches the script's path backwards until it finds the matching base directory.
             :return the path to JabRef's base directory as pathlib.Path object.
             """
-            if pathlib.Path.cwd().name == 'jabref':
-                return pathlib.Path.cwd()
+            cwd = pathlib.Path.cwd()
+            if cwd.name == 'jabref':
+                return cwd
             
-            scriptLocation = PathFinder.getScriptLocation()
-            for parent in scriptLocation.parents:
+            for parent in cwd.parents:
                 if parent.name == 'jabref':
                     return parent
+            # TODO What to do if base directory could not be found?
     
     # Important directories of the JabRef repository
     JABREF_BASE_DIRECTORY = PathFinder.getJabRefBaseDirectory()

From e7be7ef3eaa55691eaee32b5db804719880295e1 Mon Sep 17 00:00:00 2001
From: Stefan <st155160@stud.uni-stuttgart.de>
Date: Wed, 21 Feb 2018 03:50:45 +0100
Subject: [PATCH 16/40] =?UTF-8?q?Added=20=C2=B4BASE=5FDIRECTORY=5FNAME?=
 =?UTF-8?q?=C2=B4=20variable=20to=20PathFinder=20class?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 scripts/syncLang.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/scripts/syncLang.py b/scripts/syncLang.py
index 0a679231f1a..3046eb42b75 100644
--- a/scripts/syncLang.py
+++ b/scripts/syncLang.py
@@ -26,6 +26,8 @@ class PathFinder:
         requires Python 3.4 or higher
         """
         
+        BASE_DIRECTORY_NAME = 'jabref'
+        
         @staticmethod
         def getJabRefBaseDirectory():
             """
@@ -33,11 +35,11 @@ def getJabRefBaseDirectory():
             :return the path to JabRef's base directory as pathlib.Path object.
             """
             cwd = pathlib.Path.cwd()
-            if cwd.name == 'jabref':
+            if cwd.name == PathFinder.BASE_DIRECTORY_NAME:
                 return cwd
             
             for parent in cwd.parents:
-                if parent.name == 'jabref':
+                if parent.name == PathFinder.BASE_DIRECTORY_NAME:
                     return parent
             # TODO What to do if base directory could not be found?
     

From cb21464b6173d9a52d5b2abeb6c20825d5099746 Mon Sep 17 00:00:00 2001
From: Stefan <st155160@stud.uni-stuttgart.de>
Date: Thu, 22 Feb 2018 12:53:58 +0100
Subject: [PATCH 17/40] Print commands will now use localization directory by
 default

---
 scripts/syncLang.py | 52 +++++++++++++++++++++++++++++++++++++--------
 1 file changed, 43 insertions(+), 9 deletions(-)

diff --git a/scripts/syncLang.py b/scripts/syncLang.py
index 3046eb42b75..8dfb267edab 100644
--- a/scripts/syncLang.py
+++ b/scripts/syncLang.py
@@ -213,6 +213,14 @@ def __init__(self, extended_logging=False):
     def set_extended_logging_enabled(self, value):
         self.extended_logging = bool(value)
         
+    def print_missing_keys(self):
+        for file in self.__other_jabref_properties():
+            file_name = self.__format_filename(file)
+            self.print_missing_keys_for_file(file_name)
+        for file in self.__other_menu_properties():
+            file_name = self.__format_filename(file)
+            self.print_missing_keys_for_file(file_name)
+        
     def print_missing_keys_for_file(self, file_name):
         file_status = self.__get_status_for_file(file_name)
         if file_status:
@@ -223,6 +231,15 @@ def print_missing_keys_for_file(self, file_name):
                 self.__print_keys(keys_missing)
             else:
                 logging.info("No missing keys found for file:" + file_name)
+                
+    def print_obsolete_keys(self):
+        for file in self.__other_jabref_properties():
+            file_name = self.__format_filename(file)
+            self.print_obsolete_keys_for_file(file_name)
+        for file in self.__other_menu_properties():
+            file_name = self.__format_filename(file)
+            self.print_obsolete_keys_for_file(file_name)
+                
     
     def print_obsolete_keys_for_file(self, file_name):
         file_status = self.__get_status_for_file(file_name)
@@ -235,6 +252,14 @@ def print_obsolete_keys_for_file(self, file_name):
                 self.__print_keys(keys_obsolete)
             else:
                 logging.info("No obsolete keys found for file: " + file_name)
+                
+    def print_duplicate_keys(self):
+        for file in self.__other_jabref_properties():
+            file_name = self.__format_filename(file)
+            self.print_duplicate_keys_for_file(file_name)
+        for file in self.__other_menu_properties():
+            file_name = self.__format_filename(file)
+            self.print_duplicate_keys_for_file(file_name)
 
     def print_duplicate_keys_for_file(self, file_name):
         file_status = self.__get_status_for_file(file_name)
@@ -569,16 +594,25 @@ def update_command(args):
         syncer.update_properties()
 
     def print_missing(args):
-        file_name = args.f
-        syncer.print_missing_keys_for_file(file_name)
+        file_name = args.file
+        if file_name:
+            syncer.print_missing_keys_for_file(file_name)
+        else:
+            syncer.print_missing_keys()
 
     def print_obsolete(args):
-        file_name = args.f
-        syncer.print_obsolete_keys_for_file(file_name)
+        file_name = args.file
+        if file_name:
+            syncer.print_obsolete_keys_for_file(file_name)
+        else:
+            syncer.print_obsolete_keys()
 
     def print_duplicates(args):
-        file_name = args.f
-        syncer.print_duplicate_keys_for_file(file_name)
+        file_name = args.file
+        if file_name:
+            syncer.print_duplicate_keys_for_file(file_name)
+        else:
+            syncer.print_duplicate_keys()
     
     parser = argparse.ArgumentParser(add_help=True)
     parser.description = "This script is used to synchronize the keys of different *.properties files."
@@ -586,7 +620,7 @@ def print_duplicates(args):
     shared_arguments = argparse.ArgumentParser(add_help=False)
     extended_argument = shared_arguments.add_argument("-e", "--extended", help="Prints extended information about the process to the terminal", required=False, action='store_true', default=False)
     
-    subcommands = parser.add_subparsers(title="Subcommands", description="Provide different options for the user")
+    subcommands = parser.add_subparsers(title="Subcommands", description="Provide different options for the user", dest="subcommand")
     
     # markdown parser
     markdown_parser = subcommands.add_parser("markdown", description="Creates a markdown file of the current status")
@@ -605,9 +639,9 @@ def print_duplicates(args):
     print_parser = subcommands.add_parser("print", description="Prints specific status info to the console")
     
     shared_print_arguments = argparse.ArgumentParser(add_help=False)
-    file_argument = shared_print_arguments.add_argument("-f", "-file", help="Specifies a file for the command to run with", required=True, action='store')
+    file_argument = shared_print_arguments.add_argument("-f", "--file", help="Specifies a file for the command to run with", required=False, action='store')
     
-    print_options = print_parser.add_subparsers(title="Print Options", description="Different options for printing")
+    print_options = print_parser.add_subparsers(title="Print Options", description="Different options for printing", dest="print_option_name")
     
     missing_parser = print_options.add_parser("missing", description="Prints all missing keys", parents=[shared_print_arguments])
     missing_parser.set_defaults(func=print_missing)

From fb3bba0b751cf29253f548d51319b2ddd3de07db Mon Sep 17 00:00:00 2001
From: Stefan <st155160@stud.uni-stuttgart.de>
Date: Wed, 28 Feb 2018 20:45:33 +0100
Subject: [PATCH 18/40] Missing keys will no longer be written to the
 properties files

---
 scripts/syncLang.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/scripts/syncLang.py b/scripts/syncLang.py
index 8dfb267edab..0dbe32d86b6 100644
--- a/scripts/syncLang.py
+++ b/scripts/syncLang.py
@@ -445,9 +445,9 @@ def __update_properties(self, main_property_file, other_property_files):
             num_keys_missing = len(keys_missing)
             num_keys_obsolete = len(keys_obsolete)
 
-            for missing_key in keys_missing:
+            # for missing_key in keys_missing:
                 # Missing keys are added with main translation by default.
-                keys[missing_key] = main_keys_dict[missing_key]
+                # keys[missing_key] = main_keys_dict[missing_key]
 
             for obsolete_key in keys_obsolete:
                 del keys[obsolete_key]

From 432a92bb31d9737e6466cf7d64e89020ecbefdf6 Mon Sep 17 00:00:00 2001
From: Stefan <st155160@stud.uni-stuttgart.de>
Date: Fri, 2 Mar 2018 15:44:05 +0100
Subject: [PATCH 19/40] Fixed missing key issue

---
 scripts/syncLang.py | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/scripts/syncLang.py b/scripts/syncLang.py
index 0dbe32d86b6..0b2386b3617 100644
--- a/scripts/syncLang.py
+++ b/scripts/syncLang.py
@@ -456,9 +456,10 @@ def __update_properties(self, main_property_file, other_property_files):
             for line in main_lines:
                 key = main_keys.key_from_line(line)
                 if key is not None:
-                    # Do not write empty keys
-                    if keys[key] != "":
-                        other_lines_to_write.append(Keys.format_key_and_value(key=key, value=keys[key]) + "\n")
+                    if keys.has_key(key):
+                        # Do not write empty keys
+                        if keys[key] != "":
+                            other_lines_to_write.append(Keys.format_key_and_value(key=key, value=keys[key]) + "\n")
                 else:
                     other_lines_to_write.append(line)
 

From 262ebc5fed183298550de7b6691eb52e56da40b5 Mon Sep 17 00:00:00 2001
From: Tobias Diez <tobiasdiez@gmx.de>
Date: Fri, 4 Oct 2019 21:55:47 +0200
Subject: [PATCH 20/40] Add UUID for upgrading

In my understanding generating two installers with different versions and same --win-upgrade-uuid should uninstall another version during installation, i.e. this is needed to have a proper upgrade instead of a parallel installation of two JabRef versions.
---
 build.gradle | 1 +
 1 file changed, 1 insertion(+)

diff --git a/build.gradle b/build.gradle
index 2a95dc4d428..10b9632072a 100644
--- a/build.gradle
+++ b/build.gradle
@@ -582,6 +582,7 @@ jlink {
             installerOptions = [
                     '--vendor', 'JabRef',
                     '--app-version', "${project.version}",
+                    '--win-upgrade-uuid', 'd636b4ee-6f10-451e-bf57-c89656780e36'
                     '--win-dir-chooser',
                     '--win-shortcut'
             ]

From a53b137dd1111d4fa4c2df75af6a7c6fcb1c8812 Mon Sep 17 00:00:00 2001
From: matthiasgeiger <matthias.geiger@uni-bamberg.de>
Date: Sat, 5 Oct 2019 10:29:22 +0200
Subject: [PATCH 21/40] add missing ','

---
 build.gradle | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index 10b9632072a..b3d7851f76a 100644
--- a/build.gradle
+++ b/build.gradle
@@ -582,7 +582,7 @@ jlink {
             installerOptions = [
                     '--vendor', 'JabRef',
                     '--app-version', "${project.version}",
-                    '--win-upgrade-uuid', 'd636b4ee-6f10-451e-bf57-c89656780e36'
+                    '--win-upgrade-uuid', 'd636b4ee-6f10-451e-bf57-c89656780e36',
                     '--win-dir-chooser',
                     '--win-shortcut'
             ]

From baa47ff95f13764f6ecb9f9ab38762f56752c342 Mon Sep 17 00:00:00 2001
From: matthiasgeiger <matthias.geiger@uni-bamberg.de>
Date: Sat, 5 Oct 2019 11:22:39 +0200
Subject: [PATCH 22/40] use submodules to fetch CSL styles properly

---
 .github/workflows/deployment.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/deployment.yml b/.github/workflows/deployment.yml
index 2e3f869b953..7181f896579 100644
--- a/.github/workflows/deployment.yml
+++ b/.github/workflows/deployment.yml
@@ -33,6 +33,7 @@ jobs:
       uses: actions/checkout@v1
       with:
         fetch-depth: 1
+        submodules: true
     - name: Set up JDK
       uses: actions/setup-java@v1
       with:

From bbab95021364be54ed21e678fcf89ee9d1529766 Mon Sep 17 00:00:00 2001
From: matthiasgeiger <matthias.geiger@uni-bamberg.de>
Date: Sat, 5 Oct 2019 11:36:19 +0200
Subject: [PATCH 23/40] revert 3fbe0a2b57340f03d7d1271eeeb30a061d724134

---
 .github/workflows/deployment.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.github/workflows/deployment.yml b/.github/workflows/deployment.yml
index 7181f896579..2889d2e2cac 100644
--- a/.github/workflows/deployment.yml
+++ b/.github/workflows/deployment.yml
@@ -32,7 +32,6 @@ jobs:
     - name: Checkout source
       uses: actions/checkout@v1
       with:
-        fetch-depth: 1
         submodules: true
     - name: Set up JDK
       uses: actions/setup-java@v1

From d3fd6f930db846c04339c12eaa77907c8d1f082b Mon Sep 17 00:00:00 2001
From: Christoph <siedlerkiller@gmail.com>
Date: Sat, 5 Oct 2019 18:09:51 +0200
Subject: [PATCH 24/40] Update deployment.yml

Readd depth
---
 .github/workflows/deployment.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/deployment.yml b/.github/workflows/deployment.yml
index 2889d2e2cac..bec5380f3d1 100644
--- a/.github/workflows/deployment.yml
+++ b/.github/workflows/deployment.yml
@@ -32,6 +32,7 @@ jobs:
     - name: Checkout source
       uses: actions/checkout@v1
       with:
+        depth: 1
         submodules: true
     - name: Set up JDK
       uses: actions/setup-java@v1

