def handle_tool_dependencies( app, tool_shed_repository, tool_dependencies_config, tool_dependencies ):
"""
Install and build tool dependencies defined in the tool_dependencies_config. This config's tag sets can currently refer to installation
methods in Galaxy's tool_dependencies module. In the future, proprietary fabric scripts contained in the repository will be supported.
Future enhancements to handling tool dependencies may provide installation processes in addition to fabric based processes. The dependencies
will be installed in:
~/<app.config.tool_dependency_dir>/<package_name>/<package_version>/<repo_owner>/<repo_name>/<repo_installed_changeset_revision>
"""
# The received list of tool_dependencies are the database records for those dependencies defined in the received tool_dependencies_config
# that should be installed. This allows for filtering out dependencies that have not been checked for installation on the 'Manage tool
# dependencies' page for an installed tool shed repository.
attr_tups_of_dependencies_for_install = [ ( td.name, td.version, td.type ) for td in tool_dependencies ]
context = app.install_model.context
installed_tool_dependencies = []
# Parse the tool_dependencies.xml config.
tree, error_message = xml_util.parse_xml( tool_dependencies_config )
if tree is None:
return installed_tool_dependencies
root = tree.getroot()
fabric_version_checked = False
for elem in root:
if elem.tag == 'package':
# Only install the tool_dependency if it is not already installed and it is associated with a database record in the received
# tool_dependencies.
package_name = elem.get( 'name', None )
package_version = elem.get( 'version', None )
if package_name and package_version:
attr_tup = ( package_name, package_version, 'package' )
try:
index = attr_tups_of_dependencies_for_install.index( attr_tup )
except Exception, e:
index = None
if index is not None:
tool_dependency = tool_dependencies[ index ]
if tool_dependency.can_install:
# The database record is currently in a state that allows us to install the package on the file system.
try:
dependencies_ignored = not app.toolbox.dependency_manager.uses_tool_shed_dependencies()
if dependencies_ignored:
log.debug( "Skipping package %s because tool shed dependency resolver not enabled." % str( package_name ) )
# Tool dependency resolves have been configured and they do not include the tool shed. Do not install package.
if app.toolbox.dependency_manager.find_dep( package_name, package_version, type='package') != INDETERMINATE_DEPENDENCY:
## TODO: Do something here such as marking it installed or
## configured externally.
pass
tool_dependency = \
tool_dependency_util.set_tool_dependency_attributes( app,
tool_dependency=tool_dependency,
status=app.install_model.ToolDependency.installation_status.ERROR,
error_message=None,
remove_from_disk=False )
else:
tool_dependency = install_package( app, elem, tool_shed_repository, tool_dependencies=tool_dependencies )
except Exception, e:
error_message = "Error installing tool dependency %s version %s: %s" % ( str( package_name ), str( package_version ), str( e ) )
log.exception( error_message )
if tool_dependency:
# Since there was an installation error, update the tool dependency status to Error. The remove_installation_path option must
# be left False here.
tool_dependency = tool_dependency_util.handle_tool_dependency_installation_error( app,
tool_dependency,
error_message,
remove_installation_path=False )
if tool_dependency and tool_dependency.status in [ app.install_model.ToolDependency.installation_status.INSTALLED,
app.install_model.ToolDependency.installation_status.ERROR ]:
installed_tool_dependencies.append( tool_dependency )
# Add the tool_dependency to the in-memory dictionaries in the installed_repository_manager.
app.installed_repository_manager.handle_tool_dependency_install( tool_shed_repository, tool_dependency )
# Add the tool_dependency to the in-memory dictionaries in the installed_repository_manager.
app.installed_repository_manager.handle_tool_dependency_install( tool_shed_repository, tool_dependency )
elif elem.tag == 'set_environment':
# <set_environment version="1.0">
# <environment_variable name="R_SCRIPT_PATH"action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>
# </set_environment>
try:
tool_dependency = set_environment( app, elem, tool_shed_repository, attr_tups_of_dependencies_for_install )
except Exception, e:
error_message = "Error setting environment for tool dependency: %s" % str( e )
log.debug( error_message )
if tool_dependency:
# Since there was an installation error, update the tool dependency status to Error. The remove_installation_path option must
# be left False here.
tool_dependency = tool_dependency_util.handle_tool_dependency_installation_error( app,
tool_dependency,
error_message,
remove_installation_path=False )
if tool_dependency and tool_dependency.status in [ app.install_model.ToolDependency.installation_status.INSTALLED,
app.install_model.ToolDependency.installation_status.ERROR ]:
installed_tool_dependencies.append( tool_dependency )
return installed_tool_dependencies
def repository_dependency_needed_only_for_compiling_tool_dependency( repository, repository_dependency ):
for rd_tup in repository.tuples_of_repository_dependencies_needed_for_compiling_td:
tool_shed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td = rd_tup
# TODO: we may discover that we need to check more than just installed_changeset_revision and changeset_revision here, in which
# case we'll need to contact the tool shed to get the list of all possible changeset_revisions.
if repository_dependency.tool_shed == tool_shed and \
repository_dependency.name == name and \
repository_dependency.owner == owner and \
( repository_dependency.installed_changeset_revision == changeset_revision or \
