From 14c3ffbbc27fc94b56c446ae215ff561593b62c7 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Fri, 14 Oct 2022 23:21:52 +0000
Subject: Add redis_conn as argument to get_samplelist calls

---
 wqflask/wqflask/marker_regression/gemma_mapping.py | 3 ++-
 wqflask/wqflask/marker_regression/rqtl_mapping.py  | 3 ++-
 2 files changed, 4 insertions(+), 2 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py
index 08a38527..4420796c 100644
--- a/wqflask/wqflask/marker_regression/gemma_mapping.py
+++ b/wqflask/wqflask/marker_regression/gemma_mapping.py
@@ -7,6 +7,7 @@ import json
 from base import webqtlConfig
 from base.trait import create_trait
 from base.data_set import create_dataset
+from utility.redis_tools import get_redis_conn
 from utility.tools import flat_files, assert_file
 from utility.tools import GEMMA_WRAPPER_COMMAND
 from utility.tools import TEMPDIR
@@ -163,7 +164,7 @@ def gen_covariates_file(this_dataset, covariates, samples):
         trait_ob = create_trait(dataset=dataset_ob,
                                 name=trait_name,
                                 cellid=None)
-        this_dataset.group.get_samplelist()
+        this_dataset.group.get_samplelist(redis_conn=get_redis_conn())
         trait_samples = this_dataset.group.samplelist
         trait_sample_data = trait_ob.data
         for index, sample in enumerate(trait_samples):
diff --git a/wqflask/wqflask/marker_regression/rqtl_mapping.py b/wqflask/wqflask/marker_regression/rqtl_mapping.py
index 1fca5468..9a42bc35 100644
--- a/wqflask/wqflask/marker_regression/rqtl_mapping.py
+++ b/wqflask/wqflask/marker_regression/rqtl_mapping.py
@@ -13,6 +13,7 @@ import numpy as np
 
 from base.webqtlConfig import TMPDIR
 from base.trait import create_trait
+from utility.redis_tools import get_redis_conn
 from utility.tools import locate, GN3_LOCAL_URL
 from wqflask.database import database_connection
 
@@ -148,7 +149,7 @@ def cofactors_to_dict(cofactors: str, dataset_ob, samples) -> Dict:
     """
     cofactor_dict = {}
     if cofactors:
-        dataset_ob.group.get_samplelist()
+        dataset_ob.group.get_samplelist(redis_conn=get_redis_conn())
         sample_list = dataset_ob.group.samplelist
         for cofactor in cofactors.split(","):
             cofactor_name, cofactor_dataset = cofactor.split(":")
-- 
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