1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/changeset/9ad75ecd32da/ changeset: 9ad75ecd32da user: greg date: 2011-11-14 22:59:26 summary: Revert file content checks when up0loading to a tool shed repository as they're currently too restrictive. affected #: 1 file

diff -r f640c7bd6ffc4904996859e06157a5f67671f978 -r 9ad75ecd32daa6d97f20bf6ff9db354e7052d5b7 lib/galaxy/webapps/community/controllers/upload.py --- a/lib/galaxy/webapps/community/controllers/upload.py +++ b/lib/galaxy/webapps/community/controllers/upload.py @@ -101,32 +101,34 @@ full_path = os.path.abspath( os.path.join( repo_dir, upload_point, uploaded_file_filename ) ) else: full_path = os.path.abspath( os.path.join( repo_dir, uploaded_file_filename ) ) - ok, message = self.__check_file_content( uploaded_file_name ) - if ok: - # Move the uploaded file to the load_point within the repository hierarchy. - shutil.move( uploaded_file_name, full_path ) - commands.add( repo.ui, repo, full_path ) - try: - commands.commit( repo.ui, repo, full_path, user=trans.user.username, message=commit_message ) - except Exception, e: - # I never have a problem with commands.commit on a Mac, but in the test/production - # tool shed environment, it occasionally throws a "TypeError: array item must be char" - # exception. If this happens, we'll try the following. - repo.dirstate.write() - repo.commit( user=trans.user.username, text=commit_message ) - if full_path.endswith( 'tool_data_table_conf.xml.sample' ): - # Handle the special case where a tool_data_table_conf.xml.sample - # file is being uploaded by parsing the file and adding new entries - # to the in-memory trans.app.tool_data_tables dictionary as well as - # appending them to the shed's tool_data_table_conf.xml file on disk. - error, error_message = handle_sample_tool_data_table_conf_file( trans, full_path ) - if error: - message = '%s<br/>%s' % ( message, error_message ) - if full_path.endswith( '.loc.sample' ): - # Handle the special case where a xxx.loc.sample file is - # being uploaded by copying it to ~/tool-data/xxx.loc. - copy_sample_loc_file( trans, full_path ) - handle_email_alerts( trans, repository ) + # TODO: enhance this method to set a flag and alert an admin to review content since + # the hard checks are too restrictive. + #ok, message = self.__check_file_content( uploaded_file_name ) + #if ok: + # Move the uploaded file to the load_point within the repository hierarchy. + shutil.move( uploaded_file_name, full_path ) + commands.add( repo.ui, repo, full_path ) + try: + commands.commit( repo.ui, repo, full_path, user=trans.user.username, message=commit_message ) + except Exception, e: + # I never have a problem with commands.commit on a Mac, but in the test/production + # tool shed environment, it occasionally throws a "TypeError: array item must be char" + # exception. If this happens, we'll try the following. + repo.dirstate.write() + repo.commit( user=trans.user.username, text=commit_message ) + if full_path.endswith( 'tool_data_table_conf.xml.sample' ): + # Handle the special case where a tool_data_table_conf.xml.sample + # file is being uploaded by parsing the file and adding new entries + # to the in-memory trans.app.tool_data_tables dictionary as well as + # appending them to the shed's tool_data_table_conf.xml file on disk. + error, error_message = handle_sample_tool_data_table_conf_file( trans, full_path ) + if error: + message = '%s<br/>%s' % ( message, error_message ) + if full_path.endswith( '.loc.sample' ): + # Handle the special case where a xxx.loc.sample file is + # being uploaded by copying it to ~/tool-data/xxx.loc. + copy_sample_loc_file( trans, full_path ) + handle_email_alerts( trans, repository ) if ok: # Update the repository files for browsing. update_for_browsing( trans, repository, current_working_dir, commit_message=commit_message ) @@ -192,6 +194,9 @@ tar.extractall( path=full_path ) tar.close() uploaded_file.close() + """ + # TODO: enhance this method to set a flag and alert an admin to review content since + # the hard checks are too restrictive. for filename_in_archive in filenames_in_archive: if os.path.isfile( filename_in_archive ): ok, message = self.__check_file_content( filename_in_archive ) @@ -200,6 +205,7 @@ current_working_dir = os.getcwd() update_for_browsing( trans, repository, current_working_dir ) return False, message, [] + """ if remove_repo_files_not_in_tar and not repository.is_new: # We have a repository that is not new (it contains files), so discover # those files that are in the repository, but not in the uploaded archive. @@ -343,13 +349,15 @@ return False, message return True, '' def __check_file_content( self, file_path ): + return True, '' message = '' ok = True + head, tail = os.path.split( file_path ) if check_html( file_path ): - message = 'Files containing HTML content cannot be uploaded to a Galaxy tool shed.' + message = 'The file <b>%s</b> contains HTML content which cannot be uploaded to a Galaxy tool shed.' % str( tail ) ok = False elif check_image( file_path ): # For now we won't allow images to be uploaded. - message = 'Files containing images cannot be uploaded to a Galaxy tool shed.' + message = 'The file <b>%s</b> contains image content that cannot be uploaded to a Galaxy tool shed.' % str( tail ) ok = False return ok, message

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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