Source code for galaxy.tool_util.verify.asserts

import logging
import sys
from inspect import (
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}"
        # Dynamically import module
        assertion_module = sys.modules[full_assertion_module_name]
    except Exception:
        log.exception("Failed to load assertion module: %s", assertion_module_name)
    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(, mode="rb", compressed_formats=None) as fh: data = 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/ 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)