Merge branch 'testing' into scroller_testing

42 files changed, 1388 insertions, 558 deletions

diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index afffe780..2f1549ae 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -150,10 +150,12 @@ Publish or ProbeSet. E.g.
             "geno": "Geno",
         }
 
+        group_name = name
         if t in ['pheno', 'other_pheno']:
-            name = name.replace("Publish", "")
+            group_name = name.replace("Publish", "")
 
-        if bool(len(g.db.execute(sql_query_mapping[t].format(name)).fetchone())):
+        results = g.db.execute(sql_query_mapping[t].format(group_name)).fetchone()
+        if results:
             self.datasets[name] = dataset_name_mapping[t]
             self.redis_instance.set("dataset_structure", json.dumps(self.datasets))
             return True
@@ -1173,40 +1175,6 @@ class TempDataSet(DataSet):
         self.fullname = 'Temporary Storage'
         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"
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index 7666348e..7ebbc4bb 100644
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -1,4 +1,10 @@
 from __future__ import absolute_import, division, print_function
+from utility.logger import getLogger
+from flask import Flask, g, request, url_for, redirect, make_response, render_template
+from pprint import pformat as pf
+from MySQLdb import escape_string as escape
+import simplejson as json
+from wqflask import app
 
 import os
 import string
@@ -16,22 +22,19 @@ from utility import webqtlUtil
 from utility import hmac
 from utility.authentication_tools import check_resource_availability
 from utility.tools import GN2_BASE_URL, GN_VERSION
-from utility.redis_tools import get_redis_conn, get_resource_id, get_resource_info
-Redis = get_redis_conn()
+from utility.redis_tools import get_redis_conn
+from utility.redis_tools import get_resource_id
+from utility.redis_tools import get_resource_info
 
-from wqflask import app
+Redis = get_redis_conn()
 
-import simplejson as json
-from MySQLdb import escape_string as escape
-from pprint import pformat as pf
 
-from flask import Flask, g, request, url_for, redirect, make_response, render_template
+logger = getLogger(__name__)
 
-from utility.logger import getLogger
-logger = getLogger(__name__ )
 
 def create_trait(**kw):
-    assert bool(kw.get('dataset')) != bool(kw.get('dataset_name')), "Needs dataset ob. or name";
+    assert bool(kw.get('dataset')) != bool(
+        kw.get('dataset_name')), "Needs dataset ob. or name"
 
     permitted = True
     if kw.get('name'):
@@ -43,18 +46,21 @@ def create_trait(**kw):
 
         if kw.get('dataset_name') != "Temp":
             if dataset.type == 'Publish':
-                permissions = check_resource_availability(dataset, kw.get('name'))
+                permissions = check_resource_availability(
+                    dataset, kw.get('name'))
             else:
                 permissions = check_resource_availability(dataset)
 
     if "view" in permissions['data']:
         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'))
+            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(object):
     """
     Trait class defines a trait in webqtl, can be either Microarray,
@@ -64,12 +70,15 @@ 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:
@@ -77,7 +86,8 @@ 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
 
@@ -125,11 +135,11 @@ class GeneralTrait(object):
                     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
@@ -149,7 +159,7 @@ class GeneralTrait(object):
 
     @property
     def alias_fmt(self):
-        '''Return a text formatted alias'''
+        """Return a text formatted alias"""
 
         alias = 'Not available'
         if getattr(self, "alias", None):
@@ -160,16 +170,20 @@ class GeneralTrait(object):
 
     @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()
@@ -183,31 +197,31 @@ 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?)
 
