Merge github.com:genenetwork/genenetwork2 into acenteno

7 files changed, 766 insertions, 731 deletions

diff --git a/wqflask/base/GeneralObject.py b/wqflask/base/GeneralObject.py
index 02a1ef06..ce8e60b8 100644
--- a/wqflask/base/GeneralObject.py
+++ b/wqflask/base/GeneralObject.py
@@ -25,44 +25,42 @@
 # Last updated by GeneNetwork Core Team 2010/10/20
 
 class GeneralObject:
-	"""
-	Base class to define an Object.
-	a = [Spam(1, 4), Spam(9, 3), Spam(4,6)]
-	a.sort(lambda x, y: cmp(x.eggs, y.eggs))
-	"""
+    """
+    Base class to define an Object.
+    a = [Spam(1, 4), Spam(9, 3), Spam(4,6)]
+    a.sort(key = lambda x: x.eggs)
+    """
 
-	def __init__(self, *args, **kw):
-		self.contents = list(args)
-		for name, value in kw.items():
-			setattr(self, name, value)
-			
-	def __setitem__(self, key, value):
-		setattr(self, key, value)
-		
-	def __getitem__(self, key):
-		return getattr(self, key)
-		
-	def __getattr__(self, key):
-		if key in self.__dict__.keys():
-			return self.__dict__[key]
-		else:
-			return eval("self.__dict__.%s" % key)
-			
-	def __len__(self):
-		return len(self.__dict__) - 1
-				
-	def __str__(self):
-		s = ''
-		for key in self.__dict__.keys():
-			if key != 'contents':
-				s += '%s = %s\n' % (key,self.__dict__[key])
-		return s
-	
-	def __repr__(self):
-		s = ''
-		for key in self.__dict__.keys():
-			s += '%s = %s\n' % (key,self.__dict__[key])
-		return s
-	
-	def __cmp__(self,other):
-		return len(self.__dict__.keys()).__cmp__(len(other.__dict__.keys()))
\ No newline at end of file
+    def __init__(self, *args, **kw):
+        self.contents = list(args)
+        for name, value in list(kw.items()):
+            setattr(self, name, value)
+
+    def __setitem__(self, key, value):
+        setattr(self, key, value)
+
+    def __getitem__(self, key):
+        return getattr(self, key)
+
+    def __getattr__(self, key):
+        return eval("self.__dict__.%s" % key)
+
+    def __len__(self):
+        return len(self.__dict__) - 1
+
+    def __str__(self):
+        s = ''
+        for key in list(self.__dict__.keys()):
+            if key != 'contents':
+                s += '%s = %s\n' % (key, self.__dict__[key])
+        return s
+
+    def __repr__(self):
+        s = ''
+        for key in list(self.__dict__.keys()):
+            s += '%s = %s\n' % (key, self.__dict__[key])
+        return s
+
+    def __eq__(self, other):
+        return (len(list(self.__dict__.keys()))
+                == len(list(other.__dict__.keys())))
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 1457ba8d..8906ab69 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -17,8 +17,28 @@
 # at rwilliams@uthsc.edu and xzhou15@uthsc.edu
 #
 # This module is used by GeneNetwork project (www.genenetwork.org)
-
-from __future__ import absolute_import, print_function, division
+from dataclasses import dataclass
+from dataclasses import field
+from dataclasses import InitVar
+from typing import Optional, Dict
+from db.call import fetchall, fetchone, fetch1
+from utility.logger import getLogger
+from utility.tools import USE_GN_SERVER, USE_REDIS, flat_files, flat_file_exists, GN2_BASE_URL
+from db.gn_server import menu_main
+from pprint import pformat as pf
+from utility.db_tools import escape
+from utility.db_tools import mescape
+from utility.db_tools import create_in_clause
+from maintenance import get_group_samplelists
+from utility.tools import locate, locate_ignore_error, flat_files
+from utility import gen_geno_ob
+from utility import chunks
+from utility.benchmark import Bench
+from utility import webqtlUtil
+from db import webqtlDatabaseFunction
+from base import species
+from base import webqtlConfig
+from flask import Flask, g
 import os
 import math
 import string
@@ -28,43 +48,25 @@ import codecs
 import json
 import requests
 import gzip
-import cPickle as pickle
+import pickle as pickle
 import itertools
 
 from redis import Redis
-Redis = Redis()
 
-from flask import Flask, g
+r = Redis()
 
-import reaper
-
-from base import webqtlConfig
-from base import species
-from db import webqtlDatabaseFunction
-from utility import webqtlUtil
-from utility.benchmark import Bench
-from utility import chunks
-from utility import gen_geno_ob
-from utility.tools import locate, locate_ignore_error, flat_files
-
-from wqflask.api import gen_menu
-
-from maintenance import get_group_samplelists
-
-from MySQLdb import escape_string as escape
-from pprint import pformat as pf
-from db.gn_server import menu_main
-from db.call import fetchall,fetchone,fetch1
-
-from utility.tools import USE_GN_SERVER, USE_REDIS, flat_files, flat_file_exists, GN2_BASE_URL
-from utility.logger import getLogger
-logger = getLogger(__name__ )
+logger = getLogger(__name__)
 
 # Used by create_database to instantiate objects
 # Each subclass will add to this
 DS_NAME_MAP = {}
 
-def create_dataset(dataset_name, dataset_type = None, get_samplelist = True, group_name = None):
+
+def create_dataset(dataset_name, dataset_type=None,
+                   get_samplelist=True, group_name=None):
+    if dataset_name == "Temp":
+        dataset_type = "Temp"
+
     if not dataset_type:
         dataset_type = Dataset_Getter(dataset_name)
 
@@ -75,11 +77,11 @@ def create_dataset(dataset_name, dataset_type = None, get_samplelist = True, gro
     else:
         return dataset_class(dataset_name, get_samplelist)
 
-class Dataset_Types(object):
 
-    def __init__(self):
-        """Create a dictionary of samples where the value is set to Geno,
-Publish or ProbeSet. E.g.
+@dataclass
+class DatasetType:
+    """Create a dictionary of samples where the value is set to Geno,
+    Publish or ProbeSet. E.g.
 
         {'AD-cases-controls-MyersGeno': 'Geno',
          'AD-cases-controls-MyersPublish': 'Publish',
@@ -90,20 +92,28 @@ Publish or ProbeSet. E.g.
          'All Phenotypes': 'Publish',
          'B139_K_1206_M': 'ProbeSet',
          'B139_K_1206_R': 'ProbeSet' ...
-
+        }
         """
-        self.datasets = {}
+    redis_instance: InitVar[Redis]
+    datasets: Optional[Dict] = field(init=False, default_factory=dict)
+    data: Optional[Dict] = field(init=False)
 
-        data = Redis.get("dataset_structure")
+    def __post_init__(self, redis_instance):
+        self.redis_instance = redis_instance
+        data = redis_instance.get("dataset_structure")
         if data:
             self.datasets = json.loads(data)
-        else: #ZS: I don't think this should ever run unless Redis is emptied
+        else:
+            # ZS: I don't think this should ever run unless Redis is
+            # emptied
             try:
-                data = json.loads(requests.get(GN2_BASE_URL + "/api/v_pre1/gen_dropdown", timeout = 5).content)
-                for species in data['datasets']:
-                    for group in data['datasets'][species]:
-                        for dataset_type in data['datasets'][species][group]:
-                            for dataset in data['datasets'][species][group][dataset_type]:
+                data = json.loads(requests.get(
+                    GN2_BASE_URL + "/api/v_pre1/gen_dropdown",
+                    timeout=5).content)
+                for _species in data['datasets']:
+                    for group in data['datasets'][_species]:
+                        for dataset_type in data['datasets'][_species][group]:
+                            for dataset in data['datasets'][_species][group][dataset_type]:
                                 short_dataset_name = dataset[1]
                                 if dataset_type == "Phenotypes":
                                     new_type = "Publish"
@@ -112,84 +122,77 @@ Publish or ProbeSet. E.g.
                                 else:
                                     new_type = "ProbeSet"
                                 self.datasets[short_dataset_name] = new_type
-            except:
+            except Exception:  # Do nothing
                 pass
 
-            Redis.set("dataset_structure", json.dumps(self.datasets))
+            self.redis_instance.set("dataset_structure",
+                                    json.dumps(self.datasets))
+        self.data = data
 
-        # Set LOG_LEVEL_DEBUG=5 to see the following:
-        logger.debugf(5, "datasets",self.datasets)
+    def set_dataset_key(self, t, name):
+        """If name is not in the object's dataset dictionary, set it, and
+        update dataset_structure in Redis
+        args:
+          t: Type of dataset structure which can be: 'mrna_expr', 'pheno',
+             'other_pheno', 'geno'
+          name: The name of the key to inserted in the datasets dictionary
 
-    def __call__(self, name):
-        if name not in self.datasets:
-            mrna_expr_query = """
-                            SELECT
-                                ProbeSetFreeze.Id
-                            FROM
-                                ProbeSetFreeze
-                            WHERE
-                                ProbeSetFreeze.Name = "{0}"
-                            """.format(name)
+        """
+        sql_query_mapping = {
+            'mrna_expr': ("SELECT ProbeSetFreeze.Id FROM "
+                          "ProbeSetFreeze WHERE "
+                          "ProbeSetFreeze.Name = \"%s\" "),
+            'pheno': ("SELECT InfoFiles.GN_AccesionId "
+                      "FROM InfoFiles, PublishFreeze, InbredSet "
+                      "WHERE InbredSet.Name = '%s' AND "
+                      "PublishFreeze.InbredSetId = InbredSet.Id AND "
+                      "InfoFiles.InfoPageName = PublishFreeze.Name"),
+            'other_pheno': ("SELECT PublishFreeze.Name "
+                            "FROM PublishFreeze, InbredSet "
+                            "WHERE InbredSet.Name = '%s' AND "
+                            "PublishFreeze.InbredSetId = InbredSet.Id"),
+            'geno': ("SELECT GenoFreeze.Id FROM GenoFreeze WHERE "
+                     "GenoFreeze.Name = \"%s\" ")
+        }
+
+        dataset_name_mapping = {
+            "mrna_expr": "ProbeSet",
+            "pheno": "Publish",
+            "other_pheno": "Publish",
+            "geno": "Geno",
+        }
+
+        group_name = name
+        if t in ['pheno', 'other_pheno']:
+            group_name = name.replace("Publish", "")
 
-            results = g.db.execute(mrna_expr_query).fetchall()
-            if len(results):
-                self.datasets[name] = "ProbeSet"
-                Redis.set("dataset_structure", json.dumps(self.datasets))
-                return self.datasets[name]
+        results = g.db.execute(sql_query_mapping[t] % group_name).fetchone()
+        if results:
+            self.datasets[name] = dataset_name_mapping[t]
+            self.redis_instance.set(
+                "dataset_structure", json.dumps(self.datasets))
+            return True
+        return None
 
-            group_name = name.replace("Publish", "")
+    def __call__(self, name):
+        if name not in self.datasets:
+            for t in ["mrna_expr", "pheno", "other_pheno", "geno"]:
+                # This has side-effects, with the end result being a
+                # truth-y value
+                if(self.set_dataset_key(t, name)):
+                    break
+        # Return None if name has not been set
+        return self.datasets.get(name, None)
 
-            pheno_query = """SELECT InfoFiles.GN_AccesionId
-                             FROM InfoFiles, PublishFreeze, InbredSet
-                             WHERE InbredSet.Name = '{0}' AND
-                                   PublishFreeze.InbredSetId = InbredSet.Id AND
-                                   InfoFiles.InfoPageName = PublishFreeze.Name""".format(group_name)
-
-            results = g.db.execute(pheno_query).fetchall()
-            if len(results):
-                self.datasets[name] = "Publish"
-                Redis.set("dataset_structure", json.dumps(self.datasets))
-                return self.datasets[name]
-
-            #ZS: For when there isn't an InfoFiles ID; not sure if this and the preceding query are both necessary
-            other_pheno_query = """SELECT PublishFreeze.Name
-                                   FROM PublishFreeze, InbredSet
-                                   WHERE InbredSet.Name = '{}' AND
-                                         PublishFreeze.InbredSetId = InbredSet.Id""".format(group_name)
-
-            results = g.db.execute(other_pheno_query).fetchall()
-            if len(results):
-                self.datasets[name] = "Publish"
-                Redis.set("dataset_structure", json.dumps(self.datasets))
-                return self.datasets[name]
-
-            geno_query =    """
-                                SELECT
-                                    GenoFreeze.Id
-                                FROM
-                                    GenoFreeze
-                                WHERE
-                                    GenoFreeze.Name = "{0}"
-                            """.format(name)
-
-            results = g.db.execute(geno_query).fetchall()
-            if len(results):
-                self.datasets[name] = "Geno"
-                Redis.set("dataset_structure", json.dumps(self.datasets))
-                return self.datasets[name]
-
-            #ZS: It shouldn't ever reach this
-            return None
-        else:
-            return self.datasets[name]
 
