def test_build_sample_empty_strings(sample_key):
# GIVEN a sample_data dict with requiered key 'SampleID' and a sample_key with empty string as value
sample_data = {"SampleID": "2020-07452-02", sample_key: " "}
# WHEN building a mongo sample
mongo_sample = build_sample(sample_data=sample_data)
# THEN the the sample_key will not be loaded into the mongo_sample dict
assert mongo_sample == {"_id": "2020-07452-02"}
def test_build_sample_zero_values(sample_key):
# GIVEN a sample_data dict with requiered key 'SampleID' and a sample_key with value 0
sample_data = {"SampleID": "2020-07452-02", sample_key: 0}
# WHEN building a mongo sample
mongo_sample = build_sample(sample_data=sample_data)
# THEN the the sample_key will be loaded into the mongo_sample dict
assert mongo_sample == {"_id": "2020-07452-02", sample_key: 0}
def test_build_sample_str_values(sample_key):
# GIVEN a sample_data dict with requiered key 'SampleID' and a sample_key with some str value
sample_data = {"SampleID": "2020-07452-02", sample_key: "Value"}
# WHEN building a mongo sample
mongo_sample = build_sample(sample_data=sample_data)
# THEN the the sample_key will be loaded into the mongo_sample dict
if sample_key == "SampleID":
assert mongo_sample == {"_id": "2020-07452-02", sample_key: "Value"}
def load_one_batch(adapter, nipt_results_path: str):
"""Function to load one lims sample into the database.
Raises:
MissingResultsError: when parsing file that is empty"""
batch_data = parse_batch_file(nipt_results_path)
for sample in batch_data:
mongo_sample = build_sample(sample)
adapter.add_or_update_document(mongo_sample, adapter.sample_collection)
mongo_batch = build_batch(batch_data[0])
adapter.add_or_update_document(mongo_batch, adapter.batch_collection)
def test_build_sample_wrong_keys():
# GIVEN a sample_data with not accepted keys: key1 key2 key3
sample_data = {
"SampleID": "2020-07452-02",
"key1": " ",
"key2": 201862,
"key3": -10.1836097044367,
}
# WHEN building a mongo sample
mongo_sample = build_sample(sample_data=sample_data)
# THEN the unaccepted keys will not be part of the mongo_sample"
assert mongo_sample == {"_id": "2020-07452-02"}
def test_build_sample_SampleProject_key():
# GIVEN a sample_data with requiered key 'SampleID' and 'SampleProject' in int format
sample_data = {
"SampleID": "2020-07452-02",
"SampleProject": 201862,
}
# WHEN building a mongo sample
mongo_sample = build_sample(sample_data=sample_data)
# THEN the value of "SampleProject" is in str format
assert mongo_sample == {
"_id": "2020-07452-02",
"SampleProject": "201862",
}
def test_build_sample():
# GIVEN a sample_data with requiered key 'SampleID'
sample_data = {
"SampleID": "2020-07452-02",
"Description": " ",
"Zscore_13": -10.1836097044367,
}
# WHEN building a mongo sample
mongo_sample = build_sample(sample_data=sample_data)
# THEN the mongo_sample has a key "_id" with the value of "SampleID"
assert mongo_sample == {
"_id": "2020-07452-02",
"Zscore_13": -10.1836097044367,
}