-        '''
+        """
 
         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:
         samplelist = []
@@ -225,16 +239,19 @@ 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
@@ -250,7 +267,8 @@ def get_sample_data():
         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['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
@@ -260,22 +278,24 @@ def get_sample_data():
                 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() }])
+        return json.dumps([trait_dict, {key: value.value for key, value in trait_ob.data.iteritems()}])
     else:
         return None
-    
+
+
 def jsonable(trait):
     """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)
-    
+    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,
                     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,
@@ -287,7 +307,7 @@ def jsonable(trait):
         if trait.pubmed_id:
             return dict(name=trait.name,
                         dataset=dataset.name,
-                        dataset_name = dataset.shortname,
+                        dataset_name=dataset.shortname,
                         description=trait.description_display,
                         abbreviation=trait.abbreviation,
                         authors=trait.authors,
@@ -300,7 +320,7 @@ def jsonable(trait):
         else:
             return dict(name=trait.name,
                         dataset=dataset.name,
-                        dataset_name = dataset.shortname,
+                        dataset_name=dataset.shortname,
                         description=trait.description_display,
                         abbreviation=trait.abbreviation,
                         authors=trait.authors,
@@ -312,19 +332,20 @@ def jsonable(trait):
     elif dataset.type == "Geno":
         return dict(name=trait.name,
                     dataset=dataset.name,
-                    dataset_name = dataset.shortname,
+                    dataset_name=dataset.shortname,
                     location=trait.location_repr
                     )
     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"
@@ -336,11 +357,13 @@ def jsonable_table_row(trait, dataset_name, index):
             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>',
+                '<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, 
+                mean,
                 trait.LRS_score_repr,
                 trait.LRS_location_repr,
                 additive]
@@ -352,7 +375,9 @@ def jsonable_table_row(trait, dataset_name, index):
         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>',
+                    '<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>',
@@ -362,7 +387,9 @@ def jsonable_table_row(trait, dataset_name, index):
         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>',
+                    '<a href="/show_trait?trait_id=' +
+                    str(trait.name)+'&dataset='+dataset.name +
+                    '">'+str(trait.name)+'</a>',
                     trait.description_display,
                     trait.authors,
                     trait.pubmed_text,
@@ -372,7 +399,9 @@ def jsonable_table_row(trait, dataset_name, index):
     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>',
+                '<a href="/show_trait?trait_id=' +
+                str(trait.name)+'&dataset='+dataset.name +
+                '">'+str(trait.name)+'</a>',
                 trait.location_repr]
     else:
         return dict()
@@ -383,14 +412,16 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
 
     resource_id = get_resource_id(dataset, trait.name)
     if dataset.type == 'Publish':
-        the_url = "http://localhost:8080/run-action?resource={}&user={}&branch=data&action=view".format(resource_id, g.user_session.user_id)
+        the_url = "http://localhost:8080/run-action?resource={}&user={}&branch=data&action=view".format(
+            resource_id, g.user_session.user_id)
     else:
-        the_url = "http://localhost:8080/run-action?resource={}&user={}&branch=data&action=view&trait={}".format(resource_id, g.user_session.user_id, trait.name)
+        the_url = "http://localhost:8080/run-action?resource={}&user={}&branch=data&action=view&trait={}".format(
+            resource_id, g.user_session.user_id, trait.name)
 
     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
+    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
@@ -419,8 +450,8 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
             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.
+        # 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
@@ -433,14 +464,15 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
                             ProbeSetFreeze.Name = '%s' AND
                             ProbeSet.Name = '%s'
                     """ % (escape(display_fields_string),
-                        escape(dataset.name),
-                        escape(str(trait.name)))
+                           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
+        # 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 = string.join(
+                dataset.display_fields, ',Geno.')
             display_fields_string = 'Geno.' + display_fields_string
             query = """
                     SELECT %s
@@ -451,21 +483,21 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
                             GenoFreeze.Name = '%s' AND
                             Geno.Name = '%s'
                     """ % (escape(display_fields_string),
-                        escape(dataset.name),
-                        escape(trait.name))
+                           escape(dataset.name),
+                           escape(trait.name))
             logger.sql(query)
             trait_info = g.db.execute(query).fetchone()
-        else: #Temp type
+        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()
+                                      (string.join(dataset.display_fields, ','),
+                                       dataset.type, trait.name)).fetchone()
 
