Break dependence on `wqflask.utility.tools` to fix circular imports

Remove the `wqflask.utility.tools` and retrieve the `SQL_URI` setting
directly from the environment or the settings file. This breaks the
circular imports and makes the `wqflask.database` module standalone.

Move the `parse_db_url` function to the `wqflask.database` module,
where it is more sensible to be.

2 files changed, 27 insertions, 19 deletions

diff --git a/wqflask/wqflask/__init__.py b/wqflask/wqflask/__init__.py
index ab8b9e66..118a7ff3 100644
--- a/wqflask/wqflask/__init__.py
+++ b/wqflask/wqflask/__init__.py
@@ -11,6 +11,8 @@ from utility import formatting
 
 from gn3.authentication import DataRole, AdminRole
 
+from wqflask.database import parse_db_url
+
 from wqflask.group_manager import group_management
 from wqflask.resource_manager import resource_management
 from wqflask.metadata_edits import metadata_edit
@@ -29,17 +31,6 @@ from wqflask.jupyter_notebooks import jupyter_notebooks
 app = Flask(__name__)
 
 
-# Helper function for getting the SQL objects
-def parse_db_url(sql_uri: str) -> Tuple:
-    """Parse SQL_URI env variable from an sql URI
-    e.g. 'mysql://user:pass@host_name/db_name'
-
-    """
-    parsed_db = urlparse(sql_uri)
-    return (parsed_db.hostname, parsed_db.username,
-            parsed_db.password, parsed_db.path[1:])
-
-
 # See http://flask.pocoo.org/docs/config/#configuring-from-files
 # Note no longer use the badly named WQFLASK_OVERRIDES (nyi)
 app.config.from_envvar('GN2_SETTINGS')
diff --git a/wqflask/wqflask/database.py b/wqflask/wqflask/database.py
index e485bcf1..cbf01346 100644
--- a/wqflask/wqflask/database.py
+++ b/wqflask/wqflask/database.py
@@ -1,15 +1,27 @@
 # Module to initialize sqlalchemy with flask
+import os
+import sys
+import importlib
+
 import MySQLdb
 
 from sqlalchemy import create_engine
 from sqlalchemy.orm import scoped_session, sessionmaker
 from sqlalchemy.ext.declarative import declarative_base
-from utility.tools import SQL_URI
 
-from flask import current_app
+def read_from_pyfile(pyfile, setting):
+    orig_sys_path = sys.path[:]
+    sys.path.insert(0, os.path.dirname(pyfile))
+    module = importlib.import_module(os.path.basename(pyfile).strip(".py"))
+    sys.path = orig_sys_path[:]
+    return module.__dict__.get(setting)
 
+def sql_uri():
+    """Read the SQL_URI from the environment or settings file."""
+    return os.environ.get(
+        "SQL_URI", read_from_pyfile(os.environ.get("GN2_SETTINGS"), "SQL_URI"))
 
-engine = create_engine(SQL_URI, encoding="latin1")
+engine = create_engine(sql_uri(), encoding="latin1")
 
 db_session = scoped_session(sessionmaker(autocommit=False,
                                          autoflush=False,
@@ -20,11 +32,16 @@ Base.query = db_session.query_property()
 # Initialise the db
 Base.metadata.create_all(bind=engine)
 
+def parse_db_url(sql_uri: str) -> Tuple:
+    """
+    Parse SQL_URI env variable from an sql URI
+    e.g. 'mysql://user:pass@host_name/db_name'
+    """
+    parsed_db = urlparse(sql_uri)
+    return (parsed_db.hostname, parsed_db.username,
+            parsed_db.password, parsed_db.path[1:])
 
 def database_connection():
     """Returns a database connection"""
-    return MySQLdb.Connect(
-        db=current_app.config.get("DB_NAME"),
-        user=current_app.config.get("DB_USER"),
-        passwd=current_app.config.get("DB_PASS"),
-        host=current_app.config.get("DB_HOST"))
+    host, user, passwd, db_name = parse_db_url(sql_uri())
+    return MySQLdb.Connect(db=db_name, user=user, passwd=passwd, host=host)