From 875b48e8456c2861296f5be29a53c045dea840e2 Mon Sep 17 00:00:00 2001
From: Matthias Geiger <matthias.geiger@uni-bamberg.de>
Date: Sun, 6 Oct 2019 07:47:23 +0200
Subject: [PATCH 25/40] Reenable prevcycle (#5385)

* fixes 5369 - fallback to 0 in case stored preview cycle pos does no longer exist

* reenable preview cycling

* remove ref to BasePanel

* unused imports

* update changelog

* incorporated suggestions

* add next/previousPreviewStyle() to EntryEditorTab

* checkstyle...
---
 CHANGELOG.md                                  |  5 ++
 src/main/java/org/jabref/gui/BasePanel.java   | 25 +++-------
 .../jabref/gui/entryeditor/EntryEditor.java   | 13 +++--
 .../gui/entryeditor/EntryEditorTab.java       | 14 ++++++
 .../gui/entryeditor/FieldsEditorTab.java      | 14 +++++-
 .../org/jabref/gui/preview/PreviewPanel.java  | 50 +++++++++++--------
 6 files changed, 73 insertions(+), 48 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index b71f0091dcd..c2285cad78e 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -33,6 +33,11 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - We fixed an exception which occured when trying to open a non existing file from the "Recent files"-menu [#5334](https://github.com/JabRef/jabref/issues/5334)
 - The context menu for fields in the entry editor is back. [#5254](https://github.com/JabRef/jabref/issues/5254)
 - We fixed an exception which occurred when trying to open a non existing file from the "Recent files"-menu [#5334](https://github.com/JabRef/jabref/issues/5334)
+- We re-introduced the feature to switch between different preview styles. [#5221](https://github.com/JabRef/jabref/issues/5221)
+
+
+
+
 
 ### Removed
 
diff --git a/src/main/java/org/jabref/gui/BasePanel.java b/src/main/java/org/jabref/gui/BasePanel.java
index b35a6bdce4d..30cc6f4aecb 100644
--- a/src/main/java/org/jabref/gui/BasePanel.java
+++ b/src/main/java/org/jabref/gui/BasePanel.java
@@ -95,7 +95,6 @@
 import org.jabref.model.entry.field.SpecialFieldValue;
 import org.jabref.model.entry.field.StandardField;
 import org.jabref.preferences.JabRefPreferences;
-import org.jabref.preferences.PreviewPreferences;
 
 import com.google.common.eventbus.Subscribe;
 import org.fxmisc.easybind.EasyBind;
@@ -352,6 +351,13 @@ private void setupActions() {
                     new SpecialFieldViewModel(SpecialField.READ_STATUS, undoManager).getSpecialFieldAction(status, this.frame));
         }
 
+        actions.put(Actions.NEXT_PREVIEW_STYLE, () -> {
+            entryEditor.nextPreviewStyle();
+        });
+        actions.put(Actions.PREVIOUS_PREVIEW_STYLE, () -> {
+            entryEditor.previousPreviewStyle();
+        });
+
         actions.put(Actions.SEND_AS_EMAIL, new SendAsEMailAction(frame));
 
         actions.put(Actions.WRITE_XMP, new WriteXMPAction(this)::execute);
@@ -844,23 +850,6 @@ private void showAndEdit() {
         }
     }
 
-    public void nextPreviewStyle() {
-        cyclePreview(Globals.prefs.getPreviewPreferences().getPreviewCyclePosition() + 1);
-    }
-
-    public void previousPreviewStyle() {
-        cyclePreview(Globals.prefs.getPreviewPreferences().getPreviewCyclePosition() - 1);
-    }
-
-    private void cyclePreview(int newPosition) {
-        PreviewPreferences previewPreferences = Globals.prefs.getPreviewPreferences()
-                                                             .getBuilder()
-                                                             .withPreviewCyclePosition(newPosition)
-                                                             .build();
-        Globals.prefs.storePreviewPreferences(previewPreferences);
-        entryEditor.updatePreviewInTabs(previewPreferences);
-    }
-
     /**
      * Removes the bottom component.
      */
diff --git a/src/main/java/org/jabref/gui/entryeditor/EntryEditor.java b/src/main/java/org/jabref/gui/entryeditor/EntryEditor.java
index dadcad8be9c..9bd2a2a9c4c 100644
--- a/src/main/java/org/jabref/gui/entryeditor/EntryEditor.java
+++ b/src/main/java/org/jabref/gui/entryeditor/EntryEditor.java
@@ -50,7 +50,6 @@
 import org.jabref.model.entry.field.Field;
 import org.jabref.model.util.FileUpdateMonitor;
 import org.jabref.preferences.PreferencesService;
-import org.jabref.preferences.PreviewPreferences;
 
 import com.airhacks.afterburner.views.ViewLoader;
 import org.fxmisc.easybind.EasyBind;
@@ -404,11 +403,11 @@ public void setFocusToField(Field field) {
         });
     }
 
-    public void updatePreviewInTabs(PreviewPreferences previewPreferences) {
-        for (Tab tab : this.entryEditorTabs) {
-            if (tab instanceof FieldsEditorTab) {
-                ((FieldsEditorTab) tab).previewPanel.updateLayout(previewPreferences);
-            }
-        }
+    public void nextPreviewStyle() {
+        this.entryEditorTabs.forEach(EntryEditorTab::nextPreviewStyle);
+    }
+
+    public void previousPreviewStyle() {
+        this.entryEditorTabs.forEach(EntryEditorTab::previousPreviewStyle);
     }
 }
diff --git a/src/main/java/org/jabref/gui/entryeditor/EntryEditorTab.java b/src/main/java/org/jabref/gui/entryeditor/EntryEditorTab.java
index a0b91a914f7..6c5da5ec0f6 100644
--- a/src/main/java/org/jabref/gui/entryeditor/EntryEditorTab.java
+++ b/src/main/java/org/jabref/gui/entryeditor/EntryEditorTab.java
@@ -44,4 +44,18 @@ public void notifyAboutFocus(BibEntry entry) {
         handleFocus();
     }
 
+    /**
+     * Switch to next Preview style - should be overriden if a EntryEditorTab is actually showing a preview
+     */
+    protected void nextPreviewStyle() {
+        // do nothing by default
+    }
+
+    /**
+     * Switch to previous Preview style - should be overriden if a EntryEditorTab is actually showing a preview
+     */
+    protected void previousPreviewStyle() {
+        // do nothing by default
+    }
+
 }
diff --git a/src/main/java/org/jabref/gui/entryeditor/FieldsEditorTab.java b/src/main/java/org/jabref/gui/entryeditor/FieldsEditorTab.java
index ce226b512f8..eba5b206523 100644
--- a/src/main/java/org/jabref/gui/entryeditor/FieldsEditorTab.java
+++ b/src/main/java/org/jabref/gui/entryeditor/FieldsEditorTab.java
@@ -40,12 +40,12 @@
  * A single tab displayed in the EntryEditor holding several FieldEditors.
  */
 abstract class FieldsEditorTab extends EntryEditorTab {
-    public PreviewPanel previewPanel;
     protected final BibDatabaseContext databaseContext;
     private final Map<Field, FieldEditorFX> editors = new LinkedHashMap<>();
     private final boolean isCompressed;
     private final SuggestionProviders suggestionProviders;
     private final DialogService dialogService;
+    private PreviewPanel previewPanel;
     private FieldEditorFX activeField;
     private UndoManager undoManager;
     private Collection<Field> fields = new ArrayList<>();
@@ -197,6 +197,16 @@ protected void bindToEntry(BibEntry entry) {
         });
     }
 
+    @Override
+    protected void nextPreviewStyle() {
+        previewPanel.nextPreviewStyle();
+    }
+
+    @Override
+    protected void previousPreviewStyle() {
+        previewPanel.previousPreviewStyle();
+    }
+
     protected abstract SortedSet<Field> determineFieldsToShow(BibEntry entry);
 
     public Collection<Field> getShownFields() {
@@ -208,7 +218,7 @@ private void initPanel() {
             gridPane = new GridPane();
             gridPane.getStyleClass().add("editorPane");
 
-            previewPanel = new PreviewPanel(databaseContext, null, dialogService, ExternalFileTypes.getInstance(), Globals.getKeyPrefs(), Globals.prefs.getPreviewPreferences());
+            previewPanel = new PreviewPanel(databaseContext, dialogService, ExternalFileTypes.getInstance(), Globals.getKeyPrefs(), Globals.prefs);
 
             // Warp everything in a scroll-pane
             ScrollPane scrollPane = new ScrollPane();
diff --git a/src/main/java/org/jabref/gui/preview/PreviewPanel.java b/src/main/java/org/jabref/gui/preview/PreviewPanel.java
index c4fbde25a1e..3f25375cf5b 100644
--- a/src/main/java/org/jabref/gui/preview/PreviewPanel.java
+++ b/src/main/java/org/jabref/gui/preview/PreviewPanel.java
@@ -17,7 +17,6 @@
 import javafx.scene.layout.VBox;
 
 import org.jabref.Globals;
-import org.jabref.gui.BasePanel;
 import org.jabref.gui.DialogService;
 import org.jabref.gui.externalfiles.ExternalFilesEntryLinker;
 import org.jabref.gui.externalfiletype.ExternalFileTypes;
@@ -28,6 +27,7 @@
 import org.jabref.logic.l10n.Localization;
 import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.entry.BibEntry;
+import org.jabref.preferences.JabRefPreferences;
 import org.jabref.preferences.PreviewPreferences;
 
 import org.slf4j.Logger;
@@ -40,18 +40,19 @@ public class PreviewPanel extends VBox {
     private final ExternalFilesEntryLinker fileLinker;
     private final KeyBindingRepository keyBindingRepository;
     private final PreviewViewer previewView;
+    private final JabRefPreferences preferences;
     private BibEntry entry;
-    private BasePanel basePanel;
     private DialogService dialogService;
 
-    public PreviewPanel(BibDatabaseContext database, BasePanel basePanel, DialogService dialogService, ExternalFileTypes externalFileTypes, KeyBindingRepository keyBindingRepository, PreviewPreferences preferences) {
-        this.basePanel = basePanel;
+    public PreviewPanel(BibDatabaseContext database, DialogService dialogService, ExternalFileTypes externalFileTypes, KeyBindingRepository keyBindingRepository, JabRefPreferences preferences) {
         this.keyBindingRepository = keyBindingRepository;
         this.dialogService = dialogService;
-        fileLinker = new ExternalFilesEntryLinker(externalFileTypes, Globals.prefs.getFilePreferences(), database);
+        this.preferences = preferences;
+        fileLinker = new ExternalFilesEntryLinker(externalFileTypes, preferences.getFilePreferences(), database);
 
+        PreviewPreferences previewPreferences = preferences.getPreviewPreferences();
         previewView = new PreviewViewer(database, dialogService, Globals.stateManager);
-        previewView.setLayout(preferences.getCurrentPreviewStyle());
+        previewView.setLayout(previewPreferences.getCurrentPreviewStyle());
         previewView.setContextMenu(createPopupMenu());
         previewView.setOnDragDetected(event -> {
             previewView.startFullDrag();
@@ -97,11 +98,7 @@ public PreviewPanel(BibDatabaseContext database, BasePanel basePanel, DialogServ
         this.getChildren().add(previewView);
 
         createKeyBindings();
-        updateLayout(preferences, true);
-    }
-
-    public void close() {
-        basePanel.closeBottomPane();
+        updateLayout(previewPreferences, true);
     }
 
     public void updateLayout(PreviewPreferences previewPreferences) {
@@ -111,6 +108,7 @@ public void updateLayout(PreviewPreferences previewPreferences) {
     private void updateLayout(PreviewPreferences previewPreferences, boolean init) {
         PreviewLayout currentPreviewStyle = previewPreferences.getCurrentPreviewStyle();
         previewView.setLayout(currentPreviewStyle);
+        preferences.storePreviewPreferences(previewPreferences);
         if (!init) {
             dialogService.notify(Localization.lang("Preview style changed to: %0", currentPreviewStyle.getName()));
         }
@@ -125,10 +123,6 @@ private void createKeyBindings() {
                         previewView.copyPreviewToClipBoard();
                         event.consume();
                         break;
-                    case CLOSE:
-                        close();
-                        event.consume();
-                        break;
                     default:
                 }
             }
@@ -141,21 +135,19 @@ private ContextMenu createPopupMenu() {
         copyPreview.setOnAction(event -> previewView.copyPreviewToClipBoard());
         MenuItem printEntryPreview = new MenuItem(Localization.lang("Print entry preview"), IconTheme.JabRefIcons.PRINTED.getGraphicNode());
         printEntryPreview.setOnAction(event -> previewView.print());
-        /* Deleted since it does not work anymore. Needs refactoring.
         MenuItem previousPreviewLayout = new MenuItem(Localization.lang("Previous preview layout"));
         previousPreviewLayout.setAccelerator(keyBindingRepository.getKeyCombination(KeyBinding.PREVIOUS_PREVIEW_LAYOUT));
-        previousPreviewLayout.setOnAction(event -> basePanel.previousPreviewStyle());
+        previousPreviewLayout.setOnAction(event -> this.previousPreviewStyle());
         MenuItem nextPreviewLayout = new MenuItem(Localization.lang("Next preview layout"));
         nextPreviewLayout.setAccelerator(keyBindingRepository.getKeyCombination(KeyBinding.NEXT_PREVIEW_LAYOUT));
-        nextPreviewLayout.setOnAction(event -> basePanel.nextPreviewStyle());
-        */
+        nextPreviewLayout.setOnAction(event -> this.nextPreviewStyle());
 
