def test_get_env_shell_file_paths_from_setup_environment_elem():
xml = """<action name="setup_r_environment">
<repository name="package_r_3_0_1" owner="bgruening" toolshed="toolshed.g2.bx.psu.edu" changeset_revision="1234567">
<package name="R" version="3.0.1" />
</repository>
</action>
"""
mock_app = MockApp()
action_elem = parse_xml_string( xml )
required_for_install_env_sh = '/path/to/existing.sh'
all_env_paths = [ required_for_install_env_sh ]
action_dict = {}
env_manager = EnvManager( mock_app )
r_env_sh = '/path/to/go/env.sh'
def mock_get_env_shell_file_paths( elem ):
assert elem.get( 'name' ) == "package_r_3_0_1"
return [ r_env_sh ]
with __mock_common_util_method( env_manager, "get_env_shell_file_paths", mock_get_env_shell_file_paths ):
env_manager.get_env_shell_file_paths_from_setup_environment_elem( all_env_paths, action_elem, action_dict )
## Verify old env files weren't deleted.
assert required_for_install_env_sh in all_env_paths
## Verify new ones added.
assert r_env_sh in all_env_paths
## env_shell_file_paths includes everything
assert all( [ env in action_dict[ 'env_shell_file_paths' ] for env in all_env_paths ] )
## action_shell_file_paths includes only env files defined in
## inside the setup_ action element.
assert required_for_install_env_sh not in action_dict[ 'action_shell_file_paths' ]
assert r_env_sh in action_dict[ 'action_shell_file_paths' ]
def test_get_env_shell_file_paths_from_setup_environment_elem():
xml = """<action name="setup_r_environment">
<repository name="package_r_3_0_1" owner="bgruening" toolshed="toolshed.g2.bx.psu.edu" changeset_revision="1234567">
<package name="R" version="3.0.1" />
</repository>
<repository name="package_zlib_1_2_8" owner="iuc" toolshed="toolshed.g2.bx.psu.edu" changeset_revision="7654321">
<package name="zlib" version="1.2.8" />
</repository>
</action>
"""
mock_app = MockApp()
action_elem = parse_xml_string(xml)
required_for_install_env_sh = '/path/to/existing.sh'
all_env_paths = [required_for_install_env_sh]
action_dict = {}
env_manager = EnvManager(mock_app)
r_env_sh = '/path/to/go/env.sh'
def mock_get_env_shell_file_paths(elem):
assert elem.get('name') in ["package_r_3_0_1", "package_zlib_1_2_8"]
return [r_env_sh]
with __mock_common_util_method(env_manager, "get_env_shell_file_paths",
mock_get_env_shell_file_paths):
env_manager.get_env_shell_file_paths_from_setup_environment_elem(
all_env_paths, action_elem, action_dict)
# Verify old env files weren't deleted.
assert required_for_install_env_sh in all_env_paths
# Verify new ones added.
assert r_env_sh in all_env_paths
# env_shell_file_paths includes everything
assert all([
env in action_dict['env_shell_file_paths'] for env in all_env_paths
])
# for every given repository there should be one env
# file + the required_for_install_env_sh file
assert len(action_dict['env_shell_file_paths']) == 3
# action_shell_file_paths includes only env files defined
# inside the setup_ action element.
assert required_for_install_env_sh in action_dict[
'action_shell_file_paths']
assert r_env_sh in action_dict['action_shell_file_paths']
def set_environment( self, elem, tool_shed_repository, attr_tups_of_dependencies_for_install ):
"""
Create a ToolDependency to set an environment variable. This is different from the process used to
set an environment variable that is associated with a package. An example entry in a tool_dependencies.xml
file is::
<set_environment version="1.0">
<environment_variable name="R_SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>
</set_environment>
This method must also handle the sub-element tag::
<environment_variable name="R_SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>
"""
# TODO: Add support for a repository dependency definition within this tool dependency type's tag set. This should look something like
