Merge branch 'testing' of github.com:genenetwork/genenetwork2 into testing

3 files changed, 53 insertions, 50 deletions

diff --git a/wqflask/wqflask/collect.py b/wqflask/wqflask/collect.py
index 0f72b29d..ffc698de 100644
--- a/wqflask/wqflask/collect.py
+++ b/wqflask/wqflask/collect.py
@@ -36,6 +36,10 @@ from utility.formatting import numify
 from base import trait
 from base.data_set import create_dataset
 
+import logging
+from utility.logger import getLogger
+logger = getLogger(__name__)
+
 def get_collection():
     if g.user_session.logged_in:
         return UserCollection()
@@ -93,7 +97,7 @@ class AnonCollection(object):
         self.traits = list(process_traits(params['traits']))
         #len_before = len(Redis.smembers(self.key))
         existing_collections = Redis.get(self.key)
-        print("existing_collections:", existing_collections)
+        logger.debug("existing_collections:", existing_collections)
         if existing_collections != None and existing_collections != "None":
             collections_list = json.loads(existing_collections)
             collection_position = 0 #ZS: Position of collection in collection_list, if it exists
@@ -158,8 +162,8 @@ class UserCollection(object):
     """User is logged in"""
 
     def add_traits(self, params, collection_name):
-        print("---> params are:", params.keys())
-        print("     type(params):", type(params))
+        logger.debug("---> params are:", params.keys())
+        logger.debug("     type(params):", type(params))
         if collection_name=="Default":
             uc = g.user_session.user_ob.get_collection_by_name("Default")
             # Doesn't exist so we'll create it
@@ -187,7 +191,7 @@ class UserCollection(object):
 
         db_session.commit()
 
-        print("added to existing, now set is:" + str(uc.members))
+        logger.debug("added to existing, now set is:" + str(uc.members))
         report_change(len_before, len_now)
 
         # Probably have to change that
@@ -210,12 +214,12 @@ def process_traits(unprocessed_traits):
 def report_change(len_before, len_now):
     new_length = len_now - len_before
     if new_length:
-        print("We've added {} to your collection.".format(
+        logger.debug("We've added {} to your collection.".format(
             numify(new_length, 'new trait', 'new traits')))
         flash("We've added {} to your collection.".format(
             numify(new_length, 'new trait', 'new traits')))
     else:
-        print("No new traits were added.")
+        logger.debug("No new traits were added.")
 
 
 @app.route("/collections/add")
@@ -223,8 +227,9 @@ def collections_add():
     traits=request.args['traits']
 
     if g.user_session.logged_in:
+        logger.debug("user_session",g.user_session)
         user_collections = g.user_session.user_ob.user_collections
-        print("user_collections are:", user_collections)
+        logger.debug("user_collections are:", user_collections)
         return render_template("collections/add.html",
                                traits = traits,
                                collections = user_collections,
@@ -246,11 +251,11 @@ def collections_new():
     if "sign_in" in params:
         return redirect(url_for('login'))
     if "create_new" in params:
-        print("in create_new")
+        logger.debug("in create_new")
         collection_name = params['new_collection']
         return create_new(collection_name)
     elif "add_to_existing" in params:
-        print("in add to existing")
+        logger.debug("in add to existing")
         collection_name = params['existing_collection'].split(":")[1]
         if g.user_session.logged_in:
             return UserCollection().add_traits(params, collection_name)
@@ -270,7 +275,7 @@ def create_new(collection_name):
     if g.user_session.logged_in:
         uc = model.UserCollection()
         uc.name = collection_name
-        print("user_session:", g.user_session.__dict__)
+        logger.debug("user_session:", g.user_session.__dict__)
         uc.user = g.user_session.user_id
         uc.members = json.dumps(list(traits))
         db_session.add(uc)
@@ -286,17 +291,17 @@ def create_new(collection_name):
 @app.route("/collections/list")
 def list_collections():
     params = request.args
-    print("PARAMS:", params)
+    logger.debug("PARAMS:", params)
     if g.user_session.logged_in:
         user_collections = list(g.user_session.user_ob.user_collections)
-        print("user_collections are:", user_collections)
+        logger.debug("user_collections are:", user_collections)
         return render_template("collections/list.html",
                                params = params,
                                collections = user_collections,
                                )
     else:
         anon_collections = user_manager.AnonUser().get_collections()
-        print("anon_collections are:", anon_collections)
+        logger.debug("anon_collections are:", anon_collections)
         return render_template("collections/list.html",
                                params = params,
                                collections = anon_collections)
@@ -305,17 +310,17 @@ def list_collections():
 @app.route("/collections/remove", methods=('POST',))
 def remove_traits():
     params = request.form
-    print("params are:", params)
+    logger.debug("params are:", params)
 