         ContextMenu menu = new ContextMenu();
         menu.getItems().add(copyPreview);
         menu.getItems().add(printEntryPreview);
         menu.getItems().add(new SeparatorMenuItem());
-        // menu.getItems().add(nextPreviewLayout);
-        // menu.getItems().add(previousPreviewLayout);
+        menu.getItems().add(nextPreviewLayout);
+        menu.getItems().add(previousPreviewLayout);
         return menu;
     }
 
@@ -167,4 +159,20 @@ public void setEntry(BibEntry entry) {
     public void print() {
         previewView.print();
     }
+
+    public void nextPreviewStyle() {
+        cyclePreview(preferences.getPreviewPreferences().getPreviewCyclePosition() + 1);
+    }
+
+    public void previousPreviewStyle() {
+        cyclePreview(preferences.getPreviewPreferences().getPreviewCyclePosition() - 1);
+    }
+
+    private void cyclePreview(int newPosition) {
+        PreviewPreferences previewPreferences = preferences.getPreviewPreferences()
+                .getBuilder()
+                .withPreviewCyclePosition(newPosition)
+                .build();
+        updateLayout(previewPreferences);
+    }
 }

From bebea3cfa179150aaa53d57384d4f0ab18944d49 Mon Sep 17 00:00:00 2001
From: Tobias Diez <tobiasdiez@gmx.de>
Date: Sun, 6 Oct 2019 09:55:25 +0200
Subject: [PATCH 26/40] Fix exception when merging entries

The problem was that `sourceChanged` was invoked asynchronous and thus the information in the change event could be obsolete if another thread changed the underlying list in the meantime. Solution: run `sourceChanged` on the JavaFX thread but synchronously.
Fixes #5169.
---
 CHANGELOG.md                                  |  1 +
 .../org/jabref/gui/util/UiThreadList.java     | 22 ++++++++++++++++++-
 2 files changed, 22 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index b71f0091dcd..815537f3f2f 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -23,6 +23,7 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - The "All entries group" is no longer shown when no library is open.
 - We fixed an exception which occurred when closing JabRef. [#5348](https://github.com/JabRef/jabref/issues/5348)
 - We fixed an error where the groups containing an entry loose their highlight color when scrolling. [#5022](https://github.com/JabRef/jabref/issues/5022) 
+- We fixed an error where an exception was thrown when merging entries. [#5169](https://github.com/JabRef/jabref/issues/5169)
 - After assigning an entry to a group, the item count is now properly colored to reflect the new membership of the entry. [#3112](https://github.com/JabRef/jabref/issues/3112)
 - The group panel is now properly updated when switching between libraries (or when closing/opening one). [#3142](https://github.com/JabRef/jabref/issues/3142)
 - We fixed an error where the number of matched entries shown in the group pane was not updated correctly. [#4441](https://github.com/JabRef/jabref/issues/4441)
diff --git a/src/main/java/org/jabref/gui/util/UiThreadList.java b/src/main/java/org/jabref/gui/util/UiThreadList.java
index a09efa8957c..b9f8b8853c7 100644
--- a/src/main/java/org/jabref/gui/util/UiThreadList.java
+++ b/src/main/java/org/jabref/gui/util/UiThreadList.java
@@ -1,18 +1,38 @@
 package org.jabref.gui.util;
 
+import java.util.concurrent.CountDownLatch;
+
 import javafx.application.Platform;
 import javafx.collections.ListChangeListener;
 import javafx.collections.ObservableList;
 import javafx.collections.transformation.TransformationList;
 
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
 class UiThreadList<T> extends TransformationList<T, T> {
+    private static final Logger LOGGER = LoggerFactory.getLogger(UiThreadList.class);
     public UiThreadList(ObservableList<? extends T> source) {
         super(source);
     }
 
     @Override
     protected void sourceChanged(ListChangeListener.Change<? extends T> change) {
-        Platform.runLater(() -> fireChange(change));
+        if (Platform.isFxApplicationThread()) {
+            fireChange(change);
+        } else {
+            CountDownLatch latch = new CountDownLatch(1);
+            Platform.runLater(() -> {
+                fireChange(change);
+                latch.countDown();
+            });
+
+            try {
+                latch.await();
+            } catch (InterruptedException e) {
+                LOGGER.error("Error while running on JavaFX thread", e);
+            }
+        }
     }
 
     @Override

From 9c7f7f61c40443b3688af16c0d95c54a78900f87 Mon Sep 17 00:00:00 2001
From: Matthias Geiger <matthias.geiger@uni-bamberg.de>
Date: Sun, 6 Oct 2019 10:19:14 +0200
Subject: [PATCH 27/40] Fix 5359: Writing of Editor field is duplicated (#5392)

* add (failing) test for #5359

* fixes #5359 - correction writing of OrFields in BibEntryWriter

* add changelog entry
---
 CHANGELOG.md                                  |  5 +-
 .../jabref/logic/bibtex/BibEntryWriter.java   |  2 +-
 .../logic/bibtex/BibEntryWriterTest.java      | 58 +++++++++++++++++++
 3 files changed, 60 insertions(+), 5 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index c2285cad78e..9a4e50fdea6 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -33,12 +33,9 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - We fixed an exception which occured when trying to open a non existing file from the "Recent files"-menu [#5334](https://github.com/JabRef/jabref/issues/5334)
 - The context menu for fields in the entry editor is back. [#5254](https://github.com/JabRef/jabref/issues/5254)
 - We fixed an exception which occurred when trying to open a non existing file from the "Recent files"-menu [#5334](https://github.com/JabRef/jabref/issues/5334)
+- We fixed a problem where the "editor" information has been duplicated during saving a .bib-Database. [#5359](https://github.com/JabRef/jabref/issues/5359)
 - We re-introduced the feature to switch between different preview styles. [#5221](https://github.com/JabRef/jabref/issues/5221)
 
-
-
-
-
 ### Removed
 
 
diff --git a/src/main/java/org/jabref/logic/bibtex/BibEntryWriter.java b/src/main/java/org/jabref/logic/bibtex/BibEntryWriter.java
index 4169df2da8f..2f1bce49674 100644
--- a/src/main/java/org/jabref/logic/bibtex/BibEntryWriter.java
+++ b/src/main/java/org/jabref/logic/bibtex/BibEntryWriter.java
@@ -111,7 +111,7 @@ private void writeRequiredFieldsFirstRemainingFieldsSecond(BibEntry entry, Write
             for (OrFields value : type.get().getRequiredFields()) {
                 for (Field field : value) {
                     writeField(entry, out, field, indentation);
-                    written.add(value.getPrimary());
+                    written.add(field);
                 }
             }
             // Then optional fields.
diff --git a/src/test/java/org/jabref/logic/bibtex/BibEntryWriterTest.java b/src/test/java/org/jabref/logic/bibtex/BibEntryWriterTest.java
index 3c158a64d53..5b2d91b77c3 100644
--- a/src/test/java/org/jabref/logic/bibtex/BibEntryWriterTest.java
+++ b/src/test/java/org/jabref/logic/bibtex/BibEntryWriterTest.java
@@ -106,6 +106,64 @@ void writeEntryWithFile() throws Exception {
                 + "}" + OS.NEWLINE, stringWriter.toString());
     }
 
+    @Test
+    void writeEntryWithOrField() throws Exception {
+            StringWriter stringWriter = new StringWriter();
+
+            BibEntry entry = new BibEntry(StandardEntryType.InBook);
+            //set an required OR field (author/editor)
+            entry.setField(StandardField.EDITOR, "Foo Bar");
+            entry.setField(StandardField.JOURNAL, "International Journal of Something");
+            //set an optional field
+            entry.setField(StandardField.NUMBER, "1");
+            entry.setField(StandardField.NOTE, "some note");
+
+            writer.write(entry, stringWriter, BibDatabaseMode.BIBTEX);
+
+            String actual = stringWriter.toString();
+
+            // @formatter:off
+            String expected = OS.NEWLINE + "@InBook{," + OS.NEWLINE +
+                    "  editor  = {Foo Bar}," + OS.NEWLINE +
+                    "  note    = {some note}," + OS.NEWLINE +
+                    "  number  = {1}," + OS.NEWLINE +
+                    "  journal = {International Journal of Something}," + OS.NEWLINE +
+                    "}" + OS.NEWLINE;
+            // @formatter:on
+
+            assertEquals(expected, actual);
+    }
+
+    @Test
+    void writeEntryWithOrFieldBothFieldsPresent() throws Exception {
+        StringWriter stringWriter = new StringWriter();
+
+        BibEntry entry = new BibEntry(StandardEntryType.InBook);
+        //set an required OR field with both fields(author/editor)
+        entry.setField(StandardField.AUTHOR, "Foo Thor");
+        entry.setField(StandardField.EDITOR, "Edi Bar");
+        entry.setField(StandardField.JOURNAL, "International Journal of Something");
+        //set an optional field
+        entry.setField(StandardField.NUMBER, "1");
+        entry.setField(StandardField.NOTE, "some note");
+
+        writer.write(entry, stringWriter, BibDatabaseMode.BIBTEX);
+
+        String actual = stringWriter.toString();
+
+        // @formatter:off
+        String expected = OS.NEWLINE + "@InBook{," + OS.NEWLINE +
+                "  author  = {Foo Thor}," + OS.NEWLINE +
+                "  editor  = {Edi Bar}," + OS.NEWLINE +
+                "  note    = {some note}," + OS.NEWLINE +
+                "  number  = {1}," + OS.NEWLINE +
+                "  journal = {International Journal of Something}," + OS.NEWLINE +
+                "}" + OS.NEWLINE;
+        // @formatter:on
+
+        assertEquals(expected, actual);
+    }
+
     @Test
     public void writeReallyUnknownTypeTest() throws Exception {
         String expected = OS.NEWLINE + "@Reallyunknowntype{test," + OS.NEWLINE +

From 9117fff18e771f2b1cb23e0dfcc83b0550f63fac Mon Sep 17 00:00:00 2001
From: Matthias Geiger <matthias.geiger@uni-bamberg.de>
Date: Sun, 6 Oct 2019 11:25:14 +0200
Subject: [PATCH 28/40] Fix various copy to clipboard issues (#5340)

* fix plain text copy in preview viewer

* put textual representation also to clipboard

* fix tests

* improve "Export to Clipboard" function

* fix checkstyle

* fix plain text copy in preview viewer (a bit more intelligent ;-))

* filter exporter list to supported exporters only

* update CHANGELOG.md

* fix checkstyle

* improve exception handling

* checkstyle
---
 CHANGELOG.md                                  |  4 ++
 .../gui/exporter/ExportToClipboardAction.java | 40 +++++++++++++++----
 .../CitationStyleToClipboardWorker.java       | 12 ++++--
 .../org/jabref/gui/preview/PreviewViewer.java | 12 +-----
 .../CitationStyleToClipboardWorkerTest.java   |  7 ++--
 5 files changed, 50 insertions(+), 25 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 9a4e50fdea6..2f9f21900f8 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -35,6 +35,10 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - We fixed an exception which occurred when trying to open a non existing file from the "Recent files"-menu [#5334](https://github.com/JabRef/jabref/issues/5334)
 - We fixed a problem where the "editor" information has been duplicated during saving a .bib-Database. [#5359](https://github.com/JabRef/jabref/issues/5359)
 - We re-introduced the feature to switch between different preview styles. [#5221](https://github.com/JabRef/jabref/issues/5221)
+- We fixed various issues (including [#5263](https://github.com/JabRef/jabref/issues/5263)) related to copying entries to the clipboard
+
+
+
 
 ### Removed
 
diff --git a/src/main/java/org/jabref/gui/exporter/ExportToClipboardAction.java b/src/main/java/org/jabref/gui/exporter/ExportToClipboardAction.java
index 122b5baf610..94b63150d15 100644
--- a/src/main/java/org/jabref/gui/exporter/ExportToClipboardAction.java
+++ b/src/main/java/org/jabref/gui/exporter/ExportToClipboardAction.java
@@ -5,6 +5,7 @@
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.Comparator;
 import java.util.List;
 import java.util.Optional;
@@ -20,6 +21,7 @@
 import org.jabref.gui.util.BackgroundTask;
 import org.jabref.logic.exporter.Exporter;
 import org.jabref.logic.l10n.Localization;
+import org.jabref.logic.util.FileType;
 import org.jabref.logic.util.OS;
 import org.jabref.model.entry.BibEntry;
 import org.jabref.preferences.JabRefPreferences;
@@ -31,6 +33,9 @@ public class ExportToClipboardAction extends SimpleCommand {
 
     private static final Logger LOGGER = LoggerFactory.getLogger(ExportToClipboardAction.class);
 
+    // Only text based exporters can be used
+    private static final List<String> SUPPORTED_FILETYPES = Arrays.asList("txt", "rtf", "rdf", "xml", "html", "htm", "csv", "ris");
+
     private JabRefFrame frame;
     private final DialogService dialogService;
     private BasePanel panel;
@@ -59,6 +64,7 @@ public void execute() {
 
         List<Exporter> exporters = Globals.exportFactory.getExporters().stream()
                                                         .sorted(Comparator.comparing(Exporter::getName))
+                                                        .filter(exporter -> SUPPORTED_FILETYPES.containsAll(exporter.getFileType().getExtensions()))
                                                         .collect(Collectors.toList());
 
         //Find default choice, if any
@@ -71,12 +77,12 @@ public void execute() {
                 Localization.lang("Export"), defaultChoice, exporters);
 
         selectedExporter.ifPresent(exporter -> BackgroundTask.wrap(() -> exportToClipboard(exporter))
-                                                             .onSuccess(this::setContentToClipboard)
-                                                             .executeWith(Globals.TASK_EXECUTOR));
-
+                                                                .onSuccess(this::setContentToClipboard)
+                                                                .onFailure(ex -> { /* swallow as already logged */ })
+                                                                .executeWith(Globals.TASK_EXECUTOR));
     }
 
