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

8 files changed, 82 insertions, 79 deletions

diff --git a/wqflask/utility/startup_config.py b/wqflask/utility/startup_config.py
index 5a62cc50..817284dd 100644
--- a/wqflask/utility/startup_config.py
+++ b/wqflask/utility/startup_config.py
@@ -33,7 +33,7 @@ def app_config():
         if page.status_code != 200:
             raise Exception("API server not found!")
 
-    import utility.elasticsearch_tools as es
-    es.test_elasticsearch_connection()
+    # import utility.elasticsearch_tools as es
+    # es.test_elasticsearch_connection()
 
     print("GN2 is running. Visit %s[http://localhost:%s/%s](%s)" % (BLUE,str(port),ENDC,get_setting("WEBSERVER_URL")))
diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py
index 75bddb24..0fbedccb 100644
--- a/wqflask/utility/tools.py
+++ b/wqflask/utility/tools.py
@@ -267,10 +267,10 @@ if ORCID_CLIENT_ID != 'UNKNOWN' and ORCID_CLIENT_SECRET:
                       ORCID_CLIENT_ID+"&client_secret="+ORCID_CLIENT_SECRET
     ORCID_TOKEN_URL = get_setting('ORCID_TOKEN_URL')
 
-ELASTICSEARCH_HOST = get_setting('ELASTICSEARCH_HOST')
-ELASTICSEARCH_PORT = get_setting('ELASTICSEARCH_PORT')
-import utility.elasticsearch_tools as es
-es.test_elasticsearch_connection()
+# ELASTICSEARCH_HOST = get_setting('ELASTICSEARCH_HOST')
+# ELASTICSEARCH_PORT = get_setting('ELASTICSEARCH_PORT')
+# import utility.elasticsearch_tools as es
+# es.test_elasticsearch_connection()
 
 SMTP_CONNECT = get_setting('SMTP_CONNECT')
 SMTP_USERNAME = get_setting('SMTP_USERNAME')
diff --git a/wqflask/wqflask/collect.py b/wqflask/wqflask/collect.py
index fa6e03b4..1d74b699 100644
--- a/wqflask/wqflask/collect.py
+++ b/wqflask/wqflask/collect.py
@@ -108,7 +108,7 @@ def collections_new():
         if 'existing_collection' not in params:
             collections = g.user_session.user_collections
             for collection in collections:
-                if collection["name"] == "Default Collection":
+                if collection["name"] == "Your Default Collection":
                     collection_id = collection["id"]
                     collection_name = collection["name"]
                     default_collection_exists = True
diff --git a/wqflask/wqflask/show_trait/SampleList.py b/wqflask/wqflask/show_trait/SampleList.py
index 7e126a36..ad78ebcc 100644
--- a/wqflask/wqflask/show_trait/SampleList.py
+++ b/wqflask/wqflask/show_trait/SampleList.py
@@ -14,8 +14,6 @@ import simplejson as json
 
 import itertools
 
-from utility.elasticsearch_tools import get_elasticsearch_connection
-
 import utility.logger
 logger = utility.logger.getLogger(__name__ )
 
@@ -158,47 +156,47 @@ class SampleList(object):
 
         return any(sample.variance for sample in self.sample_list)
 
-def get_transform_vals(dataset, trait):
-    es = get_elasticsearch_connection(for_user=False)
-
-    logger.info("DATASET NAME:", dataset.name)
-
-    query = '{"bool": {"must": [{"match": {"name": "%s"}}, {"match": {"dataset": "%s"}}]}}' % (trait.name, dataset.name)
-
-    es_body = {
-          "query": {
-            "bool": {
-              "must": [
-                {
-                  "match": {
-                    "name": "%s" % (trait.name)
-                  }
-                },
-                {
-                  "match": {
-                    "dataset": "%s" % (dataset.name)
-                  }
-                }
-              ]
-            }
-          }
-    }
-
-    response = es.search( index = "traits", doc_type = "trait", body = es_body )
-    logger.info("THE RESPONSE:", response)
-    results = response['hits']['hits']
-
-    if len(results) > 0:
-        samples = results[0]['_source']['samples']
-
-        sample_dict = {}
-        for sample in samples:
-            sample_dict[sample['name']] = sample['qnorm']
-
-        #logger.info("SAMPLE DICT:", sample_dict)
-        return sample_dict
-    else:
-        return None
+# def get_transform_vals(dataset, trait):
+#     es = get_elasticsearch_connection(for_user=False)
+
+#     logger.info("DATASET NAME:", dataset.name)
+
+#     query = '{"bool": {"must": [{"match": {"name": "%s"}}, {"match": {"dataset": "%s"}}]}}' % (trait.name, dataset.name)
+
+#     es_body = {
+#           "query": {
+#             "bool": {
+#               "must": [
+#                 {
+#                   "match": {
+#                     "name": "%s" % (trait.name)
+#                   }
+#                 },
+#                 {
+#                   "match": {
+#                     "dataset": "%s" % (dataset.name)
+#                   }
+#                 }
+#               ]
+#             }
+#           }
+#     }
+
+#     response = es.search( index = "traits", doc_type = "trait", body = es_body )
+#     logger.info("THE RESPONSE:", response)
+#     results = response['hits']['hits']
+
+#     if len(results) > 0:
+#         samples = results[0]['_source']['samples']
+
+#         sample_dict = {}
+#         for sample in samples:
+#             sample_dict[sample['name']] = sample['qnorm']
+
+#         #logger.info("SAMPLE DICT:", sample_dict)
+#         return sample_dict
+#     else:
+#         return None
 
