def clinvar(institute_id, case_name, variant_id):
"""Build a clinVar submission form for a variant."""
data = clinvar_export(store, institute_id, case_name, variant_id)
if request.method == "GET":
return data
# POST
form_dict = {}
# flatten up HPO and OMIM terms lists into string of keys separated by semicolon
for key, value in request.form.items():
if key.startswith("conditions@") or key.startswith("clin_features@"):
conditions = request.form.getlist(
key) # can be HPO or OMIM conditions
if conditions:
variant_id = key.split("@")[1]
cond_types = []
cond_values = []
for condition in conditions:
cond_types.append(
condition.split("_")[0]) # 'HPO' or 'OMIM'
cond_values.append(
condition.split("_")[1]) # HPO id or OMIM ID
if key.startswith(
"conditions@"
): # Filling in 'condition_id_type' and 'condition_id_value' in variant data
form_dict["@".join(["condition_id_type",
variant_id])] = ";".join(
cond_types) # Flattened list
form_dict["@".join(["condition_id_value",
variant_id])] = ";".join(
cond_values) # Flattened list
elif key.startswith(
"clin_features@"
): # Filling in 'clin_features' in casedata
form_dict["@".join(["clin_features",
variant_id])] = ";".join(
cond_values) # Flattened list
else:
form_dict[key] = value
# A tuple of submission objects (variants and casedata objects):
submission_objects = set_submission_objects(form_dict)
# Add submission data to an open clinvar submission object,
# or create a new if no open submission is found in database
open_submission = store.get_open_clinvar_submission(institute_id)
updated_submission = store.add_to_submission(open_submission["_id"],
submission_objects)
# Redirect to clinvar submissions handling page, and pass it the updated_submission_object
return redirect(
url_for("cases.clinvar_submissions", institute_id=institute_id))
def test_parse_clinvar_form():
"""Test create list of submission objects (variants and casedata) from clinvar page form"""
# Given a filled in form
form_fields_dict = get_submission_dict()
# Retrieve the IDs of variants in the form
variant_ids = get_submission_variants(form_fields_dict)
assert len(variant_ids) == 2
# obtain variant and casedata objects to include in submission
subm_objs = set_submission_objects(form_fields_dict)
assert len(subm_objs[0]) == 2 # one snv and one sv variant
assert len(subm_objs[1]) ==1 # one case data object
def clinvar(institute_id, case_name, variant_id):
"""Build a clinVar submission form for a variant."""
data = controllers.clinvar_export(store, institute_id, case_name, variant_id)
if request.method == 'GET':
return data
else: #POST
form_dict = request.form.to_dict()
submission_objects = set_submission_objects(form_dict) # A tuple of submission objects (variants and casedata objects)
# Add submission data to an open clinvar submission object,
# or create a new if no open submission is found in database
open_submission = store.get_open_clinvar_submission(current_user.email, institute_id)
updated_submission = store.add_to_submission(open_submission['_id'], submission_objects)
# Redirect to clinvar submissions handling page, and pass it the updated_submission_object
return redirect(url_for('cases.clinvar_submissions', institute_id=institute_id))
def clinvar(institute_id, case_name, variant_id):
"""Build a clinVar submission form for a variant."""
data = controllers.clinvar_export(store, institute_id, case_name, variant_id)
if request.method == 'GET':
return data
else: #POST
form_dict = request.form.to_dict()
submission_objects = set_submission_objects(form_dict) # A tuple of submission objects (variants and casedata objects)
# Add submission data to an open clinvar submission object,
# or create a new if no open submission is found in database
open_submission = store.get_open_clinvar_submission(current_user.email, institute_id)
updated_submission = store.add_to_submission(open_submission['_id'], submission_objects)
# Redirect to clinvar submissions handling page, and pass it the updated_submission_object
return redirect(url_for('cases.clinvar_submissions', institute_id=institute_id))
def build_clinvar_submission(store, request, institute_id, case_name, variant_id):
"""Add some variants to a ClinVar submission object or create a new ClinVar submission
Args:
store(scout.adapter.MongoAdapter)
request(flask.Request)
institute_id(str): institute_obj['_id']
case_name(str): case_obj['display_name']
variant_id(str): variant_obj['document_id']
"""
form_dict = {}
# flatten up HPO and OMIM terms lists into string of keys separated by semicolon
for key, value in request.form.items():
if "@" in key:
variant_id = key.split("@")[1]
if key.startswith("hpo_terms") and f"omim_terms@{variant_id}" not in request.form:
form_dict["@".join(["condition_id_type", variant_id])] = "HPO"
form_dict["@".join(["condition_id_value", variant_id])] = ";".join(
request.form.getlist(key)
)
elif key.startswith("omim_terms"):
form_dict["@".join(["condition_id_type", variant_id])] = "OMIM"
form_dict["@".join(["condition_id_value", variant_id])] = ";".join(
request.form.getlist(key)
)
elif key.startswith("clin_features"):
form_dict[key] = ";".join(request.form.getlist(key))
else:
form_dict[key] = value
# A tuple of submission objects (variants and casedata objects):
submission_objects = set_submission_objects(form_dict)
# Add submission data to an open clinvar submission object,
# or create a new if no open submission is found in database
open_submission = store.get_open_clinvar_submission(institute_id)
updated_submission = store.add_to_submission(open_submission["_id"], submission_objects)