-    private String exportToClipboard(Exporter exporter) {
+    private ExportResult exportToClipboard(Exporter exporter) throws Exception {
         // Set the global variable for this database's file directory before exporting,
         // so formatters can resolve linked files correctly.
         // (This is an ugly hack!)
@@ -102,9 +108,10 @@ private String exportToClipboard(Exporter exporter) {
                             entries);
             // Read the file and put the contents on the clipboard:
 
-            return readFileToString(tmp);
+            return new ExportResult(readFileToString(tmp), exporter.getFileType());
         } catch (Exception e) {
             LOGGER.error("Error exporting to clipboard", e);
+            throw new Exception("Rethrow ", e);
         } finally {
             // Clean up:
             if ((tmp != null) && Files.exists(tmp)) {
@@ -115,12 +122,19 @@ private String exportToClipboard(Exporter exporter) {
                 }
             }
         }
-        return "";
     }
 
-    private void setContentToClipboard(String content) {
+    private void setContentToClipboard(ExportResult result) {
         ClipboardContent clipboardContent = new ClipboardContent();
-        clipboardContent.putRtf(content);
+        List<String> extensions = result.fileType.getExtensions();
+        if (extensions.contains("html")) {
+            clipboardContent.putHtml(result.content);
+        } else if (extensions.contains("rtf")) {
+            clipboardContent.putRtf(result.content);
+        } else if (extensions.contains("rdf")) {
+            clipboardContent.putRtf(result.content);
+        }
+        clipboardContent.putString(result.content);
         Globals.clipboardManager.setContent(clipboardContent);
 
         dialogService.notify(Localization.lang("Entries exported to clipboard") + ": " + entries.size());
@@ -135,4 +149,14 @@ private String readFileToString(Path tmp) throws IOException {
             return reader.lines().collect(Collectors.joining(OS.NEWLINE));
         }
     }
+
+    private class ExportResult {
+        final String content;
+        final FileType fileType;
+
+        ExportResult(String content, FileType fileType) {
+            this.content = content;
+            this.fileType = fileType;
+        }
+    }
 }
diff --git a/src/main/java/org/jabref/gui/preview/CitationStyleToClipboardWorker.java b/src/main/java/org/jabref/gui/preview/CitationStyleToClipboardWorker.java
index 80299068046..23a4f056d36 100644
--- a/src/main/java/org/jabref/gui/preview/CitationStyleToClipboardWorker.java
+++ b/src/main/java/org/jabref/gui/preview/CitationStyleToClipboardWorker.java
@@ -87,8 +87,11 @@ private List<String> generateCitations() throws IOException {
      * Generates a plain text string out of the preview and copies it additionally to the html to the clipboard
      * (WYSIWYG Editors use the HTML, plain text editors the text)
      */
-    protected static String processPreview(List<String> citations) {
-        return String.join(CitationStyleOutputFormat.HTML.getLineSeparator(), citations);
+    protected static ClipboardContent processPreview(List<String> citations) {
+        ClipboardContent content = new ClipboardContent();
+        content.putHtml(String.join(CitationStyleOutputFormat.HTML.getLineSeparator(), citations));
+        content.putString(String.join(CitationStyleOutputFormat.HTML.getLineSeparator(), citations));
+        return content;
     }
 
     /**
@@ -108,6 +111,7 @@ protected static ClipboardContent processRtf(List<String> citations) {
                         String.join(CitationStyleOutputFormat.RTF.getLineSeparator(), citations) +
                         "}";
         ClipboardContent content = new ClipboardContent();
+        content.putString(result);
         content.putRtf(result);
         return content;
     }
@@ -134,6 +138,7 @@ protected static ClipboardContent processXslFo(List<String> citations) {
                   "</fo:root>" + OS.NEWLINE;
 
         ClipboardContent content = new ClipboardContent();
+        content.putString(result);
         content.put(ClipBoardManager.XML, result);
         return content;
     }
@@ -155,6 +160,7 @@ protected static ClipboardContent processHtml(List<String> citations) {
                   "</html>" + OS.NEWLINE;
 
         ClipboardContent content = new ClipboardContent();
+        content.putString(result);
         content.putHtml(result);
         return content;
     }
@@ -162,7 +168,7 @@ protected static ClipboardContent processHtml(List<String> citations) {
     private void setClipBoardContent(List<String> citations) {
         // if it's not a citation style take care of the preview
         if (!(style instanceof  CitationStylePreviewLayout)) {
-            clipBoardManager.setHtmlContent(processPreview(citations));
+            clipBoardManager.setContent(processPreview(citations));
         } else {
             // if it's generated by a citation style take care of each output format
             ClipboardContent content;
diff --git a/src/main/java/org/jabref/gui/preview/PreviewViewer.java b/src/main/java/org/jabref/gui/preview/PreviewViewer.java
index 8811d398b88..c3d0ec4b405 100644
--- a/src/main/java/org/jabref/gui/preview/PreviewViewer.java
+++ b/src/main/java/org/jabref/gui/preview/PreviewViewer.java
@@ -29,8 +29,6 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.w3c.dom.Document;
-import org.w3c.dom.Element;
-import org.w3c.dom.NodeList;
 
 /**
  * Displays an BibEntry using the given layout format.
@@ -175,16 +173,8 @@ public void copyPreviewToClipBoard() {
         StringBuilder previewStringContent = new StringBuilder();
         Document document = previewView.getEngine().getDocument();
 
-        NodeList nodeList = document.getElementsByTagName("html");
-
-        //Nodelist does not implement iterable
-        for (int i = 0; i < nodeList.getLength(); i++) {
-            Element element = (Element) nodeList.item(i);
-            previewStringContent.append(element.getTextContent());
-        }
-
         ClipboardContent content = new ClipboardContent();
-        content.putString(previewStringContent.toString());
+        content.putString(document.getElementById("content").getTextContent());
         content.putHtml((String) previewView.getEngine().executeScript("document.documentElement.outerHTML"));
 
         clipBoardManager.setContent(content);
diff --git a/src/test/java/org/jabref/gui/preview/CitationStyleToClipboardWorkerTest.java b/src/test/java/org/jabref/gui/preview/CitationStyleToClipboardWorkerTest.java
index 0ac88a6d323..82501d0e182 100644
--- a/src/test/java/org/jabref/gui/preview/CitationStyleToClipboardWorkerTest.java
+++ b/src/test/java/org/jabref/gui/preview/CitationStyleToClipboardWorkerTest.java
@@ -39,7 +39,8 @@ void processPreviewText() throws Exception {
                 OS.NEWLINE +
                 "Abstract:  This entry describes a test scenario which may be useful in JabRef. By providing a test entry it is possible to see how certain things will look in this graphical BIB-file mananger. ";
 
-        String actual = CitationStyleToClipboardWorker.processPreview(Arrays.asList(citation, citation));
+        ClipboardContent clipboardContent = CitationStyleToClipboardWorker.processPreview(Arrays.asList(citation, citation));
+        String actual = clipboardContent.getString();
 
         assertEquals(expected, actual);
     }
@@ -91,8 +92,8 @@ void processPreviewHtml() throws Exception {
                 "</dd>" + OS.NEWLINE +
                 "<p></p></font>";
 
-        String actual = CitationStyleToClipboardWorker.processPreview(Arrays.asList(citation, citation));
-
+        ClipboardContent clipboardContent = CitationStyleToClipboardWorker.processPreview(Arrays.asList(citation, citation));
+        String actual = clipboardContent.getString();
         assertEquals(expected, actual);
     }
 

From b7b93a4d17c48b5b750cd2acc90f9fbc0f621650 Mon Sep 17 00:00:00 2001
From: Steffin Stanly <32876873+steffinstanly@users.noreply.github.com>
Date: Sun, 6 Oct 2019 17:01:11 +0530
Subject: [PATCH 29/40] Update CHANGELOG.md

---
 CHANGELOG.md | 32 ++++++++++++++++----------------
 1 file changed, 16 insertions(+), 16 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 2f9f21900f8..d4e0815b371 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -13,7 +13,7 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 
 ### Changed
 
-- We added a short DOI field formatter which shortens DOI to more human readable form. [koppor#343](https://github.com/koppor/jabref/issues/343)
+- We added a short DOI field formatter which shortens DOI to more human-readable form. [koppor#343](https://github.com/koppor/jabref/issues/343)
 - We improved the display of group memberships by adding multiple colored bars if the entry belongs to more than one group. [#4574](https://github.com/JabRef/jabref/issues/4574)
 
