Merge pull request #5344 from mvdbeek/history_import_fixes

[17.09] History import fixes

lib/galaxy/tools/imp_exp/imp_history_from_archive.xml

@@ -1,7 +1,7 @@
 <tool id="__IMPORT_HISTORY__" name="Import History" version="0.1" tool_type="import_history">
   <type class="ImportHistoryTool" module="galaxy.tools"/>
   <action module="galaxy.tools.actions.history_imp_exp" class="ImportHistoryToolAction"/>
-  <command interpreter="python">unpack_tar_gz_archive.py "${ str( $__ARCHIVE_SOURCE__ ).encode( 'base64' ) }" "${ str( $__DEST_DIR__ ).encode( 'base64' ) }" --$__ARCHIVE_TYPE__ --encoded</command>
+  <command>python '$__tool_directory__/unpack_tar_gz_archive.py' '${ str( $__ARCHIVE_SOURCE__ ).encode( 'base64' ) }' '${ str( $__DEST_DIR__ ).encode( 'base64' ) }' --$__ARCHIVE_TYPE__ --encoded</command>
   <inputs>
     <param name="__ARCHIVE_SOURCE__" type="text">
       <sanitizer sanitize="False"/>

lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py

@@ -49,7 +49,7 @@ def check_archive(archive_file, dest_dir):
     Ensure that a tar archive has no absolute paths or relative paths outside
     the archive.
     """
-    with tarfile.open(archive_file, mode='r:gz') as archive_fp:
+    with tarfile.open(archive_file, mode='r') as archive_fp:
         for arc_path in archive_fp.getnames():
             assert os.path.normpath(
                 os.path.join(
@@ -64,7 +64,7 @@ def unpack_archive(archive_file, dest_dir):
     """
     Unpack a tar and/or gzipped archive into a destination directory.
     """
-    archive_fp = tarfile.open(archive_file, mode='r:gz')
+    archive_fp = tarfile.open(archive_file, mode='r')
     archive_fp.extractall(path=dest_dir)
     archive_fp.close()
 

lib/galaxy/webapps/galaxy/controllers/history.py

@@ -1155,6 +1155,9 @@ class HistoryController(BaseUIController, SharableMixin, UsesAnnotations, UsesIt
         archive_url = kwargs.get('archive_url', None)
         archive_source = None
         if hasattr(archive_file, 'file'):
+            # archive_file.file is a TemporaryFile and will be deleted once it is closed.
+            # We prevent this by setting `delete` to `False`.
+            archive_file.file.delete = False
             archive_source = archive_file.file.name
             archive_type = 'file'
         elif archive_url: