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

2 files changed, 44 insertions, 20 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})
diff --git a/gn3/computations/partial_correlations.py b/gn3/computations/partial_correlations.py
index 0041684..07c73db 100644
--- a/gn3/computations/partial_correlations.py
+++ b/gn3/computations/partial_correlations.py
@@ -555,9 +555,9 @@ def trait_for_output(trait):
     }
     return {key: val for key, val in trait.items() if val is not None}
 
-def check_for_common_errors(conn, primary_trait_name, control_trait_names):
+def check_for_common_errors(
+        conn, primary_trait_name, control_trait_names, threshold):
     """Check for common errors"""
-    threshold = 0
     corr_min_informative = 4
     non_error_result = {"status": "success"}
 
@@ -671,8 +671,10 @@ def partial_correlations_with_target_db(# pylint: disable=[R0913, R0914, R0911]
     functionality into smaller functions that do fewer things.
     """
 
+    threshold = 0
+
     check_res = check_for_common_errors(
-        conn, primary_trait_name, control_trait_names)
+        conn, primary_trait_name, control_trait_names, threshold)
     if check_res.get("status") == "error":
         return error_check_results
 
@@ -680,7 +682,7 @@ def partial_correlations_with_target_db(# pylint: disable=[R0913, R0914, R0911]
     input_trait_geneid = primary_trait.get("geneid", 0)
     input_trait_symbol = primary_trait.get("symbol", "")
     input_trait_mouse_geneid = translate_to_mouse_gene_id(
-        species, input_trait_geneid, conn)
+        check_res["species"], input_trait_geneid, conn)
 
     tissue_probeset_freeze_id = 1
     db_type = primary_trait["db"]["dataset_type"]
@@ -744,8 +746,8 @@ def partial_correlations_with_target_db(# pylint: disable=[R0913, R0914, R0911]
     database_filename = get_filename(conn, target_db_name, TEXTDIR)
     _total_traits, all_correlations = partial_corrs(
         conn, check_res["common_primary_control_samples"],
-        check_res["fixed_primary_values"], check_res["fixed_control_vals"],
-        len(check_res["fixed_primary_vals"]), check_res["species"],
+        check_res["fixed_primary_values"], check_res["fixed_control_values"],
+        len(check_res["fixed_primary_values"]), check_res["species"],
         input_trait_geneid, input_trait_symbol, tissue_probeset_freeze_id,
         method, {**target_dataset, "dataset_type": target_dataset["type"]},
         database_filename)
@@ -764,7 +766,7 @@ def partial_correlations_with_target_db(# pylint: disable=[R0913, R0914, R0911]
         return __by_partial_corr_p_value__
 
     add_lit_corr_and_tiss_corr = compose(
-        partial(literature_correlation_by_list, conn, species),
+        partial(literature_correlation_by_list, conn, check_res["species"]),
         partial(
             tissue_correlation_by_list, conn, input_trait_symbol,
             tissue_probeset_freeze_id, method))
@@ -801,7 +803,7 @@ def partial_correlations_with_target_db(# pylint: disable=[R0913, R0914, R0911]
         "results": {
             "primary_trait": trait_for_output(primary_trait),
             "control_traits": tuple(
-                trait_for_output(trait) for trait in cntrl_traits),
+                trait_for_output(trait) for trait in check_res["control_traits"]),
             "correlations": tuple(
                 trait_for_output(trait) for trait in trait_list),
             "dataset_type": target_dataset["type"],
@@ -818,7 +820,7 @@ def partial_correlations_with_target_traits(
     """
     threshold = 0
     check_res = check_for_common_errors(
-        conn, primary_trait_name, control_trait_names)
+        conn, primary_trait_name, control_trait_names, threshold)
     if check_res.get("status") == "error":
         return error_check_results