Merge branch 'master' of git://github.com/biocore/qiita into alpha-0.1-release

Fixes #1134

Author: ElDeveloper

qiita_core/util.py

@@ -80,7 +80,6 @@ def setUp(self):
             @reset_test_database
             def tearDown(self):
                 super(DecoratedClass, self).tearDown()
-                del self.conn_handler
 
         return DecoratedClass
     return class_modifier

qiita_db/environment_manager.py

@@ -270,6 +270,7 @@ def drop_environment(ask_for_confirmation):
             do_drop = True
 
     if do_drop:
+        SQLConnectionHandler.close()
         admin_conn = SQLConnectionHandler(admin='admin_without_database')
         admin_conn.set_autocommit('on')
         admin_conn.execute('DROP DATABASE %s' % qiita_config.database)

qiita_db/sql_connection.py

@@ -122,6 +122,38 @@ class SQLConnectionHandler(object):
         2275: str,  # cstring
     }
 
+    _user_args = {
+        'user': qiita_config.user,
+        'password': qiita_config.password,
+        'database': qiita_config.database,
+        'host': qiita_config.host,
+        'port': qiita_config.port}
+
+    _admin_args = {
+        'user': qiita_config.admin_user,
+        'password': qiita_config.admin_password,
+        'database': qiita_config.database,
+        'host': qiita_config.host,
+        'port': qiita_config.port}
+
+    _admin_nodb_args = {
+        'user': qiita_config.admin_user,
+        'password': qiita_config.admin_password,
+        'host': qiita_config.host,
+        'port': qiita_config.port}
+
+    _user_conn = None
+    _admin_conn = None
+    _admin_nodb_conn = None
+
+    _conn_map = {'no_admin': '_user_conn',
+                 'admin_with_database': '_admin_conn',
+                 'admin_without_database': '_admin_nodb_conn'}
+
+    _args_map = {'no_admin': '_user_args',
+                 'admin_with_database': '_admin_args',
+                 'admin_without_database': '_admin_nodb_args'}
+
     """Encapsulates the DB connection with the Postgres DB
 
     Parameters
@@ -142,39 +174,25 @@ def __init__(self, admin='no_admin'):
                                "'admin_without_database'}")
 
         self.admin = admin
+
+        self._conn_attr = self._conn_map[self.admin]
+        self._args_attr = self._args_map[self.admin]
+        self._conn_args = getattr(SQLConnectionHandler, self._args_attr)
+        self._connection = getattr(SQLConnectionHandler, self._conn_attr)
         self._open_connection()
+
         # queues for transaction blocks. Format is {str: list} where the str
         # is the queue name and the list is the queue of SQL commands
         self.queues = {}
 
-    def __del__(self):
-        # make sure if connection close fails it doesn't raise error
-        # should only error if connection already closed
-        try:
-            self._connection.close()
-        except:
-            pass
-
     def _open_connection(self):
-        # connection string arguments for a normal user
-        args = {
-            'user': qiita_config.user,
-            'password': qiita_config.password,
-            'database': qiita_config.database,
-            'host': qiita_config.host,
-            'port': qiita_config.port}
-
-        # if this is an admin user, use the admin credentials
-        if self.admin != 'no_admin':
-            args['user'] = qiita_config.admin_user
-            args['password'] = qiita_config.admin_password
-
-        # Do not connect to a particular database unless requested
-        if self.admin == 'admin_without_database':
-            del args['database']
+        # if the connection has been created and is not closed
+        if self._connection is not None and self._connection.closed == 0:
+            return
 
         try:
-            self._connection = connect(**args)
+            setattr(SQLConnectionHandler, self._conn_attr,
+                    connect(**self._conn_args))
         except OperationalError as e:
             # catch threee known common exceptions and raise runtime errors
             try:
@@ -202,6 +220,19 @@ def _open_connection(self):
                      '\n\n\t%s\n%s For more information, review `INSTALL.md`'
                      ' in the Qiita installation base directory.')
             raise RuntimeError(ebase % (e.message, etext))
+        else:
+            self._connection = getattr(SQLConnectionHandler, self._conn_attr)
+
+    @staticmethod
+    def close():
+        if SQLConnectionHandler._user_conn is not None:
+            SQLConnectionHandler._user_conn.close()
+
+        if SQLConnectionHandler._admin_conn is not None:
+            SQLConnectionHandler._admin_conn.close()
+
+        if SQLConnectionHandler._admin_nodb_conn is not None:
+            SQLConnectionHandler._admin_nodb_conn.close()
 
     @contextmanager
     def get_postgres_cursor(self):
@@ -213,9 +244,7 @@ def get_postgres_cursor(self):
 
         Raises a QiitaDBConnectionError if the cursor cannot be created
         """
-        if self._connection.closed:
-            # Currently defaults to non-admin connection
-            self._open_connection()
+        self._open_connection()
 
         try:
             with self._connection.cursor(cursor_factory=DictCursor) as cur:

qiita_db/test/test_sql_connection.py

@@ -11,6 +11,11 @@ def test_create_queue(self):
         self.conn_handler.create_queue("toy_queue")
         self.assertEqual(self.conn_handler.list_queues(), ["toy_queue"])
 
+    def test_close(self):
+        self.assertEqual(self.conn_handler._user_conn.closed, 0)
+        self.conn_handler.close()
+        self.assertNotEqual(self.conn_handler._user_conn.closed, 0)
+
     def test_run_queue(self):
         self.conn_handler.create_queue("toy_queue")
         self.conn_handler.add_to_queue(

qiita_pet/handlers/auth_handlers.py

@@ -52,8 +52,7 @@ def post(self):
                 msg = ("Unable to send verification email. Please contact the "
                        "qiita developers at <a href='mailto:qiita-help"
                        "@gmail.com'>qiita-help@gmail.com</a>")
-                error_msg = u"?error=" + url_escape(msg)
-                self.redirect(u"/?level=danger&message=" + error_msg)
+                self.redirect(u"/?level=danger&message=" + url_escape(msg))
                 return
             self.redirect(u"/")
         else:

qiita_pet/handlers/base_handlers.py

@@ -59,7 +59,9 @@ def head(self):
 class MainHandler(BaseHandler):
     '''Index page'''
     def get(self):
-        self.render("index.html", message='', level='')
+        msg = self.get_argument('message', '')
+        lvl = self.get_argument('level', '')
+        self.render("index.html", message=msg, level=lvl)
 
 
 class MockupHandler(BaseHandler):