def test_hide_compounds_follow_filter_in(app, variant_obj):
"""Test hiding compounds from view given hide compounds follow filter options"""
# GIVEN a variant
compound_variant_obj = {
"_id": "a_compound",
"case_id": variant_obj["case_id"],
"chromosome": variant_obj["chromosome"],
"position": variant_obj["position"] + 3,
"end": variant_obj["position"] + 3,
"reference": "A",
"alternative": "G",
"category": "sv",
"sub_category": "del",
}
store.variant_collection.insert_one(compound_variant_obj)
compound_variant_dict = {
"variant": "a_compound",
"is_dismissed": False,
}
# GIVEN a variant with the other variant as an only compound
variant_obj["compounds"] = [compound_variant_dict]
print("variant obj", variant_obj)
# WHEN asking for hiding compounds that do match a subtype annotation
query_form = {"svtype": ["dup", "del"], "compound_follow_filter": True}
# WHEN calling the function
hide_compounds_query(store, variant_obj, query_form)
# WHEN checking its compounds
compounds = variant_obj.get("compounds")
# THEN the only compound now appears included
assert compounds[0]["is_dismissed"] is False
# WHEN asking for hiding compounds that do not match a subtype annotation
query_form = {"svtype": ["inv"], "compound_follow_filter": True}
# WHEN calling the function
hide_compounds_query(store, variant_obj, query_form)
# WHEN checking its compounds
compounds = variant_obj.get("compounds")
# THEN the only compound now appears dismissed
assert compounds[0]["is_dismissed"]
def test_hide_compounds_follow_filter_clnsig(app, variant_obj):
"""Test hiding compounds from view given hide compounds follow filter options"""
# GIVEN a variant
compound_variant_obj = {
"_id":
"a_compound",
"case_id":
variant_obj["case_id"],
"chromosome":
variant_obj["chromosome"],
"position":
variant_obj["position"] + 3,
"end":
variant_obj["position"] + 3,
"reference":
"A",
"alternative":
"G",
"clnsig": [{
"value": "Pathogenic",
"accession": "RCV00123456.7",
"revstat": "single"
}],
}
store.variant_collection.insert_one(compound_variant_obj)
compound_variant_dict = {
"variant": "a_compound",
"is_dismissed": False,
}
# GIVEN a variant with the other variant as an only compound
variant_obj["compounds"] = [compound_variant_dict]
print("variant obj", variant_obj)
# WHEN asking for hiding compounds that do match a ClinVar annotation
query_form = {"clinsig": [4, 5], "compound_follow_filter": True}
# WHEN calling the function
hide_compounds_query(store, variant_obj, query_form)
# WHEN checking its compounds
compounds = variant_obj.get("compounds")
# THEN the only compound appears included
assert compounds[0]["is_dismissed"] is False
def test_hide_compounds_query_rank(app, variant_obj):
"""Test hiding compounds from view given a compound rank score filter option"""
# GIVEN a variant
test_rank_score = 4
compound_variant_obj = {
"_id": "a_compound",
"case_id": variant_obj["case_id"],
"chromosome": variant_obj["chromosome"],
"position": variant_obj["position"] + 3,
"reference": "A",
"alternative": "G",
"rank_score": test_rank_score,
"is_dismissed": False,
}
store.variant_collection.insert_one(compound_variant_obj)
# GIVEN a variant with the other as an only compound
variant_obj["compounds"] = [compound_variant_obj]
# WHEN asking for a lower score threshold
query_form = {"compound_rank_score": test_rank_score - 1}
# WHEN calling the function
hide_compounds_query(store, variant_obj, query_form)
# WHEN checking its compounds
compounds = variant_obj.get("compounds")
# THEN the only compound is still not dismissed
assert compounds[0]["is_dismissed"] is False
# WHEN asking for hiding compounds with higher rank score threshold
query_form = {"compound_rank_score": test_rank_score + 1}
# WHEN calling the function
hide_compounds_query(store, variant_obj, query_form)
# WHEN checking its compounds
compounds = variant_obj.get("compounds")
# THEN the only compound now appears dismissed
assert compounds[0]["is_dismissed"]
def test_hide_compounds_follow_filter(app, variant_obj):
"""Test hiding compounds from view given hide compounds follow filter options"""
# GIVEN a variant
test_cadd = 15
compound_variant_obj = {
"_id": "a_compound",
"case_id": variant_obj["case_id"],
"chromosome": variant_obj["chromosome"],
"position": variant_obj["position"] + 3,
"end": variant_obj["position"] + 3,
"reference": "A",
"alternative": "G",
"cadd_score": test_cadd,
"local_obs_old": 10,
}
store.variant_collection.insert_one(compound_variant_obj)
compound_variant_dict = {
"variant": "a_compound",
"is_dismissed": False,
}
# GIVEN a variant with the other variant as an only compound
variant_obj["compounds"] = [compound_variant_dict]
# CADD
# WHEN asking for hiding compounds with higher cadd score threshold
query_form = {"cadd_score": test_cadd + 1, "compound_follow_filter": True}
# WHEN calling the function
hide_compounds_query(store, variant_obj, query_form)
# WHEN checking its compounds
compounds = variant_obj.get("compounds")