 # Do the intensive work at startup one time only
-Dataset_Getter = Dataset_Types()
+Dataset_Getter = DatasetType(r)
+
 
 def create_datasets_list():
     if USE_REDIS:
         key = "all_datasets"
-        result = Redis.get(key)
+        result = r.get(key)
 
         if result:
             logger.debug("Redis cache hit")
@@ -205,38 +208,25 @@ def create_datasets_list():
             for dataset_type in type_dict:
                 query = "SELECT Name FROM {}".format(type_dict[dataset_type])
                 for result in fetchall(query):
-                    #The query at the beginning of this function isn't
-                    #necessary here, but still would rather just reuse
-                    #it logger.debug("type: {}\tname:
-                    #{}".format(dataset_type, result.Name))
+                    # The query at the beginning of this function isn't
+                    # necessary here, but still would rather just reuse
+                    # it logger.debug("type: {}\tname:
+                    # {}".format(dataset_type, result.Name))
                     dataset = create_dataset(result.Name, dataset_type)
                     datasets.append(dataset)
 
         if USE_REDIS:
-            Redis.set(key, pickle.dumps(datasets, pickle.HIGHEST_PROTOCOL))
-            Redis.expire(key, 60*60)
+            r.set(key, pickle.dumps(datasets, pickle.HIGHEST_PROTOCOL))
+            r.expire(key, 60 * 60)
 
     return datasets
 
 
-def create_in_clause(items):
-    """Create an in clause for mysql"""
-    in_clause = ', '.join("'{}'".format(x) for x in mescape(*items))
-    in_clause = '( {} )'.format(in_clause)
-    return in_clause
-
-
-def mescape(*items):
-    """Multiple escape"""
-    escaped = [escape(str(item)) for item in items]
-    #logger.debug("escaped is:", escaped)
-    return escaped
-
-
-class Markers(object):
+class Markers:
     """Todo: Build in cacheing so it saves us reading the same file more than once"""
+
     def __init__(self, name):
-        json_data_fh = open(locate(name + ".json",'genotype/json'))
+        json_data_fh = open(locate(name + ".json", 'genotype/json'))
 
         markers = []
         with open("%s/%s_snps.txt" % (flat_files('genotype/bimbam'), name), 'r') as bimbam_fh:
@@ -251,7 +241,8 @@ class Markers(object):
             for line in bimbam_fh:
                 marker = {}
                 marker['name'] = line.split(delimiter)[0].rstrip()
-                marker['Mb'] = float(line.split(delimiter)[1].rstrip())/1000000
+                marker['Mb'] = float(line.split(delimiter)[
+                                     1].rstrip()) / 1000000
                 marker['chr'] = line.split(delimiter)[2].rstrip()
                 markers.append(marker)
 
@@ -266,12 +257,12 @@ class Markers(object):
         logger.debug("length of self.markers:", len(self.markers))
         logger.debug("length of p_values:", len(p_values))
 
-        if type(p_values) is list:
+        if isinstance(p_values, list):
             # THIS IS only needed for the case when we are limiting the number of p-values calculated
-            #if len(self.markers) > len(p_values):
+            # if len(self.markers) > len(p_values):
             #    self.markers = self.markers[:len(p_values)]
 
-            for marker, p_value in itertools.izip(self.markers, p_values):
+            for marker, p_value in zip(self.markers, p_values):
                 if not p_value:
                     continue
                 marker['p_value'] = float(p_value)
@@ -280,38 +271,32 @@ class Markers(object):
                     marker['lrs_value'] = 0
                 else:
                     marker['lod_score'] = -math.log10(marker['p_value'])
-                    #Using -log(p) for the LRS; need to ask Rob how he wants to get LRS from p-values
+                    # Using -log(p) for the LRS; need to ask Rob how he wants to get LRS from p-values
                     marker['lrs_value'] = -math.log10(marker['p_value']) * 4.61
-        elif type(p_values) is dict:
+        elif isinstance(p_values, dict):
             filtered_markers = []
             for marker in self.markers:
-                #logger.debug("marker[name]", marker['name'])
-                #logger.debug("p_values:", p_values)
                 if marker['name'] in p_values:
-                    #logger.debug("marker {} IS in p_values".format(i))
                     marker['p_value'] = p_values[marker['name']]
                     if math.isnan(marker['p_value']) or (marker['p_value'] <= 0):
                         marker['lod_score'] = 0
                         marker['lrs_value'] = 0
                     else:
                         marker['lod_score'] = -math.log10(marker['p_value'])
-                        #Using -log(p) for the LRS; need to ask Rob how he wants to get LRS from p-values
-                        marker['lrs_value'] = -math.log10(marker['p_value']) * 4.61
+                        # Using -log(p) for the LRS; need to ask Rob how he wants to get LRS from p-values
+                        marker['lrs_value'] = - \
+                            math.log10(marker['p_value']) * 4.61
                     filtered_markers.append(marker)
-                #else:
-                    #logger.debug("marker {} NOT in p_values".format(i))
-                    #self.markers.remove(marker)
-                    #del self.markers[i]
             self.markers = filtered_markers
 
+
 class HumanMarkers(Markers):
 
-    def __init__(self, name, specified_markers = []):
+    def __init__(self, name, specified_markers=[]):
         marker_data_fh = open(flat_files('mapping') + '/' + name + '.bim')
         self.markers = []
         for line in marker_data_fh:
             splat = line.strip().split()
-            #logger.debug("splat:", splat)
             if len(specified_markers) > 0:
                 if splat[1] in specified_markers:
                     marker = {}
@@ -327,14 +312,11 @@ class HumanMarkers(Markers):
                 marker['Mb'] = float(splat[3]) / 1000000
             self.markers.append(marker)
 
-        #logger.debug("markers is: ", pf(self.markers))
-
-
     def add_pvalues(self, p_values):
         super(HumanMarkers, self).add_pvalues(p_values)
 
 
-class DatasetGroup(object):
+class DatasetGroup:
     """
     Each group has multiple datasets; each species has multiple groups.
 
@@ -342,12 +324,15 @@ class DatasetGroup(object):
     has multiple datasets associated with it.
 
     """
+
     def __init__(self, dataset, name=None):
         """This sets self.group and self.group_id"""
         if name == None:
-            self.name, self.id, self.genetic_type = fetchone(dataset.query_for_group)
+            self.name, self.id, self.genetic_type = fetchone(
+                dataset.query_for_group)
         else:
-            self.name, self.id, self.genetic_type = fetchone("SELECT InbredSet.Name, InbredSet.Id, InbredSet.GeneticType FROM InbredSet where Name='%s'" % name)
+            self.name, self.id, self.genetic_type = fetchone(
+                "SELECT InbredSet.Name, InbredSet.Id, InbredSet.GeneticType FROM InbredSet where Name='%s'" % name)
         if self.name == 'BXD300':
             self.name = "BXD"
 
@@ -366,7 +351,8 @@ class DatasetGroup(object):
 
     def get_mapping_methods(self):
 
-        mapping_id = g.db.execute("select MappingMethodId from InbredSet where Name= '%s'" % self.name).fetchone()[0]
+        mapping_id = g.db.execute(
+            "select MappingMethodId from InbredSet where Name= '%s'" % self.name).fetchone()[0]
         if mapping_id == "1":
             mapping_names = ["GEMMA", "QTLReaper", "R/qtl"]
         elif mapping_id == "2":
@@ -383,8 +369,8 @@ class DatasetGroup(object):
     def get_markers(self):
         def check_plink_gemma():
             if flat_file_exists("mapping"):
-                MAPPING_PATH = flat_files("mapping")+"/"
-                if os.path.isfile(MAPPING_PATH+self.name+".bed"):
+                MAPPING_PATH = flat_files("mapping") + "/"
+                if os.path.isfile(MAPPING_PATH + self.name + ".bed"):
                     return True
             return False
 
@@ -410,6 +396,15 @@ class DatasetGroup(object):
         if maternal and paternal:
             self.parlist = [maternal, paternal]
 
+    def get_study_samplelists(self):
+        study_sample_file = locate_ignore_error(self.name + ".json", 'study_sample_lists')
+        try:
+            f = open(study_sample_file)
+        except:
+            return []
+        study_samples = json.load(f)
+        return study_samples
+
     def get_genofiles(self):
         jsonfile = "%s/%s.json" % (webqtlConfig.GENODIR, self.name)
         try:
@@ -423,22 +418,23 @@ class DatasetGroup(object):
         result = None
         key = "samplelist:v3:" + self.name
         if USE_REDIS:
-            result = Redis.get(key)
+            result = r.get(key)
 
         if result is not None:
             self.samplelist = json.loads(result)
         else:
             logger.debug("Cache not hit")
 
-            genotype_fn = locate_ignore_error(self.name+".geno",'genotype')
+            genotype_fn = locate_ignore_error(self.name + ".geno", 'genotype')
             if genotype_fn:
-                self.samplelist = get_group_samplelists.get_samplelist("geno", genotype_fn)
+                self.samplelist = get_group_samplelists.get_samplelist(
+                    "geno", genotype_fn)
             else:
                 self.samplelist = None
 
             if USE_REDIS:
-                Redis.set(key, json.dumps(self.samplelist))
-                Redis.expire(key, 60*5)
+                r.set(key, json.dumps(self.samplelist))
+                r.expire(key, 60 * 5)
 
     def all_samples_ordered(self):
         result = []
@@ -448,32 +444,28 @@ class DatasetGroup(object):
 
     def read_genotype_file(self, use_reaper=False):
         '''Read genotype from .geno file instead of database'''
-        #genotype_1 is Dataset Object without parents and f1
-        #genotype_2 is Dataset Object with parents and f1 (not for intercross)
+        # genotype_1 is Dataset Object without parents and f1
+        # genotype_2 is Dataset Object with parents and f1 (not for intercross)
 
-        #genotype_1 = reaper.Dataset()
 
         # reaper barfs on unicode filenames, so here we ensure it's a string
         if self.genofile:
-            if "RData" in self.genofile: #ZS: This is a temporary fix; I need to change the way the JSON files that point to multiple genotype files are structured to point to other file types like RData
-                full_filename = str(locate(self.genofile.split(".")[0] + ".geno", 'genotype'))
+            if "RData" in self.genofile:  # ZS: This is a temporary fix; I need to change the way the JSON files that point to multiple genotype files are structured to point to other file types like RData
+                full_filename = str(
+                    locate(self.genofile.split(".")[0] + ".geno", 'genotype'))
             else:
                 full_filename = str(locate(self.genofile, 'genotype'))
         else:
             full_filename = str(locate(self.name + '.geno', 'genotype'))
-
-        if use_reaper:
-            genotype_1 = reaper.Dataset()
-            genotype_1.read(full_filename)
-        else:
-            genotype_1 = gen_geno_ob.genotype(full_filename)
+        genotype_1 = gen_geno_ob.genotype(full_filename)
 
         if genotype_1.type == "group" and self.parlist:
-            genotype_2 = genotype_1.add(Mat=self.parlist[0], Pat=self.parlist[1])       #, F1=_f1)
+            genotype_2 = genotype_1.add(
+                Mat=self.parlist[0], Pat=self.parlist[1])  # , F1=_f1)
         else:
             genotype_2 = genotype_1
 
-        #determine default genotype object
+        # determine default genotype object
         if self.incparentsf1 and genotype_1.type != "intercross":
             genotype = genotype_2
         else:
@@ -484,27 +476,21 @@ class DatasetGroup(object):
 
         return genotype
 
-def datasets(group_name, this_group = None):
+
+def datasets(group_name, this_group=None):
     key = "group_dataset_menu:v2:" + group_name
-    logger.debug("key is2:", key)
     dataset_menu = []
-    logger.debug("[tape4] webqtlConfig.PUBLICTHRESH:", webqtlConfig.PUBLICTHRESH)
-    logger.debug("[tape4] type webqtlConfig.PUBLICTHRESH:", type(webqtlConfig.PUBLICTHRESH))
     the_results = fetchall('''
          (SELECT '#PublishFreeze',PublishFreeze.FullName,PublishFreeze.Name
           FROM PublishFreeze,InbredSet
           WHERE PublishFreeze.InbredSetId = InbredSet.Id
             and InbredSet.Name = '%s'
-            and PublishFreeze.public > %s
-            and PublishFreeze.confidentiality < 1
           ORDER BY PublishFreeze.Id ASC)
          UNION
          (SELECT '#GenoFreeze',GenoFreeze.FullName,GenoFreeze.Name
           FROM GenoFreeze, InbredSet
           WHERE GenoFreeze.InbredSetId = InbredSet.Id
-            and InbredSet.Name = '%s'
-            and GenoFreeze.public > %s
-            and GenoFreeze.confidentiality < 1)
+            and InbredSet.Name = '%s')
          UNION
          (SELECT Tissue.Name, ProbeSetFreeze.FullName,ProbeSetFreeze.Name
           FROM ProbeSetFreeze, ProbeFreeze, InbredSet, Tissue
@@ -512,16 +498,15 @@ def datasets(group_name, this_group = None):
             and ProbeFreeze.TissueId = Tissue.Id
             and ProbeFreeze.InbredSetId = InbredSet.Id
             and InbredSet.Name like %s
-            and ProbeSetFreeze.public > %s
-            and ProbeSetFreeze.confidentiality < 1
           ORDER BY Tissue.Name, ProbeSetFreeze.OrderList DESC)
-        ''' % (group_name, webqtlConfig.PUBLICTHRESH,
-              group_name, webqtlConfig.PUBLICTHRESH,
-              "'" + group_name + "'", webqtlConfig.PUBLICTHRESH))
+        ''' % (group_name,
+               group_name,
+               "'" + group_name + "'"))
 
     sorted_results = sorted(the_results, key=lambda kv: kv[0])
 