 def natural_sort_key(x):
     """Get expected results when using as a key for sort - ints or strings are sorted properly"""
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index d35ba749..8883e627 100644
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -364,8 +364,8 @@ class ShowTrait(object):
                 if self.dataset:
                     dataset_menu_selected = self.dataset.name
 
-                return_results_menu = (100, 200, 500, 1000, 2000, 5000, 10000, 15000, 20000)
-                return_results_menu_selected = 500
+            return_results_menu = (100, 200, 500, 1000, 2000, 5000, 10000, 15000, 20000)
+            return_results_menu_selected = 500
 
             self.corr_tools = dict(dataset_menu = dataset_menu,
                                           dataset_menu_selected = dataset_menu_selected,
diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html
index 33221e0f..0f5c39b0 100644
--- a/wqflask/wqflask/templates/search_result_page.html
+++ b/wqflask/wqflask/templates/search_result_page.html
@@ -27,6 +27,8 @@
                     with <u>GeneWiki</u> containing <strong>{{ word.search_term[0] }}</strong>{% if loop.last %}.{% else %} and {% endif %}
                     {% elif word.key|lower == "mean" %}
                     with <u>MEAN</u> between <strong>{{ word.search_term[0] }}</strong> and <strong>{{ word.search_term[1] }}</strong>{% if loop.last %}.{% else %} and {% endif %}
+                    {% elif word.key|lower == "range" %}
+                    with <u>RANGE</u> between <strong>{{ word.search_term[0] }}</strong> and <strong>{{ word.search_term[1] }}</strong>{% if loop.last %}.{% else %} and {% endif %}
                     {% elif word.key|lower == "lrs" or word.key|lower == "lod" or word.key|lower == "translrs" or word.key|lower == "cislrs" or word.key|lower == "translod" or word.key|lower == "cislod" %}
                     {% if word.search_term|length == 1 %}
                     with {% if word.key|lower == "translrs" %}trans{% elif word.key|lower == "cislrs" %}cis{% endif %}LRS {% if word.separator == ">" %} greater than {% elif word.separator == "<" %} less than {% elif word.separator == ">=" %} greater than or equal to {% elif word.separator == "<=" %} less than or equal to {% endif %} <strong>{{ word.search_term[0] }}</strong>{% if loop.last %}.{% else %} and {% endif %}
diff --git a/wqflask/wqflask/user_login.py b/wqflask/wqflask/user_login.py
index da3cc504..40d9925c 100644
--- a/wqflask/wqflask/user_login.py
+++ b/wqflask/wqflask/user_login.py
@@ -6,7 +6,6 @@ import datetime
 import time
 import logging
 import uuid
-import hashlib
 import hmac
 import base64
 import requests
@@ -42,17 +41,23 @@ def basic_info():
                 ip_address = request.remote_addr,
                 user_agent = request.headers.get('User-Agent'))
 
-def encode_password(pass_gen_fields):
+def encode_password(pass_gen_fields, unencrypted_password):
+    logger.debug("THE TYPE:", type(pass_gen_fields))
+    logger.debug("pass_gen_fields:", pass_gen_fields)
+    logger.debug("hashfunc:", pass_gen_fields['hashfunc'])
     hashfunc = getattr(hashlib, pass_gen_fields['hashfunc'])
 
     salt = base64.b64decode(pass_gen_fields['salt'])
-    password = pbkdf2.pbkdf2_hex(str(pass_gen_fields['unencrypted_password']), 
+    encrypted_password = pbkdf2.pbkdf2_hex(str(unencrypted_password), 
                                  pass_gen_fields['salt'], 
                                  pass_gen_fields['iterations'], 
                                  pass_gen_fields['keylength'], 
                                  hashfunc)
 
