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Fix move_directory_files tool dependency action when destination is not empty

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Historically this action moves the contents of the source directory to the
destination directory. Commit d38936bd8d
broke the install when e.g. the destination is $INSTALL_DIR, which is
created by Galaxy and is not empty (contains INSTALLATION.log after first
action).
This commit is contained in:
Nicola Soranzo
2016-06-21 17:59:17 +01:00
parent 4bfa2f62fb
commit 89890d4f60
1 changed files with 11 additions and 5 deletions
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lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
+11 -5
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@@ -847,11 +847,17 @@ class MoveDirectoryFiles( RecipeStep ):
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 )
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 )
destination_directory = os.path.abspath(os.path.join(destination_dir))
if not os.path.isdir(destination_directory):
os.makedirs(destination_directory)
for dir_entry in os.listdir(source_directory):
source_entry = os.path.join(source_directory, dir_entry)
if os.path.islink(source_entry):
destination_entry = os.path.join(destination_directory, dir_entry)
os.symlink(os.readlink(source_entry), destination_entry)
os.remove(source_entry)
else:
shutil.move(source_entry, destination_directory)
def prepare_step( self, tool_dependency, action_elem, action_dict, install_environment, is_binary_download ):
# <action type="move_directory_files">