-    pheno_inserted = False #ZS: This is kind of awkward, but need to ensure Phenotypes show up before Genotypes in dropdown
+    # ZS: This is kind of awkward, but need to ensure Phenotypes show up before Genotypes in dropdown
+    pheno_inserted = False
     geno_inserted = False
     for dataset_item in sorted_results:
         tissue_name = dataset_item[0]
@@ -529,13 +514,16 @@ def datasets(group_name, this_group = None):
         dataset_short = dataset_item[2]
         if tissue_name in ['#PublishFreeze', '#GenoFreeze']:
             if tissue_name == '#PublishFreeze' and (dataset_short == group_name + 'Publish'):
-                dataset_menu.insert(0, dict(tissue=None, datasets=[(dataset, dataset_short)]))
+                dataset_menu.insert(
+                    0, dict(tissue=None, datasets=[(dataset, dataset_short)]))
                 pheno_inserted = True
             elif pheno_inserted and tissue_name == '#GenoFreeze':
-                dataset_menu.insert(1, dict(tissue=None, datasets=[(dataset, dataset_short)]))
+                dataset_menu.insert(
+                    1, dict(tissue=None, datasets=[(dataset, dataset_short)]))
                 geno_inserted = True
             else:
-                dataset_menu.append(dict(tissue=None, datasets=[(dataset, dataset_short)]))
+                dataset_menu.append(
+                    dict(tissue=None, datasets=[(dataset, dataset_short)]))
         else:
             tissue_already_exists = False
             for i, tissue_dict in enumerate(dataset_menu):
@@ -544,15 +532,14 @@ def datasets(group_name, this_group = None):
                     break
 
             if tissue_already_exists:
-                #logger.debug("dataset_menu:", dataset_menu[i]['datasets'])
                 dataset_menu[i]['datasets'].append((dataset, dataset_short))
             else:
                 dataset_menu.append(dict(tissue=tissue_name,
-                                    datasets=[(dataset, dataset_short)]))
+                                         datasets=[(dataset, dataset_short)]))
 
     if USE_REDIS:
-        Redis.set(key, pickle.dumps(dataset_menu, pickle.HIGHEST_PROTOCOL))
-        Redis.expire(key, 60*5)
+        r.set(key, pickle.dumps(dataset_menu, pickle.HIGHEST_PROTOCOL))
+        r.expire(key, 60 * 5)
 
     if this_group != None:
         this_group._datasets = dataset_menu
@@ -560,14 +547,15 @@ def datasets(group_name, this_group = None):
     else:
         return dataset_menu
 
-class DataSet(object):
+
+class DataSet:
     """
     DataSet class defines a dataset in webqtl, can be either Microarray,
     Published phenotype, genotype, or user input dataset(temp)
 
     """
 
-    def __init__(self, name, get_samplelist = True, group_name = None):
+    def __init__(self, name, get_samplelist=True, group_name=None):
 
         assert name, "Need a name"
         self.name = name
@@ -575,30 +563,34 @@ class DataSet(object):
         self.shortname = None
         self.fullname = None
         self.type = None
-        self.data_scale = None #ZS: For example log2
+        self.data_scale = None  # ZS: For example log2
+        self.accession_id = None
 
         self.setup()
 
-        if self.type == "Temp": #Need to supply group name as input if temp trait
-            self.group = DatasetGroup(self, name=group_name)   # sets self.group and self.group_id and gets genotype
+        if self.type == "Temp":  # Need to supply group name as input if temp trait
+            # sets self.group and self.group_id and gets genotype
+            self.group = DatasetGroup(self, name=group_name)
         else:
             self.check_confidentiality()
             self.retrieve_other_names()
-            self.group = DatasetGroup(self)   # sets self.group and self.group_id and gets genotype
+            # sets self.group and self.group_id and gets genotype
+            self.group = DatasetGroup(self)
             self.accession_id = self.get_accession_id()
         if get_samplelist == True:
-             self.group.get_samplelist()
+            self.group.get_samplelist()
         self.species = species.TheSpecies(self)
 
-
-    def get_desc(self):
-        """Gets overridden later, at least for Temp...used by trait's get_given_name"""
-        return None
-
-    # Delete this eventually
-    @property
-    def riset():
-        Weve_Renamed_This_As_Group
+    def as_dict(self):
+        return {
+            'name': self.name,
+            'shortname': self.shortname,
+            'fullname': self.fullname,
+            'type': self.type,
+            'data_scale': self.data_scale,
+            'group': self.group.name,
+            'accession_id': self.accession_id
+        }
 
     def get_accession_id(self):
         if self.type == "Publish":
@@ -637,29 +629,26 @@ class DataSet(object):
 
         """
 
-
         try:
             if self.type == "ProbeSet":
                 query_args = tuple(escape(x) for x in (
-                    str(webqtlConfig.PUBLICTHRESH),
                     self.name,
                     self.name,
                     self.name))
 
                 self.id, self.name, self.fullname, self.shortname, self.data_scale, self.tissue = fetch1("""
-SELECT ProbeSetFreeze.Id, ProbeSetFreeze.Name, ProbeSetFreeze.FullName, ProbeSetFreeze.ShortName, ProbeSetFreeze.DataScale, Tissue.Name
-FROM ProbeSetFreeze, ProbeFreeze, Tissue
-WHERE ProbeSetFreeze.public > %s
-AND ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id
-AND ProbeFreeze.TissueId = Tissue.Id
-AND (ProbeSetFreeze.Name = '%s' OR ProbeSetFreeze.FullName = '%s' OR ProbeSetFreeze.ShortName = '%s')
-                """ % (query_args),"/dataset/"+self.name+".json",
-            lambda r: (r["id"],r["name"],r["full_name"],r["short_name"],r["data_scale"],r["tissue"])
+    SELECT ProbeSetFreeze.Id, ProbeSetFreeze.Name, ProbeSetFreeze.FullName, ProbeSetFreeze.ShortName, ProbeSetFreeze.DataScale, Tissue.Name
+    FROM ProbeSetFreeze, ProbeFreeze, Tissue
+    WHERE ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id
+    AND ProbeFreeze.TissueId = Tissue.Id
+    AND (ProbeSetFreeze.Name = '%s' OR ProbeSetFreeze.FullName = '%s' OR ProbeSetFreeze.ShortName = '%s')
+                """ % (query_args), "/dataset/" + self.name + ".json",
+                    lambda r: (r["id"], r["name"], r["full_name"],
+                               r["short_name"], r["data_scale"], r["tissue"])
                 )
             else:
                 query_args = tuple(escape(x) for x in (
                     (self.type + "Freeze"),
-                    str(webqtlConfig.PUBLICTHRESH),
                     self.name,
                     self.name,
                     self.name))
@@ -668,14 +657,77 @@ AND (ProbeSetFreeze.Name = '%s' OR ProbeSetFreeze.FullName = '%s' OR ProbeSetFre
                 self.id, self.name, self.fullname, self.shortname = fetchone("""
                         SELECT Id, Name, FullName, ShortName
                         FROM %s
-                        WHERE public > %s AND
-                             (Name = '%s' OR FullName = '%s' OR ShortName = '%s')
-                  """ % (query_args))
+                        WHERE (Name = '%s' OR FullName = '%s' OR ShortName = '%s')
+                    """ % (query_args))
 
         except TypeError:
-            logger.debug("Dataset {} is not yet available in GeneNetwork.".format(self.name))
+            logger.debug(
+                "Dataset {} is not yet available in GeneNetwork.".format(self.name))
             pass
 
+    def chunk_dataset(self, dataset, n):
+
+        results = {}
+
+        query = """
+                SELECT ProbeSetXRef.DataId,ProbeSet.Name
+                FROM ProbeSet, ProbeSetXRef, ProbeSetFreeze
+                WHERE ProbeSetFreeze.Name = '{}' AND
+                      ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id AND
+                      ProbeSetXRef.ProbeSetId = ProbeSet.Id
+        """.format(self.name)
+
+        # should cache this
+
+        traits_name_dict = dict(g.db.execute(query).fetchall())
+
+        for i in range(0, len(dataset), n):
+            matrix = list(dataset[i:i + n])
+            trait_name = traits_name_dict[matrix[0][0]]
+
+            my_values = [value for (trait_name, strain, value) in matrix]
+            results[trait_name] = my_values
+        return results
+
+    def get_probeset_data(self, sample_list=None, trait_ids=None):
+
+        # improvement of get trait data--->>>
+        if sample_list:
+            self.samplelist = sample_list
+
+        else:
+            self.samplelist = self.group.samplelist
+
+        if self.group.parlist != None and self.group.f1list != None:
+            if (self.group.parlist + self.group.f1list) in self.samplelist:
+                self.samplelist += self.group.parlist + self.group.f1list
+
+        query = """
+            SELECT Strain.Name, Strain.Id FROM Strain, Species
+            WHERE Strain.Name IN {}
+            and Strain.SpeciesId=Species.Id
+            and Species.name = '{}'
+            """.format(create_in_clause(self.samplelist), *mescape(self.group.species))
+        results = dict(g.db.execute(query).fetchall())
+        sample_ids = [results[item] for item in self.samplelist]
+
+        sorted_samplelist = [strain_name for strain_name, strain_id in sorted(
+            results.items(), key=lambda item: item[1])]
+
+        query = """SELECT * from ProbeSetData
+                where StrainID in {}
+                and id in (SELECT ProbeSetXRef.DataId
+                FROM (ProbeSet, ProbeSetXRef, ProbeSetFreeze)
+                WHERE ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id
+                and ProbeSetFreeze.Name = '{}'
+                and ProbeSet.Id = ProbeSetXRef.ProbeSetId)""".format(create_in_clause(sample_ids), self.name)
+
+        query_results = list(g.db.execute(query).fetchall())
+        data_results = self.chunk_dataset(query_results, len(sample_ids))
+        self.samplelist = sorted_samplelist
+        self.trait_data = data_results
+        
+
     def get_trait_data(self, sample_list=None):
         if sample_list:
             self.samplelist = sample_list
@@ -692,7 +744,6 @@ AND (ProbeSetFreeze.Name = '%s' OR ProbeSetFreeze.FullName = '%s' OR ProbeSetFre
             and Strain.SpeciesId=Species.Id
             and Species.name = '{}'
             """.format(create_in_clause(self.samplelist), *mescape(self.group.species))
-        logger.sql(query)
         results = dict(g.db.execute(query).fetchall())
         sample_ids = [results[item] for item in self.samplelist]
 
@@ -713,7 +764,7 @@ AND (ProbeSetFreeze.Name = '%s' OR ProbeSetFreeze.FullName = '%s' OR ProbeSetFre
             else:
                 query = "SELECT {}.Name,".format(escape(dataset_type))
             data_start_pos = 1
-            query += string.join(temp, ', ')
+            query += ', '.join(temp)
             query += ' FROM ({}, {}XRef, {}Freeze) '.format(*mescape(dataset_type,
                                                                      self.type,
                                                                      self.type))
@@ -731,7 +782,7 @@ AND (ProbeSetFreeze.Name = '%s' OR ProbeSetFreeze.FullName = '%s' OR ProbeSetFre
                         and {}.Id = {}XRef.{}Id
                         order by {}.Id
                         """.format(*mescape(self.type, self.type, self.type, self.name,
-                                    dataset_type, self.type, dataset_type, dataset_type))
+                                            dataset_type, self.type, dataset_type, dataset_type))
             else:
                 query += """
                         WHERE {}XRef.{}FreezeId = {}Freeze.Id
@@ -739,13 +790,9 @@ AND (ProbeSetFreeze.Name = '%s' OR ProbeSetFreeze.FullName = '%s' OR ProbeSetFre
                         and {}.Id = {}XRef.{}Id
                         order by {}.Id
                         """.format(*mescape(self.type, self.type, self.type, self.type,
-                                   self.name, dataset_type, self.type, self.type, dataset_type))
+                                            self.name, dataset_type, self.type, self.type, dataset_type))
 