     if trait_info:
         trait.haveinfo = True
         for i, field in enumerate(dataset.display_fields):
-            holder =  trait_info[i]
+            holder = trait_info[i]
             setattr(trait, field, holder)
 
         if dataset.type == 'Publish':
@@ -478,9 +510,9 @@ 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 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:
                 trait.abbreviation = trait.pre_publication_abbreviation
                 trait.description_display = trait.pre_publication_description
@@ -491,9 +523,12 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
                 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")
+            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"
@@ -504,16 +539,19 @@ 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 = unicode(
+                str(trait.description).strip(codecs.BOM_UTF8), 'utf-8')
+            target_string = unicode(
+                str(trait.probe_target_description).strip(codecs.BOM_UTF8), 'utf-8')
 
-            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
@@ -521,15 +559,17 @@ 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 = ""
@@ -599,12 +639,12 @@ 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, `trait.name`+ ' information is not found in the database.'
+
+    return trait
diff --git a/wqflask/tests/base/test_data_set.py b/wqflask/tests/base/test_data_set.py
index 94780a5d..dd7f5051 100644
--- a/wqflask/tests/base/test_data_set.py
+++ b/wqflask/tests/base/test_data_set.py
@@ -66,7 +66,7 @@ class TestDataSetTypes(unittest.TestCase):
     @mock.patch('base.data_set.g')
     def test_set_dataset_key_mrna(self, db_mock):
         with app.app_context():
-            db_mock.db.execute.return_value = [1, 2, 3]
+            db_mock.db.execute.return_value.fetchone.return_value = [1, 2, 3]
             redis_mock = mock.Mock()
             redis_mock.get.return_value = self.test_dataset
             data_set = DatasetType(redis_mock)
@@ -84,7 +84,7 @@ class TestDataSetTypes(unittest.TestCase):
     @mock.patch('base.data_set.g')
     def test_set_dataset_key_pheno(self, db_mock):
         with app.app_context():
-            db_mock.db.execute.return_value = [1, 2, 3]
+            db_mock.db.execute.return_value.fetchone.return_value = [1, 2, 3]
             redis_mock = mock.Mock()
             redis_mock.get.return_value = self.test_dataset
             data_set = DatasetType(redis_mock)
@@ -93,7 +93,6 @@ class TestDataSetTypes(unittest.TestCase):
             redis_mock.set.assert_called_once_with(
                 "dataset_structure",
                 '{"Aging-Brain-UCIPublish": "Publish", "AKXDGeno": "Geno", "B139_K_1206_M": "ProbeSet", "AD-cases-controls-MyersGeno": "Geno", "AD-cases-controls-MyersPublish": "Publish", "All Phenotypes": "Publish", "Test": "Publish", "AXBXAPublish": "Publish", "B139_K_1206_R": "ProbeSet", "AXBXAGeno": "Geno"}')
-            expected_db_call = """"""
             db_mock.db.execute.assert_called_with(
                 ("SELECT InfoFiles.GN_AccesionId " +
                  "FROM InfoFiles, PublishFreeze, InbredSet " +
@@ -105,7 +104,7 @@ class TestDataSetTypes(unittest.TestCase):
     @mock.patch('base.data_set.g')
     def test_set_dataset_other_pheno(self, db_mock):
         with app.app_context():
-            db_mock.db.execute.return_value = [1, 2, 3]
+            db_mock.db.execute.return_value.fetchone.return_value = [1, 2, 3]
             redis_mock = mock.Mock()
             redis_mock.get.return_value = self.test_dataset
             data_set = DatasetType(redis_mock)
@@ -114,7 +113,6 @@ class TestDataSetTypes(unittest.TestCase):
             redis_mock.set.assert_called_once_with(
                 "dataset_structure",
