1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/641cb928bd4b/ Changeset: 641cb928bd4b User: greg Date: 2013-10-10 16:35:37 Summary: Fixes and code cleanup for installing tool dependencies defined in tool shed repository definition file via fabric. Affected #: 2 files diff -r f86731617df8422ac7364bc299c7a53978af16e6 -r 641cb928bd4bf3c9c209f880472b14b202ef1d5d 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 @@ -16,49 +16,55 @@ eggs.require( 'Fabric' ) from fabric.api import env +from fabric.api import hide from fabric.api import lcd from fabric.api import local from fabric.api import settings -from fabric.api import hide log = logging.getLogger( __name__ ) INSTALLATION_LOG = 'INSTALLATION.log' VIRTUALENV_URL = 'https://pypi.python.org/packages/source/v/virtualenv/virtualenv-1.9.1.tar.gz' -def add_to_env_shell_file( text, env_shell_file ): +def check_fabric_version(): + version = env.version + if int( version.split( "." )[ 0 ] ) < 1: + raise NotImplementedError( "Install Fabric version 1.0 or later." ) + +def file_append( text, file_path, skip_if_contained=True, make_executable=True ): ''' - Append a line to a file, if this line does not already exist in the file. Creates the file and sets the mode to - executable if the file does not exist. Equivalent to a local version of fabric.contrib.files.append. + Append a line to a file unless skip_if_contained is True and the line already exists in the file. This method creates the file + if it doesn't exist. If make_executable is True, the permissions on the file are set to executable by the owner. This method + is similar to a local version of fabric.contrib.files.append. ''' - if not os.path.exists( env_shell_file ): - local( 'touch %s' % env_shell_file ) - # Explicitly set env.sh executable. - with settings( hide( 'everything' ), warn_only=True ): - local( 'chmod +x %s' % env_shell_file ) + if not os.path.exists( file_path ): + local( 'touch %s' % file_path ) + if make_executable: + # Explicitly set the file to the received mode if valid. + with settings( hide( 'everything' ), warn_only=True ): + local( 'chmod +x %s' % file_path ) return_code = 0 - # Convert the contents to a list, in order to support adding one or more lines to env.sh. + # Convert the received text to a list, in order to support adding one or more lines to the file. if isinstance( text, basestring ): text = [ text ] for line in text: # Build a regex to search for the relevant line in env.sh. regex = td_common_util.egrep_escape( line ) - # If the line exists, egrep will return a success. - with settings( hide( 'everything' ), warn_only=True ): - egrep_cmd = 'egrep "^%s$" %s' % ( regex, env_shell_file ) - contains_line = local( egrep_cmd ).succeeded - if contains_line: - continue - # If not, then append the line, escaping any single quotes in the shell command. + if skip_if_contained: + # If the line exists in the file, egrep will return a success. + with settings( hide( 'everything' ), warn_only=True ): + egrep_cmd = 'egrep "^%s$" %s' % ( regex, file_path ) + contains_line = local( egrep_cmd ).succeeded + if contains_line: + continue + # Append the current line to the file, escaping any single quotes in the line. line = line.replace( "'", r"'\\''" ) - return_code = local( "echo '%s' >> %s" % ( line, env_shell_file ) ).return_code + return_code = local( "echo '%s' >> %s" % ( line, file_path ) ).return_code + if return_code: + # Return upon the first error encountered. + return return_code return return_code -def check_fabric_version(): - version = env.version - 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 = [] @@ -331,7 +337,7 @@ # Check for the presence of the $ENV[] key string and populate it if possible. env_var_dict = handle_environment_variables( app, tool_dependency, install_dir, env_var_dict, cmds ) env_entry, env_file = td_common_util.create_or_update_env_shell_file( install_dir, env_var_dict ) - return_code = add_to_env_shell_file( env_entry, env_file ) + return_code = file_append( env_entry, env_file, skip_if_contained=True, make_executable=True ) if return_code: return elif action_type == 'set_environment_for_install': @@ -373,13 +379,13 @@ log.error( "virtualenv's site-packages directory '%s' does not exist", output.stdout ) return modify_env_command_dict = dict( name="PYTHONPATH", action="prepend_to", value=output.stdout ) - env_entry, env_file = td_common_util.create_or_update_env_shell_file( install_dir, env_var_dict ) - return_code = add_to_env_shell_file( env_entry, env_file ) + env_entry, env_file = td_common_util.create_or_update_env_shell_file( install_dir, modify_env_command_dict ) + return_code = file_append( env_entry, env_file, skip_if_contained=True, make_executable=True ) if return_code: return modify_env_command_dict = dict( name="PATH", action="prepend_to", value=os.path.join( venv_directory, "bin" ) ) env_entry, env_file = td_common_util.create_or_update_env_shell_file( install_dir, modify_env_command_dict ) - return_code = add_to_env_shell_file( env_entry, env_file ) + return_code = file_append( env_entry, env_file, skip_if_contained=True, make_executable=True ) if return_code: return elif action_type == 'shell_command': diff -r f86731617df8422ac7364bc299c7a53978af16e6 -r 641cb928bd4bf3c9c209f880472b14b202ef1d5d 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 @@ -823,7 +823,7 @@ env_entry, env_file = td_common_util.create_or_update_env_shell_file( install_dir, env_var_dict ) if env_var_version == '1.0': # Handle setting environment variables using a fabric method. - fabric_util.add_to_env_shell_file( env_entry, env_file ) + fabric_util.file_append( env_entry, env_file, skip_if_contained=True, make_executable=True ) sa_session.refresh( tool_dependency ) if tool_dependency.status != app.model.ToolDependency.installation_status.ERROR: tool_dependency.status = app.model.ToolDependency.installation_status.INSTALLED Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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