Fixed Pylint issues

PecanProject · Apr 5, 2021 · 43bcff6 · 43bcff6
1 parent 88f122b
commit 43bcff6
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Showing 6 changed files with 352 additions and 303 deletions.
diff --git a/app/db.py b/app/db.py
@@ -3,84 +3,93 @@
 from sqlalchemy.sql import text
 from setup import setup_environment
 
-def insert_table(table,data):
-	#Make PostgreSQL Connection
-	engine = setup_environment.get_database()
-	data.to_sql(table, engine, if_exists = 'append', index=False)
 
-def insert_sites_table(table,data):
-	#Make PostgreSQL Connection
-	csv.field_size_limit(sys.maxsize)
-	engine = setup_environment.get_database()
-	connection = None
-	connection = engine.raw_connection()
-	cur = connection.cursor()
-	with open(data, 'r') as f:
-		reader = csv.reader(f)
-		next(reader) # Skip the header row.
-		for row in reader:
-			cur.execute("INSERT INTO sites (sitename,city,state,country,notes,greenhouse,geometry,time_zone,soil,soilnotes) VALUES (%s, %s, %s, %s,%s, %s, ST_MakeValid(ST_Geomfromtext(%s,4326)), %s,%s, %s)",row)
-			print(row)			
-		connection.commit()
-		connection.close()
-
+def insert_table(table, data):
+    # Make PostgreSQL Connection
+    engine = setup_environment.get_database()
+    data.to_sql(table, engine, if_exists="append", index=False)
+
+
+def insert_sites_table(table, data):
+    # Make PostgreSQL Connection
+    csv.field_size_limit(sys.maxsize)
+    engine = setup_environment.get_database()
+    connection = None
+    connection = engine.raw_connection()
+    cur = connection.cursor()
+    with open(data, "r") as f:
+        reader = csv.reader(f)
+        next(reader)  # Skip the header row.
+        for row in reader:
+            cur.execute(
+                "INSERT INTO sites (sitename,city,state,country,notes,greenhouse,geometry,time_zone,soil,soilnotes) VALUES (%s, %s, %s, %s,%s, %s, ST_MakeValid(ST_Geomfromtext(%s,4326)), %s,%s, %s)",
+                row,
+            )
+            print(row)
+        connection.commit()
+        connection.close()
+
 
 def fetch_specie_id(species):
     # Make PostgreSQL Connection
-	engine = setup_environment.get_database()
-	connection = None
-	connection = engine.connect()
-	query = 'select id from species where scientificname = :name'
-	result_set = connection.execute(text(query), name = species).fetchone()
-	connection.close()
-	for r in result_set:
-		return r
+    engine = setup_environment.get_database()
+    connection = None
+    connection = engine.connect()
+    query = "select id from species where scientificname = :name"
+    result_set = connection.execute(text(query), name=species).fetchone()
+    connection.close()
+    for r in result_set:
+        return r
 
 
 def fetch_sites_id(sitename):
     # Make PostgreSQL Connection
-	engine = setup_environment.get_database()
-	connection = None
-	connection = engine.connect()
-	query = 'select id from sites where sitename = :name'
-	result_set = connection.execute(text(query), name = sitename).fetchone()
-	connection.close()
-	for r in result_set:
-		return r
+    engine = setup_environment.get_database()
+    connection = None
+    connection = engine.connect()
+    query = "select id from sites where sitename = :name"
+    result_set = connection.execute(text(query), name=sitename).fetchone()
+    connection.close()
+    for r in result_set:
+        return r
 
 
-def fetch_cultivars_id(name,specie_id):
+def fetch_cultivars_id(name, specie_id):
     # Make PostgreSQL Connection
-	engine = setup_environment.get_database()
-	connection = None
-	connection = engine.connect()
-	query = 'select id from cultivars where name = :name and specie_id = :specie_id'
-	result_set = connection.execute(text(query), name = name,specie_id=specie_id).fetchone()
-	connection.close()
-	for r in result_set:
-		return r
+    engine = setup_environment.get_database()
+    connection = None
+    connection = engine.connect()
+    query = "select id from cultivars where name = :name and specie_id = :specie_id"
+    result_set = connection.execute(
+        text(query), name=name, specie_id=specie_id
+    ).fetchone()
+    connection.close()
+    for r in result_set:
+        return r
 
 
-def fetch_citations_id(author,year,title):
+def fetch_citations_id(author, year, title):
     # Make PostgreSQL Connection
-	engine = setup_environment.get_database()
-	connection = None
-	connection = engine.connect()
-	query = 'select id from citations where author = :author and year = :year and title = :title'
-	result_set = connection.execute(text(query),author=author,year=year, title = title).fetchone()
-	connection.close()
-	for r in result_set:
-		return r
+    engine = setup_environment.get_database()
+    connection = None
+    connection = engine.connect()
+    query = "select id from citations where author = :author and year = :year and title = :title"
+    result_set = connection.execute(
+        text(query), author=author, year=year, title=title
+    ).fetchone()
+    connection.close()
+    for r in result_set:
+        return r
 
