"""This module contains a linting functions for tool tests."""
import typing
from inspect import (
Parameter,
signature,
)
from galaxy.util import asbool
from ._util import is_datasource
from ..verify import asserts
[docs]def check_compare_attribs(element, lint_ctx, test_idx):
COMPARE_COMPATIBILITY = {
"sort": ["diff", "re_match", "re_match_multiline"],
"lines_diff": ["diff", "re_match", "contains"],
"decompress": ["diff"],
"delta": ["sim_size"],
"delta_frac": ["sim_size"],
}
compare = element.get("compare", "diff")
for attrib in COMPARE_COMPATIBILITY:
if attrib in element.attrib and compare not in COMPARE_COMPATIBILITY[attrib]:
lint_ctx.error(
f'Test {test_idx}: Attribute {attrib} is incompatible with compare="{compare}".', node=element
)
[docs]def lint_tests(tool_xml, lint_ctx):
# determine node to report for general problems with tests
tests = tool_xml.findall("./tests/test")
general_node = tool_xml.find("./tests")
if general_node is None:
general_node = tool_xml.getroot()
datasource = is_datasource(tool_xml)
if not tests:
if not datasource:
lint_ctx.warn("No tests found, most tools should define test cases.", node=general_node)
elif datasource:
lint_ctx.info("No tests found, that should be OK for data_sources.", node=general_node)
return
num_valid_tests = 0
for test_idx, test in enumerate(tests, start=1):
has_test = False
test_expect = ("expect_failure", "expect_exit_code", "expect_num_outputs")
for te in test_expect:
if te in test.attrib:
has_test = True
break
test_assert = ("assert_stdout", "assert_stderr", "assert_command")
for ta in test_assert:
assertions = test.findall(ta)
if len(assertions) == 0:
continue
if len(assertions) > 1:
lint_ctx.error(f"Test {test_idx}: More than one {ta} found. Only the first is considered.", node=test)
has_test = True
_check_asserts(test_idx, assertions, lint_ctx)
_check_asserts(test_idx, test.findall(".//assert_contents"), lint_ctx)
# check if expect_num_outputs is set if there are outputs with filters
filter = tool_xml.findall("./outputs//filter")
if len(filter) > 0 and "expect_num_outputs" not in test.attrib:
lint_ctx.warn("Test should specify 'expect_num_outputs' if outputs have filters", node=test)
# really simple test that test parameters are also present in the inputs
for param in test.findall("param"):
name = param.attrib.get("name", None)
if not name:
lint_ctx.error(f"Test {test_idx}: Found test param tag without a name defined.", node=param)
continue
name = name.split("|")[-1]
xpaths = [f"@name='{name}'", f"@argument='{name}'", f"@argument='-{name}'", f"@argument='--{name}'"]
if "_" in name:
xpaths += [f"@argument='-{name.replace('_', '-')}'", f"@argument='--{name.replace('_', '-')}'"]
found = False
for xp in xpaths:
inxpath = f".//inputs//param[{xp}]"
inparam = tool_xml.findall(inxpath)
if len(inparam) > 0:
found = True
break
if not found:
lint_ctx.error(f"Test {test_idx}: Test param {name} not found in the inputs", node=param)
output_data_or_collection = _collect_output_names(tool_xml)
found_output_test = False
for output in test.findall("output") + test.findall("output_collection"):
found_output_test = True
name = output.attrib.get("name", None)
if not name:
lint_ctx.error(f"Test {test_idx}: Found {output.tag} tag without a name defined.", node=output)
continue
if name not in output_data_or_collection:
lint_ctx.error(
f"Test {test_idx}: Found {output.tag} tag with unknown name [{name}], valid names {list(output_data_or_collection)}",
node=output,
)
continue
if output.tag == "output":
check_compare_attribs(output, lint_ctx, test_idx)
elements = output.findall("./element")
if elements:
for element in elements:
check_compare_attribs(element, lint_ctx, test_idx)
# check that
# - test/output corresponds to outputs/data and
# - test/collection to outputs/output_collection
corresponding_output = output_data_or_collection[name]
if output.tag == "output" and corresponding_output.tag != "data":
lint_ctx.error(
f"Test {test_idx}: test output {name} does not correspond to a 'data' output, but a '{corresponding_output.tag}'",
node=output,
)
elif output.tag == "output_collection" and corresponding_output.tag != "collection":
