Hook up pcorrs with target traits computations

Enable the endpoint to actually compute partial correlations with selected
target traits rather than against an entire dataset.

Fix some issues caused by recent refactor that broke pcorrs against a dataset

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})