 ### Fixed
@@ -30,9 +30,9 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - We fixed an error where the default color of a new group was white instead of dark gray. [#4868](https://github.com/JabRef/jabref/issues/4868)
 - We fixed an error mentioning "javafx.controls/com.sun.javafx.scene.control" that was thrown when interacting with the toolbar.
 - We fixed an error where a cleared search was restored after switching libraries. [#4846](https://github.com/JabRef/jabref/issues/4846) 
-- We fixed an exception which occured when trying to open a non existing file from the "Recent files"-menu [#5334](https://github.com/JabRef/jabref/issues/5334)
+- We fixed an exception which occurred when trying to open a non-existing file from the "Recent files"-menu [#5334](https://github.com/JabRef/jabref/issues/5334)
 - The context menu for fields in the entry editor is back. [#5254](https://github.com/JabRef/jabref/issues/5254)
-- We fixed an exception which occurred when trying to open a non existing file from the "Recent files"-menu [#5334](https://github.com/JabRef/jabref/issues/5334)
+- We fixed an exception which occurred when trying to open a non-existing file from the "Recent files"-menu [#5334](https://github.com/JabRef/jabref/issues/5334)
 - We fixed a problem where the "editor" information has been duplicated during saving a .bib-Database. [#5359](https://github.com/JabRef/jabref/issues/5359)
 - We re-introduced the feature to switch between different preview styles. [#5221](https://github.com/JabRef/jabref/issues/5221)
 - We fixed various issues (including [#5263](https://github.com/JabRef/jabref/issues/5263)) related to copying entries to the clipboard
@@ -107,11 +107,11 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
   - Moreover, empty deprecated fields are no longer shown
 - Added server timezone parameter when connecting to a shared database.
 - We updated the dialog for setting up general fields.
-- URL field formatting is updated. All whitespace chars, located at the beginning/ending of the url, are trimmed automatically
+- URL field formatting is updated. All whitespace chars, located at the beginning/ending of the URL, are trimmed automatically
 - We changed the behavior of the field formatting dialog such that the `bibtexkey` is not changed when formatting all fields or all text fields.
 - We added a "Move file to file directory and rename file" option for simultaneously moving and renaming of document file. [#4166](https://github.com/JabRef/jabref/issues/4166)
 - Use integrated graphics card instead of discrete on macOS [#4070](https://github.com/JabRef/jabref/issues/4070)
-- We added a cleanup operation that detects an arXiv identifier in the note, journal or url field and moves it to the `eprint` field.
+- We added a cleanup operation that detects an arXiv identifier in the note, journal or URL field and moves it to the `eprint` field.
   Because of this change, the last-used cleanup operations were reset.
 - We changed the minimum required version of Java to 1.8.0_171, as this is the latest release for which the automatic Java update works.  [#4093](https://github.com/JabRef/jabref/issues/4093)
 - The special fields like `Printed` and `Read status` now show gray icons when the row is hovered.
@@ -130,18 +130,18 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - Files without a defined external file type are now directly opened with the default application of the operating system
 - We streamlined the process to rename and move files by removing the confirmation dialogs.
 - We removed the redundant new lines of markings and wrapped the summary in the File annotation tab. [#3823](https://github.com/JabRef/jabref/issues/3823)
-- We add auto url formatting when user paste link to URL field in entry editor. [koppor#254](https://github.com/koppor/jabref/issues/254)
-- We added a minimal height for the entry editor so that it can no longer be hidden by accident. [#4279](https://github.com/JabRef/jabref/issues/4279)
+- We add auto URL formatting when user paste link to URL field in entry editor. [koppor#254](https://github.com/koppor/jabref/issues/254)
+- We added a minimum height for the entry editor so that it can no longer be hidden by accident. [#4279](https://github.com/JabRef/jabref/issues/4279)
 - We added a new keyboard shortcut so that the entry editor could be closed by <kbd>Ctrl</kbd> + <kbd>E</kbd>. [#4222] (https://github.com/JabRef/jabref/issues/4222)
 - We added an option in the preference dialog box, that allows user to pick the dark or light theme option. [#4130] (https://github.com/JabRef/jabref/issues/4130)
-- We updated updated the Related Articles tab to accept JSON from the new version of the Mr. DLib service
+- We updated the Related Articles tab to accept JSON from the new version of the Mr. DLib service
 - We added an option in the preference dialog box that allows user to choose behavior after dragging and dropping files in Entry Editor. [#4356](https://github.com/JabRef/jabref/issues/4356)
 - We added the ability to have an export preference where previously "File"-->"Export"/"Export selected entries" would not save the user's preference[#4495](https://github.com/JabRef/jabref/issues/4495)
 - We optimized the code responsible for connecting to an external database, which should lead to huge improvements in performance.
 - For automatically created groups, added ability to filter groups by entry type. [#4539](https://github.com/JabRef/jabref/issues/4539)
 - We added the ability to add field names from the Preferences Dialog [#4546](https://github.com/JabRef/jabref/issues/4546)
-- We added the ability change the column widths directly in the main table. [#4546](https://github.com/JabRef/jabref/issues/4546)
-- We added description of how recommendations where chosen and better error handling to Related Articles tab
+- We added the ability to change the column widths directly in the main table. [#4546](https://github.com/JabRef/jabref/issues/4546)
+- We added a description of how recommendations were chosen and better error handling to Related Articles tab
 - We added the ability to execute default action in dialog by using with <kbd>Ctrl</kbd> + <kbd>Enter</kbd> combination [#4496](https://github.com/JabRef/jabref/issues/4496)
 - We grouped and reordered the Main Menu (File, Edit, Library, Quality, Tools, and View tabs & icons). [#4666](https://github.com/JabRef/jabref/issues/4666) [#4667](https://github.com/JabRef/jabref/issues/4667) [#4668](https://github.com/JabRef/jabref/issues/4668) [#4669](https://github.com/JabRef/jabref/issues/4669) [#4670](https://github.com/JabRef/jabref/issues/4670) [#4671](https://github.com/JabRef/jabref/issues/4671) [#4672](https://github.com/JabRef/jabref/issues/4672) [#4673](https://github.com/JabRef/jabref/issues/4673)
 - We added additional modifiers (capitalize, titlecase and sentencecase) to the Bibtex key generator. [#1506](https://github.com/JabRef/jabref/issues/1506)
@@ -150,7 +150,7 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - We added a browse button next to the path text field for aux-based groups. [#4586](https://github.com/JabRef/jabref/issues/4586)
 - We changed the title of Group Dialog to "Add subgroup" from "Edit group" when we select Add subgroup option.
 - We enable import button only if entries are selected. [#4755](https://github.com/JabRef/jabref/issues/4755)
-- We made modifications to improve contrast of UI elements. [#4583](https://github.com/JabRef/jabref/issues/4583)
+- We made modifications to improve the contrast of UI elements. [#4583](https://github.com/JabRef/jabref/issues/4583)
 - We added a warning for empty BibTeX keys in the entry editor. [#4440](https://github.com/JabRef/jabref/issues/4440)
 - We added an option in the settings to set the default action in JabRef when right clicking on any entry in any database and selecting "Open folder". [#4763](https://github.com/JabRef/jabref/issues/4763)
 - The Medline fetcher now normalizes the author names according to the BibTeX-Standard [#4345](https://github.com/JabRef/jabref/issues/4345)
@@ -177,7 +177,7 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - We fixed an issue where the group tree was not updated correctly after an entry was changed. https://github.com/JabRef/jabref/issues/3618
 - We fixed an issue where a right-click in the main table selected a wrong entry. https://github.com/JabRef/jabref/issues/3267
 - We fixed an issue where in rare cases entries where overlayed in the main table. https://github.com/JabRef/jabref/issues/3281
-- 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 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)
@@ -210,9 +210,9 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - We fixed an issue where "Move to group" would always move the first entry in the library and not the selected [#4414](https://github.com/JabRef/jabref/issues/4414)
 - We fixed an issue where an older dialog appears when downloading full texts from the quality menu. [#4489](https://github.com/JabRef/jabref/issues/4489)
 - We fixed an issue where right clicking on any entry in any database and selecting "Open folder" results in the NullPointer exception. [#4763](https://github.com/JabRef/jabref/issues/4763)
-- We fixed an issue where option 'open terminal here' with custom command was passing wrong argument. [#4802](https://github.com/JabRef/jabref/issues/4802)
+- We fixed an issue where option 'open terminal here' with custom command was passing the wrong argument. [#4802](https://github.com/JabRef/jabref/issues/4802)
 - We fixed an issue where ranking an entry would generate an IllegalArgumentException. [#4754](https://github.com/JabRef/jabref/issues/4754)
-- We fixed an issue where special characters where removed from non label key generation pattern parts [#4767](https://github.com/JabRef/jabref/issues/4767)
+- We fixed an issue where special characters where removed from non-label key generation pattern parts [#4767](https://github.com/JabRef/jabref/issues/4767)
 - We fixed an issue where the RIS import would overwite the article date with the value of the acessed date [#4816](https://github.com/JabRef/jabref/issues/4816)
 - We fixed an issue where an NullPointer exception was thrown when a referenced entry in an Open/Libre Office document was no longer present in the library. Now an error message with the reference marker of the missing entry is shown. [#4932](https://github.com/JabRef/jabref/issues/4932)
 - We fixed an issue where a database exception related to a missing timezone was too big. [#4827](https://github.com/JabRef/jabref/issues/4827)
@@ -228,13 +228,13 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - The feature to "mark entries" was removed and merged with the groups functionality.  For migration, a group is created for every value of the `__markedentry` field and the entry is added to this group.
 - The number column was removed.
 - We removed the global search feature.
-- We removed the coloring of cells in the maintable according to whether the field is optional/required.
+- We removed the coloring of cells in the main table according to whether the field is optional/required.
 - We removed the feature to find and resolve duplicate BibTeX keys (as this use case is already covered by the integrity check).
 - We removed a few commands from the right-click menu that are not needed often and thus don't need to be placed that prominently:
   - Print entry preview: available through entry preview
   - All commands related to marking: marking is not yet reimplemented
   - Set/clear/append/rename fields: available through Edit menu
-  - Manage keywords: available through Edit menu
+  - Manage keywords: available through the Edit menu
   - Copy linked files to folder: available through File menu
   - Add/move/remove from group: removed completely (functionality still available through group interface)
 - We removed the option to change the column widths in the preferences dialog. [#4546](https://github.com/JabRef/jabref/issues/4546)

From 551ff4c8dd258d7c230d4bc9018b1b8b191c9cef Mon Sep 17 00:00:00 2001
From: Oliver Kopp <kopp.dev@gmail.com>
Date: Sun, 6 Oct 2019 13:34:37 +0200
Subject: [PATCH 30/40] Add hacktoberfest shields.io badge

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 40910c6466a..880a8eaa086 100644
--- a/README.md
+++ b/README.md
@@ -1,4 +1,4 @@
-# JabRef Bibliography Management
+# JabRef Bibliography Management [![Hacktoberfest](https://img.shields.io/github/hacktoberfest/2019/JabRef/jabref?suggestion_label=hacktoberfest)](https://www.jabref.org/hacktoberfest/2019.html)
 
 [![Build Status](https://travis-ci.org/JabRef/jabref.svg?branch=master)](https://travis-ci.org/JabRef/jabref)
 [![codecov.io](https://codecov.io/github/JabRef/jabref/coverage.svg?branch=master)](https://codecov.io/github/JabRef/jabref?branch=master)

From 29026c383a6ed68a7541f0230160a0ac8dcc2654 Mon Sep 17 00:00:00 2001
From: Steffin Stanly <32876873+steffinstanly@users.noreply.github.com>
Date: Sun, 6 Oct 2019 19:49:24 +0530
Subject: [PATCH 31/40] Update CHANGELOG.md

---
 CHANGELOG.md | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index d4e0815b371..aae419279ca 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -140,7 +140,8 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - We optimized the code responsible for connecting to an external database, which should lead to huge improvements in performance.
 - For automatically created groups, added ability to filter groups by entry type. [#4539](https://github.com/JabRef/jabref/issues/4539)
 - We added the ability to add field names from the Preferences Dialog [#4546](https://github.com/JabRef/jabref/issues/4546)
-- We added the ability to change the column widths directly in the main table. [#4546](https://github.com/JabRef/jabref/issues/4546)
+- We added the ability to change the column widths directly in the main 
+. [#4546](https://github.com/JabRef/jabref/issues/4546)
 - We added a description of how recommendations were chosen and better error handling to Related Articles tab
 - We added the ability to execute default action in dialog by using with <kbd>Ctrl</kbd> + <kbd>Enter</kbd> combination [#4496](https://github.com/JabRef/jabref/issues/4496)
 - We grouped and reordered the Main Menu (File, Edit, Library, Quality, Tools, and View tabs & icons). [#4666](https://github.com/JabRef/jabref/issues/4666) [#4667](https://github.com/JabRef/jabref/issues/4667) [#4668](https://github.com/JabRef/jabref/issues/4668) [#4669](https://github.com/JabRef/jabref/issues/4669) [#4670](https://github.com/JabRef/jabref/issues/4670) [#4671](https://github.com/JabRef/jabref/issues/4671) [#4672](https://github.com/JabRef/jabref/issues/4672) [#4673](https://github.com/JabRef/jabref/issues/4673)
@@ -177,7 +178,7 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - We fixed an issue where the group tree was not updated correctly after an entry was changed. https://github.com/JabRef/jabref/issues/3618
 - We fixed an issue where a right-click in the main table selected a wrong entry. https://github.com/JabRef/jabref/issues/3267
 - We fixed an issue where in rare cases entries where overlayed in the main table. https://github.com/JabRef/jabref/issues/3281
-- 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 selecting a group messed up the focus of the main table and the 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)

From 8ba046c048509e1d8047c3edb3a0287bc3f5c0cc Mon Sep 17 00:00:00 2001
From: Tobias Diez <tobiasdiez@gmx.de>
Date: Sun, 6 Oct 2019 22:28:35 +0200
Subject: [PATCH 32/40] Fix JabFox integration

With the new jpackage build JabFox stopped working because the registry values were not specified correctly. This fixes #4303 and fixes #4737. Moreover, the correct icon is now displayed in the installer.
---
 CHANGELOG.md                            |   1 +
 build.gradle                            |  17 +++++++++++-
 buildres/JabRef-post-image.wsf          |  35 ++++++++++++++++++++++++
 buildres/{JabRef.bat => JabRefHost.bat} |   2 +-
 buildres/{JabRef.ps1 => JabRefHost.ps1} |  15 +++++-----
 buildres/JabRefTopBanner.bmp            | Bin 0 -> 85894 bytes
 buildres/jabref.json                    |   2 +-
 7 files changed, 61 insertions(+), 11 deletions(-)
 create mode 100644 buildres/JabRef-post-image.wsf
 rename buildres/{JabRef.bat => JabRefHost.bat} (60%)
 rename buildres/{JabRef.ps1 => JabRefHost.ps1} (72%)
 create mode 100644 buildres/JabRefTopBanner.bmp

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 9a4e50fdea6..5da79394ebc 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -22,6 +22,7 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - We fixed an issue where it was no longer possible to connect to LibreOffice. [#5261](https://github.com/JabRef/jabref/issues/5261)
 - The "All entries group" is no longer shown when no library is open.
 - We fixed an exception which occurred when closing JabRef. [#5348](https://github.com/JabRef/jabref/issues/5348)
+- We fixed a few problems that prevented JabFox to communicate with JabRef. [#4737](https://github.com/JabRef/jabref/issues/4737) [#4303](https://github.com/JabRef/jabref/issues/4303)
 - We fixed an error where the groups containing an entry loose their highlight color when scrolling. [#5022](https://github.com/JabRef/jabref/issues/5022) 
 - After assigning an entry to a group, the item count is now properly colored to reflect the new membership of the entry. [#3112](https://github.com/JabRef/jabref/issues/3112)
 - The group panel is now properly updated when switching between libraries (or when closing/opening one). [#3142](https://github.com/JabRef/jabref/issues/3142)
diff --git a/build.gradle b/build.gradle
index b3d7851f76a..6ee658af349 100644
--- a/build.gradle
+++ b/build.gradle
@@ -514,6 +514,11 @@ task generateFinalJabRefPS1File(type: Copy) {
     filter(org.apache.tools.ant.filters.ReplaceTokens, tokens: [jabRefJarFileName: jar.archiveName])
 }
 
+task deleteInstallerTemp(type: Delete) {
+    delete "$buildDir/installer"
+}
+
+jpackage.dependsOn deleteInstallerTemp
 jlink {
     options = ['--strip-debug', '--compress', '2', '--no-header-files', '--no-man-pages']
     launcher {
@@ -584,7 +589,9 @@ jlink {
                     '--app-version', "${project.version}",
                     '--win-upgrade-uuid', 'd636b4ee-6f10-451e-bf57-c89656780e36',
                     '--win-dir-chooser',
-                    '--win-shortcut'
+                    '--win-shortcut',
+                    '--temp', "$buildDir/installer",
+                    '--resource-dir', "${projectDir}/buildres"
             ]
         }
 