# THEN the only compound now appears dismissed
assert compounds[0]["is_dismissed"]
# POSITION
# WHEN setting it back to visible
compound_variant_dict["is_dismissed"] = False
# WHEN asking for hiding compounds with position in the range
query_form = {
"position": variant_obj["position"] - 1,
"end": variant_obj["position"] + 5,
"compound_follow_filter": True,
}
# WHEN calling the function
hide_compounds_query(store, variant_obj, query_form)
# WHEN checking its compounds
compounds = variant_obj.get("compounds")
# THEN the only compound now appears dismissed
assert compounds[0]["is_dismissed"]
# FREQ
# WHEN setting it back to visible
compound_variant_dict["is_dismissed"] = False
# WHEN asking for hiding compounds with more counts
query_form = {"local_obs": 5, "compound_follow_filter": True}
# WHEN calling the function
hide_compounds_query(store, variant_obj, query_form)
# WHEN checking its compounds
compounds = variant_obj.get("compounds")
# THEN the only compound now appears dismissed
assert compounds[0]["is_dismissed"]
def test_hide_compounds_follow_filter_region(app, variant_obj):
"""Test hiding compounds from view given hide compounds follow filter options"""
# GIVEN a variant
test_cadd = 15
compound_variant_obj = {
"_id": "a_compound",
"case_id": variant_obj["case_id"],
"chromosome": variant_obj["chromosome"],
"position": variant_obj["position"] + 3,
"end": variant_obj["position"] + 3,
"reference": "A",
"alternative": "G",
"cadd_score": test_cadd,
"spidex": -1.5,
"local_obs_old": 10,
}
store.variant_collection.insert_one(compound_variant_obj)
compound_variant_dict = {
"variant": "a_compound",
"is_dismissed": False,
"region_annotations": ["exonic"],
}
# GIVEN a variant with the other variant as an only compound
variant_obj["compounds"] = [compound_variant_dict]
print("variant obj", variant_obj)
# WHEN asking for hiding compounds that do match a region annotation
query_form = {
"region_annotations": ["exonic"],
"compound_follow_filter": True
}
# WHEN calling the function
hide_compounds_query(store, variant_obj, query_form)
# WHEN checking its compounds
compounds = variant_obj.get("compounds")
# THEN the only compound now appears included
assert compounds[0]["is_dismissed"] is False
# but WHEN asking for hiding compounds that do not match a region annotation
query_form = {
"region_annotations": ["intronic"],
"compound_follow_filter": True
}
# WHEN calling the function
hide_compounds_query(store, variant_obj, query_form)
# WHEN checking its compounds
compounds = variant_obj.get("compounds")
# THEN the only compound now appears hidden
assert compounds[0]["is_dismissed"]
# WHEN setting it back to visible
compound_variant_dict["is_dismissed"] = False
def test_hide_compounds_follow_filter_spidex(app, variant_obj):
"""Test hiding compounds from view given hide compounds follow filter options"""
# GIVEN a variant
compound_variant_obj = {
"_id": "a_compound",
"case_id": variant_obj["case_id"],
"chromosome": variant_obj["chromosome"],
"position": variant_obj["position"] + 3,
"end": variant_obj["position"] + 3,
"reference": "A",
"alternative": "G",
"spidex": -1.5, # medium
}
store.variant_collection.insert_one(compound_variant_obj)
compound_variant_dict = {
"variant": "a_compound",
"is_dismissed": False,
}
# GIVEN a variant with the other variant as an only compound
variant_obj["compounds"] = [compound_variant_dict]
# WHEN asking for hiding compounds with higher rank score threshold
query_form = {"spidex_human": ["high"], "compound_follow_filter": True}
# WHEN calling the function
hide_compounds_query(store, variant_obj, query_form)
# WHEN checking its compounds
compounds = variant_obj.get("compounds")
# THEN the only compound appears dismissed
assert compounds[0]["is_dismissed"]
# WHEN setting it back to visible
compound_variant_dict["is_dismissed"] = False
# GIVEN a variant with the other variant as an only compound
variant_obj["compounds"] = [compound_variant_dict]
# WHEN asking for hiding compounds within the spidex score interval
query_form = {"spidex_human": ["medium"], "compound_follow_filter": True}
# WHEN calling the function
hide_compounds_query(store, variant_obj, query_form)
# WHEN checking its compounds
compounds = variant_obj.get("compounds")
# THEN the only compound does not appear dismissed
assert not compounds[0]["is_dismissed"]
# WHEN setting it back to visible
compound_variant_dict["is_dismissed"] = False
# GIVEN a variant with the other variant as an only compound
variant_obj["compounds"] = [compound_variant_dict]
# WHEN asking for hiding compounds within a spidex score interval with both the containing and the higher level
query_form = {
"spidex_human": ["medium", "high"],
"compound_follow_filter": True
}
# WHEN calling the function
hide_compounds_query(store, variant_obj, query_form)
# WHEN checking its compounds
compounds = variant_obj.get("compounds")
# THEN the only compound again appears not dismissed
assert not compounds[0]["is_dismissed"]