def test_get_acmg_pathogenic():
acmg_terms = ["PVS1", "PS1"]
res = get_acmg(acmg_terms)
assert res == "pathogenic"
acmg_terms = ["PVS1", "PS1", "BS1"]
res = get_acmg(acmg_terms)
assert res == "pathogenic"
def test_get_acmg_uncertain():
acmg_terms = ["PVS1"]
res = get_acmg(acmg_terms)
assert res == "uncertain_significance"
acmg_terms = ["PVS1", "PS1", "BA1"]
res = get_acmg(acmg_terms)
assert res == "uncertain_significance"
def test_get_acmg_uncertain():
acmg_terms = ['PVS1']
res = get_acmg(acmg_terms)
assert res == 'uncertain_significance'
acmg_terms = ['PVS1', 'PS1', 'BA1']
res = get_acmg(acmg_terms)
assert res == 'uncertain_significance'
def test_get_acmg_uncertain():
acmg_terms = ['PVS1']
res = get_acmg(acmg_terms)
assert res == 'uncertain_significance'
acmg_terms = ['PVS1', 'PS1', 'BA1']
res = get_acmg(acmg_terms)
assert res == 'uncertain_significance'
def test_get_acmg_pathogenic():
acmg_terms = ['PVS1', 'PS1']
res = get_acmg(acmg_terms)
assert res == 'pathogenic'
acmg_terms = ['PVS1', 'PS1', 'BS1']
res = get_acmg(acmg_terms)
assert res == 'pathogenic'
def test_get_acmg_pathogenic():
acmg_terms = ['PVS1', 'PS1']
res = get_acmg(acmg_terms)
assert res == 'pathogenic'
acmg_terms = ['PVS1', 'PS1', 'BS1']
res = get_acmg(acmg_terms)
assert res == 'pathogenic'
def submit_evaluation(self, variant_obj, user_obj, institute_obj, case_obj,
link, criteria):
"""Submit an evaluation to the database
Get all the relevant information, build a evaluation_obj
Args:
variant_obj(dict)
user_obj(dict)
institute_obj(dict)
case_obj(dict)
link(str): variant url
criteria(list(dict)):
[
{
'term': str,
'comment': str,
'links': list(str)
},
.
.
]
"""
variant_specific = variant_obj['_id']
variant_id = variant_obj['variant_id']
user_id = user_obj['_id']
user_name = user_obj.get('name', user_obj['_id'])
institute_id = institute_obj['_id']
case_id = case_obj['_id']
evaluation_terms = [
evluation_info['term'] for evluation_info in criteria
]
classification = get_acmg(evaluation_terms)
evaluation_obj = build_evaluation(variant_specific=variant_specific,
variant_id=variant_id,
user_id=user_id,
user_name=user_name,
institute_id=institute_id,
case_id=case_id,
classification=classification,
criteria=criteria)
self._load_evaluation(evaluation_obj)
# Update the acmg classification for the variant:
self.update_acmg(institute_obj, case_obj, user_obj, link, variant_obj,
classification)
return classification
def submit_evaluation(self, variant_obj, user_obj, institute_obj, case_obj, link, criteria):
"""Submit an evaluation to the database
Get all the relevant information, build a evaluation_obj
Args:
variant_obj(dict)
user_obj(dict)
institute_obj(dict)
case_obj(dict)
link(str): variant url
criteria(list(dict)):
[
{
'term': str,
'comment': str,
'links': list(str)
},
.
.
]
"""
variant_specific = variant_obj['_id']
variant_id = variant_obj['variant_id']
user_id = user_obj['_id']
user_name = user_obj.get('name', user_obj['_id'])
institute_id = institute_obj['_id']
case_id = case_obj['_id']
evaluation_terms = [evluation_info['term'] for evluation_info in criteria]
classification = get_acmg(evaluation_terms)
evaluation_obj = build_evaluation(
variant_specific=variant_specific,
variant_id=variant_id,
user_id=user_id,
user_name=user_name,
institute_id=institute_id,
case_id=case_id,
classification=classification,
criteria=criteria
)
self._load_evaluation(evaluation_obj)
# Update the acmg classification for the variant:
self.update_acmg(institute_obj, case_obj, user_obj, link, variant_obj, classification)
return classification
def acmg():
"""Calculate an ACMG classification from submitted criteria."""
criteria = request.args.getlist("criterion")
classification = get_acmg(criteria)
return jsonify(dict(classification=classification))
def test_get_acmg_no_terms():
acmg_terms = []
res = get_acmg(acmg_terms)
assert res == None
def test_get_acmg_no_terms():
acmg_terms = []
res = get_acmg(acmg_terms)
assert res == 'uncertain_significance'
def submit_evaluation(
self,
variant_obj,
user_obj,
institute_obj,
case_obj,
link,
criteria=None,
classification=None,
):
"""Submit an evaluation to the database
Get all the relevant information, build a evaluation_obj
Args:
variant_obj(dict)
user_obj(dict)
institute_obj(dict)
case_obj(dict)
link(str): variant url
criteria(list(dict)):
[
{
'term': str,
'comment': str,
'links': list(str)
},
.
.
]
classification(int)
"""
criteria = criteria or []
variant_specific = variant_obj["_id"]
variant_id = variant_obj["variant_id"]
user_id = user_obj["_id"]
user_name = user_obj.get("name", user_obj["_id"])
institute_id = institute_obj["_id"]
case_id = case_obj["_id"]
evaluation_terms = [evluation_info["term"] for evluation_info in criteria]
if classification is None:
classification = get_acmg(evaluation_terms)
if classification:
evaluation_obj = build_evaluation(
variant_specific=variant_specific,
variant_id=variant_id,
user_id=user_id,
user_name=user_name,
institute_id=institute_id,
case_id=case_id,
classification=classification,
criteria=criteria,
)
self._load_evaluation(evaluation_obj)
# Update the acmg classification for the variant:
self.update_acmg(
institute_obj, case_obj, user_obj, link, variant_obj, classification
)
return classification
def test_get_acmg_no_terms():
acmg_terms = []
res = get_acmg(acmg_terms)
assert res == 'uncertain_significance'
def acmg():
"""Calculate an ACMG classification from submitted criteria."""
criteria = request.args.getlist('criterion')
classification = get_acmg(criteria)
return jsonify(dict(classification=classification))
