def testRequiredFields(self):
required = MIMS.required_fields()
self.assertEqual(type(required), tuple,
"required_fields() returns a list.")
self.assertTrue(
len(required) > 0, "required_fields() return is not empty.")
def testRequiredFields(self):
required = MIMS.required_fields()
self.assertEqual(type(required), tuple,
"required_fields() returns a list.")
self.assertTrue(len(required) > 0,
"required_fields() return is not empty.")
def testInsufficientData(self):
""" Test the MIMS class with insufficient data. """
too_little = {"adapters": "test_adapters"}
valid = MIMS.check_dict(too_little)
self.assertFalse(valid, "False result for superfluous data.")
def testSuperfluousData(self):
""" Test the MIMS class with excess data. """
too_much = {
"adapters": "test_adapters",
"annot_source": "test_annot_source",
"assembly": "test_assembly",
"assembly_name": "test_assembly_name",
"biome": "test_biome",
"collection_date": "test_collection_date",
"env_package": "test_env_package",
"extrachrom_elements": "test_extrachrom_elements",
"encoded_traits": "test_encoded_traits",
"experimental_factor": "test_experimental_factor",
"feature": "test_feature",
"findex": "test_findex",
"finishing_strategy": "test_finishing_strategy",
"geo_loc_name": "test_geo_loc_name",
"investigation_type": "test_investigation_type",
"lat_lon": "test_lat_long",
"lib_const_meth": "test_lib_const_meth",
"lib_reads_seqd": "test_lib_reads_seqd",
"lib_screen": "test_lib_screen",
"lib_size": 2000,
"lib_vector": "test_lib_vector",
"material": "test_material",
"nucl_acid_amp": "test_nucl_acid_amp",
"nucl_acid_ext": "test_nucl_acid_ext",
"project_name": "test_project_name",
"rel_to_oxygen": "test_rel_to_oxygen",
"rindex": "test_rindex",
"samp_collect_device": "test_samp_collect_device",
"samp_mat_process": "test_samp_map_process",
"samp_size": "test_samp_size",
"seq_meth": "test_seq_meth",
"sop": ["a", "b", "c"],
"source_mat_id": ["a", "b", "c"],
"submitted_to_insdc": True,
"url": ["a", "b", "c"],
# And now for some spurious data
"ned": "stark",
"sansa": "stark",
"ramsay": "bolton"
}
valid = MIMS.check_dict(too_much)
self.assertFalse(valid, "False result for superfluous data.")
def testSuperfluousData(self):
too_much = {
"adapters": "test_adapters",
"annot_source": "test_annot_source",
"assembly": "test_assembly",
"assembly_name": "test_assembly_name",
"biome": "test_biome",
"collection_date": "test_collection_date",
"env_package": "test_env_package",
"extrachrom_elements": "test_extrachrom_elements",
"encoded_traits": "test_encoded_traits",
"experimental_factor": "test_experimental_factor",
"feature": "test_feature",
"findex": "test_findex",
"finishing_strategy": "test_finishing_strategy",
"geo_loc_name": "test_geo_loc_name",
"investigation_type": "test_investigation_type",
"lat_lon": "test_lat_long",
"lib_const_meth": "test_lib_const_meth",
"lib_reads_seqd": "test_lib_reads_seqd",
"lib_screen": "test_lib_screen",
"lib_size": 2000,
"lib_vector": "test_lib_vector",
"material": "test_material",
"nucl_acid_amp": "test_nucl_acid_amp",
"nucl_acid_ext": "test_nucl_acid_ext",
"project_name": "test_project_name",
"rel_to_oxygen": "test_rel_to_oxygen",
"rindex": "test_rindex",
"samp_collect_device": "test_samp_collect_device",
"samp_mat_process": "test_samp_map_process",
"samp_size": "test_samp_size",
"seq_meth": "test_seq_meth",
"sop": [ "a", "b", "c" ],
"source_mat_id": [ "a", "b", "c" ],
"submitted_to_insdc": True,
"url": ["a", "b", "c" ],
# And now for some spurious data
"ned": "stark",
"sansa": "stark",
"ramsay": "bolton"
}
valid = MIMS.check_dict(too_much)
self.assertFalse(valid, "False result for superfluous data.")