# the following. See the implementation of support for this in the tool dependency package type's method above.
# This function is only called for set environment actions as defined below, not within an <install version="1.0"> tool
# dependency type. Here is an example of the tag set this function does handle:
# <action type="set_environment">
# <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
# </action>
# Here is an example of the tag set this function does not handle:
# <set_environment version="1.0">
# <repository toolshed="<tool shed>" name="<repository name>" owner="<repository owner>" changeset_revision="<changeset revision>" />
# </set_environment>
env_manager = EnvManager( self.app )
tool_dependencies = []
env_var_version = elem.get( 'version', '1.0' )
tool_shed_repository_install_dir = os.path.abspath( tool_shed_repository.repo_files_directory( self.app ) )
if elem.tag == 'environment_variable':
# <environment_variable name="R_SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>
elems = [ elem ]
else:
# <set_environment version="1.0">
# <environment_variable name="R_SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>
# </set_environment>
elems = [ env_var_elem for env_var_elem in elem ]
for env_var_elem in elems:
env_var_name = env_var_elem.get( 'name', None )
# The value of env_var_name must match the text value of at least 1 <requirement> tag in the
# tool config's <requirements> tag set whose "type" attribute is "set_environment" (e.g.,
# <requirement type="set_environment">R_SCRIPT_PATH</requirement>).
env_var_action = env_var_elem.get( 'action', None )
if env_var_name and env_var_action:
# Tool dependencies of type "set_environment" always have the version attribute set to None.
attr_tup = ( env_var_name, None, 'set_environment' )
if attr_tup in attr_tups_of_dependencies_for_install:
install_dir = \
tool_dependency_util.get_tool_dependency_install_dir( app=self.app,
repository_name=tool_shed_repository.name,
repository_owner=tool_shed_repository.owner,
repository_changeset_revision=tool_shed_repository.installed_changeset_revision,
tool_dependency_type='set_environment',
tool_dependency_name=env_var_name,
tool_dependency_version=None )
install_environment = InstallEnvironment( app=self.app,
tool_shed_repository_install_dir=tool_shed_repository_install_dir,
install_dir=install_dir )
env_var_dict = env_manager.create_env_var_dict( elem=env_var_elem,
install_environment=install_environment )
if env_var_dict:
if not os.path.exists( install_dir ):
os.makedirs( install_dir )
status = self.app.install_model.ToolDependency.installation_status.INSTALLING
tool_dependency = \
tool_dependency_util.create_or_update_tool_dependency( app=self.app,
tool_shed_repository=tool_shed_repository,
name=env_var_name,
version=None,
type='set_environment',
status=status,
set_status=True )
if env_var_version == '1.0':
# Create this tool dependency's env.sh file.
env_file_builder = EnvFileBuilder( install_dir )
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 ) )
log.debug( error_message )
status = self.app.install_model.ToolDependency.installation_status.ERROR
tool_dependency = \
tool_dependency_util.set_tool_dependency_attributes( self.app,
tool_dependency=tool_dependency,
status=status,
error_message=error_message )
else:
if tool_dependency.status not in [ self.app.install_model.ToolDependency.installation_status.ERROR,
self.app.install_model.ToolDependency.installation_status.INSTALLED ]:
status = self.app.install_model.ToolDependency.installation_status.INSTALLED
tool_dependency = \
tool_dependency_util.set_tool_dependency_attributes( self.app,
tool_dependency=tool_dependency,
status=status )
log.debug( 'Environment variable %s set in %s for tool dependency %s.' %
( str( env_var_name ), str( install_dir ), str( tool_dependency.name ) ) )
else:
error_message = 'Only set_environment version 1.0 is currently supported (i.e., change your tag to be <set_environment version="1.0">).'
status = self.app.install_model.ToolDependency.installation_status.ERROR
tool_dependency = \
tool_dependency_util.set_tool_dependency_attributes( self.app,
tool_dependency=tool_dependency,
status=status,
error_message=error_message )
tool_dependencies.append( tool_dependency )
return tool_dependencies