1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/commits/739287adeac8/ Changeset: 739287adeac8 User: davebgx Date: 2014-02-27 21:46:03 Summary: Eliminate the use of shell commands to perform functions that can be done internally with the elimination of fabric.local for tool dependency installation. Affected #: 2 files

diff -r cb00a217028c903a0868bad0b370b325893eb708 -r 739287adeac8561c32d6dcf24d7eb9309d992da3 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 @@ -5,6 +5,7 @@ import os import Queue import shutil +import stat import subprocess import sys import tempfile @@ -72,10 +73,10 @@ self.install_dir = install_dir self.return_code = 0

- def append_line( self, skip_if_contained=True, make_executable=True, **kwd ): + def append_line( self, make_executable=True, **kwd ): env_var_dict = dict( **kwd ) env_entry, env_file = self.create_or_update_env_shell_file( self.install_dir, env_var_dict ) - return_code = file_append( env_entry, env_file, skip_if_contained=skip_if_contained, make_executable=make_executable ) + return_code = file_append( env_entry, env_file, make_executable=make_executable ) self.return_code = self.return_code or return_code return self.return_code

@@ -194,42 +195,56 @@ stderr_queue.put( output ) stderr_queue.put( None )

-def file_append( text, file_path, skip_if_contained=True, make_executable=True ): +def file_append( text, file_path, make_executable=True ): """ - 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. + Append a line to a file unless 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. """ - if not os.path.exists( file_path ): - return_code = handle_simple_command( 'touch %s' % file_path ) - if return_code: - return return_code + file_dir = os.path.dirname( file_path ) + if not os.path.exists( file_dir ): + try: + os.makedirs( file_dir ) + except Exception, e: + log.exception( str( e ) ) + return 1 + if os.path.exists( file_path ): + try: + new_env_file_contents = [] + env_file_contents = file( file_path, 'a+' ).readlines() + # Clean out blank lines from the env.sh file. + for line in env_file_contents: + line = line.rstrip() + if line: + new_env_file_contents.append( line ) + env_file_contents = new_env_file_contents + except Exception, e: + log.exception( str( e ) ) + return 1 + else: + env_file_handle = open( file_path, 'w' ) + env_file_handle.close() + env_file_contents = [] if make_executable: - # Explicitly set the file to the received mode if valid. - with settings( hide( 'everything' ), warn_only=True ): - return_code = handle_simple_command( 'chmod +x %s' % file_path ) - if return_code: - return return_code + # Explicitly set the file's executable bits. + try: + os.chmod( file_path, int( '111', base=8) | os.stat( file_path )[ stat.ST_MODE ] ) + except Exception, e: + log.exception( str( e ) ) + return 1 return_code = 0 # 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 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 ) - return_code = handle_simple_command( egrep_cmd ) - if return_code == 0: - continue - # Append the current line to the file, escaping any single quotes in the line. - line = line.replace( "'", r"'\''" ) - return_code = handle_simple_command( "echo '%s' >> %s" % ( line, file_path ) ) - if return_code: - # Return upon the first error encountered. - return return_code + line = line.rstrip() + if line not in env_file_contents: + env_file_contents.append( line ) + try: + file( file_path, 'w' ).write( '\n'.join( env_file_contents ) ) + except Exception, e: + log.exception( str( e ) ) + return 1 return return_code

def filter_actions_after_binary_installation( actions ): @@ -278,8 +293,8 @@ """ Wrap subprocess.Popen in such a way that the stderr and stdout from running a shell command will be captured and logged in nearly real time. This is similar to fabric.local, but allows us to - retain control over the process. This method is considered "complex" because it uses queues and - threads - see handle_simple_command(). + retain control over the process. This method is named "complex" because it uses queues and + threads to execute a command while capturing and displaying the output. """ wrapped_command = shlex.split( "/bin/sh -c '%s'" % str( command ) ) # Launch the command as subprocess. A bufsize of 1 means line buffered. @@ -456,30 +471,6 @@ env_var_dict[ 'value' ] = env_var_value return env_var_dict

-def handle_simple_command( command ): - """ - Use this instead of fabric.local to retain control over the process spawned to run the - received command. - """ - wrapped_command = shlex.split( "/bin/sh -c '%s'" % str( command ) ) - # Launch the command as subprocess. A bufsize of 1 means line buffered. - try: - process_handle = subprocess.Popen( wrapped_command, - stdout=subprocess.PIPE, - stderr=subprocess.PIPE, - bufsize=1, - close_fds=False, - cwd=state.env[ 'lcwd' ] ) - except OSError, e: - # We don't have a working directory. - process_handle = subprocess.Popen( wrapped_command, - stdout=subprocess.PIPE, - stderr=subprocess.PIPE ) - stdout, stderr = process_handle.communicate() - if stderr: - log.debug( "Problem executing command %s: %s." % ( wrapped_command, stderr ) ) - return process_handle.returncode - def install_virtualenv( app, venv_dir ): if not os.path.exists( venv_dir ): with make_tmp_dir() as work_dir: @@ -951,7 +942,10 @@ work_dir = tempfile.mkdtemp( prefix="tmp-toolshed-mtd" ) yield work_dir if os.path.exists( work_dir ): - return_code = handle_simple_command( 'rm -rf %s' % work_dir ) + try: + shutil.rmtree( work_dir ) + except Exception, e: + log.exception( str( e ) )

def set_galaxy_environment( galaxy_user, tool_dependency_dir, host='localhost', shell='/bin/bash -l -c' ): """General Galaxy environment configuration. This method is not currently used."""

diff -r cb00a217028c903a0868bad0b370b325893eb708 -r 739287adeac8561c32d6dcf24d7eb9309d992da3 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 @@ -884,7 +884,7 @@ if env_var_version == '1.0': # Create this tool dependency's env.sh file. env_file_builder = fabric_util.EnvFileBuilder( install_dir ) - return_code = env_file_builder.append_line( skip_if_contained=True, make_executable=True, **env_var_dict ) + return_code = env_file_builder.append_line( make_executable=True, **env_var_dict ) if return_code: error_message = 'Error creating env.sh file for tool dependency %s, return_code: %s' % \ ( str( tool_dependency.name ), str( return_code ) )

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

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