diff options
Diffstat (limited to 'gn3/api')
| -rw-r--r-- | gn3/api/correlation.py | 44 |
1 files changed, 33 insertions, 11 deletions
diff --git a/gn3/api/correlation.py b/gn3/api/correlation.py index 7eb7cd6..aeb7f8c 100644 --- a/gn3/api/correlation.py +++ b/gn3/api/correlation.py @@ -16,6 +16,8 @@ from gn3.computations.correlations import map_shared_keys_to_values from gn3.computations.correlations import compute_tissue_correlation from gn3.computations.correlations import compute_all_lit_correlation from gn3.computations.correlations import compute_all_sample_correlation +from gn3.computations.partial_correlations import ( + partial_correlations_with_target_traits) correlation = Blueprint("correlation", __name__) @@ -111,22 +113,42 @@ def partial_correlation(): return reduce(__field_errors__(request_data), fields, errors) args = request.get_json() - request_errors = __errors__( - args, ("primary_trait", "control_traits", "target_db", "method")) + with_target_db = args.get("with_target_db", True) + request_errors = None + if with_target_db: + request_errors = __errors__( + args, ("primary_trait", "control_traits", "target_db", "method")) + else: + request_errors = __errors__( + args, ("primary_trait", "control_traits", "target_traits", "method")) if request_errors: return build_response({ "status": "error", "messages": request_errors, "error_type": "Client Error"}) - return build_response({ - "status": "success", - "results": queue_cmd( - conn=redis.Redis(), - cmd=compose_pcorrs_command( + + if with_target_db: + return build_response({ + "status": "queued", + "results": queue_cmd( + conn=redis.Redis(), + cmd=compose_pcorrs_command( + trait_fullname(args["primary_trait"]), + tuple( + trait_fullname(trait) for trait in args["control_traits"]), + args["method"], args["target_db"], + int(args.get("criteria", 500))), + job_queue=current_app.config.get("REDIS_JOB_QUEUE"), + env = {"PYTHONPATH": ":".join(sys.path), "SQL_URI": SQL_URI})}) + else: + with database_connector() as conn: + results = partial_correlations_with_target_traits( + conn, trait_fullname(args["primary_trait"]), tuple( trait_fullname(trait) for trait in args["control_traits"]), - args["method"], args["target_db"], - int(args.get("criteria", 500))), - job_queue=current_app.config.get("REDIS_JOB_QUEUE"), - env = {"PYTHONPATH": ":".join(sys.path), "SQL_URI": SQL_URI})}) + tuple( + trait_fullname(trait) for trait in args["target_traits"]), + args["method"]) + + return build_response({"status": "success", "results": results}) |