`flask.current_app.config["SQL_URI"]` ==> `utility.tools.SQL_URI`

Genenetwork2 configs are a tad weird, and instead of using the configs
in `flask.current_app`, we need to use those in `utility.tools`.

2 files changed, 10 insertions, 11 deletions

diff --git a/wqflask/wqflask/correlation/correlation_gn3_api.py b/wqflask/wqflask/correlation/correlation_gn3_api.py
index b09f3ae2..cffcda60 100644
--- a/wqflask/wqflask/correlation/correlation_gn3_api.py
+++ b/wqflask/wqflask/correlation/correlation_gn3_api.py
@@ -3,7 +3,7 @@ import json
 import time
 from functools import wraps
 
-from flask import current_app
+from utility.tools import SQL_URI
 
 from wqflask.correlation import correlation_functions
 from wqflask.correlation.pre_computes import fetch_precompute_results
@@ -148,7 +148,7 @@ def lit_for_trait_list(corr_results, this_dataset, this_trait):
     geneid_dict = {trait_name: geneid for (trait_name, geneid) in geneid_dict.items() if
                    trait_lists.get(trait_name)}
 
-    with database_connection(current_app.config["SQL_URI"]) as conn:
+    with database_connection(SQL_URI) as conn:
         correlation_results = compute_all_lit_correlation(
             conn=conn, trait_lists=list(geneid_dict.items()),
             species=species, gene_id=this_trait_geneid)
diff --git a/wqflask/wqflask/correlation/rust_correlation.py b/wqflask/wqflask/correlation/rust_correlation.py
index cfec1ae3..67bd5ff5 100644
--- a/wqflask/wqflask/correlation/rust_correlation.py
+++ b/wqflask/wqflask/correlation/rust_correlation.py
@@ -2,8 +2,7 @@
 import json
 from functools import reduce
 
-from flask import current_app
-
+from utility.tools import SQL_URI
 from utility.db_tools import mescape
 from utility.db_tools import create_in_clause
 from wqflask.correlation.correlation_functions\
@@ -29,7 +28,7 @@ def query_probes_metadata(dataset, trait_list):
     if not bool(trait_list) or dataset.type!="ProbeSet":
         return []
 
-    with database_connection(current_app.config["SQL_URI"]) as conn:
+    with database_connection(SQL_URI) as conn:
         with conn.cursor() as cursor:
 
             query = """
@@ -99,7 +98,7 @@ def chunk_dataset(dataset, steps, name):
                   ProbeSetXRef.ProbeSetId = ProbeSet.Id
     """.format(name)
 
-    with database_connection(current_app.config["SQL_URI"]) as conn:
+    with database_connection(SQL_URI) as conn:
         with conn.cursor() as curr:
             curr.execute(query)
             traits_name_dict = dict(curr.fetchall())
@@ -123,7 +122,7 @@ def compute_top_n_sample(start_vars, dataset, trait_list):
             sample_data=json.loads(samples_vals),
             dataset_samples=dataset.group.all_samples_ordered())
 
-        with database_connection(current_app.config["SQL_URI"]) as conn:
+        with database_connection(SQL_URI) as conn:
             with conn.cursor() as curr:
                 curr.execute(
                     """
@@ -141,7 +140,7 @@ def compute_top_n_sample(start_vars, dataset, trait_list):
     if len(trait_list) == 0:
         return {}
 
-    with database_connection(current_app.config["SQL_URI"]) as conn:
+    with database_connection(SQL_URI) as conn:
         with conn.cursor() as curr:
             # fetching strain data in bulk
             query = (
@@ -177,7 +176,7 @@ def compute_top_n_lit(corr_results, target_dataset, this_trait) -> dict:
     geneid_dict = {trait_name: geneid for (trait_name, geneid)
                    in geneid_dict.items() if
                    corr_results.get(trait_name)}
-    with database_connection(current_app.config["SQL_URI"]) as conn:
+    with database_connection(SQL_URI) as conn:
         return reduce(
             lambda acc, corr: {**acc, **corr},
             compute_all_lit_correlation(
@@ -252,7 +251,7 @@ def __compute_sample_corr__(
 
 
     if target_dataset.type == "ProbeSet" and start_vars.get("use_cache") == "true":
-        with database_connection(current_app.config["SQL_URI"]) as conn:
+        with database_connection(SQL_URI) as conn:
             file_path = fetch_text_file(target_dataset.name, conn)
             if file_path:
                 (sample_vals, target_data) = read_text_file(
@@ -339,7 +338,7 @@ def __compute_lit_corr__(
     (this_trait_geneid, geneid_dict, species) = do_lit_correlation(
         this_trait, target_dataset)
 
-    with database_connection(current_app.config["SQL_URI"]) as conn:
+    with database_connection(SQL_URI) as conn:
         return reduce(
             lambda acc, lit: {**acc, **lit},
             compute_all_lit_correlation(