Merge branch 'release_16.04' into dev

galaxyproject · Jun 15, 2016 · 0fd152c · 0fd152c
2 parents dca91da + 37242c8
commit 0fd152c
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Showing 2 changed files with 7 additions and 21 deletions.
diff --git a/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py b/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
@@ -848,22 +848,10 @@ def execute_step( self, tool_dependency, package_name, actions, action_dict, fil
     def move_directory_files( self, current_dir, source_dir, destination_dir ):
         source_directory = os.path.abspath( os.path.join( current_dir, source_dir ) )
         destination_directory = os.path.join( destination_dir )
-        if not os.path.isdir( destination_directory ):
-            os.makedirs( destination_directory )
-        symlinks = []
-        regular_files = []
-        for file_name in os.listdir( source_directory ):
-            source_file = os.path.join( source_directory, file_name )
-            destination_file = os.path.join( destination_directory, file_name )
-            files_tuple = ( source_file, destination_file )
-            if os.path.islink( source_file ):
-                symlinks.append( files_tuple )
-            else:
-                regular_files.append( files_tuple )
-        for source_file, destination_file in symlinks:
-            shutil.move( source_file, destination_file )
-        for source_file, destination_file in regular_files:
-            shutil.move( source_file, destination_file )
+        destination_parent_directory = os.path.dirname(destination_directory)
+        if not os.path.isdir( destination_parent_directory ):
+            os.makedirs( destination_parent_directory )
+        shutil.move( source_directory, destination_directory )
 
     def prepare_step( self, tool_dependency, action_elem, action_dict, install_environment, is_binary_download ):
         # <action type="move_directory_files">

diff --git a/lib/tool_shed/util/basic_util.py b/lib/tool_shed/util/basic_util.py
@@ -90,13 +90,11 @@ def get_file_type_str( changeset_revision, file_type ):
 
 def move_file( current_dir, source, destination, rename_to=None ):
     source_path = os.path.abspath( os.path.join( current_dir, source ) )
-    source_file = os.path.basename( source_path )
+    destination_directory = os.path.join( destination )
     if rename_to is not None:
-        destination_file = rename_to
-        destination_directory = os.path.join( destination )
-        destination_path = os.path.join( destination_directory, destination_file )
+        destination_path = os.path.join( destination_directory, rename_to )
     else:
-        destination_directory = os.path.join( destination )
+        source_file = os.path.basename( source_path )
         destination_path = os.path.join( destination_directory, source_file )
     if not os.path.exists( destination_directory ):
         os.makedirs( destination_directory )