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authorFrederick Muriuki Muriithi2023-04-06 13:58:36 +0300
committerFrederick Muriuki Muriithi2023-04-06 13:58:36 +0300
commitcee15ae774691f706cf2de31e8dadba7d2d4930a (patch)
tree765a749d7637f809e28d98e2bdd79019c2ba8f23 /wqflask
parent753493121177d92221e199b9f1ca9f35b50f3556 (diff)
downloadgenenetwork2-cee15ae774691f706cf2de31e8dadba7d2d4930a.tar.gz
`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`.
Diffstat (limited to 'wqflask')
-rw-r--r--wqflask/wqflask/correlation/correlation_gn3_api.py4
-rw-r--r--wqflask/wqflask/correlation/rust_correlation.py17
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(