@@ -609,6 +616,14 @@ jlink {
         }
     }
 }
+tasks.jpackageImage.doLast {
+    copy {
+        from("/buildres/") {
+            include "jabref.json", "JabRefHost.bat", "JabRefHost.ps1"
+        }
+        into "$buildDir/distribution/JabRef"
+    }
+}
 
 jmh {
     warmupIterations = 5
diff --git a/buildres/JabRef-post-image.wsf b/buildres/JabRef-post-image.wsf
new file mode 100644
index 00000000000..56ddd9097f4
--- /dev/null
+++ b/buildres/JabRef-post-image.wsf
@@ -0,0 +1,35 @@
+<?xml version="1.0" ?>
+<package>
+   <job id="postImage">
+    <script language="jscript">
+     <![CDATA[
+        var fileSystem = new ActiveXObject("Scripting.FileSystemObject");
+        // The script is invoked in the "image" folder and not in "config" for some reason
+        var jabRefRoot = fileSystem.GetFolder(".").ParentFolder.ParentFolder.ParentFolder.ParentFolder.Path;
+        var installerConfig = jabRefRoot + "/build/installer/config/";
+
+        // Copy additional installer resources
+        fileSystem.CopyFile(jabRefRoot + "/buildres/JabRefTopBanner.bmp", installerConfig);
+
+        var wxsFilePath = installerConfig + "JabRef.wxs";
+        wxsFile = fileSystem.OpenTextFile(wxsFilePath, 1);
+        var contents = wxsFile.ReadAll();
+        wxsFile.Close();
+
+        // Add registry values for JabFox
+        contents = contents.replace("</Product>", "<DirectoryRef Id=\"TARGETDIR\"><Component Id=\"RegistryJabFoxEntries\" Guid=\"b6bc55ad-905c-4258-89b1-8b37abbe559c\" Win64=\"yes\"><RegistryKey Root=\"HKMU\" Key=\"SOFTWARE\\Mozilla\\NativeMessagingHosts\\org.jabref.jabref\" Action=\"createAndRemoveOnUninstall\" ForceCreateOnInstall=\"yes\"><RegistryValue Type=\"string\" Value=\"[APPLICATIONFOLDER]jabref.json\"/></RegistryKey></Component></DirectoryRef><Feature Id=\"JabFox\" Level=\"1\"><ComponentRef Id=\"RegistryJabFoxEntries\" /></Feature></Product>");
+
+        // Specify correct icon in Add/Remove Programs
+        contents = contents.replace("</Product>", "<Property Id=\"ARPPRODUCTICON\" Value=\"DesktopIcon.exe\" /></Product>");
+
+        // Specify banner
+        contents = contents.replace("</Product>", "<WixVariable Id=\"WixUIBannerBmp\" Value=\"JabRefTopBanner.bmp\" /></Product>");
+        //contents = contents.replace("</Product>", "<WixVariable Id=\"WixUIDialogBmp\" Value=\"\" /></Product>");
+
+         wxsFile = fileSystem.OpenTextFile(wxsFilePath, 2, true);
+         wxsFile.Write(contents);
+         wxsFile.Close();
+     ]]>
+    </script>
+   </job>
+</package>
diff --git a/buildres/JabRef.bat b/buildres/JabRefHost.bat
similarity index 60%
rename from buildres/JabRef.bat
rename to buildres/JabRefHost.bat
index 7a2cee363b0..d44d94f282c 100644
--- a/buildres/JabRef.bat
+++ b/buildres/JabRefHost.bat
@@ -1,3 +1,3 @@
 @echo off
 pushd %~dp0
-@powershell.exe -ExecutionPolicy Bypass -NoLogo -NonInteractive -NoProfile -WindowStyle Hidden -File ".\JabRef.ps1"
+@powershell.exe -ExecutionPolicy Bypass -NoLogo -NonInteractive -NoProfile -WindowStyle Hidden -File ".\JabRefHost.ps1"
diff --git a/buildres/JabRef.ps1 b/buildres/JabRefHost.ps1
similarity index 72%
rename from buildres/JabRef.ps1
rename to buildres/JabRefHost.ps1
index fe814e6013e..f31df86f74e 100644
--- a/buildres/JabRef.ps1
+++ b/buildres/JabRefHost.ps1
@@ -11,8 +11,7 @@ function Respond($response) {
     }
 }
 
-$jabRefJarFileName = "@jabRefJarFileName@"
-$jabRefJar = [System.IO.Path]::Combine($PSScriptRoot, $jabRefJarFileName)
+$jabRefExe = [System.IO.Path]::Combine($PSScriptRoot, "JabRef.exe")
 
 try {
     $reader = New-Object System.IO.BinaryReader([System.Console]::OpenStandardInput())
@@ -21,16 +20,16 @@ try {
     $message = $messageRaw | ConvertFrom-Json
 
     if ($message.Status -eq "validate") {
-        if (-not (Test-Path $jabRefJar)) {
-            return Respond @{message="jarNotFound";path=$jabRefJar}
+        if (-not (Test-Path $jabRefExe)) {
+            return Respond @{message="jarNotFound";path=$jabRefExe}
         } else {
             return Respond @{message="jarFound"}
         }
     }
-    
-    if (-not (Test-Path $jabRefJar)) {
+
+    if (-not (Test-Path $jabRefExe)) {
         $wshell = New-Object -ComObject Wscript.Shell
-        $popup = "Unable to locate '$jabRefJarFileName' in '$([System.IO.Path]::GetDirectoryName($jabRefJar))'."
+        $popup = "Unable to locate '$jabRefExe'."
         $wshell.Popup($popup,0,"JabRef", 0x0 + 0x30)
         return
     }
@@ -39,7 +38,7 @@ try {
     #$wshell.Popup($message.Text,0,"JabRef", 0x0 + 0x30)
 
     $messageText = $message.Text
-    $output = & java -jar $jabRefJar -importBibtex "$messageText" 2>&1
+    $output = & $jabRefExe -importBibtex "$messageText" 2>&1
     #$output = & echoargs -importBibtex $messageText 2>&1
     #$wshell.Popup($output,0,"JabRef", 0x0 + 0x30)
     return Respond @{message="ok";output="$output"}
diff --git a/buildres/JabRefTopBanner.bmp b/buildres/JabRefTopBanner.bmp
new file mode 100644
index 0000000000000000000000000000000000000000..7e95c3b8fd763ce3cdc4b35620daf7902dcd8df4
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literal 0
HcmV?d00001

diff --git a/buildres/jabref.json b/buildres/jabref.json
index dee50f008fe..9024c5b17f4 100644
--- a/buildres/jabref.json
+++ b/buildres/jabref.json
@@ -1,7 +1,7 @@
 {
   "name": "org.jabref.jabref",
   "description": "JabRef",
-  "path": "JabRef.bat",
+  "path": "JabRefHost.bat",
   "type": "stdio",
   "allowed_extensions": [
     "@jabfox"

From a6948ea0de5c8f13da452a5f029129952cc99ca3 Mon Sep 17 00:00:00 2001
From: Tobias Diez <tobiasdiez@gmx.de>
Date: Sun, 6 Oct 2019 22:32:47 +0200
Subject: [PATCH 33/40] Remove unnecessary code

---
 build.gradle | 8 --------
 1 file changed, 8 deletions(-)

diff --git a/build.gradle b/build.gradle
index 6ee658af349..7192e613482 100644
--- a/build.gradle
+++ b/build.gradle
@@ -506,14 +506,6 @@ modernizer {
 }
 
 // Release tasks
-task generateFinalJabRefPS1File(type: Copy) {
-    from('buildres') {
-        include 'JabRef.ps1'
-    }
-    into 'build'
-    filter(org.apache.tools.ant.filters.ReplaceTokens, tokens: [jabRefJarFileName: jar.archiveName])
-}
-
 task deleteInstallerTemp(type: Delete) {
     delete "$buildDir/installer"
 }

From ef445c55300bde42fb81667f3048b011f645479d Mon Sep 17 00:00:00 2001
From: "dependabot-preview[bot]"
 <27856297+dependabot-preview[bot]@users.noreply.github.com>
Date: Mon, 7 Oct 2019 12:26:57 +0200
Subject: [PATCH 34/40] Bump slf4j-api from 2.0.0-alpha0 to 2.0.0-alpha1
 (#5403)

* Bump slf4j-api from 2.0.0-alpha0 to 2.0.0-alpha1

Bumps [slf4j-api](https://github.com/qos-ch/slf4j) from 2.0.0-alpha0 to 2.0.0-alpha1.
- [Release notes](https://github.com/qos-ch/slf4j/releases)
- [Commits](https://github.com/qos-ch/slf4j/commits/v_2.0.0-alpha1)

Signed-off-by: dependabot-preview[bot] <support@dependabot.com>

* Pin log4j.plugins
---
 build.gradle | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index b3d7851f76a..f96d0451254 100644
--- a/build.gradle
+++ b/build.gradle
@@ -164,9 +164,10 @@ dependencies {
     compile 'org.jsoup:jsoup:1.12.1'
     compile 'com.mashape.unirest:unirest-java:1.4.9'
 
-    compile 'org.slf4j:slf4j-api:2.0.0-alpha0'
+    compile 'org.slf4j:slf4j-api:2.0.0-alpha1'
     compile group: 'org.apache.logging.log4j', name: 'log4j-jcl', version: '3.0.0-20190915.182410-364'
     compile group: 'org.apache.logging.log4j', name: 'log4j-slf4j18-impl', version: '3.0.0-20190915.182922-250'
+    compile group: 'org.apache.logging.log4j', name: 'log4j-plugins', version: '3.0.0-20190915.182837-57'
     implementation group: 'org.apache.logging.log4j', name: 'log4j-api', version: '3.0.0-20190915.182113-372'
     compile group: 'org.apache.logging.log4j', name: 'log4j-core', version: '3.0.0-20190915.182215-368'
     annotationProcessor group: 'org.apache.logging.log4j', name: 'log4j-core', version: '3.0.0-20190915.182215-368'

From 845481a05638d722d8756f7ae20a619790836340 Mon Sep 17 00:00:00 2001
From: "dependabot-preview[bot]"
 <27856297+dependabot-preview[bot]@users.noreply.github.com>
Date: Mon, 7 Oct 2019 10:28:58 +0000
Subject: [PATCH 35/40] Bump mockito-core from 3.0.0 to 3.1.0

Bumps [mockito-core](https://github.com/mockito/mockito) from 3.0.0 to 3.1.0.
- [Release notes](https://github.com/mockito/mockito/releases)
- [Commits](https://github.com/mockito/mockito/compare/v3.0.0...v3.1.0)

Signed-off-by: dependabot-preview[bot] <support@dependabot.com>
---
 build.gradle | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index f96d0451254..d7cc1395d17 100644
--- a/build.gradle
+++ b/build.gradle
@@ -206,7 +206,7 @@ dependencies {
     testCompile 'net.bytebuddy:byte-buddy-parent:1.10.1'
     testRuntime group: 'org.apache.logging.log4j', name: 'log4j-core', version: '3.0.0-20190915.182215-368'
     testRuntime group: 'org.apache.logging.log4j', name: 'log4j-jul', version: '3.0.0-20190915.182552-364'
-    testCompile 'org.mockito:mockito-core:3.0.0'
+    testCompile 'org.mockito:mockito-core:3.1.0'
     //testCompile 'com.github.tomakehurst:wiremock:2.24.1'
     testCompile ('org.reflections:reflections:0.9.11') {
         exclude module: "jsr305"

From 33755c23c579d7bab34db2e4d18730e5eacbff0b Mon Sep 17 00:00:00 2001
From: "dependabot-preview[bot]"
 <27856297+dependabot-preview[bot]@users.noreply.github.com>
Date: Mon, 7 Oct 2019 10:29:13 +0000
Subject: [PATCH 36/40] Bump mariadb-java-client from 2.4.4 to 2.5.0

Bumps [mariadb-java-client](https://github.com/MariaDB/mariadb-connector-j) from 2.4.4 to 2.5.0.
- [Release notes](https://github.com/MariaDB/mariadb-connector-j/releases)
- [Commits](https://github.com/MariaDB/mariadb-connector-j/compare/2.4.4...2.5.0)

Signed-off-by: dependabot-preview[bot] <support@dependabot.com>
---
 build.gradle | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build.gradle b/build.gradle
index f96d0451254..ab774f3b820 100644
--- a/build.gradle
+++ b/build.gradle
@@ -138,7 +138,7 @@ dependencies {
     antlr4 'org.antlr:antlr4:4.7.2'
     compile 'org.antlr:antlr4-runtime:4.7.2'
 
-    compile group: 'org.mariadb.jdbc', name: 'mariadb-java-client', version: '2.4.4'
+    compile group: 'org.mariadb.jdbc', name: 'mariadb-java-client', version: '2.5.0'
 
     compile 'org.postgresql:postgresql:42.2.8'
 

From 7c5597caebef018efbbd188b8c8e33d76dde2381 Mon Sep 17 00:00:00 2001
From: "dependabot-preview[bot]"
 <27856297+dependabot-preview[bot]@users.noreply.github.com>
Date: Mon, 7 Oct 2019 10:51:24 +0000
Subject: [PATCH 37/40] Bump src/main/resources/csl-styles from `36ac1f6` to
 `6169061`

Bumps [src/main/resources/csl-styles](https://github.com/citation-style-language/styles) from `36ac1f6` to `6169061`.
- [Release notes](https://github.com/citation-style-language/styles/releases)
- [Commits](https://github.com/citation-style-language/styles/compare/36ac1f63004b1b85c8aed51f7111a8bed3fb7208...6169061a140068e897337de95f917008037fcd3b)

Signed-off-by: dependabot-preview[bot] <support@dependabot.com>
---
 src/main/resources/csl-styles | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/main/resources/csl-styles b/src/main/resources/csl-styles
index 36ac1f63004..6169061a140 160000
--- a/src/main/resources/csl-styles
+++ b/src/main/resources/csl-styles
@@ -1 +1 @@
-Subproject commit 36ac1f63004b1b85c8aed51f7111a8bed3fb7208
+Subproject commit 6169061a140068e897337de95f917008037fcd3b

From 9af26e9645799dda3c4922ea653ad0d921f3fec5 Mon Sep 17 00:00:00 2001
From: "dependabot-preview[bot]"
 <27856297+dependabot-preview[bot]@users.noreply.github.com>
Date: Mon, 7 Oct 2019 10:51:40 +0000
Subject: [PATCH 38/40] Bump src/main/resources/csl-locales from `e89e6b0` to
 `9785a6e`

Bumps [src/main/resources/csl-locales](https://github.com/citation-style-language/locales) from `e89e6b0` to `9785a6e`.
- [Release notes](https://github.com/citation-style-language/locales/releases)
- [Commits](https://github.com/citation-style-language/locales/compare/e89e6b08b5c621a414fc7114f2129efac5f8c7d5...9785a6e3584e8c903df3d5a53f0e800dcabd282b)

Signed-off-by: dependabot-preview[bot] <support@dependabot.com>
---
 src/main/resources/csl-locales | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/main/resources/csl-locales b/src/main/resources/csl-locales
index e89e6b08b5c..9785a6e3584 160000
--- a/src/main/resources/csl-locales
+++ b/src/main/resources/csl-locales
@@ -1 +1 @@
-Subproject commit e89e6b08b5c621a414fc7114f2129efac5f8c7d5
+Subproject commit 9785a6e3584e8c903df3d5a53f0e800dcabd282b

From 1c3802edd9c8d84905f5374810013f1305dc44f3 Mon Sep 17 00:00:00 2001
From: Galileo Sartor <galileo.sartor@gmail.com>
Date: Mon, 7 Oct 2019 16:19:27 +0200
Subject: [PATCH 39/40] Snap GitHub ci (#5379)

* Build snap from java package

* add snap to github ci

* Use docker snapcraft

* Add container to ubuntu matrix item

* move snap workflow to matrix

* add matrix to snapbuild

* add transfer.sh link

* Use tar from build/distribution

* Add stable snapcraft

* Remove explicit container

* Attempt at a github actions integration

* Try to make it work...

