def test_mutation_get_center_input_files():
"""
Test to make sure center input files are gotten
including the vcf files since process vcf is specified
"""
syn_get_effects = [
sample_clinical_entity, patient_clinical_entity, vcf1_entity,
vcf2_entity
]
expected_center_file_list = [[vcf1_entity], [vcf2_entity],
[
sample_clinical_entity,
patient_clinical_entity
]]
calls = [
mock.call(sample_clinical_synid, downloadFile=True),
mock.call(patient_clinical_synid, downloadFile=True),
mock.call(vcf1synid, downloadFile=True),
mock.call(vcf2synid, downloadFile=True)
]
with patch.object(synapseutils, "walk",
return_value=walk_return()) as patch_synapseutils_walk,\
patch.object(syn, "get",
side_effect=syn_get_effects) as patch_syn_get:
center_file_list = input_to_database.get_center_input_files(
syn, "syn12345", center, process="mutation")
assert len(center_file_list) == len(expected_center_file_list)
assert len(center_file_list[2]) == 2
assert center_file_list == expected_center_file_list
patch_synapseutils_walk.assert_called_once_with(syn, 'syn12345')
patch_syn_get.assert_has_calls(calls)
def test_main_get_center_input_files():
'''Test to make sure center input files are retrieved.
'''
syn_get_effects = [
sample_clinical_entity, patient_clinical_entity, vcf1_entity,
vcf2_entity
]
expected_center_file_list = [[vcf1_entity], [vcf2_entity],
[
sample_clinical_entity,
patient_clinical_entity
]]
calls = [
mock.call(sample_clinical_synid),
mock.call(patient_clinical_synid),
mock.call(vcf1synid),
mock.call(vcf2synid)
]
with patch.object(synapseutils, "walk",
return_value=walk_return()) as patch_synapseutils_walk,\
patch.object(syn, "get",
side_effect=syn_get_effects) as patch_syn_get:
center_file_list = input_to_database.get_center_input_files(
syn, "syn12345", center, process="vcf")
assert len(center_file_list) == len(expected_center_file_list)
assert len(center_file_list[2]) == 2
assert center_file_list == expected_center_file_list
patch_synapseutils_walk.assert_called_once_with(syn, 'syn12345')
patch_syn_get.assert_has_calls(calls)
def test_empty_get_center_input_files():
'''
Test that center input files is empty if directory
pass in is empty
'''
with patch.object(
synapseutils, "walk",
return_value=walk_return_empty()) as patch_synapseutils_walk:
center_file_list = input_to_database.get_center_input_files(
syn, "syn12345", center, process="vcf")
assert center_file_list == []
patch_synapseutils_walk.assert_called_once_with(syn, 'syn12345')