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Add timeout of 2hours to template #33

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Add timeout of 2hours to template #33

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5c31100
Add timeout of 2hours to template
patrickimran Jul 31, 2021
a50a56d
FIX setUP/tearDown now classmethods + combined tests manipulating fil…
patrickimran Aug 5, 2021
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2 changes: 1 addition & 1 deletion q2_mlab/templates/array_job_template.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -89,7 +89,7 @@ do
then
echo $RESULTS already exists, execution skipped
else
qiime mlab unit-benchmark --i-table {{ TABLE_FP }} \
timeout -s SIGKILL 2h qiime mlab unit-benchmark --i-table {{ TABLE_FP }} \
--i-metadata {{ METADATA_FP }} \
--p-algorithm {{ ALGORITHM }} \
--p-params "${params}" \
Expand Down
13 changes: 8 additions & 5 deletions q2_mlab/tests/test_doctor.py
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Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,8 @@


class DoctorTests(unittest.TestCase):
def setUp(self):
@classmethod
def setUpClass(self):

self.TEST_DIR = os.path.split(__file__)[0]
self.dataset_file = os.path.join(self.TEST_DIR, "data/table.qza")
Expand Down Expand Up @@ -89,7 +90,8 @@ def setUp(self):
inserted_path = os.path.join(inserted_dir, artifact)
os.rename(uninserted_path, inserted_path)

def tearDown(self):
@classmethod
def tearDownClass(self):

# Remove files we generated
files_generated = [
Expand Down Expand Up @@ -169,20 +171,21 @@ def test_parse_info(self):
}
self.assertDictEqual(info_dict, expected_dict)

def test_get_uninserted_results(self):
def test_getting_filtering_results(self):

# Test getting uninserted results
results_list = get_results(self.results_dir)
for fname in results_list:
self.assertTrue(fname.endswith(".qza"))
self.assertEqual(len(results_list), 110)

def test_get_inserted_results(self):
# Test getting inserted results
inserted_dir = os.path.join(self.results_dir, "inserted")
results_list = get_results(inserted_dir)
for fname in results_list:
self.assertTrue(fname.endswith(".qza"))
self.assertEqual(len(results_list), 2)

def test_filter_duplicate_parameter_results(self):
results_list = get_results(self.results_dir)
self.assertEqual(len(results_list), 110)
self.assertTrue(
Expand Down