* Try to fix ?

* Build without docker

* Build with latest docker

* Add docker image based on bionic

* Temporarily revert to version-script

* Uncomment upload to builds.jabref

* Make sure to move only jabref snap to build folder

* Update and rename deployment.yml to snap-deployment.yml

Modify to push again

* Update and rename snap-deployment.yml to deployment.yml

* Reenable checks for PRs

* Temporarily disable master branch check to test

* I'm tired...

* Fix branch name detection for PRs

* Try to fix branch name detection

* Update deployment.yml

* Update deployment.yml

* Remove on PR
---
 .github/workflows/deployment.yml |  18 +-
 snap/plugins/x_gradle.py         | 301 -------------------------------
 snap/snapcraft.yaml              |  51 ++----
 3 files changed, 26 insertions(+), 344 deletions(-)
 delete mode 100644 snap/plugins/x_gradle.py

diff --git a/.github/workflows/deployment.yml b/.github/workflows/deployment.yml
index bec5380f3d1..49eae5fb82f 100644
--- a/.github/workflows/deployment.yml
+++ b/.github/workflows/deployment.yml
@@ -34,6 +34,14 @@ jobs:
       with:
         depth: 1
         submodules: true
+    - name: Extract branch name
+      shell: bash
+      run: |
+         ref=${GITHUB_REF#refs/heads/}
+         ref=${ref#refs/pull/}
+         ref=${ref%/merge}
+         echo "##[set-output name=branch;]${ref}"
+      id: extract_branch
     - name: Set up JDK
       uses: actions/setup-java@v1
       with:
@@ -75,10 +83,14 @@ jobs:
     - name: Package application image
       run: ${{ matrix.archivePortable }}
       shell: bash
-    - name: Extract branch name
+    - name: Build and publish snap
+      if: matrix.os == 'ubuntu-latest' && steps.extract_branch.outputs.branch == 'master'
+      env:
+        SNAPCRAFT_LOGIN_FILE: ${{ secrets.SNAPCRAFT_LOGIN_FILE }}
+      run: |
+          docker run -v $(pwd):$(pwd) -t lyzardking/snapcraft-bionic sh -c "apt update -qq && cd $(pwd) && snapcraft && mv jabref*.snap build/distribution/"
+          # cd build/distribution/ && mdkir .snapcraft && echo ${SNAPCRAFT_LOGIN_FILE} | base64 --decode --ignore-garbage > .snapcraft/snapcraft.cfg && snapcraft push --release=beta *.snap
       shell: bash
-      run: echo "##[set-output name=branch;]$(echo ${GITHUB_REF#refs/heads/})"
-      id: extract_branch
     - name: Upload to builds.jabref.org
       uses: garygrossgarten/github-action-scp@release
       with:
diff --git a/snap/plugins/x_gradle.py b/snap/plugins/x_gradle.py
deleted file mode 100644
index 899d6567712..00000000000
--- a/snap/plugins/x_gradle.py
+++ /dev/null
@@ -1,301 +0,0 @@
-# -*- Mode:Python; indent-tabs-mode:nil; tab-width:4 -*-
-#
-# Copyright (C) 2016, 2018 Canonical Ltd
-#
-# This program is free software: you can redistribute it and/or modify
-# it under the terms of the GNU General Public License version 3 as
-# published by the Free Software Foundation.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program.  If not, see <http://www.gnu.org/licenses/>.
-
-"""This plugin is useful for building parts that use gradle.
-
-The gradle build system is commonly used to build Java projects.
-The plugin requires a pom.xml in the root of the source tree.
-
-This plugin uses the common plugin keywords as well as those for "sources".
-For more information check the 'plugins' topic for the former and the
-'sources' topic for the latter.
-
-Additionally, this plugin uses the following plugin-specific keywords:
-
-    - gradle-options:
-      (list of strings)
-      Flags to pass to the build using the gradle semantics for parameters.
-      The 'jar' option is always passed in as the last parameter.
-
-    - gradle-output-dir:
-      (string; default: 'build/libs')
-      The output directory where the resulting jar or war files from gradle[w]
-      are generated.
-
-    - gradle-version:
-      (string)
-      The version of gradle you want to use to build the source artifacts.
-      Defaults to the current release downloadable from
-      https://services.gradle.org/distributions/
-      The entry is ignored if gradlew is found.
-
-    - gradle-version-checksum:
-      (string)
-      The checksum for gradle-version in the form of <digest-type>/<digest>.
-      As an example "sha512/2a803f578f341e164f6753e410413d16ab60fab...".
-
-    - gradle-openjdk-version:
-      (string)
-      openjdk version available to the base to use. If not set the latest
-      version available to the base will be used.
-"""
-
-import logging
-import os
-import urllib.parse
-from glob import glob
-from typing import Sequence
-
-import snapcraft
-from snapcraft import file_utils, formatting_utils
-from snapcraft.internal import errors, sources
-
-logger = logging.getLogger(__name__)
-
-
-_DEFAULT_GRADLE_VERSION = "4.10.2"
-_DEFAULT_GRADLE_CHECKSUM = (
-    "sha256/b49c6da1b2cb67a0caf6c7480630b51c70a11ca2016ff2f555eaeda863143a29"
-)
-_GRADLE_URL = "https://services.gradle.org/distributions/gradle-{version}-bin.zip"
-
-
-class UnsupportedJDKVersionError(errors.SnapcraftError):
-
-    fmt = (
-        "The gradle-openjdk-version plugin property was set to {version!r}.\n"
-        "Valid values for the {base!r} base are: {valid_versions}."
-    )
-
-    def __init__(
-        self, *, base: str, version: str, valid_versions: Sequence[str]
-    ) -> None:
-        super().__init__(
-            base=base,
-            version=version,
-            valid_versions=formatting_utils.humanize_list(
-                valid_versions, conjunction="or"
-            ),
-        )
-
-
-class GradlePlugin(snapcraft.BasePlugin):
-    @classmethod
-    def schema(cls):
-        schema = super().schema()
-        schema["properties"]["gradle-options"] = {
-            "type": "array",
-            "minitems": 1,
-            "uniqueItems": True,
-            "items": {"type": "string"},
-            "default": [],
-        }
-        schema["properties"]["gradle-output-dir"] = {
-            "type": "string",
-            "default": "build/libs",
-        }
-
-        schema["properties"]["gradle-version"] = {"type": "string"}
-
-        schema["properties"]["gradle-version-checksum"] = {"type": "string"}
-
-        schema["properties"]["gradle-openjdk-version"] = {
-            "type": "string",
-            "default": "",
-        }
-
-        schema["required"] = ["source"]
-
-        return schema
-
-    @classmethod
-    def get_pull_properties(cls):
-        # Inform Snapcraft of the properties associated with pulling. If these
-        # change in the YAML Snapcraft will consider the pull step dirty.
-        return ["gradle-version", "gradle-version-checksum", "gradle-openjdk-version"]
-
-    @classmethod
-    def get_build_properties(cls):
-        # Inform Snapcraft of the properties associated with building. If these
-        # change in the YAML Snapcraft will consider the build step dirty.
-        return super().get_build_properties() + ["gradle-options", "gradle-output-dir"]
-
-    @property
-    def _gradle_tar(self):
-        if self._gradle_tar_handle is None:
-            gradle_uri = _GRADLE_URL.format(version=self._gradle_version)
-            self._gradle_tar_handle = sources.Zip(
-                gradle_uri, self._gradle_dir, source_checksum=self._gradle_checksum
-            )
-        return self._gradle_tar_handle
-
-    def __init__(self, name, options, project):
-        super().__init__(name, options, project)
-
-        self._setup_gradle()
-        self._setup_base_tools(project.info.get_build_base())
-
-    def _setup_base_tools(self, base):
-        if base not in ("core", "core16", "core18"):
-            raise errors.PluginBaseError(
-                part_name=self.name, base=self.project.info.get_build_base()
-            )
-
-        if base in ("core", "core16"):
-            valid_versions = ["8", "9"]
-        elif base == "core18":
-            valid_versions = ["8", "11"]
-
-        version = self.options.gradle_openjdk_version
-        if not version:
-            version = valid_versions[-1]
-        elif version not in valid_versions:
-            raise UnsupportedJDKVersionError(
-                version=version, base=base, valid_versions=valid_versions
-            )
-
-        self.stage_packages.append("openjdk-{}-jre-headless".format(version))
-        self.build_packages.append("openjdk-{}-jdk-headless".format(version))
-        self.build_packages.append("ca-certificates-java")
-        self._java_version = version
-
-    def _using_gradlew(self) -> bool:
-        return os.path.isfile(os.path.join(self.sourcedir, "gradlew"))
-
-    def _setup_gradle(self):
-        self._gradle_tar_handle = None
-        self._gradle_dir = os.path.join(self.partdir, "gradle")
-        if self.options.gradle_version:
-            self._gradle_version = self.options.gradle_version
-            self._gradle_checksum = self.options.gradle_version_checksum
-        else:
-            self._gradle_version = _DEFAULT_GRADLE_VERSION
-            self._gradle_checksum = _DEFAULT_GRADLE_CHECKSUM
-
-    def pull(self):
-        super().pull()
-
-        if self._using_gradlew():
-            logger.info("Found gradlew, skipping gradle setup.")
-            return
-
-        os.makedirs(self._gradle_dir, exist_ok=True)
-        self._gradle_tar.download()
-
-    def build(self):
-        super().build()
-
-        if self._using_gradlew():
-            gradle_cmd = ["./gradlew"]
-        else:
-            self._gradle_tar.provision(self._gradle_dir, keep_zip=True)
-            gradle_cmd = ["gradle"]
-        self.run(
-            gradle_cmd
-            + self._get_proxy_options()
-            + self.options.gradle_options,
-            rootdir=self.builddir,
-        )
-
-        src = os.path.join(self.builddir, self.options.gradle_output_dir)
-        basedir = "jabref"
-        # jarfiles = glob(os.path.join(src, "*.jar"))
-        # warfiles = glob(os.path.join(src, "*.war"))
-
-        # if len(jarfiles) > 0:
-        #     basedir = "jar"
-        # elif len(warfiles) > 0:
-        #     basedir = "war"
-        #     jarfiles = warfiles
-        # else:
-        #     raise RuntimeError("Could not find any built jar files for part")
-
-        file_utils.link_or_copy_tree(
-            src,
-            os.path.join(self.installdir, basedir),
-            copy_function=lambda src, dst: file_utils.link_or_copy(
-                src, dst, self.installdir
-            ),
-        )
-
-        self._create_symlinks()
-
-    def _create_symlinks(self):
-        if self.project.info.get_build_base() not in ("core18", "core16", "core"):
-            raise errors.PluginBaseError(
-                part_name=self.name, base=self.project.info.get_build_base()
-            )
-
-        os.makedirs(os.path.join(self.installdir, "bin"), exist_ok=True)
-        java_bin = glob(
-            os.path.join(
-                self.installdir,
-                "usr",
-                "lib",
-                "jvm",
-                "java-{}-openjdk-*".format(self._java_version),
-                "bin",
-                "java",
-            )
-        )[0]
-        os.symlink(
-            os.path.relpath(java_bin, os.path.join(self.installdir, "bin")),
-            os.path.join(self.installdir, "bin", "java"),
-        )
-
-    def run(self, cmd, rootdir):
-        super().run(cmd, cwd=rootdir, env=self._build_environment())
-
-    def _build_environment(self):
-        if self._using_gradlew():
-            return
-
-        env = os.environ.copy()
-        gradle_bin = os.path.join(
-            self._gradle_dir, "gradle-{}".format(self._gradle_version), "bin"
-        )
-        print(gradle_bin)
-
-        if env.get("PATH"):
-            new_path = "{}:{}".format(gradle_bin, env.get("PATH"))
-        else:
-            new_path = gradle_bin
-
-        env["PATH"] = new_path
-        return env
-
-    def _get_proxy_options(self):
-        proxy_options = []
-        for var in ("http", "https"):
-            proxy = os.environ.get("{}_proxy".format(var), False)
-            if proxy:
-                parsed_url = urllib.parse.urlparse(proxy)
-                proxy_options.append(
-                    "-D{}.proxyHost={}".format(var, parsed_url.hostname)
-                )
-                if parsed_url.port:
-                    proxy_options.append(
-                        "-D{}.proxyPort={}".format(var, parsed_url.port)
-                    )
-                if parsed_url.username:
-                    proxy_options.append(
-                        "-D{}.proxyUser={}".format(var, parsed_url.username)
-                    )
-                if parsed_url.password:
-                    proxy_options.append(
-                        "-D{}.proxyPassword={}".format(var, parsed_url.password)
-                    )
-        return proxy_options
diff --git a/snap/snapcraft.yaml b/snap/snapcraft.yaml
index b62d2d571e3..a60eadd2d4d 100644
--- a/snap/snapcraft.yaml
+++ b/snap/snapcraft.yaml
@@ -1,7 +1,9 @@
 name: jabref
-version: "git"
+# adopt-info: jabref
+version: 'master'
 version-script: cat build.gradle | grep "^version =" | cut -d'"' -f2
-#icon: snap/gui/jabref.png
+icon: snap/gui/jabref.png
+license: MIT
 summary: Bibliography manager
 description: JabRef is an open source bibliography reference manager. The native file format used by JabRef is BibTeX, the standard LaTeX bibliography format.
 
