def lint_tool_source_with(lint_context, tool_source, extra_modules=[]):
import galaxy.tools.linters
tool_xml = getattr(tool_source, "xml_tree", None)
linter_modules = submodules.import_submodules(galaxy.tools.linters, ordered=True)
linter_modules.extend(extra_modules)
for module in linter_modules:
tool_type = tool_source.parse_tool_type() or "default"
lint_tool_types = getattr(module, "lint_tool_types", ["default"])
if not ("*" in lint_tool_types or tool_type in lint_tool_types):
continue
for (name, value) in inspect.getmembers(module):
if callable(value) and name.startswith("lint_"):
# Look at the first argument to the linter to decide
# if we should lint the XML description or the abstract
# tool parser object.
first_arg = inspect.getargspec(value).args[0]
if first_arg == "tool_xml":
if tool_xml is None:
# XML linter and non-XML tool, skip for now
continue
else:
lint_context.lint(name, value, tool_xml)
else:
lint_context.lint(name, value, tool_source)
def lint_tool_source_with(lint_context, tool_source, extra_modules=[]):
import galaxy.tool_util.linters
tool_xml = getattr(tool_source, "xml_tree", None)
linter_modules = submodules.import_submodules(galaxy.tool_util.linters,
ordered=True)
linter_modules.extend(extra_modules)
for module in linter_modules:
tool_type = tool_source.parse_tool_type() or "default"
lint_tool_types = getattr(module, "lint_tool_types", ["default"])
if not ("*" in lint_tool_types or tool_type in lint_tool_types):
continue
for (name, value) in inspect.getmembers(module):
if callable(value) and name.startswith("lint_"):
# Look at the first argument to the linter to decide
# if we should lint the XML description or the abstract
# tool parser object.
first_arg = getfullargspec(value).args[0]
if first_arg == "tool_xml":
if tool_xml is None:
# XML linter and non-XML tool, skip for now
continue
else:
lint_context.lint(name, value, tool_xml)
else:
lint_context.lint(name, value, tool_source)
def _get_interface_modules():
interfaces = []
modules = import_submodules(sys.modules[__name__])
for module in modules:
module_names = [getattr(module, _) for _ in dir(module)]
classes = [_ for _ in module_names if inspect.isclass(_) and
not _ == ContainerInterface and issubclass(_, ContainerInterface)]
interfaces.extend(classes)
return {x.container_type: x for x in interfaces}
def _get_interface_modules():
interfaces = []
modules = import_submodules(sys.modules[__name__])
for module in modules:
module_names = [getattr(module, _) for _ in dir(module)]
classes = [_ for _ in module_names if inspect.isclass(_) and
not _ == ContainerInterface and issubclass(_, ContainerInterface)]
interfaces.extend(classes)
return dict((x.container_type, x) for x in interfaces)
def _get_state_handlers_dict():
state_handlers = {}
for module in import_submodules(galaxy.jobs.runners.state_handlers, ordered=True):
for func in getattr(module, "__all__", []):
if func not in state_handlers:
state_handlers[func] = []
state_handlers[func].append(getattr(module, func))
log.debug("Loaded '%s' state handler from module %s", func, module.__name__)
return state_handlers
def __get_rule_modules_or_defaults(self, rules_module_name):
"""
Returns the rules under the given rules_module_name or default
to returning the rules of the top-level rules module for the plugin
"""
if rules_module_name:
rules_module = importlib.import_module(rules_module_name)
else:
rules_module = self.rules_module
return import_submodules(rules_module, ordered=True)
def __get_rule_modules_or_defaults(self, rules_module_name):
"""
Returns the rules under the given rules_module_name or default
to returning the rules of the top-level rules module for the plugin
"""
if rules_module_name:
rules_module = importlib.import_module(rules_module_name)
else:
rules_module = self.rules_module
return import_submodules(rules_module, ordered=True)
def _get_state_handlers_dict():
state_handlers = {}
for module in import_submodules(galaxy.jobs.runners.state_handlers,
ordered=True):
for func in getattr(module, "__all__", []):
if func not in state_handlers:
state_handlers[func] = []
state_handlers[func].append(getattr(module, func))
log.debug("Loaded '%s' state handler from module %s", func,
module.__name__)
return state_handlers
def plugins_dict(module, plugin_type_identifier):
""" Walk through all classes in submodules of module and find ones labelled
with specified plugin_type_identifier and throw in a dictionary to allow
constructions from plugins by these types later on.
"""
plugin_dict = {}
for plugin_module in import_submodules(module, ordered=True):
for clazz in __plugin_classes_in_module(plugin_module):
plugin_type = getattr(clazz, plugin_type_identifier, None)
if plugin_type:
plugin_dict[plugin_type] = clazz
return plugin_dict
def plugins_dict(module, plugin_type_identifier):
""" Walk through all classes in submodules of module and find ones labelled
with specified plugin_type_identifier and throw in a dictionary to allow
constructions from plugins by these types later on.
"""
plugin_dict = {}
for plugin_module in import_submodules(module, ordered=True):
# FIXME: this is not how one is suppose to use __all__ why did you do
# this past John?
for clazz in getattr(plugin_module, "__all__", []):
try:
clazz = getattr(plugin_module, clazz)
except TypeError:
clazz = clazz
plugin_type = getattr(clazz, plugin_type_identifier, None)
if plugin_type:
plugin_dict[plugin_type] = clazz
return plugin_dict
def plugins_dict(module, plugin_type_identifier):
""" Walk through all classes in submodules of module and find ones labelled
with specified plugin_type_identifier and throw in a dictionary to allow
constructions from plugins by these types later on.
"""
plugin_dict = {}
for plugin_module in import_submodules(module, ordered=True):
# FIXME: this is not how one is suppose to use __all__ why did you do
# this past John?
for clazz in getattr(plugin_module, "__all__", []):
try:
clazz = getattr(plugin_module, clazz)
except TypeError:
clazz = clazz
plugin_type = getattr(clazz, plugin_type_identifier, None)
if plugin_type:
plugin_dict[plugin_type] = clazz
return plugin_dict