lint_ctx.error(
f"Test {test_idx}: test collection output '{name}' does not correspond to a 'output_collection' output, but a '{corresponding_output.tag}'",
node=output,
)
# check that discovered data is tested sufficiently
discover_datasets = corresponding_output.find(".//discover_datasets")
if discover_datasets is not None:
if output.tag == "output":
if "count" not in output.attrib and output.find("./discovered_dataset") is None:
lint_ctx.error(
f"Test {test_idx}: test output '{name}' must have a 'count' attribute and/or 'discovered_dataset' children",
node=output,
)
else:
if "count" not in output.attrib and len(elements) == 0:
lint_ctx.error(
f"Test {test_idx}: test collection '{name}' must have a 'count' attribute or 'element' children",
node=output,
)
if corresponding_output.get("type", "") in ["list:list", "list:paired"]:
nested_elements = output.find("./element/element")
element_with_count = output.find("./element[@count]")
if nested_elements is None and element_with_count is None:
lint_ctx.error(
f"Test {test_idx}: test collection '{name}' must contain nested 'element' tags and/or element childen with a 'count' attribute",
node=output,
)
if "expect_failure" in test.attrib and asbool(test.attrib["expect_failure"]):
if found_output_test:
lint_ctx.error(f"Test {test_idx}: Cannot specify outputs in a test expecting failure.", node=test)
continue
if "expect_num_outputs" in test.attrib:
lint_ctx.error(
f"Test {test_idx}: Cannot make assumptions on the number of outputs in a test expecting failure.",
node=test,
)
continue
has_test = has_test or found_output_test
if not has_test:
lint_ctx.warn(
f"Test {test_idx}: No outputs or expectations defined for tests, this test is likely invalid.",
node=test,
)
else:
num_valid_tests += 1
if num_valid_tests or datasource:
lint_ctx.valid(f"{num_valid_tests} test(s) found.", node=general_node)
else:
lint_ctx.warn("No valid test(s) found.", node=general_node)
def _check_asserts(test_idx, assertions, lint_ctx):
"""
assertions is a list of assert_contents, assert_stdout, assert_stderr, assert_command
in practice only for the first case the list may be longer than one
"""
for assertion in assertions:
for i, a in enumerate(assertion.iter()):
if i == 0: # skip root note itself
continue
assert_function_name = "assert_" + a.tag
if assert_function_name not in asserts.assertion_functions:
lint_ctx.error(f"Test {test_idx}: unknown assertion '{a.tag}'", node=a)
continue
assert_function_sig = signature(asserts.assertion_functions[assert_function_name])
# check of the attributes
for attrib in a.attrib:
if attrib not in assert_function_sig.parameters:
lint_ctx.error(f"Test {test_idx}: unknown attribute '{attrib}' for '{a.tag}'", node=a)
continue
# check missing required attributes
for p in assert_function_sig.parameters:
if p in ["output", "output_bytes", "verify_assertions_function", "children"]:
continue
if assert_function_sig.parameters[p].default is Parameter.empty and p not in a.attrib:
lint_ctx.error(f"Test {test_idx}: missing attribute '{p}' for '{a.tag}'", node=a)
# has_n_lines, has_n_columns, and has_size need to specify n/value, min, or max
if a.tag in ["has_n_lines", "has_n_columns"]:
if "n" not in a.attrib and "min" not in a.attrib and "max" not in a.attrib:
lint_ctx.error(f"Test {test_idx}: '{a.tag}' needs to specify 'n', 'min', or 'max'", node=a)
if a.tag == "has_size":
if "value" not in a.attrib and "min" not in a.attrib and "max" not in a.attrib:
lint_ctx.error(f"Test {test_idx}: '{a.tag}' needs to specify 'value', 'min', or 'max'", node=a)
def _handle_optionals(annotation):
as_dict = annotation.__dict__
if "__origin__" in as_dict and as_dict["__origin__"] == typing.Union:
return as_dict["__args__"][0]
return annotation
def _collect_output_names(tool_xml):
"""
determine dict mapping the names of data and collection outputs to the
corresponding nodes
"""
output_data_or_collection = {}
outputs = tool_xml.findall("./outputs")
if len(outputs) == 1:
for output in list(outputs[0]):
name = output.attrib.get("name", None)
if not name:
continue
output_data_or_collection[name] = output
return output_data_or_collection