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test_test_engines.py
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import json
import os
from tempfile import NamedTemporaryFile
from planemo.engine.test import test_runnables as t_runnables
from planemo.runnable import for_paths
from .test_utils import (
create_test_context,
mark,
PROJECT_TEMPLATES_DIR,
skip_if_environ,
skip_unless_module,
target_galaxy_branch,
TEST_DATA_DIR,
)
@skip_if_environ("PLANEMO_SKIP_CWLTOOL_TESTS")
@skip_unless_module("toil")
def test_toil_tests():
ctx = create_test_context()
test_artifact = os.path.join(TEST_DATA_DIR, "int_tool.cwl")
runnables = for_paths([test_artifact])
exit_code = t_runnables(
ctx,
runnables,
engine="toil",
)
assert exit_code == 0
@skip_if_environ("PLANEMO_SKIP_GALAXY_TESTS")
@mark.tests_galaxy_branch
def test_galaxy_wf_tests():
ctx = create_test_context()
random_lines = os.path.join(PROJECT_TEMPLATES_DIR, "demo", "randomlines.xml")
cat = os.path.join(PROJECT_TEMPLATES_DIR, "demo", "cat.xml")
test_artifact = os.path.join(TEST_DATA_DIR, "wf1.gxwf.yml")
runnables = for_paths([test_artifact])
kwds = {
"engine": "galaxy",
"no_dependency_resolution": True,
"paste_test_data_paths": False,
"galaxy_branch": target_galaxy_branch(),
"extra_tools": [random_lines, cat],
}
exit_code = t_runnables(ctx, runnables, **kwds)
assert exit_code == 0
@skip_if_environ("PLANEMO_SKIP_GALAXY_TESTS")
@mark.tests_galaxy_branch
def test_galaxy_workflow_collection_output():
ctx = create_test_context()
test_artifact = os.path.join(TEST_DATA_DIR, "wf7-collection-output.gxwf.yml")
collection_creates_pair = os.path.join(TEST_DATA_DIR, "collection_creates_pair_2.xml")
runnables = for_paths([test_artifact])
kwds = {
"engine": "galaxy",
"no_dependency_resolution": True,
"paste_test_data_paths": False,
"galaxy_branch": target_galaxy_branch(),
"extra_tools": [collection_creates_pair],
}
exit_code = t_runnables(ctx, runnables, **kwds)
assert exit_code == 0
@skip_if_environ("PLANEMO_SKIP_GALAXY_TESTS")
@mark.tests_galaxy_branch
def test_galaxy_workflow_collection_output_fail():
ctx = create_test_context()
test_artifact = os.path.join(TEST_DATA_DIR, "wf7-collection-output-fail.gxwf.yml")
collection_creates_pair = os.path.join(TEST_DATA_DIR, "collection_creates_pair_2.xml")
runnables = for_paths([test_artifact])
kwds = {
"engine": "galaxy",
"no_dependency_resolution": True,
"paste_test_data_paths": False,
"galaxy_branch": target_galaxy_branch(),
"extra_tools": [collection_creates_pair],
}
exit_code = t_runnables(ctx, runnables, **kwds)
assert exit_code == 1
@skip_if_environ("PLANEMO_SKIP_GALAXY_TESTS")
# @mark.tests_galaxy_branch only works >= 20.09 or newer
def test_galaxy_workflow_tags():
with NamedTemporaryFile(prefix="data_manager_test_json") as json_out:
ctx = create_test_context()
test_artifact = os.path.join(TEST_DATA_DIR, "wf10-tags-and-rules.gxwf.yml")
collection_cat_list = os.path.join(TEST_DATA_DIR, "cat_list.xml")
runnables = for_paths([test_artifact])
kwds = {
"engine": "galaxy",
"no_dependency_resolution": True,
"paste_test_data_paths": False,
"galaxy_branch": "dev",
"extra_tools": [collection_cat_list],
"test_output_json": json_out.name,
}
try:
exit_code = t_runnables(ctx, runnables, **kwds)
assert exit_code == 0
except Exception:
with open(json_out.name) as f:
print(f.read())
raise
@skip_if_environ("PLANEMO_SKIP_GALAXY_TESTS")
@mark.tests_galaxy_branch
def test_galaxy_workflow_nested_collection_inputs():
ctx = create_test_context()
test_artifact = os.path.join(TEST_DATA_DIR, "wf8-collection-nested-input.gxwf.yml")
collection_cat_pair = os.path.join(TEST_DATA_DIR, "cat_pair.xml")
collection_cat_list = os.path.join(TEST_DATA_DIR, "cat_list.xml")
runnables = for_paths([test_artifact])
kwds = {
"engine": "galaxy",
"no_dependency_resolution": True,
"paste_test_data_paths": False,
"galaxy_branch": target_galaxy_branch(),
"extra_tools": [collection_cat_pair, collection_cat_list],
}
exit_code = t_runnables(ctx, runnables, **kwds)
assert exit_code == 0
@skip_if_environ("PLANEMO_SKIP_GALAXY_TESTS")
@mark.tests_galaxy_branch
def test_galaxy_workflow_non_data_inputs():
ctx = create_test_context()
test_artifact = os.path.join(TEST_DATA_DIR, "wf9-int-input.gxwf.yml")
runnables = for_paths([test_artifact])
kwds = {
"engine": "galaxy",
"no_dependency_resolution": True,
"paste_test_data_paths": False,
"galaxy_branch": target_galaxy_branch(),
}
exit_code = t_runnables(ctx, runnables, **kwds)
assert exit_code == 0
@skip_if_environ("PLANEMO_SKIP_GALAXY_TESTS")
@mark.tests_galaxy_branch
def test_galaxy_workflow_step_failed():
ctx = create_test_context()
test_artifact = os.path.join(TEST_DATA_DIR, "wf_failed_step.ga")
runnables = for_paths([test_artifact])
with NamedTemporaryFile(prefix="result_json") as json_out:
kwds = {
"engine": "galaxy",
"no_dependency_resolution": True,
"paste_test_data_paths": False,
"extra_tools": ["$GALAXY_FUNCTIONAL_TEST_TOOLS"],
"test_output_json": json_out.name,
"galaxy_branch": target_galaxy_branch(),
}
exit_code = t_runnables(ctx, runnables, **kwds)
assert exit_code == 1
report = json.load(json_out)
data = report["tests"][0]["data"]
assert data["status"] == "error"
assert data["execution_problem"]
invocation_steps = data["invocation_details"]["steps"]
assert len(invocation_steps) == 2
first_step, second_step = invocation_steps.values()
assert first_step["state"] == "scheduled"
job = first_step["jobs"][0]
assert job["exit_code"] == 127
assert job["state"] == "error"
assert second_step["state"] == "scheduled"
assert second_step["jobs"][0]["state"] == "paused"