fix for fetching dataset traits data

2 files changed, 29 insertions, 18 deletions

diff --git a/gn3/api/datasets.py b/gn3/api/datasets.py
index 70ee3a1..eb4097d 100644
--- a/gn3/api/datasets.py
+++ b/gn3/api/datasets.py
@@ -32,19 +32,19 @@ def create_dataset_api(dataset_name, dataset_type=None):
 
 @dataset.route("/fetch_traits_data/<dataset_name>/<dataset_type>")
 def fetch_traits_data(dataset_name, dataset_type):
-    """endpoints fetches sample for each trait in\
-    a dataset"""
+    """test fetch_traits_data/dataset_name/dataset_type"""
     # what actually brings speed issues in correlation
-    sample_ids = [4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15,
-                  17, 18, 19, 20, 21, 22, 24, 25, 26, 28, 29, 30, 31,
-                  35, 36, 37, 39, 98, 99, 100, 103, 487, 105, 106, 110, 115,
-                  116, 117, 118, 119, 120, 919, 147,
-                  121, 40, 41, 124, 125, 128, 135, 129, 130, 131,
-                  132, 134, 138, 139, 140, 141, 142, 144,
-                  145, 148, 149, 920, 922, 2, 3, 1, 1100]
+    # should fetch this
+    trait_sample_ids = [4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15,
+                        17, 18, 19, 20, 21, 22, 24, 25, 26, 28, 29, 30, 31,
+                        35, 36, 37, 39, 98, 99, 100, 103, 487, 105, 106, 110, 115,
+                        116, 117, 118, 119, 120, 919, 147,
+                        121, 40, 41, 124, 125, 128, 135, 129, 130, 131,
+                        132, 134, 138, 139, 140, 141, 142, 144,
+                        145, 148, 149, 920, 922, 2, 3, 1, 1100]
 
     conn, _cursor = database_connector()
-    results = get_traits_data(sample_ids=sample_ids, database_instance=conn,
+    results = get_traits_data(sample_ids=trait_sample_ids, database_instance=conn,
                               dataset_name=dataset_name, dataset_type=dataset_type)
     conn.close()
 
diff --git a/gn3/api/traits.py b/gn3/api/traits.py
index a9ff906..758dcca 100644
--- a/gn3/api/traits.py
+++ b/gn3/api/traits.py
@@ -7,6 +7,8 @@ from flask import request
 
 from gn3.computations.traits import fetch_trait
 from gn3.computations.traits import get_trait_info_data
+from gn3.experimental_db import database_connector
+
 trait = Blueprint("trait", __name__)
 
 
@@ -18,14 +20,23 @@ def home():
 
 @trait.route("/<string:trait_name>/<string:dataset_name>")
 def create_trait(trait_name, dataset_name):
-    """endpoints for creating trait first should\
-    call the endpoint for creating the trait only\
-    also acts as endpoints for fetching trait data"""
-
-    trait_dataset = mock.Mock()  # xtodo should replace this with calling epoints
-    trait_dataset.name = dataset_name
-
-    trait_results = fetch_trait(dataset=trait_dataset, trait_name=trait_name)
+    """/test:trait_name/dataset_name/type :retrieve sample\
+    data for trait"""
+
+    # xtodo replace the object at most this endpoint
+    # requires dataset_type,dataset_name ,dataset_id
+    trait_dataset = {
+        "name": dataset_name,
+        "id": 12,
+        "type": "ProbeSet"  # temp values
+    }
+    conn, _cursor = database_connector()
+
+    trait_results = fetch_trait(dataset=trait_dataset,
+                                trait_name=trait_name,
+                                database=conn)
+
+    conn.close()
 
     return jsonify(trait_results)