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Fix for setting environment paths when using setup_virutalenv.

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This commit is contained in:
Daniel Blankenberg
2014-04-29 12:13:01 -04:00
parent e97f7e2804
commit 2e67b5c247
1 changed files with 35 additions and 12 deletions
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lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
+35 -12
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@@ -1158,20 +1158,15 @@ class SetupVirtualEnv( RecipeStep ):
full_setup_command = "%s; %s; %s" % ( setup_command, activate_command, install_command )
return_code = install_environment.handle_command( app, tool_dependency, install_dir, full_setup_command )
if return_code:
log.error( "Failed to do setup_virtualenv install, exit code='%s'", return_code )
# would it be better to try to set env variables anway, instead of returning here?
return tool_dependency, None, None
# Use raw strings so that python won't automatically unescape the quotes before passing the command
# to subprocess.Popen.
site_packages_command = \
r"""%s -c 'import os, sys; print os.path.join(sys.prefix, "lib", "python" + sys.version[:3], "site-packages")'""" % \
os.path.join( venv_directory, "bin", "python" )
output = install_environment.handle_command( app, tool_dependency, install_dir, site_packages_command, return_output=True )
if output.return_code:
return tool_dependency, None, None
if not os.path.exists( output.stdout ):
log.debug( "virtualenv's site-packages directory '%s' does not exist", output.stdout )
return tool_dependency, None, None
env_file_builder.append_line( name="PYTHONPATH", action="prepend_to", value=output.stdout )
site_packages_directory, site_packages_directory_list = self.__get_site_packages_directory( install_environment, app, tool_dependency, install_dir, python_cmd, venv_directory )
env_file_builder.append_line( name="PATH", action="prepend_to", value=os.path.join( venv_directory, "bin" ) )
if site_packages_directory is None:
log.error( "virtualenv's site-packages directory '%s' does not exist", site_packages_directory_list )
else:
env_file_builder.append_line( name="PYTHONPATH", action="prepend_to", value=site_packages_directory )
# The caller should check the status of the returned tool_dependency since this function does nothing
# with the return_code.
return_code = env_file_builder.return_code
@@ -1203,6 +1198,34 @@ class SetupVirtualEnv( RecipeStep ):
action_dict[ 'python' ] = action_elem.get( 'python', 'python' )
return action_dict
def __get_site_packages_directory( self, install_environment, app, tool_dependency, install_dir, python_cmd, venv_directory ):
lib_dir = os.path.join( venv_directory, "lib" )
rval = os.path.join( lib_dir, python_cmd, 'site-packages' )
site_packages_directory_list = [ rval ]
if os.path.exists( rval ):
return ( rval, site_packages_directory_list )
for ( dirpath, dirnames, filenames ) in os.walk( lib_dir ):
for dirname in dirnames:
rval = os.path.join( lib_dir, dirname, 'site-packages' )
site_packages_directory_list.append( rval )
if os.path.exists( rval ):
return ( rval, site_packages_directory_list )
break
# fall back to python call to get site packages
# FIXME: This is probably more robust?, but there is currently an issue with handling the output.stdout
# preventing the entire path from being included (it gets truncated)
# Use raw strings so that python won't automatically unescape the quotes before passing the command
# to subprocess.Popen.
for site_packages_command in [ r"""%s -c 'import site; site.getsitepackages()[0]'""" % \
os.path.join( venv_directory, "bin", "python" ),
r"""%s -c 'import os, sys; print os.path.join( sys.prefix, "lib", "python" + sys.version[:3], "site-packages" )'""" % \
os.path.join( venv_directory, "bin", "python" ) ]:
output = install_environment.handle_command( app, tool_dependency, install_dir, site_packages_command, return_output=True )
site_packages_directory_list.append( output.stdout )
if not output.return_code and os.path.exists( output.stdout ):
return ( output.stdout, site_packages_directory_list )
return ( None, site_packages_directory_list )
class ShellCommand( RecipeStep ):
def __init__( self ):