-            #logger.debug("trait data query: ", query)
-
-            logger.sql(query)
             results = g.db.execute(query).fetchall()
-            #logger.debug("query results:", results)
             trait_sample_data.append(results)
 
         trait_count = len(trait_sample_data[0])
@@ -759,25 +806,23 @@ AND (ProbeSetFreeze.Name = '%s' OR ProbeSetFreeze.FullName = '%s' OR ProbeSetFre
                 self.trait_data[trait_name] += (
                     trait_sample_data[chunk_counter][trait_counter][data_start_pos:])
 
+
 class PhenotypeDataSet(DataSet):
     DS_NAME_MAP['Publish'] = 'PhenotypeDataSet'
 
     def setup(self):
-
-        #logger.debug("IS A PHENOTYPEDATASET")
-
         # Fields in the database table
         self.search_fields = ['Phenotype.Post_publication_description',
-                            'Phenotype.Pre_publication_description',
-                            'Phenotype.Pre_publication_abbreviation',
-                            'Phenotype.Post_publication_abbreviation',
-                            'PublishXRef.mean',
-                            'Phenotype.Lab_code',
-                            'Publication.PubMed_ID',
-                            'Publication.Abstract',
-                            'Publication.Title',
-                            'Publication.Authors',
-                            'PublishXRef.Id']
+                              'Phenotype.Pre_publication_description',
+                              'Phenotype.Pre_publication_abbreviation',
+                              'Phenotype.Post_publication_abbreviation',
+                              'PublishXRef.mean',
+                              'Phenotype.Lab_code',
+                              'Publication.PubMed_ID',
+                              'Publication.Abstract',
+                              'Publication.Title',
+                              'Publication.Authors',
+                              'PublishXRef.Id']
 
         # Figure out what display_fields is
         self.display_fields = ['name', 'group_code',
@@ -799,13 +844,13 @@ class PhenotypeDataSet(DataSet):
 
         # Fields displayed in the search results table header
         self.header_fields = ['Index',
-                            'Record',
-                            'Description',
-                            'Authors',
-                            'Year',
-                            'Max LRS',
-                            'Max LRS Location',
-                            'Additive Effect']
+                              'Record',
+                              'Description',
+                              'Authors',
+                              'Year',
+                              'Max LRS',
+                              'Max LRS Location',
+                              'Additive Effect']
 
         self.type = 'Publish'
 
@@ -823,7 +868,7 @@ class PhenotypeDataSet(DataSet):
         # (Urgently?) Need to write this
         pass
 
-    def get_trait_info(self, trait_list, species = ''):
+    def get_trait_info(self, trait_list, species=''):
         for this_trait in trait_list:
 
             if not this_trait.haveinfo:
@@ -831,9 +876,9 @@ class PhenotypeDataSet(DataSet):
 
             description = this_trait.post_publication_description
 
-            #If the dataset is confidential and the user has access to confidential
-            #phenotype traits, then display the pre-publication description instead
-            #of the post-publication description
+            # If the dataset is confidential and the user has access to confidential
+            # phenotype traits, then display the pre-publication description instead
+            # of the post-publication description
             if this_trait.confidential:
                 this_trait.description_display = ""
                 continue   # for now, because no authorization features
@@ -858,7 +903,7 @@ class PhenotypeDataSet(DataSet):
             if this_trait.pubmed_id:
                 this_trait.pubmed_link = webqtlConfig.PUBMEDLINK_URL % this_trait.pubmed_id
 
-            #LRS and its location
+            # LRS and its location
             this_trait.LRS_score_repr = "N/A"
             this_trait.LRS_location_repr = "N/A"
 
@@ -869,7 +914,6 @@ class PhenotypeDataSet(DataSet):
                         Geno.Name = '%s' and
                         Geno.SpeciesId = Species.Id
                 """ % (species, this_trait.locus)
-                logger.sql(query)
                 result = g.db.execute(query).fetchone()
 
                 if result:
@@ -878,7 +922,8 @@ class PhenotypeDataSet(DataSet):
                         LRS_Mb = result[1]
 
                         this_trait.LRS_score_repr = LRS_score_repr = '%3.1f' % this_trait.lrs
-                        this_trait.LRS_location_repr = LRS_location_repr = 'Chr%s: %.6f' % (LRS_Chr, float(LRS_Mb))
+                        this_trait.LRS_location_repr = LRS_location_repr = 'Chr%s: %.6f' % (
+                            LRS_Chr, float(LRS_Mb))
 
     def retrieve_sample_data(self, trait):
         query = """
@@ -898,7 +943,6 @@ class PhenotypeDataSet(DataSet):
                     Order BY
                             Strain.Name
                     """
-        logger.sql(query)
         results = g.db.execute(query, (trait, self.id)).fetchall()
         return results
 
@@ -945,12 +989,13 @@ class GenotypeDataSet(DataSet):
                 this_trait.retrieveInfo()
 
             if this_trait.chr and this_trait.mb:
-                this_trait.location_repr = 'Chr%s: %.6f' % (this_trait.chr, float(this_trait.mb) )
+                this_trait.location_repr = 'Chr%s: %.6f' % (
+                    this_trait.chr, float(this_trait.mb))
 
     def retrieve_sample_data(self, trait):
         query = """
                     SELECT
-                            Strain.Name, GenoData.value, GenoSE.error, GenoData.Id, Strain.Name2
+                            Strain.Name, GenoData.value, GenoSE.error, "N/A", Strain.Name2
                     FROM
                             (GenoData, GenoFreeze, Strain, Geno, GenoXRef)
                     left join GenoSE on
@@ -964,7 +1009,6 @@ class GenotypeDataSet(DataSet):
                     Order BY
                             Strain.Name
                     """
-        logger.sql(query)
         results = g.db.execute(query,
                                (webqtlDatabaseFunction.retrieve_species_id(self.group.name),
                                 trait, self.name)).fetchall()
@@ -1014,14 +1058,14 @@ class MrnaAssayDataSet(DataSet):
 
         # Fields displayed in the search results table header
         self.header_fields = ['Index',
-                             'Record',
-                             'Symbol',
-                             'Description',
-                             'Location',
-                             'Mean',
-                             'Max LRS',
-                             'Max LRS Location',
-                             'Additive Effect']
+                              'Record',
+                              'Symbol',
+                              'Description',
+                              'Location',
+                              'Mean',
+                              'Max LRS',
+                              'Max LRS Location',
+                              'Additive Effect']
 
         # Todo: Obsolete or rename this field
         self.type = 'ProbeSet'
@@ -1037,7 +1081,6 @@ class MrnaAssayDataSet(DataSet):
                                 ProbeSetFreeze.Name = "%s"
                 ''' % escape(self.name)
 
-
     def check_confidentiality(self):
         return geno_mrna_confidentiality(self)
 
@@ -1055,37 +1098,37 @@ class MrnaAssayDataSet(DataSet):
             if not this_trait.symbol:
                 this_trait.symbol = "N/A"
 
-            #XZ, 12/08/2008: description
-            #XZ, 06/05/2009: Rob asked to add probe target description
-            description_string = unicode(str(this_trait.description).strip(codecs.BOM_UTF8), 'utf-8')
-            target_string = unicode(str(this_trait.probe_target_description).strip(codecs.BOM_UTF8), 'utf-8')
+            # XZ, 12/08/2008: description
+            # XZ, 06/05/2009: Rob asked to add probe target description
+            description_string = str(
+                str(this_trait.description).strip(codecs.BOM_UTF8), 'utf-8')
+            target_string = str(
+                str(this_trait.probe_target_description).strip(codecs.BOM_UTF8), 'utf-8')
 
             if len(description_string) > 1 and description_string != 'None':
                 description_display = description_string
             else:
                 description_display = this_trait.symbol
 
-            if (len(description_display) > 1 and description_display != 'N/A' and
-                    len(target_string) > 1 and target_string != 'None'):
+            if (len(description_display) > 1 and description_display != 'N/A'
+                    and len(target_string) > 1 and target_string != 'None'):
                 description_display = description_display + '; ' + target_string.strip()
 
             # Save it for the jinja2 template
             this_trait.description_display = description_display
 
             if this_trait.chr and this_trait.mb:
-                this_trait.location_repr = 'Chr%s: %.6f' % (this_trait.chr, float(this_trait.mb))
+                this_trait.location_repr = 'Chr%s: %.6f' % (
+                    this_trait.chr, float(this_trait.mb))
 
-            #Get mean expression value
+            # Get mean expression value
             query = (
-            """select ProbeSetXRef.mean from ProbeSetXRef, ProbeSet
+                """select ProbeSetXRef.mean from ProbeSetXRef, ProbeSet
                 where ProbeSetXRef.ProbeSetFreezeId = %s and
                 ProbeSet.Id = ProbeSetXRef.ProbeSetId and
                 ProbeSet.Name = '%s'
             """ % (escape(str(this_trait.dataset.id)),
                    escape(this_trait.name)))
-
-            #logger.debug("query is:", pf(query))
-            logger.sql(query)
             result = g.db.execute(query).fetchone()
 
             mean = result[0] if result else 0
@@ -1093,11 +1136,11 @@ class MrnaAssayDataSet(DataSet):
             if mean:
                 this_trait.mean = "%2.3f" % mean
 
-            #LRS and its location
+            # LRS and its location
             this_trait.LRS_score_repr = 'N/A'
             this_trait.LRS_location_repr = 'N/A'
 
-            #Max LRS and its Locus location
+            # Max LRS and its Locus location
             if this_trait.lrs and this_trait.locus:
                 query = """
                     select Geno.Chr, Geno.Mb from Geno, Species
@@ -1105,24 +1148,28 @@ class MrnaAssayDataSet(DataSet):
                         Geno.Name = '{}' and
                         Geno.SpeciesId = Species.Id
                 """.format(species, this_trait.locus)
-                logger.sql(query)
                 result = g.db.execute(query).fetchone()
 
                 if result:
                     lrs_chr, lrs_mb = result
                     this_trait.LRS_score_repr = '%3.1f' % this_trait.lrs
-                    this_trait.LRS_location_repr = 'Chr%s: %.6f' % (lrs_chr, float(lrs_mb))
+                    this_trait.LRS_location_repr = 'Chr%s: %.6f' % (
+                        lrs_chr, float(lrs_mb))
 
         return trait_list
 
     def retrieve_sample_data(self, trait):
         query = """
                     SELECT
-                            Strain.Name, ProbeSetData.value, ProbeSetSE.error, ProbeSetData.Id, Strain.Name2
+                            Strain.Name, ProbeSetData.value, ProbeSetSE.error, NStrain.count, Strain.Name2
                     FROM
-                            (ProbeSetData, ProbeSetFreeze, Strain, ProbeSet, ProbeSetXRef)
+                            (ProbeSetData, ProbeSetFreeze,
+                             Strain, ProbeSet, ProbeSetXRef)
                     left join ProbeSetSE on
                             (ProbeSetSE.DataId = ProbeSetData.Id AND ProbeSetSE.StrainId = ProbeSetData.StrainId)
+                    left join NStrain on
+                            (NStrain.DataId = ProbeSetData.Id AND
+                            NStrain.StrainId = ProbeSetData.StrainId)
                     WHERE
                             ProbeSet.Name = '%s' AND ProbeSetXRef.ProbeSetId = ProbeSet.Id AND
                             ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id AND
@@ -1132,9 +1179,7 @@ class MrnaAssayDataSet(DataSet):
                     Order BY
                             Strain.Name
                     """ % (escape(trait), escape(self.name))
-        logger.sql(query)
         results = g.db.execute(query).fetchall()
-        #logger.debug("RETRIEVED RESULTS HERE:", results)
         return results
 
     def retrieve_genes(self, column_name):
@@ -1144,7 +1189,6 @@ class MrnaAssayDataSet(DataSet):
                     where ProbeSetXRef.ProbeSetFreezeId = %s and
                     ProbeSetXRef.ProbeSetId=ProbeSet.Id;
                 """ % (column_name, escape(str(self.id)))
-        logger.sql(query)
         results = g.db.execute(query).fetchall()
 
         return dict(results)
@@ -1173,48 +1217,21 @@ class TempDataSet(DataSet):
         self.shortname = 'Temp'
 
