def test_env_file_builder():
install_dir = "/opt/galaxy/dependencies/foo/"
env_file_builder = EnvFileBuilder( install_dir )
added_lines = []
mock_return = dict(value=0)
def mock_file_append( text, file_path, **kwds ):
added_lines.append( text )
return mock_return[ "value" ]
with __mock_env_file_builder_method( env_file_builder, "file_append", mock_file_append ):
env_file_builder.append_line( name="PATH", action="prepend_to", value="/usr/bin/local/R" )
assert added_lines == [ "PATH=/usr/bin/local/R:$PATH; export PATH" ]
assert env_file_builder.return_code == 0
# Reset mock lines
del added_lines[:]
# Next time file_append will fail
mock_return["value"] = 1
env_file_builder.append_line( action="source", value="/usr/bin/local/R/env.sh" )
assert added_lines == [ "if [ -f /usr/bin/local/R/env.sh ] ; then . /usr/bin/local/R/env.sh ; fi" ]
# Check failure
assert env_file_builder.return_code == 1
mock_return["value"] = 0
env_file_builder.append_line( name="LD_LIBRARY_PATH", action="append_to", value="/usr/bin/local/R/lib" )
# Verify even though last append succeeded, previous failure still recorded.
assert env_file_builder.return_code == 1
def test_env_file_builder():
install_dir = "/opt/galaxy/dependencies/foo/"
env_file_builder = EnvFileBuilder( install_dir )
added_lines = []
mock_return = dict(value=0)
def mock_file_append( text, file_path, **kwds ):
added_lines.append( text )
return mock_return[ "value" ]
with __mock_env_file_builder_method( env_file_builder, "file_append", mock_file_append ):
env_file_builder.append_line( name="PATH", action="prepend_to", value="/usr/bin/local/R" )
assert added_lines == [ "PATH=/usr/bin/local/R:$PATH; export PATH" ]
assert env_file_builder.return_code == 0
# Reset mock lines
del added_lines[:]
# Next time file_append will fail
mock_return["value"] = 1
env_file_builder.append_line( action="source", value="/usr/bin/local/R/env.sh" )
assert added_lines == [ "if [ -f /usr/bin/local/R/env.sh ] ; then . /usr/bin/local/R/env.sh ; fi" ]
# Check failure
assert env_file_builder.return_code == 1
mock_return["value"] = 0
env_file_builder.append_line( name="LD_LIBRARY_PATH", action="append_to", value="/usr/bin/local/R/lib" )
# Verify even though last append succeeded, previous failure still recorded.
assert env_file_builder.return_code == 1
def test_create_or_update_env_shell_file():
test_path = "/usr/share/R/libs"
env_file_builder = EnvFileBuilder( test_path )
line, path = env_file_builder.create_or_update_env_shell_file( TEST_INSTALL_DIR, dict( action="append_to", name="R_LIBS", value=test_path ) )
assert path == join( TEST_INSTALL_DIR, "env.sh" )
assert line == "R_LIBS=$R_LIBS:/usr/share/R/libs; export R_LIBS"
line, path = env_file_builder.create_or_update_env_shell_file( TEST_INSTALL_DIR, dict( action="prepend_to", name="R_LIBS", value=test_path ) )
assert path == join( TEST_INSTALL_DIR, "env.sh" )
assert line == "R_LIBS=/usr/share/R/libs:$R_LIBS; export R_LIBS"
line, path = env_file_builder.create_or_update_env_shell_file( TEST_INSTALL_DIR, dict( action="set_to", name="R_LIBS", value=test_path ) )
assert path == join( TEST_INSTALL_DIR, "env.sh" )
assert line == "R_LIBS=/usr/share/R/libs; export R_LIBS"
line, path = env_file_builder.create_or_update_env_shell_file( TEST_INSTALL_DIR, dict( action="source", value=test_path ) )
assert path == join( TEST_INSTALL_DIR, "env.sh" )
assert line == "if [ -f /usr/share/R/libs ] ; then . /usr/share/R/libs ; fi"
def test_create_or_update_env_shell_file():
test_path = "/usr/share/R/libs"
env_file_builder = EnvFileBuilder(test_path)
line, path = env_file_builder.create_or_update_env_shell_file(
TEST_INSTALL_DIR,
dict(action="append_to", name="R_LIBS", value=test_path))
assert path == join(TEST_INSTALL_DIR, "env.sh")
assert line == "R_LIBS=$R_LIBS:/usr/share/R/libs; export R_LIBS"
line, path = env_file_builder.create_or_update_env_shell_file(
TEST_INSTALL_DIR,
dict(action="prepend_to", name="R_LIBS", value=test_path))
assert path == join(TEST_INSTALL_DIR, "env.sh")
assert line == "R_LIBS=/usr/share/R/libs:$R_LIBS; export R_LIBS"
line, path = env_file_builder.create_or_update_env_shell_file(
TEST_INSTALL_DIR, dict(action="set_to", name="R_LIBS",
value=test_path))
assert path == join(TEST_INSTALL_DIR, "env.sh")
assert line == "R_LIBS=/usr/share/R/libs; export R_LIBS"
line, path = env_file_builder.create_or_update_env_shell_file(
TEST_INSTALL_DIR, dict(action="source", value=test_path))
assert path == join(TEST_INSTALL_DIR, "env.sh")
assert line == "if [ -f /usr/share/R/libs ] ; then . /usr/share/R/libs ; fi"
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
def create_tool_dependency_with_initialized_env_sh_file( self, dependent_install_dir, tool_shed_repository,
required_repository, package_name, package_version,
tool_dependencies_config ):
"""
Create or get a tool_dependency record that is defined by the received package_name and package_version.
