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authorFrederick Muriuki Muriithi2021-11-22 09:06:52 +0300
committerFrederick Muriuki Muriithi2021-11-22 12:06:47 +0300
commit854416ba850b7793aa9aa95528b89bc69df26888 (patch)
treef3b61260e0c8ca030157adb3823d3227f470d033 /gn3
parent92d5766f5514181cd6aa82fc0d0f225666e892cb (diff)
downloadgenenetwork3-854416ba850b7793aa9aa95528b89bc69df26888.tar.gz
Make the DB connection argument the first
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * To make the code more composable down the line, make the database connection argument the first argument for functions that access the database, since they will always require the connection.
Diffstat (limited to 'gn3')
-rw-r--r--gn3/db/correlations.py10
1 files changed, 5 insertions, 5 deletions
diff --git a/gn3/db/correlations.py b/gn3/db/correlations.py
index 06b3310..f327dc3 100644
--- a/gn3/db/correlations.py
+++ b/gn3/db/correlations.py
@@ -34,7 +34,7 @@ def get_filename(target_db_name: str, conn: Any) -> str:
return ""
def build_temporary_literature_table(
- species: str, gene_id: int, return_number: int, conn: Any) -> str:
+ conn: Any, species: str, gene_id: int, return_number: int) -> str:
"""
Build and populate a temporary table to hold the literature correlation data
to be used in computations.
@@ -128,7 +128,7 @@ def fetch_literature_correlations(
GeneNetwork1.
"""
temp_table = build_temporary_literature_table(
- species, gene_id, return_number, conn)
+ conn, species, gene_id, return_number)
query_fns = {
"Geno": fetch_geno_literature_correlations,
# "Temp": fetch_temp_literature_correlations,
@@ -268,8 +268,8 @@ def fetch_gene_symbol_tissue_value_dict_for_trait(
return {}
def build_temporary_tissue_correlations_table(
- trait_symbol: str, probeset_freeze_id: int, method: str,
- return_number: int, conn: Any) -> str:
+ conn: Any, trait_symbol: str, probeset_freeze_id: int, method: str,
+ return_number: int) -> str:
"""
Build a temporary table to hold the tissue correlations data.
@@ -320,7 +320,7 @@ def fetch_tissue_correlations(# pylint: disable=R0913
GeneNetwork1.
"""
temp_table = build_temporary_tissue_correlations_table(
- trait_symbol, probeset_freeze_id, method, return_number, conn)
+ conn, trait_symbol, probeset_freeze_id, method, return_number)
with conn.cursor() as cursor:
cursor.execute(
(