 
-    @staticmethod
-    def handle_pca(desc):
-        if 'PCA' in desc:
-            # Todo: Modernize below lines
-            desc = desc[desc.rindex(':')+1:].strip()
-        else:
-            desc = desc[:desc.index('entered')].strip()
-        return desc
-
-    def get_desc(self):
-        query = 'SELECT description FROM Temp WHERE Name=%s' % self.name
-        logger.sql(query)
-        g.db.execute(query)
-        desc = g.db.fetchone()[0]
-        desc = self.handle_pca(desc)
-        return desc
-
-    def retrieve_sample_data(self, trait):
-        query = """
-                SELECT
-                        Strain.Name, TempData.value, TempData.SE, TempData.NStrain, TempData.Id
-                FROM
-                        TempData, Temp, Strain
-                WHERE
-                        TempData.StrainId = Strain.Id AND
-                        TempData.Id = Temp.DataId AND
-                        Temp.name = '%s'
-                Order BY
-                        Strain.Name
-                """ % escape(trait.name)
-
-        logger.sql(query)
-        results = g.db.execute(query).fetchall()
-
-
 def geno_mrna_confidentiality(ob):
     dataset_table = ob.type + "Freeze"
-    #logger.debug("dataset_table [%s]: %s" % (type(dataset_table), dataset_table))
 
     query = '''SELECT Id, Name, FullName, confidentiality,
-                        AuthorisedUsers FROM %s WHERE Name = "%s"''' % (dataset_table,ob.name)
-    logger.sql(query)
+                        AuthorisedUsers FROM %s WHERE Name = "%s"''' % (dataset_table, ob.name)
+    result = g.db.execute(query)
+
+    (dataset_id,
+     name,
+     full_name,
+     confidential,
+     authorized_users) = result.fetchall()[0]
+
+    if confidential:
+        return True
     result = g.db.execute(query)
 
     (dataset_id,
diff --git a/wqflask/base/mrna_assay_tissue_data.py b/wqflask/base/mrna_assay_tissue_data.py
index 6fec5dcd..8f8e2b0a 100644
--- a/wqflask/base/mrna_assay_tissue_data.py
+++ b/wqflask/base/mrna_assay_tissue_data.py
@@ -1,5 +1,3 @@
-from __future__ import absolute_import, print_function, division
-
 import collections
 
 from flask import g
@@ -7,14 +5,15 @@ from flask import g
 from utility import db_tools
 from utility import Bunch
 
-from MySQLdb import escape_string as escape
+from utility.db_tools import escape
+from gn3.db_utils import database_connector
 
-from pprint import pformat as pf
 
 from utility.logger import getLogger
-logger = getLogger(__name__ )
+logger = getLogger(__name__)
+
 
-class MrnaAssayTissueData(object):
+class MrnaAssayTissueData:
 
     def __init__(self, gene_symbols=None):
         self.gene_symbols = gene_symbols
@@ -23,7 +22,7 @@ class MrnaAssayTissueData(object):
 
         self.data = collections.defaultdict(Bunch)
 
-        query =  '''select t.Symbol, t.GeneId, t.DataId, t.Chr, t.Mb, t.description, t.Probe_Target_Description
+        query = '''select t.Symbol, t.GeneId, t.DataId, t.Chr, t.Mb, t.description, t.Probe_Target_Description
                         from (
                         select Symbol, max(Mean) as maxmean
                         from TissueProbeSetXRef
@@ -34,29 +33,31 @@ class MrnaAssayTissueData(object):
         # Due to the limit size of TissueProbeSetFreezeId table in DB,
         # performance of inner join is acceptable.MrnaAssayTissueData(gene_symbols=symbol_list)
         if len(gene_symbols) == 0:
-            query +=  '''Symbol!='' and Symbol Is Not Null group by Symbol)
+            query += '''Symbol!='' and Symbol Is Not Null group by Symbol)
                 as x inner join TissueProbeSetXRef as t on t.Symbol = x.Symbol
                 and t.Mean = x.maxmean;
                     '''
         else:
             in_clause = db_tools.create_in_clause(gene_symbols)
 
-            #ZS: This was in the query, not sure why: http://docs.python.org/2/library/string.html?highlight=lower#string.lower
+            # ZS: This was in the query, not sure why: http://docs.python.org/2/library/string.html?highlight=lower#string.lower
             query += ''' Symbol in {} group by Symbol)
                 as x inner join TissueProbeSetXRef as t on t.Symbol = x.Symbol
                 and t.Mean = x.maxmean;
                     '''.format(in_clause)
 
-        results = g.db.execute(query).fetchall()
 
-        lower_symbols = []
+        # lower_symbols = []
+        lower_symbols = {}
         for gene_symbol in gene_symbols:
+            # lower_symbols[gene_symbol.lower()] = True
             if gene_symbol != None:
-                lower_symbols.append(gene_symbol.lower())
-
+                lower_symbols[gene_symbol.lower()] = True
+        results = list(g.db.execute(query).fetchall())
         for result in results:
             symbol = result[0]
-            if symbol.lower() in lower_symbols:
+            if symbol  is not None and lower_symbols.get(symbol.lower()):
+
                 symbol = symbol.lower()
 
                 self.data[symbol].gene_id = result.GeneId
@@ -67,16 +68,16 @@ class MrnaAssayTissueData(object):
                 self.data[symbol].probe_target_description = result.Probe_Target_Description
 
     ###########################################################################
-    #Input: cursor, symbolList (list), dataIdDict(Dict)
-    #output: symbolValuepairDict (dictionary):one dictionary of Symbol and Value Pair,
+    # Input: cursor, symbolList (list), dataIdDict(Dict)
+    # output: symbolValuepairDict (dictionary):one dictionary of Symbol and Value Pair,
     #        key is symbol, value is one list of expression values of one probeSet;
-    #function: get one dictionary whose key is gene symbol and value is tissue expression data (list type).
-    #Attention! All keys are lower case!
+    # function: get one dictionary whose key is gene symbol and value is tissue expression data (list type).
+    # Attention! All keys are lower case!
     ###########################################################################
 
     def get_symbol_values_pairs(self):
         id_list = [self.data[symbol].data_id for symbol in self.data]
-        
+
         symbol_values_dict = {}
 
         if len(id_list) > 0:
@@ -85,11 +86,13 @@ class MrnaAssayTissueData(object):
                        WHERE TissueProbeSetData.Id IN {} and
                              TissueProbeSetXRef.DataId = TissueProbeSetData.Id""".format(db_tools.create_in_clause(id_list))
 
+
             results = g.db.execute(query).fetchall()
             for result in results:
                 if result.Symbol.lower() not in symbol_values_dict:
                     symbol_values_dict[result.Symbol.lower()] = [result.value]
                 else:
-                    symbol_values_dict[result.Symbol.lower()].append(result.value)
+                    symbol_values_dict[result.Symbol.lower()].append(
+                        result.value)
 
-        return symbol_values_dict
\ No newline at end of file
+        return symbol_values_dict
diff --git a/wqflask/base/species.py b/wqflask/base/species.py
index 6d99af65..f303aabb 100644
--- a/wqflask/base/species.py
+++ b/wqflask/base/species.py
@@ -1,62 +1,66 @@
-from __future__ import absolute_import, print_function, division
+from collections import OrderedDict
+from dataclasses import dataclass
+from dataclasses import InitVar
+from typing import Optional, Dict
+from flask import g
 
-import collections
 
-from flask import Flask, g
+@dataclass
+class TheSpecies:
+    """Data related to species."""
+    dataset: Optional[Dict] = None
+    species_name: Optional[str] = None
 
-#from MySQLdb import escape_string as escape
-
-from utility import Bunch
-
-from pprint import pformat as pf
-
-from utility.logger import getLogger
-logger = getLogger(__name__ )
-
-class TheSpecies(object):
-    def __init__(self, dataset=None, species_name=None):
-        if species_name != None:
-            self.name = species_name
+    def __post_init__(self):
+        if self.species_name is not None:
+            self.name = self.species_name
             self.chromosomes = Chromosomes(species=self.name)
         else:
-            self.dataset = dataset
             self.chromosomes = Chromosomes(dataset=self.dataset)
 
-class IndChromosome(object):
-    def __init__(self, name, length):
-        self.name = name
-        self.length = length
+
+@dataclass
+class IndChromosome:
+    """Data related to IndChromosome"""
+    name: str
+    length: int
 
     @property
     def mb_length(self):
-        """Chromosome length in megabases"""
+        """Chromosome length in mega-bases"""
         return self.length / 1000000
 
-class Chromosomes(object):
-    def __init__(self, dataset=None, species=None):
-        self.chromosomes = collections.OrderedDict()
-        if species != None:
-            query = """
-                Select
-                        Chr_Length.Name, Chr_Length.OrderId, Length from Chr_Length, Species
-                where
-                        Chr_Length.SpeciesId = Species.SpeciesId AND
-                        Species.Name = '%s'
-                Order by OrderId
-                """ % species.capitalize()
-        else:
+
+@dataclass
+class Chromosomes:
+    """Data related to a chromosome"""
+    dataset: InitVar[Dict] = None
+    species: Optional[str] = None
+
+    def __post_init__(self, dataset):
+        if self.species is None:
             self.dataset = dataset
 
-            query = """
-                Select
-                        Chr_Length.Name, Chr_Length.OrderId, Length from Chr_Length, InbredSet
-                where
-                        Chr_Length.SpeciesId = InbredSet.SpeciesId AND
-                        InbredSet.Name = '%s'
-                Order by OrderId
-                """ % self.dataset.group.name
-        logger.sql(query)
+    @property
+    def chromosomes(self):
+        """Lazily fetch the chromosomes"""
+        chromosomes = OrderedDict()
+        if self.species is not None:
+            query = (
+                "SELECT Chr_Length.Name, Chr_Length.OrderId, Length "
+                "FROM Chr_Length, Species WHERE "
+                "Chr_Length.SpeciesId = Species.SpeciesId AND "
+                "Species.Name = "
+                "'%s' ORDER BY OrderId" % self.species.capitalize())
+        else:
+            query = (
+                "SELECT Chr_Length.Name, Chr_Length.OrderId, "
+                "Length FROM Chr_Length, InbredSet WHERE "
+                "Chr_Length.SpeciesId = InbredSet.SpeciesId AND "
+                "InbredSet.Name = "
+                "'%s' ORDER BY OrderId" % self.dataset.group.name)
         results = g.db.execute(query).fetchall()
-
         for item in results:
-            self.chromosomes[item.OrderId] = IndChromosome(item.Name, item.Length)
\ No newline at end of file
+            chromosomes[item.OrderId] = IndChromosome(
+                item.Name, item.Length)
+        return chromosomes
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index e454c593..f0749858 100644
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -1,33 +1,59 @@
-from __future__ import absolute_import, division, print_function
-
-import string
-import resource
-import codecs
 import requests
-
-import redis
-Redis = redis.StrictRedis()
+import simplejson as json
+from wqflask import app
 
 from base import webqtlConfig
 from base.webqtlCaseData import webqtlCaseData
 from base.data_set import create_dataset
-from db import webqtlDatabaseFunction
-from utility import webqtlUtil
 from utility import hmac
-from utility.tools import GN2_BASE_URL
+from utility.authentication_tools import check_resource_availability
+from utility.tools import GN2_BASE_URL, GN_PROXY_URL
+from utility.redis_tools import get_redis_conn, get_resource_id
 
-from wqflask import app
-
-import simplejson as json
-from MySQLdb import escape_string as escape
-from pprint import pformat as pf
+from utility.db_tools import escape
 
-from flask import Flask, g, request, url_for
+from flask import g, request, url_for
 
 from utility.logger import getLogger
-logger = getLogger(__name__ )
 
