import inspect
import logging
import sys
from galaxy.util import unicodify
log = logging.getLogger(__name__)
assertion_module_names = ['text', 'tabular', 'xml']
# Code for loading modules containing assertion checking functions, to
# create a new module of assertion functions, create the needed python
# source file "test/base/asserts/<MODULE_NAME>.py" and add
# <MODULE_NAME> to the list of assertion module names defined above.
assertion_modules = []
for assertion_module_name in assertion_module_names:
full_assertion_module_name = 'galaxy.tools.verify.asserts.' + assertion_module_name
log.debug(full_assertion_module_name)
try:
# Dynamically import module
__import__(full_assertion_module_name)
assertion_module = sys.modules[full_assertion_module_name]
assertion_modules.append(assertion_module)
except Exception:
log.exception('Failed to load assertion module: %s', assertion_module_name)
[docs]def verify_assertions(data, assertion_description_list):
""" This function takes a list of assertions and a string to check
these assertions against. """
for assertion_description in assertion_description_list:
verify_assertion(data, assertion_description)
[docs]def verify_assertion(data, assertion_description):
tag = assertion_description["tag"]
assert_function_name = "assert_" + tag
assert_function = None
for assertion_module in assertion_modules:
if hasattr(assertion_module, assert_function_name):
assert_function = getattr(assertion_module, assert_function_name)
if assert_function is None:
errmsg = "Unable to find test function associated with XML tag '%s'. Check your tool file syntax." % tag
raise AssertionError(errmsg)
assert_function_args = inspect.getargspec(assert_function).args
args = {}
for attribute, value in assertion_description["attributes"].items():
if attribute in assert_function_args:
args[attribute] = value
# Three special arguments automatically populated independently of
# tool XML attributes. output is passed in as the contents of the
# output file. verify_assertions_function is passed in as the
# verify_assertions function defined above, this allows
# recursively checking assertions on subsections of
# output. children is the parsed version of the child elements of
# the XML element describing this assertion. See
# assert_element_text in test/base/asserts/xml.py as an example of
# how to use verify_assertions_function and children in conjuction
# to apply assertion checking to a subset of the input. The parsed
# version of an elements child elements do not need to just define
# assertions, developers of assertion functions can also use the
# child elements in novel ways to define inputs the assertion
# checking function (for instance consider the following fictional
# assertion function for checking column titles of tabular output
# - <has_column_titles><with_name name="sequence"><with_name
# name="probability"></has_column_titles>.)
if "output" in assert_function_args:
# This was read in as bytes for checksum and such, but all current
# assertions expect text data. If binary assertions are added at
# some point, just checkout for "output_bytes" for instance and pass
# data in unchanged.
args["output"] = unicodify(data)
if "verify_assertions_function" in assert_function_args:
args["verify_assertions_function"] = verify_assertions
if "children" in assert_function_args:
args["children"] = assertion_description["children"]
# TODO: Verify all needed function arguments are specified.
assert_function(**args)