An env.sh file will be created for the tool_dependency in the received dependent_install_dir.
"""
# The received required_repository refers to a tool_shed_repository record that is defined as a complex
# repository dependency for this tool_dependency. The required_repository may or may not be currently
# installed (it doesn't matter). If it is installed, it is associated with a tool_dependency that has
# an env.sh file that this new tool_dependency must be able to locate and "source". If it is not installed,
# we can still determine where that env.sh file will be, so we'll initialize this new tool_dependency's env.sh
# file in either case. If the required repository ends up with an installation error, this new tool
# dependency will still be fine because its containing repository will be defined as missing dependencies.
tool_dependencies = []
if not os.path.exists( dependent_install_dir ):
os.makedirs( dependent_install_dir )
required_tool_dependency_env_file_path = None
if tool_dependencies_config:
required_td_tree, error_message = xml_util.parse_xml( tool_dependencies_config )
if required_td_tree:
required_td_root = required_td_tree.getroot()
for required_td_elem in required_td_root:
# Find the appropriate package name and version.
if required_td_elem.tag == 'package':
# <package name="bwa" version="0.5.9">
required_td_package_name = required_td_elem.get( 'name', None )
required_td_package_version = required_td_elem.get( 'version', None )
# Check the database to see if we have a record for the required tool dependency (we may not which is ok). If we
# find a record, we need to see if it is in an error state and if so handle it appropriately.
required_tool_dependency = \
tool_dependency_util.get_tool_dependency_by_name_version_type_repository( self.app,
required_repository,
required_td_package_name,
required_td_package_version,
'package' )
if required_td_package_name == package_name and required_td_package_version == package_version:
# Get or create a database tool_dependency record with which the installed package on disk will be associated.
tool_dependency = \
tool_dependency_util.create_or_update_tool_dependency( app=self.app,
tool_shed_repository=tool_shed_repository,
name=package_name,
version=package_version,
type='package',
status=self.app.install_model.ToolDependency.installation_status.NEVER_INSTALLED,
set_status=True )
# Create an env.sh file for the tool_dependency whose first line will source the env.sh file located in
# the path defined by required_tool_dependency_env_file_path. It doesn't matter if the required env.sh
# file currently exists..
required_tool_dependency_env_file_path = \
self.get_required_repository_package_env_sh_path( package_name,
package_version,
required_repository )
env_file_builder = EnvFileBuilder( tool_dependency.installation_directory( self.app ) )
env_file_builder.append_line( action="source", value=required_tool_dependency_env_file_path )
return_code = env_file_builder.return_code
if return_code:
error_message = 'Error defining env.sh file for package %s, return_code: %s' % \
( str( package_name ), str( return_code ) )
tool_dependency = \
tool_dependency_util.set_tool_dependency_attributes(self.app,
tool_dependency=tool_dependency,
status=self.app.install_model.ToolDependency.installation_status.ERROR,
error_message=error_message)
elif required_tool_dependency is not None and required_tool_dependency.in_error_state:
error_message = "This tool dependency's required tool dependency %s version %s has status %s." % \
( str( required_tool_dependency.name ), str( required_tool_dependency.version ), str( required_tool_dependency.status ) )
tool_dependency = \
tool_dependency_util.set_tool_dependency_attributes(self.app,
tool_dependency=tool_dependency,
status=self.app.install_model.ToolDependency.installation_status.ERROR,
error_message=error_message)
else:
tool_dependency = \
tool_dependency_util.set_tool_dependency_attributes( self.app,
tool_dependency=tool_dependency,
status=self.app.install_model.ToolDependency.installation_status.INSTALLED )
tool_dependencies.append( tool_dependency )
return tool_dependencies