 
-#Fetching ID from Users,experiments,cultivars and treatments tables
-def fetch_id(value,table):
+# Fetching ID from Users,experiments,cultivars and treatments tables
+def fetch_id(value, table):
     # Make PostgreSQL Connection
-	connection = None
-	engine = setup_environment.get_database()
-	connection = engine.connect()
-	query = 'select id from '+table+' where name = :name'
-	result_set = connection.execute(text(query), name = value).fetchone()
-	connection.close()
-	for r in result_set:
-		return r
+    connection = None
+    engine = setup_environment.get_database()
+    connection = engine.connect()
+    query = "select id from " + table + " where name = :name"
+    result_set = connection.execute(text(query), name=value).fetchone()
+    connection.close()
+    for r in result_set:
+        return r
diff --git a/app/server.py b/app/server.py
@@ -2,7 +2,7 @@
 Main module of the Server file
 """
 
-#Importing moudles
+# Importing moudles
 import connexion
 import json
 from time import sleep
@@ -14,7 +14,7 @@
 sleep(5)
 
 # Read the swagger.yml file to configure the endpoints
-app.add_api("yaba.yaml",validate_responses=False)
+app.add_api("yaba.yaml", validate_responses=False)
 
 
 # create a URL route in our application for "/"
@@ -26,10 +26,12 @@ def home():
     (on docker:     localhost:5001/)
     :return:        the below json message
     """
-    return Response(json.dumps("Welcome to YABA API Index Route"), mimetype='application/json')
+    return Response(
+        json.dumps("Welcome to YABA API Index Route"), mimetype="application/json"
+    )
 
 
 if __name__ == "__main__":
-    app.run(host="0.0.0.0",port=5000,debug=False)
-    #http_server = WSGIServer(('0.0.0.0', 5000), app)
-    #http_server.serve_forever()
+    app.run(host="0.0.0.0", port=5000, debug=False)
+    # http_server = WSGIServer(('0.0.0.0', 5000), app)
+    # http_server.serve_forever()
diff --git a/app/setup/setup_environment.py b/app/setup/setup_environment.py
@@ -14,12 +14,12 @@ def get_database():
         log.info("Successfully Connected to BETY Database!")
     except IOError:
         log.exception("Failed to get database connection!")
-        return None, 'fail'
+        return None, "fail"
 
     return engine
 
 
-def get_connection_from_config(config_file_name='credentials.yaml'):
+def get_connection_from_config(config_file_name="credentials.yaml"):
     """
     Sets up database connection from config file.
     Input:
@@ -28,19 +28,25 @@ def get_connection_from_config(config_file_name='credentials.yaml'):
                       credentials for the PostgreSQL database
     """
 
-    with open(config_file_name, 'r') as f:
+    with open(config_file_name, "r") as f:
         creds = yaml.safe_load(f)
 
-    if not ('PGHOST' in creds.keys() and
-            'PGUSER' in creds.keys() and
-            'PGPASSWORD' in creds.keys() and
-            'PGDATABASE' in creds.keys() and
-            'PGPORT' in creds.keys()):
-        raise Exception('Bad config file: ' + config_file_name)
+    if not (
+        "PGHOST" in creds.keys()
+        and "PGUSER" in creds.keys()
+        and "PGPASSWORD" in creds.keys()
+        and "PGDATABASE" in creds.keys()
+        and "PGPORT" in creds.keys()
+    ):
+        raise Exception("Bad config file: " + config_file_name)
 
-    return get_engine(creds['PGDATABASE'], creds['PGUSER'],
-                      creds['PGHOST'], creds['PGPORT'],
-                      creds['PGPASSWORD'])
+    return get_engine(
+        creds["PGDATABASE"],
+        creds["PGUSER"],
+        creds["PGHOST"],
+        creds["PGPORT"],
+        creds["PGPASSWORD"],
+    )
 
 
 def get_engine(db, user, host, port, passwd):
@@ -54,7 +60,8 @@ def get_engine(db, user, host, port, passwd):
     passwd: Password for the database
     """
 
-    url = 'postgresql+psycopg2://{user}:{passwd}@{host}:{port}/{db}'.format(
-        user=user, passwd=passwd, host=host, port=port, db=db)
-    engine = create_engine(url,poolclass=QueuePool)
+    url = "postgresql+psycopg2://{user}:{passwd}@{host}:{port}/{db}".format(
+        user=user, passwd=passwd, host=host, port=port, db=db
+    )
+    engine = create_engine(url, poolclass=QueuePool)
     return engine