diff options
| -rw-r--r-- | misc/notes.txt | 7 | ||||
| -rw-r--r-- | wqflask/secure_server.py | 76 | ||||
| -rw-r--r-- | wqflask/wqflask/do_search.py | 14 |
3 files changed, 85 insertions, 12 deletions
diff --git a/misc/notes.txt b/misc/notes.txt index cdd353ea..e40dad8f 100644 --- a/misc/notes.txt +++ b/misc/notes.txt @@ -219,3 +219,10 @@ grep -ir (search string) (directory) -i ignores case -r searches recursively through subdirectories of directory you specify + +=========================================== + +MySQL Things - + +Create fulltext (MATCH AGAINST syntax) index: +CREATE FULLTEXT INDEX __________ ON Table (Column); 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)) |