import logging
import sys
from inspect import (
getfullargspec,
getmembers,
)
from tempfile import NamedTemporaryFile
from galaxy.util import unicodify
from galaxy.util.compression_utils import get_fileobj
log = logging.getLogger(__name__)
assertion_module_names = ["text", "tabular", "xml", "json", "hdf5", "archive", "size", "image"]
# 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_functions = {}
for assertion_module_name in assertion_module_names:
full_assertion_module_name = f"galaxy.tool_util.verify.asserts.{assertion_module_name}"
try:
# Dynamically import module
__import__(full_assertion_module_name)
assertion_module = sys.modules[full_assertion_module_name]
except Exception:
log.exception("Failed to load assertion module: %s", assertion_module_name)
continue
for member, value in getmembers(assertion_module):
if member.startswith("assert_"):
assertion_functions[member] = value
[docs]def verify_assertions(data: bytes, assertion_description_list, decompress: bool = False):
"""This function takes a list of assertions and a string to check
these assertions against."""
if decompress:
with NamedTemporaryFile() as tmpfh:
tmpfh.write(data)
tmpfh.flush()
with get_fileobj(tmpfh.name, mode="rb", compressed_formats=None) as fh:
data = fh.read()
for assertion_description in assertion_description_list:
verify_assertion(data, assertion_description)
[docs]def verify_assertion(data: bytes, assertion_description):
tag = assertion_description["tag"]
assert_function_name = "assert_" + tag
assert_function = assertion_functions.get(assert_function_name)
if assert_function is None:
errmsg = f"Unable to find test function associated with XML tag {tag}. Check your tool file syntax."
raise AssertionError(errmsg)
assert_function_args = getfullargspec(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 conjunction
# 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:
# If the assert_function will have an attribute called "output"
# the data passed from the test to the function will be unicodified.
# This is because most of the assert functions are working on pure
# text files.
args["output"] = unicodify(data)
if "output_bytes" in assert_function_args:
# This will read in data as bytes and will not change it prior passing
# it to the assert_function
args["output_bytes"] = 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)