scout/server/blueprints/variants/controllers.py
def get_clinvar_submission(store, institute_id, case_name, variant_id, submission_id):
    """Collects all variants from the clinvar submission collection with a specific submission_id

        Args:
            store(scout.adapter.MongoAdapter)
            institute_id(str): Institute ID
            case_name(str): case ID
            variant_id(str): variant._id
            submission_id(str): clinvar submission id, i.e. SUB76578

        Returns:
            A dictionary with all the data to display the clinvar_update.html template page
    """

    institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
    pinned = [store.variant(variant_id) or variant_id for variant_id in
                  case_obj.get('suspects', [])]
    variant_obj = store.variant(variant_id)
    clinvar_submission_objs = store.clinvars(submission_id=submission_id)
    return dict(
        today = str(date.today()),
        institute=institute_obj,
        case=case_obj,
        variant=variant_obj,
        pinned_vars=pinned,
        clinvars = clinvar_submission_objs
    )
def get_clinvar_submission(store, institute_id, case_name, variant_id, submission_id):
    institute_obj, case_obj = institute_and_case(store, institute_id, case_name)
    pinned = [store.variant(variant_id) or variant_id for variant_id in
                  case_obj.get('suspects', [])]
    variant_obj = store.variant(variant_id)
    clinvar_submission_objs = store.clinvars(submission_id=submission_id)
    return dict(
        today = str(date.today()),
        institute=institute_obj,
        case=case_obj,
        variant=variant_obj,
        pinned_vars=pinned,
        clinvars = clinvar_submission_objs
    )
def get_clinvar_submission ( store , institute_id , case_name , variant_id , submission_id ) : institute_obj , case_obj = institute_and_case ( store , institute_id , case_name ) pinned = [ store . variant ( variant_id ) or variant_id for variant_id in case_obj . get ( 'suspects' , [ ] ) ] variant_obj = store . variant ( variant_id ) clinvar_submission_objs = store . clinvars ( submission_id = submission_id ) return dict ( today = str ( date . today ( ) ) , institute = institute_obj , case = case_obj , variant = variant_obj , pinned_vars = pinned , clinvars = clinvar_submission_objs )
Collects all variants from the clinvar submission collection with a specific submission_id

        Args:
            store(scout.adapter.MongoAdapter)
            institute_id(str): Institute ID
            case_name(str): case ID
            variant_id(str): variant._id
            submission_id(str): clinvar submission id, i.e. SUB76578

        Returns:
            A dictionary with all the data to display the clinvar_update.html template page
Collects all variants from the clinvar submission collection with a specific submission_id