def test_variants_research_no_shadow_clinical_assessments(
real_variant_database, institute_obj, case_obj
):
# GIVEN a db with variants,
adapter = real_variant_database
case_id = case_obj["_id"]
# GIVEN a clinical variant from one case
variant_clinical = adapter.variant_collection.find_one(
{"case_id": case_id, "variant_type": "clinical"}
)
# GIVEN a copy of that variant marked research
variant_research = copy.deepcopy(variant_clinical)
variant_research["_id"] = "research_version"
variant_research["variant_type"] = "research"
adapter.variant_collection.insert_one(variant_research)
# WHEN filtering for that variant in research
variants_query = {"variant_type": "research"}
variants_query_res = adapter.variants(
case_obj["_id"], query=variants_query, category=variant_clinical["category"]
)
res = variants(adapter, institute_obj, case_obj, variants_query_res)
res_variants = res["variants"]
LOG.debug("Variants: {}".format(res_variants))
# THEN it is returned
assert any([variant["_id"] == variant_research["_id"] for variant in res_variants])
# THEN no previous annotations are reported back for the reseach case..
assert not any([variant.get("clinical_assessments") for variant in res_variants])
def test_variants_assessment_shared_with_group(mocker, real_variant_database,
institute_obj, case_obj):
mocker.patch(
"scout.server.blueprints.variants.controllers.user_institutes",
return_value=[{
"_id": "cust000"
}],
)
# GIVEN a db with variants,
adapter = real_variant_database
case_id = case_obj["_id"]
other_case_id = "other_" + case_id
other_case_obj = copy.deepcopy(case_obj)
other_case_obj["_id"] = other_case_id
## WHEN inserting an object with a group id
group_id = ObjectId("101010101010101010101010")
other_case_obj["group"] = [group_id]
adapter.case_collection.insert_one(other_case_obj)
# WHEN setting the same group id for the original case
adapter.case_collection.find_one_and_update(
{"_id": case_id}, {"$set": {
"group": [group_id]
}})
# GIVEN a clinical variant from one case
variant = adapter.variant_collection.find_one({
"case_id": case_id,
"variant_type": "clinical"
})
# GIVEN a copy of the variant for the other case
other_variant_obj = copy.deepcopy(variant)
other_variant_obj["case_id"] = other_case_id
other_variant_obj["_id"] = "another_variant"
adapter.variant_collection.insert_one(other_variant_obj)
# WHEN updating an assessment on the same first case variant
adapter.variant_collection.find_one_and_update(
{"_id": variant["_id"]}, {"$set": {
"acmg_classification": 4
}})
# WHEN retrieving assessments for the variant from the other case
variants_query = {"variant_type": "clinical"}
variants_query_res = adapter.variants(other_case_id,
query=variants_query,
category=variant["category"])
res = variants(adapter, institute_obj, other_case_obj, variants_query_res,
1000)
res_variants = res["variants"]
# THEN a group assessment is recalled on the other case,
# since the variant in the first case had an annotation
assert any(variant.get("group_assessments") for variant in res_variants)
def test_variants_research_shadow_clinical_assessments(real_variant_database,
institute_obj,
case_obj):
# GIVEN a db with variants,
adapter = real_variant_database
case_id = case_obj["_id"]
# GIVEN a clinical variant from one case
variant_clinical = adapter.variant_collection.find_one({
"case_id":
case_id,
"variant_type":
"clinical"
})
# GIVEN a copy of that variant marked research
variant_research = copy.deepcopy(variant_clinical)
variant_research["_id"] = "research_version"
variant_research["variant_type"] = "research"
adapter.variant_collection.insert_one(variant_research)
# WHEN updating the manual assessments of the clinical variant
adapter.variant_collection.update_one(
{"_id": variant_clinical["_id"]},
{
"$set": {
"manual_rank": 2,
"mosaic_tags": ["1"],
"dismiss_variant": ["2", "3"],
"acmg_classification": 0,
}
},
)
# WHEN filtering for that variant in research
variants_query = {"variant_type": "research"}
variants_query_res = adapter.variants(
case_obj["_id"],
query=variants_query,
category=variant_clinical["category"])
res = variants(adapter, institute_obj, case_obj, variants_query_res)
res_variants = res["variants"]
# THEN it is returned
assert any([
variant["_id"] == variant_research["_id"] for variant in res_variants
])
# THEN previous annotations are reported back for the reseach case.
assert any(
[variant.get("clinical_assessments") for variant in res_variants])
def test_variants_research_no_shadow_clinical_assessments(
mocker, real_variant_database, institute_obj, case_obj):
mocker.patch(
"scout.server.blueprints.variants.controllers.user_institutes",
return_value=[{
"_id": "cust000"
}],
)
# GIVEN a db with variants,
adapter = real_variant_database
case_id = case_obj["_id"]
# GIVEN a clinical variant from one case
variant_clinical = adapter.variant_collection.find_one({
"case_id":
case_id,
"variant_type":
"clinical"
})
# GIVEN a copy of that variant marked research
variant_research = copy.deepcopy(variant_clinical)
variant_research["_id"] = "research_version"
variant_research["variant_type"] = "research"
adapter.variant_collection.insert_one(variant_research)
# WHEN filtering for that variant in research
variants_query = {"variant_type": "research"}
variants_query_res = adapter.variants(
case_obj["_id"],
query=variants_query,
category=variant_clinical["category"])
# NOTE in tests list length will be used, in live code count_documents{query} is
# called.
number_variants = len(list(variants_query_res.clone()))
res = variants(adapter, institute_obj, case_obj, variants_query_res,
number_variants)
res_variants = res["variants"]
LOG.debug("Variants: {}".format(res_variants))
# THEN it is returned
assert any([
variant["_id"] == variant_research["_id"] for variant in res_variants
])
# THEN no previous annotations are reported back for the reseach case..
assert not any(
[variant.get("clinical_assessments") for variant in res_variants])
def test_variants_research_shadow_clinical_assessments(mocker,
real_variant_database,
institute_obj,
case_obj):
mocker.patch(
"scout.server.blueprints.variants.controllers.user_institutes",
return_value=[{
"_id": "cust000"
}],
)
# GIVEN a db with variants,
adapter = real_variant_database
case_id = case_obj["_id"]
# GIVEN a clinical variant from one case
variant_clinical = adapter.variant_collection.find_one({
"case_id":
case_id,
"variant_type":
"clinical"
})
# GIVEN a copy of that variant marked research
variant_research = copy.deepcopy(variant_clinical)
variant_research["_id"] = "research_version"
variant_research["variant_type"] = "research"
adapter.variant_collection.insert_one(variant_research)
# WHEN updating the manual assessments of the clinical variant
adapter.variant_collection.update_one(
{"_id": variant_clinical["_id"]},
{
"$set": {
"manual_rank": 2,
"mosaic_tags": ["1"],
"dismiss_variant": ["2", "3"],
"acmg_classification": 0,
}
},
)
# WHEN filtering for that variant in research
variants_query = {"variant_type": "research"}
variants_query_res = adapter.variants(
case_obj["_id"],
query=variants_query,
category=variant_clinical["category"])
# NOTE in tests list length will be used, in live code count_documents{query} is
# called.
number_variants = len(list(variants_query_res.clone()))
res = variants(adapter, institute_obj, case_obj, variants_query_res,
number_variants)
res_variants = res["variants"]
# THEN it is returned
assert any([
variant["_id"] == variant_research["_id"] for variant in res_variants
])
# THEN previous annotations are reported back for the reseach case.
assert any(
[variant.get("clinical_assessments") for variant in res_variants])