Remove self-reference to db

Author: pbashyal-nmdp

pyard/db.py

@@ -20,15 +20,11 @@
 #    > http://www.fsf.org/licensing/licenses/lgpl.html
 #    > http://www.opensource.org/licenses/lgpl-license.php
 #
-import os
 import pathlib
 import sqlite3
 from typing import Tuple, Dict, Set, List
 
-from pyard import db
-
 from .data_repository import ARSMapping
-from .load import load_serology_broad_split_mapping
 from .misc import get_imgt_db_versions, get_default_db_directory
 
 
@@ -373,22 +369,18 @@ def set_user_version(connection: sqlite3.Connection, version: int):
 
 
 def load_ars_mappings(db_connection):
-    dup_g = db.load_dict(
-        db_connection, table_name="dup_g", columns=("allele", "g_group")
-    )
-    dup_lgx = db.load_dict(
+    dup_g = load_dict(db_connection, table_name="dup_g", columns=("allele", "g_group"))
+    dup_lgx = load_dict(
         db_connection, table_name="dup_lgx", columns=("allele", "lgx_group")
     )
-    g_group = db.load_dict(db_connection, table_name="g_group", columns=("allele", "g"))
-    lgx_group = db.load_dict(
+    g_group = load_dict(db_connection, table_name="g_group", columns=("allele", "g"))
+    lgx_group = load_dict(
         db_connection, table_name="lgx_group", columns=("allele", "lgx")
     )
-    exon_group = db.load_dict(
+    exon_group = load_dict(
         db_connection, table_name="exon_group", columns=("allele", "exon")
     )
-    p_not_g = db.load_dict(
-        db_connection, table_name="p_not_g", columns=("allele", "lgx")
-    )
+    p_not_g = load_dict(db_connection, table_name="p_not_g", columns=("allele", "lgx"))
     return (
         ARSMapping(
             dup_g=dup_g,
@@ -405,34 +397,34 @@ def load_ars_mappings(db_connection):
 def save_ars_mappings(
     db_connection, dup_g, dup_lgx, exon_group, g_group, lgx_group, p_group, p_not_g
 ):
-    db.save_dict(
+    save_dict(
         db_connection,
         table_name="p_not_g",
         dictionary=p_not_g,
         columns=("allele", "lgx"),
     )
-    db.save_dict(
+    save_dict(
         db_connection,
         table_name="dup_g",
         dictionary=dup_g,
         columns=("allele", "g_group"),
     )
-    db.save_dict(
+    save_dict(
         db_connection,
         table_name="dup_lgx",
         dictionary=dup_lgx,
         columns=("allele", "lgx_group"),
     )
-    db.save_dict(
+    save_dict(
         db_connection, table_name="g_group", dictionary=g_group, columns=("allele", "g")
     )
-    db.save_dict(
+    save_dict(
         db_connection,
         table_name="lgx_group",
         dictionary=lgx_group,
         columns=("allele", "lgx"),
     )
-    db.save_dict(
+    save_dict(
         db_connection,
         table_name="exon_group",
         dictionary=exon_group,
@@ -459,46 +451,42 @@ def save_code_mappings(
     valid_alleles,
     who_alleles,
 ):
-    db.save_dict(
-        db_connection, "exp_alleles", exp_alleles, ("exp_allele", "allele_list")
-    )
-    db.save_dict(db_connection, "xx_codes", flat_xx_codes, ("allele_1d", "allele_list"))
+    save_dict(db_connection, "exp_alleles", exp_alleles, ("exp_allele", "allele_list"))
+    save_dict(db_connection, "xx_codes", flat_xx_codes, ("allele_1d", "allele_list"))
     # Save this version of the valid alleles
-    db.save_set(db_connection, "alleles", valid_alleles, "allele")
+    save_set(db_connection, "alleles", valid_alleles, "allele")
     # Save this version of the WHO alleles
-    db.save_set(db_connection, "who_alleles", who_alleles, "allele")
-    db.save_dict(
+    save_set(db_connection, "who_alleles", who_alleles, "allele")
+    save_dict(
         db_connection, "who_group", flat_who_group, columns=("who", "allele_list")
     )
 