     if "uc_id" in params:
         uc_id = params['uc_id']
         uc = model.UserCollection.query.get(uc_id)
         traits_to_remove = params.getlist('traits[]')
         traits_to_remove = process_traits(traits_to_remove)
-        print("\n\n  after processing, traits_to_remove:", traits_to_remove)
+        logger.debug("\n\n  after processing, traits_to_remove:", traits_to_remove)
         all_traits = uc.members_as_set()
         members_now = all_traits - traits_to_remove
-        print("  members_now:", members_now)
+        logger.debug("  members_now:", members_now)
         uc.members = json.dumps(list(members_now))
         uc.changed_timestamp = datetime.datetime.utcnow()
         db_session.commit()
@@ -332,7 +337,7 @@ def remove_traits():
 @app.route("/collections/delete", methods=('POST',))
 def delete_collection():
     params = request.form
-    print("params:", params)
+    logger.debug("params:", params)
     if g.user_session.logged_in:
         uc_id = params['uc_id']
         if len(uc_id.split(":")) > 1:
@@ -363,7 +368,7 @@ def delete_collection():
 @app.route("/collections/view")
 def view_collection():
     params = request.args
-    print("PARAMS in view collection:", params)
+    logger.debug("PARAMS in view collection:", params)
 
     if "uc_id" in params:
         uc_id = params['uc_id']
@@ -379,7 +384,7 @@ def view_collection():
         #this_collection = user_collections[params['collection_id']]
         traits = this_collection['members']
 
-    print("in view_collection traits are:", traits)
+    logger.debug("in view_collection traits are:", traits)
 
     trait_obs = []
     json_version = []
@@ -405,7 +410,7 @@ def view_collection():
         collection_info = dict(trait_obs=trait_obs,
                                collection_name=this_collection['name'])
     if "json" in params:
-        print("json_version:", json_version)
+        logger.debug("json_version:", json_version)
         return json.dumps(json_version)
     else:
         return render_template("collections/view.html",
diff --git a/wqflask/wqflask/static/dbdoc/TODO.md b/wqflask/wqflask/static/dbdoc/TODO.md
deleted file mode 100644
index c0a8bab7..00000000
--- a/wqflask/wqflask/static/dbdoc/TODO.md
+++ /dev/null
@@ -1 +0,0 @@
-TODO: Add all database documentation into this folder
diff --git a/wqflask/wqflask/user_manager.py b/wqflask/wqflask/user_manager.py
index c55649f3..a0605803 100644
--- a/wqflask/wqflask/user_manager.py
+++ b/wqflask/wqflask/user_manager.py
@@ -23,9 +23,6 @@ import urlparse
 
 import simplejson as json
 
-import sqlalchemy
-from sqlalchemy import orm
-
 #from redis import StrictRedis
 import redis
 Redis = redis.StrictRedis()
@@ -46,7 +43,6 @@ from wqflask.database import db_session
 from wqflask import model
 
 from utility import Bunch, Struct, after
-from utility.tools import LOG_SQL, LOG_SQL_ALCHEMY
 
 import logging
 from utility.logger import getLogger
@@ -55,7 +51,10 @@ logger = getLogger(__name__)
 from base.data_set import create_datasets_list
 
 import requests
-from utility.elasticsearch_tools import get_elasticsearch_connection, get_user_by_unique_column, save_user
+from utility.elasticsearch_tools import get_elasticsearch_connection, get_user_by_unique_column, get_item_by_unique_column, save_user, es_save_data
+
+from smtplib import SMTP
+from utility.tools import SMTP_CONNECT, SMTP_USERNAME, SMTP_PASSWORD
 
