refactoring

.gitignore

@@ -0,0 +1 @@
+__pycache__/

coronary_ref_homo.py

@@ -7,15 +7,16 @@ class CoronaryRefHomo:
 
     rsid_map:dict[str, dict] = {}
 
-    def init(self, reporter, sql_insert:str) -> None:
-        self.parent = reporter
-        self.sql_insert = sql_insert
 
+    def setup(self, parent, result_cursor:sqlite3.Cursor, data_cursor:sqlite3.Cursor, sql_insert:str) -> None:
+        self.parent = parent
+        self.sql_insert = sql_insert
+        self.result_cursor: sqlite3.Cursor = result_cursor
+        self.data_cursor: sqlite3.Cursor = data_cursor
 
-    def setup(self) -> None:
         sql:str = "SELECT rsID, Risk_allele FROM coronary_disease WHERE Ref_allele = Risk_allele"
-        self.parent.coronary_cursor.execute(sql)
-        rows:list = self.parent.coronary_cursor.fetchall()
+        self.data_cursor.execute(sql)
+        rows:list = self.data_cursor.fetchall()
         for rsid, risk_allele in rows:
             self.rsid_map[rsid] = {'exist':True, 'risk':risk_allele}
 
@@ -42,9 +43,9 @@ def end(self) -> None:
                 query:str = "SELECT Risk_allele, Gene, Genotype, Conclusion, Weight, PMID, Population, GWAS_study_design, P_value " \
                         f"FROM coronary_disease WHERE rsID = '{rsid}' AND Genotype = '{risk}';"
 
-                self.parent.coronary_cursor.execute(query)
-                row:list = self.parent.coronary_cursor.fetchone()
+                self.data_cursor.execute(query)
+                row:list = self.data_cursor.fetchone()
                 if row:
                     task:tuple = (rsid, row[1], row[0], row[0]+"/"+row[0], row[3], row[4], row[5], row[6], row[7], row[8],
                             self.parent.get_color(row[4], 0.6))
-                    self.parent.longevity_cursor.execute(self.sql_insert, task)
+                    self.result_cursor.execute(self.sql_insert, task)

just_coronary.py

@@ -27,16 +27,15 @@ def check(self):
         return True
 
     def setup (self):
-        self.ref_homo.init(self, self.sql_insert)
         modules_path:str = str(Path(__file__).parent)
         sql_file:str = modules_path + "/data/coronary.sqlite"
         if Path(sql_file).exists():
-            self.coronary_conn:sqlite3.Connection = sqlite3.connect(sql_file)
-            self.coronary_cursor:sqlite3.Cursor = self.coronary_conn.cursor()
+            self.data_conn:sqlite3.Connection = sqlite3.connect(sql_file)
+            self.data_cursor:sqlite3.Cursor = self.data_conn.cursor()
 
         self.result_path:Path = Path(self.output_dir, self.run_name + "_longevity.sqlite")
-        self.longevity_conn:sqlite3.Connection = sqlite3.connect(self.result_path)
-        self.longevity_cursor:sqlite3.Cursor = self.longevity_conn.cursor()
+        self.result_conn:sqlite3.Connection = sqlite3.connect(self.result_path)
+        self.result_cursor:sqlite3.Cursor = self.result_conn.cursor()
         sql_create:str = """ CREATE TABLE IF NOT EXISTS coronary (
             id integer NOT NULL PRIMARY KEY,
             rsid text,
@@ -51,22 +50,22 @@ def setup (self):
             pvalue text,
             weightcolor text            
             )"""
-        self.longevity_cursor.execute(sql_create)
-        self.longevity_conn.commit()
-        self.longevity_cursor.execute("DELETE FROM coronary;")
-        self.ref_homo.setup()
+        self.result_cursor.execute(sql_create)
+        self.result_conn.commit()
+        self.result_cursor.execute("DELETE FROM coronary;")
+        self.ref_homo.setup(self, self.result_cursor, self.data_cursor, self.sql_insert)
 
 
     def cleanup (self):
-        if self.longevity_cursor is not None:
-            self.longevity_cursor.close()
-        if self.longevity_conn is not None:
-            self.longevity_conn.commit()
-            self.longevity_conn.close()
-        if self.coronary_cursor is not None:
-            self.coronary_cursor.close()
-        if self.coronary_conn is not None:
-            self.coronary_conn.close()
+        if self.result_cursor is not None:
+            self.result_cursor.close()
+        if self.result_conn is not None:
+            self.result_conn.commit()
+            self.result_conn.close()
+        if self.data_cursor is not None:
+            self.data_cursor.close()
+        if self.data_conn is not None:
+            self.data_conn.close()
         return
 
 
@@ -109,8 +108,8 @@ def annotate (self, input_data):
         query:str = "SELECT Risk_allele, Gene, Genotype, Conclusion, Weight, PMID, Population, GWAS_study_design, P_value " \
                 f"FROM coronary_disease WHERE rsID = '{rsid}';"
 
-        self.coronary_cursor.execute(query)
-        rows:list[Any] = self.coronary_cursor.fetchall()
+        self.data_cursor.execute(query)
+        rows:list[Any] = self.data_cursor.fetchall()
 
         if len(rows) == 0:
             return
@@ -128,7 +127,7 @@ def annotate (self, input_data):
             if gen_set == row_gen:
                 task:tuple = (rsid, row[1], allele, genome, row[3], float(row[4]), row[5], row[6], row[7],
                         row[8], self.get_color(row[4], 0.6))
-                self.longevity_cursor.execute(self.sql_insert, task)
+                self.result_cursor.execute(self.sql_insert, task)
 
         return {"col1":""}