Added secure_server.py

Updated notes.txt

2 files changed, 78 insertions, 12 deletions

diff --git a/wqflask/secure_server.py b/wqflask/secure_server.py
new file mode 100644
index 00000000..49e0b433
--- /dev/null
+++ b/wqflask/secure_server.py
@@ -0,0 +1,76 @@
+from __future__ import print_function, division, absolute_import
+
+from wqflask import app
+
+from flask import Flask, render_template
+from flask.ext.sqlalchemy import SQLAlchemy
+from flask.ext.security import Security, SQLAlchemyUserDatastore, \
+     UserMixin, RoleMixin
+
+# Create app
+#app = Flask(__name__)
+app.config['SECRET_KEY'] = 'LjfrbDOlvdFMT5cCi9qrJqStxK4NcmxW'
+app.config['SQLALCHEMY_DATABASE_URI'] = 'mysql://webqtl:f2ZypIflRM@gn.cazhbciu2y1i.us-east-1.rds.amazonaws.com/db_webqtl'
+#app.config['SECURITY_CONFIRMABLE'] = True
+app.config['SECURITY_TRACKABLE'] = True
+
+# Create database connection object
+db = SQLAlchemy(app)
+
+# Define models
+roles_users = db.Table('roles_users',
+        db.Column('user_id', db.Integer(), db.ForeignKey('user.id')),
+        db.Column('role_id', db.Integer(), db.ForeignKey('role.id')))
+
+class Role(db.Model, RoleMixin):
+    id = db.Column(db.Integer(), primary_key=True)
+    name = db.Column(db.String(80), unique=True)
+    description = db.Column(db.String(255))
+
+class User(db.Model, UserMixin):
+    id = db.Column(db.Integer(), primary_key=True)
+    email = db.Column(db.String(255), unique=True)
+    password = db.Column(db.String(255))
+    active = db.Column(db.Boolean())
+    confirmed_at = db.Column(db.DateTime())
+    
+    last_login_at = db.Column(db.DateTime())
+    current_login_at = db.Column(db.DateTime())
+    last_login_ip_= db.Column(db.String(39))
+    current_login_ip = db.Column(db.String(39))
+    login_count = db.Column(db.Integer())
+    
+    roles = db.relationship('Role', secondary=roles_users,
+                            backref=db.backref('users', lazy='dynamic'))
+
+# Setup Flask-Security
+user_datastore = SQLAlchemyUserDatastore(db, User, Role)
+security = Security(app, user_datastore)
+
+# Create a user to test with
+#@app.before_first_request
+def create_user():
+    db.create_all()
+    user_datastore.create_user(email='matt@example.com', password='notebook')
+    db.session.commit()
+
+## Views
+#@app.route('/')
+#def home():
+#    return render_template('index.html')
+
+import logging
+#from themodule import TheHandlerYouWant
+file_handler = logging.FileHandler("/tmp/flask_gn_log")
+file_handler.setLevel(logging.DEBUG)
+app.logger.addHandler(file_handler)
+
+import logging_tree
+logging_tree.printout()
+
+if __name__ == '__main__':
+    #create_user()
+    app.run(host='0.0.0.0',
+        use_debugger=False,
+        threaded=True,
+        use_reloader=True)
diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py
index b390bdc4..2e74d991 100644
--- a/wqflask/wqflask/do_search.py
+++ b/wqflask/wqflask/do_search.py
@@ -70,12 +70,7 @@ class QuickMrnaAssaySearch(DoSearch):
                 ProbeSet.Mb as ProbeSet_Mb,
                 ProbeSet.Symbol as ProbeSet_Symbol,
                 ProbeSet.name_num as ProbeSet_name_num
-                FROM ProbeSet,
-                ProbeSetXRef,
-                ProbeSetFreeze,
-                ProbeFreeze,
-                InbredSet,
-                Species """
+                FROM ProbeSet """
                 
     header_fields = ['',
                      'Record ID',
@@ -89,12 +84,7 @@ class QuickMrnaAssaySearch(DoSearch):
         query = self.base_query + """WHERE (MATCH (ProbeSet.Name,
                     ProbeSet.description,
                     ProbeSet.symbol)
-                    AGAINST ('%s' IN BOOLEAN MODE)) and
-                    ProbeSet.Id = ProbeSetXRef.ProbeSetId and
-                    ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id and
-                    ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and
-                    ProbeFreeze.InbredSetId = InbredSet.Id and
-                    InbredSet.SpeciesId = Species.Id
+                    AGAINST ('%s' IN BOOLEAN MODE))
                             """ % (escape(self.search_term[0]))
 
         print("final query is:", pf(query))