def clinvar_header(submission_objs, csv_type):
"""Call clinvar parser to extract required fields to include in csv header from clinvar submission objects
Args:
submission_objs(list)
csv_type(str)
Returns:
clinvar_header_obj(dict) # custom csv header (dict based on constants CLINVAR_HEADER and CASEDATA_HEADER, but with required fields only)
"""
clinvar_header_obj = clinvar_submission_header(submission_objs, csv_type)
return clinvar_header_obj
def test_add_remove_subm_objects(adapter, institute_obj, case_obj):
"""Test adding variant and casedata objects to a submission"""
# Get the ID of an existing submission
submission_obj = adapter.get_open_clinvar_submission(
institute_id=institute_obj["_id"])
# Given a test variant and its associated casedata
variant_data = [get_test_submission_variant(case_obj)
] # a list of 1 dictionary element
case_data = [get_test_submission_case(case_obj)
] # a list of 1 dictionary element
subm_objs = (variant_data, case_data)
# assert that clinvar collection in database is empty
submission_objects = list(adapter.clinvar_collection.find())
assert len(submission_objects) == 0
# Add objects to submission
updated_subm = adapter.add_to_submission(submission_obj["_id"], subm_objs)
# Assert that 'variant_data' value of submission is updated
assert updated_subm["variant_data"] == [variant_data[0].get("_id")]
# Assert that 'case_data' value of submission is updated
assert updated_subm["case_data"] == [case_data[0].get("_id")]
# assert that clinvar collection in database has now 2 elements
submission_objects = list(adapter.clinvar_collection.find())
assert len(submission_objects) == 2
# check if it is possible to create CSV files header for variant and casedata objects
variants_file_header = clinvar_submission_header(submission_objects,
"variant_data")
assert len(variants_file_header.keys()) > 0
casedata_file_header = clinvar_submission_header(submission_objects,
"case_data")
assert len(casedata_file_header.keys()) > 0
# check if it is possible to create CSV files lines for variant and casedata objects
variants_file_lines = clinvar_submission_lines(submission_objects,
variants_file_header)
assert len(variants_file_lines[0].split(",")) == len(
variants_file_header.keys()
) # variant file header and line have the same number of columns
casedata_file_lines = clinvar_submission_lines(submission_objects,
casedata_file_header)
assert len(casedata_file_lines[0].split(",")) == len(
casedata_file_header.keys()
) # casedata file header and line have the same number of columns
# assert that one of these objects is the variant object
assert variant_data == adapter.clinvar_objs(submission_obj["_id"],
"variant_data")
# assert that one of these objects is the case data object
assert case_data == adapter.clinvar_objs(submission_obj["_id"],
"case_data")
# assert that a variant is present for test case
assert adapter.case_to_clinVars(case_obj["_id"]) == {
variant_data[0]["local_id"]: variant_data[0]
}
# Removal of clinvar objects from submission and from clinvar collection in database
# remove case_data object
updated_submission = adapter.delete_clinvar_object(
object_id=case_data[0]["_id"],
object_type="case_data",
submission_id=submission_obj["_id"],
)
assert updated_submission["case_data"] == []
# remove variant object
updated_submission = adapter.delete_clinvar_object(
object_id=variant_data[0]["_id"],
object_type="variant_data",
submission_id=submission_obj["_id"],
)
assert updated_submission["variant_data"] == []
# assert that there are no objects left in clinvar collection
submission_objects = list(adapter.clinvar_collection.find())
assert len(submission_objects) == 0
def clinvar_header(submission_objs, csv_type):
""" Call clinvar parser to extract required fields to include in csv header from clinvar submission objects"""
clinvar_header_obj = clinvar_submission_header(submission_objs, csv_type)
return clinvar_header_obj
def clinvar_header(submission_objs, csv_type):
""" Call clinvar parser to extract required fields to include in csv header from clinvar submission objects"""
clinvar_header_obj = clinvar_submission_header(submission_objs, csv_type)
return clinvar_header_obj
def test_add_remove_subm_objects(adapter, user_obj, institute_obj):
"""Test adding variant and casedata objects to a submission"""
# Get the ID of an existing submission
submission_obj = adapter.get_open_clinvar_submission( user_id=user_obj['_id'], institute_id=institute_obj['_id'])
# Given a test variant and its associated casedata
variant_data = [ get_test_submission_variant() ] # a list of 1 dictionary element
case_data = [ get_test_submission_case() ] # a list of 1 dictionary element
subm_objs = (variant_data, case_data)
# assert that clinvar collection in database is empty
submission_objects = list(adapter.clinvar_collection.find())
assert len(submission_objects) == 0
# Add objects to submission
updated_subm = adapter.add_to_submission( submission_obj['_id'], subm_objs)
# Assert that 'variant_data' value of submission is updated
assert updated_subm['variant_data'] == [variant_data[0].get('_id')]
# Assert that 'case_data' value of submission is updated
assert updated_subm['case_data'] == [case_data[0].get('_id')]
# assert that clinvar collection in database has now 2 elements
submission_objects = list(adapter.clinvar_collection.find())
assert len(submission_objects) == 2
# check if it is possible to create CSV files header for variant and casedata objects
variants_file_header = clinvar_submission_header(submission_objects, 'variant_data')
assert len(variants_file_header.keys()) > 0
casedata_file_header = clinvar_submission_header(submission_objects, 'case_data')
assert len(casedata_file_header.keys()) > 0
# check if it is possible to create CSV files lines for variant and casedata objects
variants_file_lines = clinvar_submission_lines(submission_objects, variants_file_header)
assert len(variants_file_lines[0].split(',')) == len(variants_file_header.keys()) # variant file header and line have the same number of columns
casedata_file_lines = clinvar_submission_lines(submission_objects, casedata_file_header)
assert len(casedata_file_lines[0].split(',')) == len(casedata_file_header.keys()) # casedata file header and line have the same number of columns
# assert that one of these objects is the variant object
assert variant_data == adapter.clinvar_objs(submission_obj['_id'], 'variant_data')
# assert that one of these objects is the case data object
assert case_data == adapter.clinvar_objs(submission_obj['_id'], 'case_data')
# assert that a variant is present for case 'case1'
assert adapter.case_to_clinVars('case1') == {variant_data[0]['local_id'] : variant_data[0]}
# Removal of clinvar objects from submission and from clinvar collection in database
# remove case_data object
updated_submission = adapter.delete_clinvar_object(object_id=case_data[0]['_id'], object_type='case_data', submission_id=submission_obj['_id'])
assert updated_submission['case_data'] == []
# remove variant object
updated_submission = adapter.delete_clinvar_object(object_id=variant_data[0]['_id'], object_type='variant_data', submission_id=submission_obj['_id'])
assert updated_submission['variant_data'] == []
# assert that there are no objects left in clinvar collection
submission_objects = list(adapter.clinvar_collection.find())
assert len(submission_objects) == 0