def testValidData(self):
""" Test the MIMS class with completely valid data. """
just_right = {
"adapters": "test_adapters",
"annot_source": "test_annot_source",
"assembly": "test_assembly",
"assembly_name": "test_assembly_name",
"biome": "test_biome",
"collection_date": "test_collection_date",
"env_package": "test_env_package",
"extrachrom_elements": "test_extrachrom_elements",
"encoded_traits": "test_encoded_traits",
"experimental_factor": "test_experimental_factor",
"feature": "test_feature",
"findex": "test_findex",
"finishing_strategy": "test_finishing_strategy",
"geo_loc_name": "test_geo_loc_name",
"investigation_type": "test_investigation_type",
"lat_lon": "test_lat_long",
"lib_const_meth": "test_lib_const_meth",
"lib_reads_seqd": "test_lib_reads_seqd",
"lib_screen": "test_lib_screen",
"lib_size": 2000,
"lib_vector": "test_lib_vector",
"material": "test_material",
"nucl_acid_amp": "test_nucl_acid_amp",
"nucl_acid_ext": "test_nucl_acid_ext",
"project_name": "test_project_name",
"rel_to_oxygen": "test_rel_to_oxygen",
"rindex": "test_rindex",
"samp_collect_device": "test_samp_collect_device",
"samp_mat_process": "test_samp_map_process",
"samp_size": "test_samp_size",
"seq_meth": "test_seq_meth",
"sop": ["a", "b", "c"],
"source_mat_id": ["a", "b", "c"],
"submitted_to_insdc": True,
"url": ["a", "b", "c"]
}
valid = MIMS.check_dict(just_right)
self.assertTrue(valid, "True result for valid data.")
def testValidData(self):
just_right = {
"adapters": "test_adapters",
"annot_source": "test_annot_source",
"assembly": "test_assembly",
"assembly_name": "test_assembly_name",
"biome": "test_biome",
"collection_date": "test_collection_date",
"env_package": "test_env_package",
"extrachrom_elements": "test_extrachrom_elements",
"encoded_traits": "test_encoded_traits",
"experimental_factor": "test_experimental_factor",
"feature": "test_feature",
"findex": "test_findex",
"finishing_strategy": "test_finishing_strategy",
"geo_loc_name": "test_geo_loc_name",
"investigation_type": "test_investigation_type",
"lat_lon": "test_lat_long",
"lib_const_meth": "test_lib_const_meth",
"lib_reads_seqd": "test_lib_reads_seqd",
"lib_screen": "test_lib_screen",
"lib_size": 2000,
"lib_vector": "test_lib_vector",
"material": "test_material",
"nucl_acid_amp": "test_nucl_acid_amp",
"nucl_acid_ext": "test_nucl_acid_ext",
"project_name": "test_project_name",
"rel_to_oxygen": "test_rel_to_oxygen",
"rindex": "test_rindex",
"samp_collect_device": "test_samp_collect_device",
"samp_mat_process": "test_samp_map_process",
"samp_size": "test_samp_size",
"seq_meth": "test_seq_meth",
"sop": [ "a", "b", "c" ],
"source_mat_id": [ "a", "b", "c" ],
"submitted_to_insdc": True,
"url": ["a", "b", "c" ]
}
valid = MIMS.check_dict(just_right)
self.assertTrue(valid, "True result for valid data.")
def testInsufficientData(self):
too_little = { "adapters": "test_adapters" }
valid = MIMS.check_dict(too_little)
self.assertFalse(valid, "False result for superfluous data.")