 
 def load_code_mappings(db_connection):
-    valid_alleles = db.load_set(db_connection, "alleles")
-    who_alleles = db.load_set(db_connection, "who_alleles")
-    who_group = db.load_dict(db_connection, "who_group", ("who", "allele_list"))
+    valid_alleles = load_set(db_connection, "alleles")
+    who_alleles = load_set(db_connection, "who_alleles")
+    who_group = load_dict(db_connection, "who_group", ("who", "allele_list"))
     who_group = {k: v.split("/") for k, v in who_group.items()}
-    xx_codes = db.load_dict(db_connection, "xx_codes", ("allele_1d", "allele_list"))
+    xx_codes = load_dict(db_connection, "xx_codes", ("allele_1d", "allele_list"))
     xx_codes = {k: v.split("/") for k, v in xx_codes.items()}
-    exp_alleles = db.load_dict(
-        db_connection, "exp_alleles", ("exp_allele", "allele_list")
-    )
+    exp_alleles = load_dict(db_connection, "exp_alleles", ("exp_allele", "allele_list"))
     exp_alleles = {k: v.split("/") for k, v in exp_alleles.items()}
     return valid_alleles, who_alleles, xx_codes, who_group, exp_alleles
 
 
 def load_shortnulls(db_connection):
-    shortnulls = db.load_dict(db_connection, "shortnulls", ("shortnull", "allele_list"))
+    shortnulls = load_dict(db_connection, "shortnulls", ("shortnull", "allele_list"))
     shortnulls = {k: v.split("/") for k, v in shortnulls.items()}
     return shortnulls
 
 
 def save_shortnulls(db_connection, shortnulls):
-    db.save_dict(db_connection, "shortnulls", shortnulls, ("shortnull", "allele_list"))
+    save_dict(db_connection, "shortnulls", shortnulls, ("shortnull", "allele_list"))
 
 
 def save_mac_codes(db_connection, mac, mac_table_name):
     # Save the mac dict to db
-    db.save_dict(
+    save_dict(
         db_connection,
         table_name=mac_table_name,
         dictionary=mac,
@@ -508,7 +496,7 @@ def save_mac_codes(db_connection, mac, mac_table_name):
 
 def save_serology_mappings(db_connection, sero_mapping):
     # Save the serology mapping to db
-    db.save_dict(
+    save_dict(
         db_connection,
         table_name="serology_mapping",
         dictionary=sero_mapping,
@@ -533,7 +521,7 @@ def load_v2_v3_mappings(db_connection):
         "A*01179": "A*01:179N",
         "DRB5*02ZB": "DRB5*02:UTV",
     }
-    db.save_dict(
+    save_dict(
         db_connection,
         table_name="v2_mapping",
         dictionary=v2_to_v3_example,
@@ -542,7 +530,7 @@ def load_v2_v3_mappings(db_connection):
 
 
 def load_serology_broad_split_mappings(db_connection):
-    sero_mapping = db.load_dict(
+    sero_mapping = load_dict(
         db_connection, "serology_broad_split_mapping", ("serology", "splits")
     )
     sero_splits = {k: v.split("/") for k, v in sero_mapping.items()}
@@ -552,7 +540,7 @@ def load_serology_broad_split_mappings(db_connection):
 def save_serology_broad_split_mappings(db_connection, sero_mapping):
     # Save the `splits` as a "/" delimited string to db
     sero_splits = {sero: "/".join(splits) for sero, splits in sero_mapping.items()}
-    db.save_dict(
+    save_dict(
         db_connection,
         table_name="serology_broad_split_mapping",
         dictionary=sero_splits,