-    return password
+    pass_gen_fields.pop("unencrypted_password", None)
+    pass_gen_fields["password"] = encrypted_password
+
+    return pass_gen_fields
 
 def set_password(password):
     pass_gen_fields = {
@@ -67,19 +72,10 @@ def set_password(password):
 
     assert len(password) >= 6, "Password shouldn't be shorter than 6 characters"
 
-    encoded_password = encode_password(pass_gen_fields)
+    encoded_password = encode_password(pass_gen_fields, pass_gen_fields['unencrypted_password'])
 
     return encoded_password
 
-def encrypt_password(unencrypted_password, pwfields):
-        hashfunc = getattr(hashlib, pwfields['hashfunc'])
-        salt = base64.b64decode(pwfields['salt'])
-        iterations = pwfields['iterations']
-        keylength = pwfields['keylength']
-        encrypted_password = pbkdf2.pbkdf2_hex(str(unencrypted_password),
-                                               salt, iterations, keylength, hashfunc)
-        return encrypted_password
-
 def get_signed_session_id(user):
     session_id = str(uuid.uuid4())
 
@@ -186,9 +182,12 @@ def login():
             password_match = False
             if user_details:
                 submitted_password = params['password']
-                pwfields = json.loads(user_details['password'])
-                encrypted_pass = encrypt_password(submitted_password, pwfields)
-                password_match = pbkdf2.safe_str_cmp(encrypted_pass, pwfields['password'])
+                pwfields = user_details['password']
+                if type(pwfields) is str:
+                    pwfields = json.loads(pwfields)
+                encrypted_pass_fields = encode_password(pwfields, submitted_password)
+                password_match = pbkdf2.safe_str_cmp(encrypted_pass_fields['password'], pwfields['password'])
+
             else: # Invalid e-mail
                 flash("Invalid e-mail address. Please try again.", "alert-danger")
                 response = make_response(redirect(url_for('login')))
@@ -226,7 +225,7 @@ def github_oauth2():
         "client_secret": GITHUB_CLIENT_SECRET,
         "code": code
     }
-    logger.debug("LOGIN DATA:", data)
+
     result = requests.post("https://github.com/login/oauth/access_token", json=data)
     result_dict = {arr[0]:arr[1] for arr in [tok.split("=") for tok in [token.encode("utf-8") for token in result.text.split("&")]]}
 
@@ -437,19 +436,18 @@ def register_user(params):
         if params.get('password_confirm') != password:
             errors.append("Passwords don't match.")
 
-        if errors:
-            return errors
-
         user_details['password'] = set_password(password)
         user_details['user_id'] = str(uuid.uuid4())
         user_details['confirmed'] = 1
 
-        user_details['registration_info'] = json.dumps(basic_info(), sort_keys=True)
+        user_details['registration_info'] = basic_info()
         save_user(user_details, user_details['user_id'])
 
+        return errors
+
 @app.route("/n/register", methods=('GET', 'POST'))
 def register():
-    errors = None
+    errors = []
 
     params = request.form if request.form else request.args
     params = params.to_dict(flat=True)
diff --git a/wqflask/wqflask/user_session.py b/wqflask/wqflask/user_session.py
index d75a03df..fd1779fb 100644
--- a/wqflask/wqflask/user_session.py
+++ b/wqflask/wqflask/user_session.py
@@ -9,6 +9,7 @@ import simplejson as json
 import redis # used for collections
 Redis = redis.StrictRedis()
 
+
 from flask import (Flask, g, render_template, url_for, request, make_response,
                    redirect, flash, abort)
 
@@ -69,19 +70,23 @@ class UserSession(object):
         if not self.record or self.record == []:
             if user_cookie:
                 self.logged_in = False
+                self.record = dict(login_time = time.time(),
+                                    user_type = "anon",
+                                    user_id = str(uuid.uuid4()))
+                Redis.hmset(self.redis_key, self.record)
+                Redis.expire(self.redis_key, THIRTY_DAYS)
+                response = make_response(redirect(url_for('login')))
+                response.set_cookie(self.user_cookie_name, '', expires=0)
 
                 ########### Grrr...this won't work because of the way flask handles cookies
                 # Delete the cookie
-                response = make_response(redirect(url_for('login')))
-                #response.set_cookie(self.cookie_name, '', expires=0)
                 flash("Due to inactivity your session has expired. If you'd like please login again.")
-                #return response
+                return response
                 #return
             else:
                 self.record = dict(login_time = time.time(),
                                     user_type = "anon",
                                     user_id = str(uuid.uuid4()))
-
                 Redis.hmset(self.redis_key, self.record)
                 Redis.expire(self.redis_key, THIRTY_DAYS)
         else: