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Merged in next-stable.

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This commit is contained in:
Dave Bouvier
2013-05-23 15:50:34 -04:00
parent ce012e9c57 6bda99e492
commit 23a145f88c
1 changed files with 34 additions and 2 deletions
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lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py
+34 -2
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@@ -22,6 +22,7 @@ from fabric.api import settings
log = logging.getLogger( __name__ )
CMD_SEPARATOR = '__CMD_SEP__'
INSTALLATION_LOG = 'INSTALLATION.log'
VIRTUALENV_URL = 'https://pypi.python.org/packages/source/v/virtualenv/virtualenv-1.9.1.tar.gz'
@@ -49,6 +50,29 @@ def handle_command( app, tool_dependency, install_dir, cmd, return_output=False
return output
return output.return_code
def handle_environment_variables( app, tool_dependency, install_dir, env_var_dict, set_prior_environment_commands ):
env_var_value = env_var_dict[ 'value' ]
if '$ENV[' in env_var_value and ']' in env_var_value:
# Pull out the name of the environment variable to populate.
inherited_env_var_name = env_var_value.split( '[' )[1].split( ']' )[0]
to_replace = '$ENV[%s]' % inherited_env_var_name
# Build a command line that outputs CMD_SEPARATOR + environment variable value + CMD_SEPARATOR.
set_prior_environment_commands.extend( [ "echo '%s'" % CMD_SEPARATOR, 'echo $%s' % inherited_env_var_name, "echo '%s'" % CMD_SEPARATOR ] )
command = ' ; '.join( set_prior_environment_commands )
# Run the command and capture the output.
command_return = handle_command( app, tool_dependency, install_dir, command, return_output=True )
# And extract anything between the two instances of CMD_SEPARATOR.
environment_variable_value = command_return.split( CMD_SEPARATOR )[1].split( CMD_SEPARATOR )[0].strip( '\n' )
if environment_variable_value:
log.info( 'Replacing %s with %s in env.sh for this repository.', to_replace, environment_variable_value )
env_var_value = env_var_value.replace( to_replace, environment_variable_value )
else:
# If the return is empty, replace the original $ENV[] with nothing, to avoid any shell misparsings later on.
log.error( 'Environment variable %s not found, removing from set_environment.', inherited_env_var_name )
env_var_value = env_var_value.replace( to_replace, '$%s' % inherited_env_var_name )
env_var_dict[ 'value' ] = env_var_value
return env_var_dict
def install_virtualenv( app, venv_dir ):
if not os.path.exists( venv_dir ):
with make_tmp_dir() as work_dir:
@@ -149,10 +173,18 @@ def install_and_build_package( app, tool_dependency, actions_dict ):
destination_dir=os.path.join( action_dict[ 'destination' ] ) )
elif action_type == 'set_environment':
# Currently the only action supported in this category is "environment_variable".
# Build a command line from the prior_installation_required, in case an environment variable is referenced
# in the set_environment action.
cmds = []
for env_shell_file_path in env_shell_file_paths:
for i, env_setting in enumerate( open( env_shell_file_path ) ):
cmds.append( env_setting.strip( '\n' ) )
env_var_dicts = action_dict[ 'environment_variable' ]
for env_var_dict in env_var_dicts:
cmd = common_util.create_or_update_env_shell_file( install_dir, env_var_dict )
return_code = handle_command( app, tool_dependency, install_dir, cmd )
# 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_command = common_util.create_or_update_env_shell_file( install_dir, env_var_dict )
return_code = handle_command( app, tool_dependency, install_dir, env_command )
if return_code:
return
elif action_type == 'set_environment_for_install':