view env/lib/python3.9/site-packages/galaxy/tool_util/linters/ @ 0:4f3585e2f14b draft default tip

"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
author shellac
date Mon, 22 Mar 2021 18:12:50 +0000
line wrap: on
line source

"""This module contains a linting functions for tool tests."""
from ._util import is_datasource

# Misspelled so as not be picked up by nosetests.
def lint_tsts(tool_xml, lint_ctx):
    tests = tool_xml.findall("./tests/test")
    datasource = is_datasource(tool_xml)

    if not tests and not datasource:
        lint_ctx.warn("No tests found, most tools should define test cases.")
    elif datasource:"No tests found, that should be OK for data_sources.")

    num_valid_tests = 0
    for test in tests:
        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
        test_assert = ("assert_stdout", "assert_stderr", "assert_command")
        for ta in test_assert:
            if len(test.findall(ta)) > 0:
                has_test = True

        output_data_names, output_collection_names = _collect_output_names(tool_xml)
        found_output_test = False
        for output in test.findall("output"):
            found_output_test = True
            name = output.attrib.get("name", None)
            if not name:
                lint_ctx.warn("Found output tag without a name defined.")
                if name not in output_data_names:
                    lint_ctx.error(f"Found output tag with unknown name [{name}], valid names [{output_data_names}]")

        for output_collection in test.findall("output_collection"):
            found_output_test = True
            name = output_collection.attrib.get("name", None)
            if not name:
                lint_ctx.warn("Found output_collection tag without a name defined.")
                if name not in output_collection_names:
                    lint_ctx.warn(f"Found output_collection tag with unknown name [{name}], valid names [{output_collection_names}]")

        has_test = has_test or found_output_test
        if not has_test:
            lint_ctx.warn("No outputs or expectations defined for tests, this test is likely invalid.")
            num_valid_tests += 1

    if num_valid_tests or datasource:
        lint_ctx.valid("%d test(s) found.", num_valid_tests)
        lint_ctx.warn("No valid test(s) found.")

def _collect_output_names(tool_xml):
    output_data_names = []
    output_collection_names = []

    outputs = tool_xml.findall("./outputs")
    if len(outputs) == 1:
        for output in list(outputs[0]):
            name = output.attrib.get("name", None)
            if not name:
            if output.tag == "data":
            elif output.tag == "collection":

    return output_data_names, output_collection_names