-class GeneralTrait(object):
+logger = getLogger(__name__)
+
+Redis = get_redis_conn()
+
+
+def create_trait(**kw):
+    assert bool(kw.get('dataset')) != bool(
+        kw.get('dataset_name')), "Needs dataset ob. or name"
+
+    assert bool(kw.get('name')), "Needs trait name"
+
+    if bool(kw.get('dataset')):
+        dataset = kw.get('dataset')
+    else:
+        if kw.get('dataset_name') != "Temp":
+            dataset = create_dataset(kw.get('dataset_name'))
+        else:
+            dataset = create_dataset("Temp", group_name=kw.get('group_name'))
+
+    if dataset.type == 'Publish':
+        permissions = check_resource_availability(
+            dataset, kw.get('name'))
+    else:
+        permissions = check_resource_availability(dataset)
+
+    if permissions['data'] != "no-access":
+        the_trait = GeneralTrait(**kw)
+        if the_trait.dataset.type != "Temp":
+            the_trait = retrieve_trait_info(
+                the_trait,
+                the_trait.dataset,
+                get_qtl_info=kw.get('get_qtl_info'))
+        return the_trait
+    else:
+        return None
+
+
+class GeneralTrait:
     """
     Trait class defines a trait in webqtl, can be either Microarray,
     Published phenotype, genotype, or user input trait
@@ -36,12 +62,17 @@ class GeneralTrait(object):
 
     def __init__(self, get_qtl_info=False, get_sample_info=True, **kw):
         # xor assertion
-        assert bool(kw.get('dataset')) != bool(kw.get('dataset_name')), "Needs dataset ob. or name";
-        self.name = kw.get('name')                 # Trait ID, ProbeSet ID, Published ID, etc.
+        assert bool(kw.get('dataset')) != bool(
+            kw.get('dataset_name')), "Needs dataset ob. or name"
+        # Trait ID, ProbeSet ID, Published ID, etc.
+        self.name = kw.get('name')
         if kw.get('dataset_name'):
             if kw.get('dataset_name') == "Temp":
                 temp_group = self.name.split("_")[2]
-                self.dataset = create_dataset(dataset_name = "Temp", dataset_type = "Temp", group_name = temp_group)
+                self.dataset = create_dataset(
+                    dataset_name="Temp",
+                    dataset_type="Temp",
+                    group_name=temp_group)
             else:
                 self.dataset = create_dataset(kw.get('dataset_name'))
         else:
@@ -49,8 +80,10 @@ class GeneralTrait(object):
         self.cellid = kw.get('cellid')
         self.identification = kw.get('identification', 'un-named trait')
         self.haveinfo = kw.get('haveinfo', False)
-        self.sequence = kw.get('sequence')         # Blat sequence, available for ProbeSet
+        # Blat sequence, available for ProbeSet
+        self.sequence = kw.get('sequence')
         self.data = kw.get('data', {})
+        self.view = True
 
         # Sets defaults
         self.locus = None
@@ -74,11 +107,10 @@ class GeneralTrait(object):
             elif len(name2) == 3:
                 self.dataset, self.name, self.cellid = name2
 
-        # Todo: These two lines are necessary most of the time, but perhaps not all of the time
-        # So we could add a simple if statement to short-circuit this if necessary
-        if self.dataset.type != "Temp":
-            self = retrieve_trait_info(self, self.dataset, get_qtl_info=get_qtl_info)
-        if get_sample_info != False:
+        # Todo: These two lines are necessary most of the time, but
+        # perhaps not all of the time So we could add a simple if
+        # statement to short-circuit this if necessary
+        if get_sample_info is not False:
             self = retrieve_sample_data(self, self.dataset)
 
     def export_informative(self, include_variance=0):
@@ -91,18 +123,18 @@ class GeneralTrait(object):
         vals = []
         the_vars = []
         sample_aliases = []
-        for sample_name, sample_data in self.data.items():
-            if sample_data.value != None:
-                if not include_variance or sample_data.variance != None:
+        for sample_name, sample_data in list(self.data.items()):
+            if sample_data.value is not None:
+                if not include_variance or sample_data.variance is not None:
                     samples.append(sample_name)
                     vals.append(sample_data.value)
                     the_vars.append(sample_data.variance)
                     sample_aliases.append(sample_data.name2)
-        return  samples, vals, the_vars, sample_aliases
+        return samples, vals, the_vars, sample_aliases
 
     @property
     def description_fmt(self):
-        '''Return a text formated description'''
+        """Return a text formated description"""
         if self.dataset.type == 'ProbeSet':
             if self.description:
                 formatted = self.description
@@ -117,31 +149,38 @@ class GeneralTrait(object):
                 formatted = self.post_publication_description
         else:
             formatted = "Not available"
+        if isinstance(formatted, bytes):
+            formatted = formatted.decode("utf-8")
         return formatted
 
     @property
     def alias_fmt(self):
-        '''Return a text formatted alias'''
+        """Return a text formatted alias"""
 
         alias = 'Not available'
-        if self.alias:
-            alias = string.replace(self.alias, ";", " ")
-            alias = string.join(string.split(alias), ", ")
+        if getattr(self, "alias", None):
+            alias = self.alias.replace(";", " ")
+            alias = ", ".join(alias.split())
 
         return alias
 
     @property
     def wikidata_alias_fmt(self):
-        '''Return a text formatted alias'''
+        """Return a text formatted alias"""
 
         alias = 'Not available'
         if self.symbol:
-            human_response = requests.get(GN2_BASE_URL + "gn3/gene/aliases/" + self.symbol.upper())
-            mouse_response = requests.get(GN2_BASE_URL + "gn3/gene/aliases/" + self.symbol.capitalize())
-            other_response = requests.get(GN2_BASE_URL + "gn3/gene/aliases/" + self.symbol.lower())
+            human_response = requests.get(
+                GN2_BASE_URL + "gn3/gene/aliases/" + self.symbol.upper())
+            mouse_response = requests.get(
+                GN2_BASE_URL + "gn3/gene/aliases/" + self.symbol.capitalize())
+            other_response = requests.get(
+                GN2_BASE_URL + "gn3/gene/aliases/" + self.symbol.lower())
 
             if human_response and mouse_response and other_response:
-                alias_list = json.loads(human_response.content) + json.loads(mouse_response.content) + json.loads(other_response.content)
+                alias_list = json.loads(human_response.content) + json.loads(
+                    mouse_response.content) + \
+                    json.loads(other_response.content)
 
                 filtered_aliases = []
                 seen = set()
@@ -155,33 +194,34 @@ class GeneralTrait(object):
 
         return alias
 
-
     @property
     def location_fmt(self):
-        '''Return a text formatted location
+        """Return a text formatted location
 
-        While we're at it we set self.location in case we need it later (do we?)
+        While we're at it we set self.location in case we need it
+        later (do we?)
 
-        '''
+        """
 
         if self.chr and self.mb:
-            self.location = 'Chr %s @ %s Mb'  % (self.chr,self.mb)
+            self.location = 'Chr %s @ %s Mb' % (self.chr, self.mb)
         elif self.chr:
             self.location = 'Chr %s @ Unknown position' % (self.chr)
         else:
             self.location = 'Not available'
 
         fmt = self.location
-        ##XZ: deal with direction
+        # XZ: deal with direction
         if self.strand_probe == '+':
             fmt += (' on the plus strand ')
         elif self.strand_probe == '-':
             fmt += (' on the minus strand ')
 
         return fmt
-        
+
+
 def retrieve_sample_data(trait, dataset, samplelist=None):
-    if samplelist == None:
+    if samplelist is None:
         samplelist = []
 
     if dataset.type == "Temp":
@@ -197,55 +237,71 @@ def retrieve_sample_data(trait, dataset, samplelist=None):
             all_samples_ordered = dataset.group.all_samples_ordered()
             for i, item in enumerate(results):
                 try:
-                    trait.data[all_samples_ordered[i]] = webqtlCaseData(all_samples_ordered[i], float(item))
+                    trait.data[all_samples_ordered[i]] = webqtlCaseData(
+                        all_samples_ordered[i], float(item))
                 except:
                     pass
         else:
             for item in results:
                 name, value, variance, num_cases, name2 = item
                 if not samplelist or (samplelist and name in samplelist):
-                    trait.data[name] = webqtlCaseData(*item)   #name, value, variance, num_cases)
+                    # name, value, variance, num_cases)
+                    trait.data[name] = webqtlCaseData(*item)
     return trait
 
+
 @app.route("/trait/get_sample_data")
 def get_sample_data():
     params = request.args
     trait = params['trait']
     dataset = params['dataset']
 
-    trait_ob = GeneralTrait(name=trait, dataset_name=dataset)
-
-    trait_dict = {}
-    trait_dict['name'] = trait
-    trait_dict['db'] = dataset
-    trait_dict['type'] = trait_ob.dataset.type
-    trait_dict['group'] = trait_ob.dataset.group.name
-    trait_dict['tissue'] = trait_ob.dataset.tissue
-    trait_dict['species'] = trait_ob.dataset.group.species
-    trait_dict['url'] = url_for('show_trait_page', trait_id = trait, dataset = dataset)
-    trait_dict['description'] = trait_ob.description_display
-    if trait_ob.dataset.type == "ProbeSet":
-        trait_dict['symbol'] = trait_ob.symbol
-        trait_dict['location'] = trait_ob.location_repr
-    elif trait_ob.dataset.type == "Publish":
-        if trait_ob.pubmed_id:
-            trait_dict['pubmed_link'] = trait_ob.pubmed_link
-        trait_dict['pubmed_text'] = trait_ob.pubmed_text
-
-    return json.dumps([trait_dict, {key: value.value for key, value in trait_ob.data.iteritems() }])
-    
-def jsonable(trait):
+    trait_ob = create_trait(name=trait, dataset_name=dataset)
+    if trait_ob:
+        trait_dict = {}
+        trait_dict['name'] = trait
+        trait_dict['db'] = dataset
+        trait_dict['type'] = trait_ob.dataset.type
+        trait_dict['group'] = trait_ob.dataset.group.name
+        trait_dict['tissue'] = trait_ob.dataset.tissue
+        trait_dict['species'] = trait_ob.dataset.group.species
+        trait_dict['url'] = url_for(
+            'show_trait_page', trait_id=trait, dataset=dataset)
+        if trait_ob.dataset.type == "ProbeSet":
+            trait_dict['symbol'] = trait_ob.symbol
+            trait_dict['location'] = trait_ob.location_repr
+            trait_dict['description'] = trait_ob.description_display
+        elif trait_ob.dataset.type == "Publish":
+            trait_dict['description'] = trait_ob.description_display
+            if trait_ob.pubmed_id:
+                trait_dict['pubmed_link'] = trait_ob.pubmed_link
+            trait_dict['pubmed_text'] = trait_ob.pubmed_text
+        else:
+            trait_dict['location'] = trait_ob.location_repr
+
+        return json.dumps([trait_dict, {key: value.value for
+                                        key, value in list(
+                                            trait_ob.data.items())}])
+    else:
+        return None
+
+
+def jsonable(trait, dataset=None):
     """Return a dict suitable for using as json
 
     Actual turning into json doesn't happen here though"""
 
-    dataset = create_dataset(dataset_name = trait.dataset.name, dataset_type = trait.dataset.type, group_name = trait.dataset.group.name)
-    
+    if not dataset:
+        dataset = create_dataset(dataset_name=trait.dataset.name,
+                                dataset_type=trait.dataset.type,
+                                group_name=trait.dataset.group.name)
+
     if dataset.type == "ProbeSet":
         return dict(name=trait.name,
+                    view=trait.view,
                     symbol=trait.symbol,
                     dataset=dataset.name,
-                    dataset_name = dataset.shortname,
+                    dataset_name=dataset.shortname,
                     description=trait.description_display,
                     mean=trait.mean,
                     location=trait.location_repr,
@@ -256,181 +312,142 @@ def jsonable(trait):
     elif dataset.type == "Publish":
         if trait.pubmed_id:
             return dict(name=trait.name,
+                        view=trait.view,
                         dataset=dataset.name,
-                        dataset_name = dataset.shortname,
+                        dataset_name=dataset.shortname,
                         description=trait.description_display,
                         abbreviation=trait.abbreviation,
                         authors=trait.authors,
+                        pubmed_id=trait.pubmed_id,
                         pubmed_text=trait.pubmed_text,
                         pubmed_link=trait.pubmed_link,
+                        mean=trait.mean,
                         lrs_score=trait.LRS_score_repr,
                         lrs_location=trait.LRS_location_repr,
                         additive=trait.additive
                         )
         else:
             return dict(name=trait.name,
+                        view=trait.view,
                         dataset=dataset.name,
-                        dataset_name = dataset.shortname,
+                        dataset_name=dataset.shortname,
                         description=trait.description_display,
                         abbreviation=trait.abbreviation,
                         authors=trait.authors,
                         pubmed_text=trait.pubmed_text,
+                        mean=trait.mean,
                         lrs_score=trait.LRS_score_repr,
                         lrs_location=trait.LRS_location_repr,
                         additive=trait.additive
                         )
     elif dataset.type == "Geno":
         return dict(name=trait.name,
+                    view=trait.view,
                     dataset=dataset.name,
-                    dataset_name = dataset.shortname,
+                    dataset_name=dataset.shortname,
                     location=trait.location_repr
                     )
+    elif dataset.name == "Temp":
+        return dict(name=trait.name,
+                    view=trait.view,
+                    dataset="Temp",
+                    dataset_name="Temp")
     else:
         return dict()
 
