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.submodules(galaxy.tools.linters)
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.tools.linters
tool_xml = getattr(tool_source, "xml_tree", None)
linter_modules = submodules.submodules(galaxy.tools.linters)
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_xml_with(lint_context, tool_xml, extra_modules=[]):
import galaxy.tools.linters
linter_modules = submodules.submodules(galaxy.tools.linters)
linter_modules.extend(extra_modules)
for module in linter_modules:
for (name, value) in inspect.getmembers(module):
if callable(value) and name.startswith("lint_"):
lint_context.lint(name, value, tool_xml)
def lint_xml_with(lint_context, tool_xml, extra_modules=[]):
import galaxy.tools.linters
linter_modules = submodules.submodules(galaxy.tools.linters)
linter_modules.extend(extra_modules)
for module in linter_modules:
for (name, value) in inspect.getmembers(module):
if callable(value) and name.startswith("lint_"):
lint_context.lint(name, value, tool_xml)
def _get_interface_modules():
interfaces = []
modules = 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 submodules(galaxy.jobs.runners.state_handlers):
for func in 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_state_handlers_dict():
state_handlers = {}
for module in submodules(galaxy.jobs.runners.state_handlers):
for func in 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_interface_modules():
interfaces = []
modules = submodules(sys.modules[__name__])
for module in modules:
classes = filter(
lambda x: inspect.isclass(x)
and not x == ContainerInterface # noqa: E131
and issubclass(x, ContainerInterface), # noqa: E131
[getattr(module, x) for x in dir(module)])
interfaces.extend(classes)
return dict([(x.container_type, x) for x in interfaces])
def _get_interface_modules():
interfaces = []
modules = submodules(sys.modules[__name__])
for module in modules:
classes = filter(
lambda x: inspect.isclass(x) and not x ==
ContainerInterface # noqa: E131
and issubclass(x, ContainerInterface), # noqa: E131
[getattr(module, x) for x in dir(module)])
interfaces.extend(classes)
return dict([(x.container_type, x) for x in interfaces])
def lint_xml(tool_xml, level=LEVEL_ALL, fail_level=LEVEL_WARN):
import galaxy.tools.linters
lint_context = LintContext(level=level)
linter_modules = submodules.submodules(galaxy.tools.linters)
for module in linter_modules:
for (name, value) in inspect.getmembers(module):
if callable(value) and name.startswith("lint_"):
lint_context.lint(module, name, value, tool_xml)
found_warns = lint_context.found_warns
found_errors = lint_context.found_errors
if level == LEVEL_WARN and (found_warns or found_errors):
return False
else:
return found_errors
def lint_xml(tool_xml, level=LEVEL_ALL, fail_level=LEVEL_WARN):
import galaxy.tools.linters
lint_context = LintContext(level=level)
linter_modules = submodules.submodules(galaxy.tools.linters)
for module in linter_modules:
for (name, value) in inspect.getmembers(module):
if callable(value) and name.startswith("lint_"):
lint_context.lint(module, name, value, tool_xml)
found_warns = lint_context.found_warns
found_errors = lint_context.found_errors
if level == LEVEL_WARN and (found_warns or found_errors):
return False
else:
return found_errors
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 submodules( module ):
# FIXME: this is not how one is suppose to use __all__ why did you do
# this past John?
for clazz in plugin_module.__all__:
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 submodules(module):
# FIXME: this is not how one is suppose to use __all__ why did you do
# this past John?
for clazz in plugin_module.__all__:
plugin_type = getattr(clazz, plugin_type_identifier, None)
if plugin_type:
plugin_dict[plugin_type] = clazz
return plugin_dict
def __plugin_modules( self ):
import galaxy.jobs.metrics.instrumenters
return submodules( galaxy.jobs.metrics.instrumenters )
def __resolver_modules(self):
import galaxy.tools.deps.resolvers
return submodules(galaxy.tools.deps.resolvers)
def __resolver_modules( self ):
import galaxy.tools.deps.resolvers
return submodules( galaxy.tools.deps.resolvers )
