2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a89bbdfd4a71/ Changeset: a89bbdfd4a71 Branch: stable User: inithello Date: 2014-02-19 22:34:01 Summary: Ensure that symlinks are moved before regular files, since this can in some cases causes a 'No such file or directory' error when the symlink target is moved before the symlink itself. Affected #: 1 file diff -r 0770af01a257818ee82f11a191d4305880ea0b91 -r a89bbdfd4a71671d575d9a0a3a9f8abeba3f7b21 lib/tool_shed/galaxy_install/tool_dependencies/td_common_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/td_common_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/td_common_util.py @@ -303,9 +303,19 @@ 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 ) def move_file( current_dir, source, destination, rename_to=None ): https://bitbucket.org/galaxy/galaxy-central/commits/85c38536c315/ Changeset: 85c38536c315 User: inithello Date: 2014-02-19 22:34:22 Summary: Merge with a89bbdfd4a71671d575d9a0a3a9f8abeba3f7b21 Affected #: 1 file diff -r ee315625cf4e394bca8a05f25c82e78c978ed50c -r 85c38536c31583ef06db42c1f54d6248b79f96a5 lib/tool_shed/galaxy_install/tool_dependencies/td_common_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/td_common_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/td_common_util.py @@ -303,9 +303,19 @@ 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 ) def move_file( current_dir, source, destination, rename_to=None ): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.