 THREE_DAYS = 60 * 60 * 24 * 3
 #THREE_DAYS = 45
@@ -220,6 +219,7 @@ class UserSession(object):
     def user_ob(self):
         """Actual sqlalchemy record"""
         # Only look it up once if needed, then store it
+        raise "OBSOLETE: use ElasticSearch instead"
         try:
             if LOG_SQL_ALCHEMY:
                 logging.getLogger('sqlalchemy.pool').setLevel(logging.DEBUG)
@@ -386,6 +386,7 @@ class ForgotPasswordEmail(VerificationEmail):
             "email_address": toaddr,
             "timestamp": timestamp()
         }
+        es = get_elasticsearch_connection()
         es_save_data(es, self.key_prefix, "local", data, verification_code)
 
         subject = self.subject
@@ -437,12 +438,12 @@ def verify_email():
 @app.route("/n/password_reset", methods=['GET'])
 def password_reset():
     logger.debug("in password_reset request.url is:", request.url)
-
     # We do this mainly just to assert that it's in proper form for displaying next page
     # Really not necessary but doesn't hurt
     # user_encode = DecodeUser(ForgotPasswordEmail.key_prefix).reencode_standalone()
     verification_code = request.args.get('code')
     hmac = request.args.get('hm')
+    es = get_elasticsearch_connection()
     if verification_code:
         code_details = get_item_by_unique_column(
             es
@@ -466,7 +467,6 @@ def password_reset():
 
 @app.route("/n/password_reset_step2", methods=('POST',))
 def password_reset_step2():
-    from utility.elasticsearch_tools import es
     logger.debug("in password_reset request.url is:", request.url)
 
     errors = []
@@ -748,6 +748,7 @@ def forgot_password():
 def forgot_password_submit():
     params = request.form
     email_address = params['email_address']
+    es = get_elasticsearch_connection()
     user_details = get_user_by_unique_column(es, "email_address", email_address)
     if user_details:
         ForgotPasswordEmail(user_details["email_address"])
@@ -840,19 +841,6 @@ def register():
     return render_template("new_security/register_user.html", values=params, errors=errors)
 
 
-
-
-#@app.route("/n/login", methods=('GET', 'POST'))
-#def login():
-#    return user_manager.login()
-#
-#@app.route("/manage/verify")
-#def verify():
-#    user_manager.verify_email()
-#    return render_template("new_security/verified.html")
-
-
-
 ################################# Sign and unsign #####################################
 
 def url_for_hmac(endpoint, **values):
@@ -914,15 +902,26 @@ app.jinja_env.globals.update(url_for_hmac=url_for_hmac,
 #     Redis.rpush("mail_queue", msg)
 
 def send_email(toaddr, msg, fromaddr="no-reply@genenetwork.org"):
-    from smtplib import SMTP
-    from utility.tools import SMTP_CONNECT, SMTP_USERNAME, SMTP_PASSWORD
-    server = SMTP(SMTP_CONNECT)
-    server.starttls()
-    server.login(SMTP_USERNAME, SMTP_PASSWORD)
-    server.sendmail(fromaddr, toaddr, msg)
-    server.quit()
-
-
+    """Send an E-mail through SMTP_CONNECT host. If SMTP_USERNAME is not
+    'UNKNOWN' TLS is used
+
+    """
+    if SMTP_USERNAME == 'UNKNOWN':
+        logger.debug("SMTP: connecting with host "+SMTP_CONNECT)
+        server = SMTP(SMTP_CONNECT)
+        server.sendmail(fromaddr, toaddr, msg)
+    else:
+        logger.debug("SMTP: connecting TLS with host "+SMTP_CONNECT)
+        server = SMTP(SMTP_CONNECT)
+        server.starttls()
+        logger.debug("SMTP: login with user "+SMTP_USERNAME)
+        server.login(SMTP_USERNAME, SMTP_PASSWORD)
+        logger.debug("SMTP: "+fromaddr)
+        logger.debug("SMTP: "+toaddr)
+        logger.debug("SMTP: "+msg)
+        server.sendmail(fromaddr, toaddr, msg)
+        server.quit()
+    logger.info("Successfully sent email to "+toaddr)
 
 class GroupsManager(object):
     def __init__(self, kw):