-def jsonable_table_row(trait, dataset_name, index):
-    """Return a list suitable for json and intended to be displayed in a table
-
-    Actual turning into json doesn't happen here though"""
-
-    dataset = create_dataset(dataset_name)
-    
-    if dataset.type == "ProbeSet":
-        if trait.mean == "":
-            mean = "N/A"
-        else:
-            mean = "%.3f" % round(float(trait.mean), 2)
-        if trait.additive == "":
-            additive = "N/A"
-        else:
-            additive = "%.3f" % round(float(trait.additive), 2)
-        return ['<input type="checkbox" name="searchResult" class="checkbox trait_checkbox" value="' + hmac.data_hmac('{}:{}'.format(str(trait.name), dataset.name)) + '">',
-                index,
-                '<a href="/show_trait?trait_id='+str(trait.name)+'&dataset='+dataset.name+'">'+str(trait.name)+'</a>',
-                trait.symbol,
-                trait.description_display,
-                trait.location_repr,
-                mean, 
-                trait.LRS_score_repr,
-                trait.LRS_location_repr,
-                additive]
-    elif dataset.type == "Publish":
-        if trait.additive == "":
-            additive = "N/A"
-        else:
-            additive = "%.2f" % round(float(trait.additive), 2)
-        if trait.pubmed_id:
-            return ['<input type="checkbox" name="searchResult" class="checkbox trait_checkbox" value="' + hmac.data_hmac('{}:{}'.format(str(trait.name), dataset.name)) + '">',
-                    index,
-                    '<a href="/show_trait?trait_id='+str(trait.name)+'&dataset='+dataset.name+'">'+str(trait.name)+'</a>',
-                    trait.description_display,
-                    trait.authors,
-                    '<a href="' + trait.pubmed_link + '">' + trait.pubmed_text + '</href>',
-                    trait.LRS_score_repr,
-                    trait.LRS_location_repr,
-                    additive]
-        else:
-            return ['<input type="checkbox" name="searchResult" class="checkbox trait_checkbox" value="' + hmac.data_hmac('{}:{}'.format(str(trait.name), dataset.name)) + '">',
-                    index,
-                    '<a href="/show_trait?trait_id='+str(trait.name)+'&dataset='+dataset.name+'">'+str(trait.name)+'</a>',
-                    trait.description_display,
-                    trait.authors,
-                    trait.pubmed_text,
-                    trait.LRS_score_repr,
-                    trait.LRS_location_repr,
-                    additive]
-    elif dataset.type == "Geno":
-        return ['<input type="checkbox" name="searchResult" class="checkbox trait_checkbox" value="' + hmac.data_hmac('{}:{}'.format(str(trait.name), dataset.name)) + '">',
-                index,
-                '<a href="/show_trait?trait_id='+str(trait.name)+'&dataset='+dataset.name+'">'+str(trait.name)+'</a>',
-                trait.location_repr]
-    else:
-        return dict()
 
 def retrieve_trait_info(trait, dataset, get_qtl_info=False):
     assert dataset, "Dataset doesn't exist"
-    
+
+    resource_id = get_resource_id(dataset, trait.name)
     if dataset.type == 'Publish':
-        query = """
-                SELECT
-                        PublishXRef.Id, InbredSet.InbredSetCode, Publication.PubMed_ID,
-                        Phenotype.Pre_publication_description, Phenotype.Post_publication_description, Phenotype.Original_description,
-                        Phenotype.Pre_publication_abbreviation, Phenotype.Post_publication_abbreviation, PublishXRef.mean,
-                        Phenotype.Lab_code, Phenotype.Submitter, Phenotype.Owner, Phenotype.Authorized_Users,
-                        Publication.Authors, Publication.Title, Publication.Abstract,
-                        Publication.Journal, Publication.Volume, Publication.Pages,
-                        Publication.Month, Publication.Year, PublishXRef.Sequence,
-                        Phenotype.Units, PublishXRef.comments
-                FROM
-                        PublishXRef, Publication, Phenotype, PublishFreeze, InbredSet
-                WHERE
-                        PublishXRef.Id = %s AND
-                        Phenotype.Id = PublishXRef.PhenotypeId AND
-                        Publication.Id = PublishXRef.PublicationId AND
-                        PublishXRef.InbredSetId = PublishFreeze.InbredSetId AND
-                        PublishXRef.InbredSetId = InbredSet.Id AND
-                        PublishFreeze.Id = %s
-                """ % (trait.name, dataset.id)
+        the_url = GN_PROXY_URL + "run-action?resource={}&user={}&branch=data&action=view".format(
+            resource_id, g.user_session.user_id)
+    else:
+        the_url = GN_PROXY_URL + "run-action?resource={}&user={}&branch=data&action=view&trait={}".format(
+            resource_id, g.user_session.user_id, trait.name)
 
-        logger.sql(query)
-        trait_info = g.db.execute(query).fetchone()
-
-
-    #XZ, 05/08/2009: Xiaodong add this block to use ProbeSet.Id to find the probeset instead of just using ProbeSet.Name
-    #XZ, 05/08/2009: to avoid the problem of same probeset name from different platforms.
-    elif dataset.type == 'ProbeSet':
-        display_fields_string = ', ProbeSet.'.join(dataset.display_fields)
-        display_fields_string = 'ProbeSet.' + display_fields_string
-        query = """
-                SELECT %s
-                FROM ProbeSet, ProbeSetFreeze, ProbeSetXRef
-                WHERE
-                        ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id AND
-                        ProbeSetXRef.ProbeSetId = ProbeSet.Id AND
-                        ProbeSetFreeze.Name = '%s' AND
-                        ProbeSet.Name = '%s'
-                """ % (escape(display_fields_string),
-                       escape(dataset.name),
-                       escape(str(trait.name)))
-        logger.sql(query)
-        trait_info = g.db.execute(query).fetchone()
-    #XZ, 05/08/2009: We also should use Geno.Id to find marker instead of just using Geno.Name
-    # to avoid the problem of same marker name from different species.
-    elif dataset.type == 'Geno':
-        display_fields_string = string.join(dataset.display_fields,',Geno.')
-        display_fields_string = 'Geno.' + display_fields_string
-        query = """
-                SELECT %s
-                FROM Geno, GenoFreeze, GenoXRef
-                WHERE
-                        GenoXRef.GenoFreezeId = GenoFreeze.Id AND
-                        GenoXRef.GenoId = Geno.Id AND
-                        GenoFreeze.Name = '%s' AND
-                        Geno.Name = '%s'
-                """ % (escape(display_fields_string),
-                       escape(dataset.name),
-                       escape(trait.name))
-        logger.sql(query)
-        trait_info = g.db.execute(query).fetchone()
-    else: #Temp type
-        query = """SELECT %s FROM %s WHERE Name = %s"""
-        logger.sql(query)
-        trait_info = g.db.execute(query,
-                                  (string.join(dataset.display_fields,','),
-                                               dataset.type, trait.name)).fetchone()
+    try:
+        response = requests.get(the_url).content
+        trait_info = json.loads(response)
+    except:  # ZS: I'm assuming the trait is viewable if the try fails for some reason; it should never reach this point unless the user has privileges, since that's dealt with in create_trait
+        if dataset.type == 'Publish':
+            query = """
+                    SELECT
+                            PublishXRef.Id, InbredSet.InbredSetCode, Publication.PubMed_ID,
+                            CAST(Phenotype.Pre_publication_description AS BINARY),
+                            CAST(Phenotype.Post_publication_description AS BINARY),
+                            CAST(Phenotype.Original_description AS BINARY),
+                            CAST(Phenotype.Pre_publication_abbreviation AS BINARY),
+                            CAST(Phenotype.Post_publication_abbreviation AS BINARY), PublishXRef.mean,
+                            Phenotype.Lab_code, Phenotype.Submitter, Phenotype.Owner, Phenotype.Authorized_Users,
+                            CAST(Publication.Authors AS BINARY), CAST(Publication.Title AS BINARY), CAST(Publication.Abstract AS BINARY),
+                            CAST(Publication.Journal AS BINARY), Publication.Volume, Publication.Pages,
+                            Publication.Month, Publication.Year, PublishXRef.Sequence,
+                            Phenotype.Units, PublishXRef.comments
+                    FROM
+                            PublishXRef, Publication, Phenotype, PublishFreeze, InbredSet
+                    WHERE
+                            PublishXRef.Id = %s AND
+                            Phenotype.Id = PublishXRef.PhenotypeId AND
+                            Publication.Id = PublishXRef.PublicationId AND
+                            PublishXRef.InbredSetId = PublishFreeze.InbredSetId AND
+                            PublishXRef.InbredSetId = InbredSet.Id AND
+                            PublishFreeze.Id = %s
+                    """ % (trait.name, dataset.id)
+
+            logger.sql(query)
+            trait_info = g.db.execute(query).fetchone()
+
+        # XZ, 05/08/2009: Xiaodong add this block to use ProbeSet.Id to find the probeset instead of just using ProbeSet.Name
+        # XZ, 05/08/2009: to avoid the problem of same probeset name from different platforms.
+        elif dataset.type == 'ProbeSet':
+            display_fields_string = ', ProbeSet.'.join(dataset.display_fields)
+            display_fields_string = 'ProbeSet.' + display_fields_string
+            query = """
+                    SELECT %s
+                    FROM ProbeSet, ProbeSetFreeze, ProbeSetXRef
+                    WHERE
+                            ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id AND
+                            ProbeSetXRef.ProbeSetId = ProbeSet.Id AND
+                            ProbeSetFreeze.Name = '%s' AND
+                            ProbeSet.Name = '%s'
+                    """ % (escape(display_fields_string),
+                           escape(dataset.name),
+                           escape(str(trait.name)))
+            logger.sql(query)
+            trait_info = g.db.execute(query).fetchone()
+        # XZ, 05/08/2009: We also should use Geno.Id to find marker instead of just using Geno.Name
+        # to avoid the problem of same marker name from different species.
+        elif dataset.type == 'Geno':
+            display_fields_string = ',Geno.'.join(dataset.display_fields)
+            display_fields_string = 'Geno.' + display_fields_string
+            query = """
+                    SELECT %s
+                    FROM Geno, GenoFreeze, GenoXRef
+                    WHERE
+                            GenoXRef.GenoFreezeId = GenoFreeze.Id AND
+                            GenoXRef.GenoId = Geno.Id AND
+                            GenoFreeze.Name = '%s' AND
+                            Geno.Name = '%s'
+                    """ % (escape(display_fields_string),
+                           escape(dataset.name),
+                           escape(trait.name))
+            logger.sql(query)
+            trait_info = g.db.execute(query).fetchone()
+        else:  # Temp type
+            query = """SELECT %s FROM %s WHERE Name = %s"""
+            logger.sql(query)
+            trait_info = g.db.execute(query,
+                                      ','.join(dataset.display_fields),
+                                      dataset.type, trait.name).fetchone()
 
     if trait_info:
         trait.haveinfo = True
-
-        #XZ: assign SQL query result to trait attributes.
         for i, field in enumerate(dataset.display_fields):
             holder = trait_info[i]
-            # if isinstance(trait_info[i], basestring):
-            #     logger.debug("HOLDER:", holder)
-            #     logger.debug("HOLDER2:", holder.decode(encoding='latin1'))
-            #     holder = unicode(trait_info[i], "utf-8", "ignore")
-            if isinstance(trait_info[i], basestring):
-                holder = holder.encode('latin1')
+            if isinstance(holder, bytes):
+                holder = holder.decode("utf-8", errors="ignore")
             setattr(trait, field, holder)
 
         if dataset.type == 'Publish':
@@ -443,29 +460,18 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
 
             description = trait.post_publication_description
 
-            #If the dataset is confidential and the user has access to confidential
-            #phenotype traits, then display the pre-publication description instead
-            #of the post-publication description
-            if trait.confidential:
+            # If the dataset is confidential and the user has access to confidential
+            # phenotype traits, then display the pre-publication description instead
+            # of the post-publication description
+            trait.description_display = "N/A"
+            if not trait.pubmed_id:
                 trait.abbreviation = trait.pre_publication_abbreviation
-                trait.description_display = trait.pre_publication_description
-
-                #if not webqtlUtil.hasAccessToConfidentialPhenotypeTrait(
-                #        privilege=self.dataset.privilege,
-                #        userName=self.dataset.userName,
-                #        authorized_users=self.authorized_users):
-                #
-                #    description = self.pre_publication_description
+                if trait.pre_publication_description:
+                    trait.description_display = trait.pre_publication_description
             else:
                 trait.abbreviation = trait.post_publication_abbreviation
                 if description:
                     trait.description_display = description.strip()
-                else:
-                    trait.description_display = ""
-
-            trait.abbreviation = unicode(str(trait.abbreviation).strip(codecs.BOM_UTF8), 'utf-8', errors="replace")
-            trait.description_display = unicode(str(trait.description_display).strip(codecs.BOM_UTF8), 'utf-8', errors="replace")
-            trait.authors = unicode(str(trait.authors).strip(codecs.BOM_UTF8), 'utf-8', errors="replace")
 
             if not trait.year.isdigit():
                 trait.pubmed_text = "N/A"
@@ -476,16 +482,17 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
                 trait.pubmed_link = webqtlConfig.PUBMEDLINK_URL % trait.pubmed_id
 
         if dataset.type == 'ProbeSet' and dataset.group:
-            description_string = unicode(str(trait.description).strip(codecs.BOM_UTF8), 'utf-8')
-            target_string = unicode(str(trait.probe_target_description).strip(codecs.BOM_UTF8), 'utf-8')
+            description_string = trait.description
+            target_string = trait.probe_target_description
 