@@ -14,11 +16,10 @@ architectures:
 
 apps:
   jabref:
-    command: desktop-launch $SNAP/jabref/bin/JabRefMain
+    command: bin/JabRef
+    extensions: [gnome-3-28]
     environment:
       _JAVA_OPTIONS: "-Duser.home=$SNAP_USER_DATA"
-      XDG_DATA_DIRS: $SNAP/share:$XDG_DATA_DIRS
-      GSETTINGS_SCHEMA_DIR: $SNAP/share/glib-2.0/schemas
     plugs:
       - desktop
       - desktop-legacy
@@ -28,43 +29,13 @@ apps:
       - opengl
       - network-bind
       - removable-media
-      - gnome-3-28-1804
-
-plugs:
-  gnome-3-28-1804:
-    interface: content
-    target: gnome-platform
-    default-provider: gnome-3-28-1804:gnome-3-28-1804
-    content: gnome-3-28-1804
-  gtk-3-themes:
-    interface: content
-    target: $SNAP/data-dir/themes
-    default-provider: gtk-common-themes:gtk-3-themes
-  icon-themes:
-    interface: content
-    target: $SNAP/data-dir/icons
-    default-provider: gtk-common-themes:icon-themes
-
 
 parts:
   jabref:
-    plugin: x_gradle
-    source: .
-    source-type: git
+    plugin: dump
+    source: build/distribution/JabRef-portable_linux.tar.gz
+    # override-pull: |
+    #   snapcraftctl pull
+    #   snapcraftctl set-version "$(cat app/JabRef.cfg | grep "app.version=" | cut -d'=' -f2)"
     stage-packages:
-      - openjdk-11-jre
-      - openjfx
       - x11-utils
-    gradle-options: [jlink, -xtest]
-    gradle-output-dir: 'build/image'
-  desktop-gnome-platform:
-    source: https://github.com/ubuntu/snapcraft-desktop-helpers.git
-    source-subdir: gtk
-    plugin: make
-    make-parameters: ["FLAVOR=gtk3"]
-    build-packages:
-      - build-essential
-      - libgtk-3-dev
-    override-build: |
-      snapcraftctl build
-      mkdir -pv $SNAPCRAFT_PART_INSTALL/gnome-platform

From facda00c148954b0ba32d859976fb0d72ce9cac6 Mon Sep 17 00:00:00 2001
From: Tobias Diez <tobiasdiez@gmx.de>
Date: Mon, 7 Oct 2019 20:46:22 +0200
Subject: [PATCH 40/40] Add test for regular expression pattern

---
 .../logic/util/BracketedPatternTest.java      | 73 ++++++++++---------
 1 file changed, 37 insertions(+), 36 deletions(-)

diff --git a/src/test/java/org/jabref/logic/util/BracketedPatternTest.java b/src/test/java/org/jabref/logic/util/BracketedPatternTest.java
index 5e2cd0511e9..41bfbad9622 100644
--- a/src/test/java/org/jabref/logic/util/BracketedPatternTest.java
+++ b/src/test/java/org/jabref/logic/util/BracketedPatternTest.java
@@ -14,14 +14,14 @@
 import static org.junit.jupiter.api.Assertions.assertNotEquals;
 import static org.junit.jupiter.api.Assertions.assertThrows;
 
-public class BracketedPatternTest {
+class BracketedPatternTest {
 
     private BibEntry bibentry;
     private BibDatabase database;
     private BibEntry dbentry;
 
     @BeforeEach
-    public void setUp() throws Exception {
+    void setUp() throws Exception {
         bibentry = new BibEntry();
         bibentry.setField(StandardField.AUTHOR, "O. Kitsune");
         bibentry.setField(StandardField.YEAR, "2017");
@@ -47,27 +47,27 @@ public void setUp() throws Exception {
     }
 
     @Test
-    public void bibentryExpansionTest() {
+    void bibentryExpansionTest() {
         BracketedPattern pattern = new BracketedPattern("[year]_[auth]_[firstpage]");
         assertEquals("2017_Kitsune_213", pattern.expand(bibentry));
     }
 
     @Test
-    public void nullDatabaseExpansionTest() {
+    void nullDatabaseExpansionTest() {
         BibDatabase another_database = null;
         BracketedPattern pattern = new BracketedPattern("[year]_[auth]_[firstpage]");
         assertEquals("2017_Kitsune_213", pattern.expand(bibentry, another_database));
     }
 
     @Test
-    public void pureauthReturnsAuthorIfEditorIsAbsent() {
+    void pureauthReturnsAuthorIfEditorIsAbsent() {
         BibDatabase emptyDatabase = new BibDatabase();
         BracketedPattern pattern = new BracketedPattern("[pureauth]");
         assertEquals("Kitsune", pattern.expand(bibentry, emptyDatabase));
     }
 
     @Test
-    public void pureauthReturnsAuthorIfEditorIsPresent() {
+    void pureauthReturnsAuthorIfEditorIsPresent() {
         BibDatabase emptyDatabase = new BibDatabase();
         BracketedPattern pattern = new BracketedPattern("[pureauth]");
         bibentry.setField(StandardField.EDITOR, "Editorlastname, Editorfirstname");
@@ -75,7 +75,7 @@ public void pureauthReturnsAuthorIfEditorIsPresent() {
     }
 
     @Test
-    public void pureauthReturnsEmptyStringIfAuthorIsAbsent() {
+    void pureauthReturnsEmptyStringIfAuthorIsAbsent() {
         BibDatabase emptyDatabase = new BibDatabase();
         BracketedPattern pattern = new BracketedPattern("[pureauth]");
         bibentry.clearField(StandardField.AUTHOR);
@@ -83,7 +83,7 @@ public void pureauthReturnsEmptyStringIfAuthorIsAbsent() {
     }
 
     @Test
-    public void pureauthReturnsEmptyStringIfAuthorIsAbsentAndEditorIsPresent() {
+    void pureauthReturnsEmptyStringIfAuthorIsAbsentAndEditorIsPresent() {
         BibDatabase emptyDatabase = new BibDatabase();
         BracketedPattern pattern = new BracketedPattern("[pureauth]");
         bibentry.clearField(StandardField.AUTHOR);
@@ -92,14 +92,14 @@ public void pureauthReturnsEmptyStringIfAuthorIsAbsentAndEditorIsPresent() {
     }
 
     @Test
-    public void emptyDatabaseExpansionTest() {
+    void emptyDatabaseExpansionTest() {
         BibDatabase another_database = new BibDatabase();
         BracketedPattern pattern = new BracketedPattern("[year]_[auth]_[firstpage]");
         assertEquals("2017_Kitsune_213", pattern.expand(bibentry, another_database));
     }
 
     @Test
-    public void databaseWithStringsExpansionTest() {
+    void databaseWithStringsExpansionTest() {
         BibDatabase another_database = new BibDatabase();
         BibtexString string = new BibtexString("sgr", "Saulius Gražulis");
         another_database.addString(string);
@@ -113,31 +113,31 @@ public void databaseWithStringsExpansionTest() {
     }
 
     @Test
-    public void unbalancedBracketsExpandToSomething() {
+    void unbalancedBracketsExpandToSomething() {
         BracketedPattern pattern = new BracketedPattern("[year]_[auth_[firstpage]");
         assertNotEquals("", pattern.expand(bibentry));
     }
 
     @Test
-    public void unbalancedLastBracketExpandsToSomething() {
+    void unbalancedLastBracketExpandsToSomething() {
         BracketedPattern pattern = new BracketedPattern("[year]_[auth]_[firstpage");
         assertNotEquals("", pattern.expand(bibentry));
     }
 
     @Test
-    public void entryTypeExpansionTest() {
+    void entryTypeExpansionTest() {
         BracketedPattern pattern = new BracketedPattern("[entrytype]:[year]_[auth]_[pages]");
         assertEquals("Misc:2017_Kitsune_213--216", pattern.expand(bibentry));
     }
 
     @Test
-    public void entryTypeExpansionLowercaseTest() {
+    void entryTypeExpansionLowercaseTest() {
         BracketedPattern pattern = new BracketedPattern("[entrytype:lower]:[year]_[auth]_[firstpage]");
         assertEquals("misc:2017_Kitsune_213", pattern.expand(bibentry));
     }
 
     @Test
-    public void suppliedBibentryBracketExpansionTest() {
+    void suppliedBibentryBracketExpansionTest() {
         BibDatabase another_database = null;
         BracketedPattern pattern = new BracketedPattern("[year]_[auth]_[firstpage]");
         BibEntry another_bibentry = new BibEntry();
@@ -148,7 +148,7 @@ public void suppliedBibentryBracketExpansionTest() {
     }
 
     @Test
-    public void nullBibentryBracketExpansionTest() {
+    void nullBibentryBracketExpansionTest() {
         BibDatabase another_database = null;
         BibEntry another_bibentry = null;
         BracketedPattern pattern = new BracketedPattern("[year]_[auth]_[firstpage]");
@@ -156,58 +156,53 @@ public void nullBibentryBracketExpansionTest() {
     }
 
     @Test
-    public void bracketedExpressionDefaultConstructorTest() {
+    void bracketedExpressionDefaultConstructorTest() {
         BibDatabase another_database = null;
         BracketedPattern pattern = new BracketedPattern();
         assertThrows(NullPointerException.class, () -> pattern.expand(bibentry, ';', another_database));
     }
 
     @Test
-    public void unknownKeyExpandsToEmptyString() {
-        Character separator = ';';
-        assertEquals("", BracketedPattern.expandBrackets("[unknownkey]", separator, dbentry, database));
+    void unknownKeyExpandsToEmptyString() {
+        assertEquals("", BracketedPattern.expandBrackets("[unknownkey]", ';', dbentry, database));
     }
 
     @Test
-    public void emptyPatternAndEmptyModifierExpandsToEmptyString() {
-        Character separator = ';';
-        assertEquals("", BracketedPattern.expandBrackets("[:]", separator, dbentry, database));
+    void emptyPatternAndEmptyModifierExpandsToEmptyString() {
+        assertEquals("", BracketedPattern.expandBrackets("[:]", ';', dbentry, database));
     }
 
     @Test
-    public void emptyPatternAndValidModifierExpandsToEmptyString() {
+    void emptyPatternAndValidModifierExpandsToEmptyString() {
         Character separator = ';';
         assertEquals("", BracketedPattern.expandBrackets("[:lower]", separator, dbentry, database));
     }
 
     @Test
-    public void bibtexkeyPatternExpandsToBibTeXKey() {
+    void bibtexkeyPatternExpandsToBibTeXKey() {
         Character separator = ';';
         assertEquals("HipKro03", BracketedPattern.expandBrackets("[bibtexkey]", separator, dbentry, database));
     }
 
     @Test
-    public void bibtexkeyPatternWithEmptyModifierExpandsToBibTeXKey() {
-        Character separator = ';';
-        assertEquals("HipKro03", BracketedPattern.expandBrackets("[bibtexkey:]", separator, dbentry, database));
+    void bibtexkeyPatternWithEmptyModifierExpandsToBibTeXKey() {
+        assertEquals("HipKro03", BracketedPattern.expandBrackets("[bibtexkey:]", ';', dbentry, database));
     }
 
     @Test
-    public void authorPatternTreatsVonNamePrefixCorrectly() {
-        Character separator = ';';
+    void authorPatternTreatsVonNamePrefixCorrectly() {
         assertEquals("Eric von Hippel and Georg von Krogh",
-                BracketedPattern.expandBrackets("[author]", separator, dbentry, database));
+                BracketedPattern.expandBrackets("[author]", ';', dbentry, database));
     }
 
     @Test
-    public void lowerFormatterWorksOnVonNamePrefixes() {
-        Character separator = ';';
+    void lowerFormatterWorksOnVonNamePrefixes() {
         assertEquals("eric von hippel and georg von krogh",
-                BracketedPattern.expandBrackets("[author:lower]", separator, dbentry, database));
+                BracketedPattern.expandBrackets("[author:lower]", ';', dbentry, database));
     }
 
     @Test
-    public void testResolvedFieldAndFormat() {
+    void testResolvedFieldAndFormat() {
         BibEntry child = new BibEntry();
         child.setField(StandardField.CROSSREF, "HipKro03");
         database.insertEntry(child);
@@ -232,7 +227,7 @@ public void testResolvedFieldAndFormat() {
     }
 
     @Test
-    public void testResolvedParentNotInDatabase() {
+    void testResolvedParentNotInDatabase() {
         BibEntry child = new BibEntry();
         child.setField(StandardField.CROSSREF, "HipKro03");
         database.removeEntry(dbentry);
@@ -240,4 +235,10 @@ public void testResolvedParentNotInDatabase() {
 
         assertEquals("", BracketedPattern.expandBrackets("[author]", ';', child, database));
     }
+
+    @Test
+    void regularExpressionReplace() {
+        assertEquals("2003-JabRef Science",
+                BracketedPattern.expandBrackets("[year]-[journal:regex(\"Organization\",\"JabRef\")]", ';', dbentry, database));
+    }
 }