1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f33c054d6d5b/ Changeset: f33c054d6d5b User: Dave Bouvier Date: 2013-08-07 03:21:10 Summary: Fix for the download_binary action type incorrectly processing downloaded compressed files. Affected #: 3 files diff -r 773941fd26a43c8522c3ff9977cfda5968f65505 -r f33c054d6d5b75ae545248d71ec559d74b4fa636 lib/tool_shed/galaxy_install/tool_dependencies/common_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/common_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/common_util.py @@ -71,23 +71,13 @@ __shellquote(env_shell_file_path)) return cmd -def download_binary_from_url( url, work_dir, install_dir ): +def download_binary( url, work_dir ): ''' - Download a pre-compiled binary from the specified URL. If the downloaded file is an archive, - extract it into install_dir and delete the archive. + Download a pre-compiled binary from the specified URL. ''' downloaded_filename = os.path.split( url )[ -1 ] - try: - dir = url_download( work_dir, downloaded_filename, url, extract=True ) - downloaded_filepath = os.path.join( work_dir, downloaded_filename ) - if is_compressed( downloaded_filepath ): - os.remove( downloaded_filepath ) - move_directory_files( current_dir=work_dir, - source_dir=dir, - destination_dir=install_dir ) - return True - except HTTPError: - return False + dir = url_download( work_dir, downloaded_filename, url, extract=False ) + return downloaded_filename def extract_tar( file_name, file_path ): if isgzip( file_name ) or isbz2( file_name ): diff -r 773941fd26a43c8522c3ff9977cfda5968f65505 -r f33c054d6d5b75ae545248d71ec559d74b4fa636 lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py @@ -31,6 +31,15 @@ if int( version.split( "." )[ 0 ] ) < 1: raise NotImplementedError( "Install Fabric version 1.0 or later." ) +def filter_actions_after_binary_installation( actions ): + '''Filter out actions that should not be processed if a binary download succeeded.''' + filtered_actions = [] + for action in actions: + action_type, action_dict = action + if action_type in [ 'set_environment', 'chmod', 'download_binary' ]: + filtered_actions.append( action ) + return filtered_actions + def handle_command( app, tool_dependency, install_dir, cmd, return_output=False ): sa_session = app.model.context.current with settings( warn_only=True ): @@ -165,8 +174,6 @@ actions = actions_dict.get( 'actions', None ) filtered_actions = [] env_shell_file_paths = [] - # Default to false so that the install process will default to compiling. - binary_found = False if actions: with make_tmp_dir() as work_dir: with lcd( work_dir ): @@ -174,20 +181,38 @@ # are currently only two supported processes; download_by_url and clone via a "shell_command" action type. action_type, action_dict = actions[ 0 ] if action_type == 'download_binary': - # Eliminate the download_binary action so remaining actions can be processed correctly. - filtered_actions = actions[ 1: ] url = action_dict[ 'url' ] + # Get the target directory for this download, if the user has specified one. Default to the root of $INSTALL_DIR. + target_directory = action_dict.get( 'target_directory', None ) # Attempt to download a binary from the specified URL. - log.debug( 'Attempting to download from %s', url ) - binary_found = common_util.download_binary_from_url( url, work_dir, install_dir ) - if binary_found: - # If the attempt succeeded, set the action_type to binary_found, in order to skip any download_by_url or shell_command actions. + log.debug( 'Attempting to download from %s to %s', url, str( target_directory ) ) + downloaded_filename = None + try: + downloaded_filename = common_util.download_binary( url, work_dir ) + # Filter out any actions that are not download_binary, chmod, or set_environment. + filtered_actions = filter_actions_after_binary_installation( actions[ 1: ] ) + # Set actions to the same, so that the current download_binary doesn't get re-run in the filtered actions below. actions = filtered_actions - action_type = 'binary_found' - else: + except