-            if len(description_string) > 1 and description_string != 'None':
+            if str(description_string or "") != "" and description_string != 'None':
                 description_display = description_string
             else:
                 description_display = trait.symbol
 
-            if (len(description_display) > 1 and description_display != 'N/A' and
-                    len(target_string) > 1 and target_string != 'None'):
+            if (str(description_display or "") != ""
+                and description_display != 'N/A'
+                    and str(target_string or "") != "" and target_string != 'None'):
                 description_display = description_display + '; ' + target_string.strip()
 
             # Save it for the jinja2 template
@@ -493,15 +500,17 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
 
             trait.location_repr = 'N/A'
             if trait.chr and trait.mb:
-                trait.location_repr = 'Chr%s: %.6f' % (trait.chr, float(trait.mb))
+                trait.location_repr = 'Chr%s: %.6f' % (
+                    trait.chr, float(trait.mb))
 
         elif dataset.type == "Geno":
             trait.location_repr = 'N/A'
             if trait.chr and trait.mb:
-                trait.location_repr = 'Chr%s: %.6f' % (trait.chr, float(trait.mb))
+                trait.location_repr = 'Chr%s: %.6f' % (
+                    trait.chr, float(trait.mb))
 
         if get_qtl_info:
-            #LRS and its location
+            # LRS and its location
             trait.LRS_score_repr = "N/A"
             trait.LRS_location_repr = "N/A"
             trait.locus = trait.locus_chr = trait.locus_mb = trait.lrs = trait.pvalue = trait.additive = ""
@@ -571,12 +580,12 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
                         trait.locus = trait.locus_chr = trait.locus_mb = trait.additive = ""
                 else:
                     trait.locus = trait.lrs = trait.additive = ""
-
-            if (dataset.type == 'Publish' or dataset.type == "ProbeSet") and trait.locus_chr != "" and trait.locus_mb != "":
-                trait.LRS_location_repr = LRS_location_repr = 'Chr%s: %.6f' % (trait.locus_chr, float(trait.locus_mb))
-                if trait.lrs != "":
+            if (dataset.type == 'Publish' or dataset.type == "ProbeSet") and str(trait.locus_chr or "") != "" and str(trait.locus_mb or "") != "":
+                trait.LRS_location_repr = LRS_location_repr = 'Chr%s: %.6f' % (
+                    trait.locus_chr, float(trait.locus_mb))
+                if str(trait.lrs or "") != "":
                     trait.LRS_score_repr = LRS_score_repr = '%3.1f' % trait.lrs
     else:
-        raise KeyError, `trait.name`+' information is not found in the database.'
-        
-    return trait
\ No newline at end of file
+        raise KeyError(repr(trait.name)
+                       + ' information is not found in the database.')
+    return trait
diff --git a/wqflask/base/webqtlCaseData.py b/wqflask/base/webqtlCaseData.py
index d8487f01..25b6cb8a 100644
--- a/wqflask/base/webqtlCaseData.py
+++ b/wqflask/base/webqtlCaseData.py
@@ -19,8 +19,7 @@
 # This module is used by GeneNetwork project (www.genenetwork.org)
 #
 # Created by GeneNetwork Core Team 2010/08/10
-#
-# Last updated by GeneNetwork Core Team 2010/10/20
+
 
 from utility.logger import getLogger
 logger = getLogger(__name__)
@@ -29,58 +28,57 @@ import utility.tools
 
 utility.tools.show_settings()
 
-class webqtlCaseData(object):
+
+class webqtlCaseData:
     """one case data in one trait"""
 
     def __init__(self, name, value=None, variance=None, num_cases=None, name2=None):
         self.name = name
-        self.name2 = name2                  # Other name (for traits like BXD65a)
+        # Other name (for traits like BXD65a)
+        self.name2 = name2
         self.value = value                  # Trait Value
         self.variance = variance            # Trait Variance
         self.num_cases = num_cases          # Number of individuals/cases
         self.extra_attributes = None
-        self.this_id = None   # Set a sane default (can't be just "id" cause that's a reserved word)
+        # Set a sane default (can't be just "id" cause that's a reserved word)
+        self.this_id = None
         self.outlier = None   # Not set to True/False until later
 
     def __repr__(self):
-        str = "<webqtlCaseData> "
-        if self.value != None:
-            str += "value=%2.3f" % self.value
-        if self.variance != None:
-            str += " variance=%2.3f" % self.variance
+        case_data_string = "<webqtlCaseData> "
+        if self.value is not None:
+            case_data_string += "value=%2.3f" % self.value
+        if self.variance is not None:
+            case_data_string += " variance=%2.3f" % self.variance
         if self.num_cases:
-            str += " ndata=%s" % self.num_cases
+            case_data_string += " ndata=%s" % self.num_cases
         if self.name:
-            str += " name=%s" % self.name
+            case_data_string += " name=%s" % self.name
         if self.name2:
-            str += " name2=%s" % self.name2
-        return str
+            case_data_string += " name2=%s" % self.name2
+        return case_data_string
 
     @property
     def class_outlier(self):
         """Template helper"""
         if self.outlier:
             return "outlier"
-        else:
-            return ""
+        return ""
 
     @property
     def display_value(self):
-        if self.value != None:
+        if self.value is not None:
             return "%2.3f" % self.value
-        else:
-            return "x"
+        return "x"
 
     @property
     def display_variance(self):
-        if self.variance != None:
+        if self.variance is not None:
             return "%2.3f" % self.variance
-        else:
-            return "x"
+        return "x"
 
     @property
     def display_num_cases(self):
-        if self.num_cases != None:
+        if self.num_cases is not None:
             return "%s" % self.num_cases
-        else:
-            return "x"
+        return "x"
diff --git a/wqflask/base/webqtlConfig.py b/wqflask/base/webqtlConfig.py
index 55407123..39947158 100644
--- a/wqflask/base/webqtlConfig.py
+++ b/wqflask/base/webqtlConfig.py
@@ -1,4 +1,4 @@
-#########################################'
+# '
 #      Environment Variables - public
 #
 # Note: much of this needs to handled by the settings/environment
@@ -10,31 +10,35 @@
 
 from utility.tools import valid_path, mk_dir, assert_dir, assert_writable_dir, flat_files, TEMPDIR
 
-#Debug Level
-#1 for debug, mod python will reload import each time
+# Debug Level
+# 1 for debug, mod python will reload import each time
 DEBUG = 1
 
-#USER privilege
-USERDICT = {'guest':1,'user':2, 'admin':3, 'root':4}
+# USER privilege
+USERDICT = {'guest': 1, 'user': 2, 'admin': 3, 'root': 4}
 
-#minimum number of informative strains
+# Set privileges
+SUPER_PRIVILEGES = {'data': 'edit', 'metadata': 'edit', 'admin': 'edit-admins'}
+DEFAULT_PRIVILEGES = {'data': 'view', 'metadata': 'view', 'admin': 'not-admin'}
+
+# minimum number of informative strains
 KMININFORMATIVE = 5
 
-#Daily download limit from one IP
+# Daily download limit from one IP
 DAILYMAXIMUM = 1000
 
-#maximum LRS value
+# maximum LRS value
 MAXLRS = 460.0
 
-#MINIMUM Database public value
+# MINIMUM Database public value
 PUBLICTHRESH = 0
 
-#EXTERNAL LINK ADDRESSES
+# EXTERNAL LINK ADDRESSES
 PUBMEDLINK_URL = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=%s&dopt=Abstract"
 UCSC_BLAT = 'http://genome.ucsc.edu/cgi-bin/hgBlat?org=%s&db=%s&type=0&sort=0&output=0&userSeq=%s'
 UTHSC_BLAT = 'http://ucscbrowser.genenetwork.org/cgi-bin/hgBlat?org=%s&db=%s&type=0&sort=0&output=0&userSeq=%s'
 UTHSC_BLAT2 = 'http://ucscbrowserbeta.genenetwork.org/cgi-bin/hgBlat?org=%s&db=%s&type=0&sort=0&output=0&userSeq=%s'
-GENOMEBROWSER_URL="https://genome.ucsc.edu/cgi-bin/hgTracks?db=%s&position=%s"
+GENOMEBROWSER_URL = "https://genome.ucsc.edu/cgi-bin/hgTracks?db=%s&position=%s"
 NCBI_LOCUSID = "http://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&dopt=Graphics&list_uids=%s"
 GENBANK_ID = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Nucleotide&cmd=search&doptcmdl=DocSum&term=%s"
 OMIM_ID = "http://www.ncbi.nlm.nih.gov/omim/%s"
@@ -52,26 +56,28 @@ GEMMA_URL = "http://www.chibi.ubc.ca/Gemma/gene/showGene.html?ncbiid=%s"
 ABA_URL = "http://mouse.brain-map.org/search/show?search_type=gene&search_term=%s"
 EBIGWAS_URL = "https://www.ebi.ac.uk/gwas/search?query=%s"
 WIKI_PI_URL = "http://severus.dbmi.pitt.edu/wiki-pi/index.php/search?q=%s"
-ENSEMBLETRANSCRIPT_URL="http://useast.ensembl.org/Mus_musculus/Transcript/Idhistory?t=%s"
+ENSEMBLETRANSCRIPT_URL = "http://useast.ensembl.org/Mus_musculus/Transcript/Idhistory?t=%s"
 DBSNP = 'http://ensembl.org/Mus_musculus/Variation/Population?v=%s'
 PROTEIN_ATLAS_URL = "http://www.proteinatlas.org/search/%s"
 OPEN_TARGETS_URL = "https://genetics.opentargets.org/gene/%s"
 UNIPROT_URL = "https://www.uniprot.org/uniprot/%s"
 RGD_URL = "https://rgd.mcw.edu/rgdweb/elasticResults.html?term=%s&category=Gene&species=%s"
 PHENOGEN_URL = "https://phenogen.org/gene.jsp?speciesCB=Rn&auto=Y&geneTxt=%s&genomeVer=rn6&section=geneEQTL"
+RRID_MOUSE_URL = "https://www.jax.org/strain/%s"
+RRID_RAT_URL = "https://rgd.mcw.edu/rgdweb/report/strain/main.html?id=%s"
 
 # Temporary storage (note that this TMPDIR can be set as an
 # environment variable - use utility.tools.TEMPDIR when you
 # want to reach this base dir
 assert_writable_dir(TEMPDIR)
 
-TMPDIR               = mk_dir(TEMPDIR+'/gn2/')
+TMPDIR = mk_dir(TEMPDIR + '/gn2/')
 assert_writable_dir(TMPDIR)
 
-CACHEDIR             = mk_dir(TMPDIR+'/cache/')
+CACHEDIR = mk_dir(TMPDIR + '/cache/')
 # We can no longer write into the git tree:
-GENERATED_IMAGE_DIR  = mk_dir(TMPDIR+'generated/')
-GENERATED_TEXT_DIR   = mk_dir(TMPDIR+'generated_text/')
+GENERATED_IMAGE_DIR = mk_dir(TMPDIR + 'generated/')
+GENERATED_TEXT_DIR = mk_dir(TMPDIR + 'generated_text/')
 
 # Make sure we have permissions to access these
 assert_writable_dir(CACHEDIR)
@@ -79,12 +85,12 @@ assert_writable_dir(GENERATED_IMAGE_DIR)
 assert_writable_dir(GENERATED_TEXT_DIR)
 
 # Flat file directories
-GENODIR              = flat_files('genotype')+'/'
+GENODIR = flat_files('genotype') + '/'
 assert_dir(GENODIR)
-assert_dir(GENODIR+'bimbam') # for gemma
+# assert_dir(GENODIR+'bimbam') # for gemma
 
 # JSON genotypes are OBSOLETE
-JSON_GENODIR         = flat_files('genotype/json')+'/'
+JSON_GENODIR = flat_files('genotype/json') + '/'
 if not valid_path(JSON_GENODIR):
     # fall back on old location (move the dir, FIXME)
     JSON_GENODIR = flat_files('json')
@@ -92,4 +98,4 @@ if not valid_path(JSON_GENODIR):
 # Are we using the following...?
 PORTADDR = "http://50.16.251.170"
 INFOPAGEHREF = '/dbdoc/%s.html'
-CGIDIR = '/webqtl/' #XZ: The variable name 'CGIDIR' should be changed to 'PYTHONDIR'
+CGIDIR = '/webqtl/'  # XZ: The variable name 'CGIDIR' should be changed to 'PYTHONDIR'