1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/46de10d8c8e5/ changeset: 46de10d8c8e5 user: greg date: 2012-06-22 20:10:53 summary: More tool shed refinements to enable working with Galaxy's ToolDataTableManager. affected #: 1 file diff -r f197c4346cc44bf3996eee6b24e2c393ad519d9d -r 46de10d8c8e5ffd537f7c13e4833aa8635ab6fcf lib/galaxy/webapps/community/controllers/common.py --- a/lib/galaxy/webapps/community/controllers/common.py +++ b/lib/galaxy/webapps/community/controllers/common.py @@ -429,6 +429,7 @@ sample_files, deleted_sample_files = get_list_of_copied_sample_files( repo, ctx, dir=work_dir ) if sample_files: trans.app.config.tool_data_path = work_dir + all_sample_files_copied = [] # Handle the tool_data_table_conf.xml.sample file if it is included in the repository. if 'tool_data_table_conf.xml.sample' in sample_files: tool_data_table_config = copy_file_from_manifest( repo, ctx, 'tool_data_table_conf.xml.sample', work_dir ) @@ -437,7 +438,13 @@ # Find all tool configs. ctx_file_name = strip_path( filename ) if ctx_file_name not in NOT_TOOL_CONFIGS and filename.endswith( '.xml' ): - is_tool_config, valid, tool, error_message = load_tool_from_tmp_directory( trans, repo, repo_dir, ctx, filename, work_dir ) + is_tool_config, valid, tool, error_message, sample_files, deleted_sample_files = load_tool_from_tmp_directory( trans, + repo, + repo_dir, + ctx, + filename, + work_dir ) + all_sample_files_copied.extend( sample_files ) if is_tool_config and valid and tool is not None: sample_files_copied, can_set_metadata, invalid_files = check_tool_input_params( trans, repo, @@ -449,33 +456,13 @@ invalid_files, original_tool_data_path, work_dir ) + all_sample_files_copied.extend( sample_files_copied ) if can_set_metadata: # Update the list of metadata dictionaries for tools in metadata_dict. repository_clone_url = generate_clone_url( trans, id ) metadata_dict = generate_tool_metadata( filename, tool, repository_clone_url, metadata_dict ) else: invalid_tool_configs.append( ctx_file_name ) - # Remove all copied sample files from both the original tool data path (~/shed-tool-data) and the temporary - # value of trans.app.config.tool_data_path, which is work_dir. - for copied_sample_file in sample_files_copied: - copied_file = copied_sample_file.replace( '.sample', '' ) - try: - os.unlink( os.path.join( trans.app.config.tool_data_path, copied_sample_file ) ) - except: - pass - try: - os.unlink( os.path.join( trans.app.config.tool_data_path, copied_file ) ) - except: - pass - if trans.app.config.tool_data_path == work_dir: - try: - os.unlink( os.path.join( original_tool_data_path, copied_sample_file ) ) - except: - pass - try: - os.unlink( os.path.join( original_tool_data_path, copied_file ) ) - except: - pass elif is_tool_config: if not error_message: error_message = 'Unknown problems loading tool.' @@ -508,6 +495,27 @@ shutil.rmtree( work_dir ) except: pass + # Remove all copied sample files from both the original tool data path (~/shed-tool-data) and the temporary + # value of trans.app.config.tool_data_path, which is work_dir. + for copied_sample_file in all_sample_files_copied: + copied_file = copied_sample_file.replace( '.sample', '' ) + try: + os.unlink( os.path.join( trans.app.config.tool_data_path, copied_sample_file ) ) + except: + pass + try: + os.unlink( os.path.join( trans.app.config.tool_data_path, copied_file ) ) + except: + pass + if trans.app.config.tool_data_path == work_dir: + try: + os.unlink( os.path.join( original_tool_data_path, copied_sample_file ) ) + except: + pass + try: + os.unlink( os.path.join( original_tool_data_path, copied_file ) ) + except: + pass return metadata_dict, invalid_files, deleted_sample_files def generate_tool_guid( trans, repository, tool ): """ @@ -810,6 +818,7 @@ except: pass return tool, message + original_tool_data_path = trans.app.config.tool_data_path tool_config_filename = strip_path( tool_config_filename ) repository = get_repository( trans, repository_id ) repo_files_dir = repository.repo_path @@ -818,6 +827,9 @@ tool = None message = '' work_dir = make_tmp_directory() + sample_files, deleted_sample_files = get_list_of_copied_sample_files( repo, ctx, dir=work_dir ) + if sample_files: + trans.app.config.tool_data_path = work_dir # Load entries into the tool_data_tables if the tool requires them. tool_data_table_config = copy_file_from_manifest( repo, ctx, 'tool_data_table_conf.xml.sample', work_dir ) if tool_data_table_config: @@ -841,12 +853,16 @@ shutil.rmtree( work_dir ) except: pass + if sample_files: + trans.app.config.tool_data_path = original_tool_data_path return tool, message def load_tool_from_tmp_directory( trans, repo, repo_dir, ctx, filename, dir ): is_tool_config = False tool = None valid = False error_message = '' + sample_files = [] + deleted_sample_files = [] tmp_config = get_named_tmpfile_from_ctx( ctx, filename, dir ) if tmp_config: if not ( check_binary( tmp_config ) or check_image( tmp_config ) or check_gzip( tmp_config )[ 0 ] @@ -860,6 +876,9 @@ log.debug( "Error parsing %s, exception: %s" % ( tmp_config, str( e ) ) ) is_tool_config = False if is_tool_config: + sample_files, deleted_sample_files = get_list_of_copied_sample_files( repo, ctx, dir=dir ) + if sample_files: + trans.app.config.tool_data_path = dir # Load entries into the tool_data_tables if the tool requires them. tool_data_table_config = copy_file_from_manifest( repo, ctx, 'tool_data_table_conf.xml.sample', dir ) if tool_data_table_config: @@ -884,7 +903,7 @@ error_message = str( e ) # Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file. reset_tool_data_tables( trans.app ) - return is_tool_config, valid, tool, error_message + return is_tool_config, valid, tool, error_message, sample_files, deleted_sample_files def new_tool_metadata_required( trans, id, metadata_dict ): """ Compare the last saved metadata for each tool in the repository with the new metadata 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.