Exception, e: + log.exception( str( e ) ) # No binary exists, or there was an error downloading the binary from the generated URL. Proceed with the remaining actions. - del actions[ 0 ] - action_type, action_dict = actions[ 0 ] + filtered_actions = actions[ 1: ] + action_type, action_dict = filtered_actions[ 0 ] + # If the downloaded file exists, move it to $INSTALL_DIR. Put this outside the try/catch above so that + # any errors in the move step are correctly sent to the tool dependency error handler. + if downloaded_filename and os.path.exists( os.path.join( work_dir, downloaded_filename ) ): + if target_directory: + target_directory = os.path.realpath( os.path.normpath( os.path.join( install_dir, target_directory ) ) ) + # Make sure the target directory is not outside of $INSTALL_DIR. + if target_directory.startswith( os.path.realpath( install_dir ) ): + full_path_to_dir = os.path.abspath( os.path.join( install_dir, target_directory ) ) + else: + full_path_to_dir = os.path.abspath( install_dir ) + else: + full_path_to_dir = os.path.abspath( install_dir ) + common_util.move_file( current_dir=work_dir, + source=downloaded_filename, + destination_dir=full_path_to_dir ) if action_type == 'download_by_url': # Eliminate the download_by_url action so remaining actions can be processed correctly. filtered_actions = actions[ 1: ] @@ -237,9 +262,6 @@ current_dir = os.path.abspath( os.path.join( work_dir, dir ) ) with lcd( current_dir ): action_type, action_dict = action_tup - # If a binary was found, we only need to process environment variables, file permissions, and any other binary downloads. - if binary_found and action_type not in [ 'set_environment', 'chmod', 'download_binary' ]: - continue if action_type == 'make_directory': common_util.make_directory( full_path=action_dict[ 'full_path' ] ) elif action_type == 'move_directory_files': @@ -374,12 +396,26 @@ os.chmod( target_file, mode ) elif action_type == 'download_binary': url = action_dict[ 'url' ] - binary_found = common_util.download_binary_from_url( url, work_dir, install_dir ) - if binary_found: - log.debug( 'Successfully downloaded binary from %s', url ) - else: - log.error( 'Unable to download binary from %s', url ) - + target_directory = action_dict.get( 'target_directory', None ) + try: + downloaded_filename = common_util.download_binary( url, work_dir ) + except Exception, e: + log.exception( str( e ) ) + # If the downloaded file exists, move it to $INSTALL_DIR. Put this outside the try/catch above so that + # any errors in the move step are correctly sent to the tool dependency error handler. + if downloaded_filename and os.path.exists( os.path.join( work_dir, downloaded_filename ) ): + if target_directory: + target_directory = os.path.realpath( os.path.normpath( os.path.join( install_dir, target_directory ) ) ) + # Make sure the target directory is not outside of $INSTALL_DIR. + if target_directory.startswith( os.path.realpath( install_dir ) ): + full_path_to_dir = os.path.abspath( os.path.join( install_dir, target_directory ) ) + else: + full_path_to_dir = os.path.abspath( install_dir ) + else: + full_path_to_dir = os.path.abspath( install_dir ) + common_util.move_file( current_dir=work_dir, + source=downloaded_filename, + destination_dir=full_path_to_dir ) def log_results( command, fabric_AttributeString, file_path ): """ diff -r 773941fd26a43c8522c3ff9977cfda5968f65505 -r f33c054d6d5b75ae545248d71ec559d74b4fa636 lib/tool_shed/galaxy_install/tool_dependencies/install_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py @@ -395,6 +395,7 @@ else: url_template_elem = url_template_elems[ 0 ] action_dict[ 'url' ] = Template( url_template_elem.text ).safe_substitute( platform_info_dict ) + action_dict[ 'target_directory' ] = action_elem.get( 'target_directory', None ) elif action_type == 'shell_command': # <action type="shell_command">make</action> action_elem_text = evaluate_template( action_elem.text ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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