                 '{"Aging-Brain-UCIPublish": "Publish", "AKXDGeno": "Geno", "B139_K_1206_M": "ProbeSet", "AD-cases-controls-MyersGeno": "Geno", "AD-cases-controls-MyersPublish": "Publish", "All Phenotypes": "Publish", "Test": "Publish", "AXBXAPublish": "Publish", "B139_K_1206_R": "ProbeSet", "AXBXAGeno": "Geno"}')
-            expected_db_call = """"""
             db_mock.db.execute.assert_called_with(
                 ("SELECT PublishFreeze.Name " +
                  "FROM PublishFreeze, InbredSet " +
@@ -125,7 +123,7 @@ class TestDataSetTypes(unittest.TestCase):
     @mock.patch('base.data_set.g')
     def test_set_dataset_geno(self, db_mock):
         with app.app_context():
-            db_mock.db.execute.return_value = [1, 2, 3]
+            db_mock.db.execute.return_value.fetchone.return_value = [1, 2, 3]
             redis_mock = mock.Mock()
             redis_mock.get.return_value = self.test_dataset
             data_set = DatasetType(redis_mock)
diff --git a/wqflask/tests/base/test_trait.py b/wqflask/tests/base/test_trait.py
new file mode 100644
index 00000000..1a3820f2
--- /dev/null
+++ b/wqflask/tests/base/test_trait.py
@@ -0,0 +1,235 @@
+# -*- coding: utf-8 -*-
+"""Tests wqflask/base/trait.py"""
+import unittest
+import mock
+
+from base.trait import GeneralTrait
+from base.trait import retrieve_trait_info
+
+
+class TestResponse:
+    """Mock Test Response after a request"""
+    @property
+    def content(self):
+        """Mock the content from Requests.get(params).content"""
+        return "[1, 2, 3, 4]"
+
+
+class TestNilResponse:
+    """Mock Test Response after a request"""
+    @property
+    def content(self):
+        """Mock the content from Requests.get(params).content"""
+        return "{}"
+
+
+class MockTrait(GeneralTrait):
+    @property
+    def wikidata_alias_fmt(self):
+        return "Mock alias"
+
+
+class TestRetrieveTraitInfo(unittest.TestCase):
+    """Tests for 'retrieve_trait_info'"""
+    def test_retrieve_trait_info_with_empty_dataset(self):
+        """Test that an exception is raised when dataset is empty"""
+        with self.assertRaises(AssertionError):
+            retrieve_trait_info(trait=mock.MagicMock(),
+                                dataset={})
+
+    @mock.patch('base.trait.requests.get')
+    @mock.patch('base.trait.g')
+    def test_retrieve_trait_info_with_empty_trait_info(self,
+                                                       g_mock,
+                                                       requests_mock):
+        """Empty trait info"""
+        requests_mock.return_value = TestNilResponse()
+        with self.assertRaises(KeyError):
+            retrieve_trait_info(trait=mock.MagicMock(),
+                                dataset=mock.MagicMock())
+
+    @mock.patch('base.trait.requests.get')
+    @mock.patch('base.trait.g')
+    def test_retrieve_trait_info_with_non_empty_trait_info(self,
+                                                           g_mock,
+                                                           requests_mock):
+        """Test that attributes are set"""
+        mock_dataset = mock.MagicMock()
+        requests_mock.return_value = TestResponse()
+        type(mock_dataset).display_fields = mock.PropertyMock(
+            return_value=["a", "b", "c", "d"])
+        test_trait = retrieve_trait_info(trait=MockTrait(dataset=mock_dataset),
+                                         dataset=mock_dataset)
+        self.assertEqual(test_trait.a, 1)
+        self.assertEqual(test_trait.b, 2)
+        self.assertEqual(test_trait.c, 3)
+        self.assertEqual(test_trait.d, 4)
+
+    @mock.patch('base.trait.requests.get')
+    @mock.patch('base.trait.g')
+    def test_retrieve_trait_info_utf8_parsing(self,
+                                              g_mock,
+                                              requests_mock):
+        """Test that utf-8 strings are parsed correctly"""
+        utf_8_string = "test_string"
+        mock_dataset = mock.MagicMock()
+        requests_mock.return_value = TestResponse()
+        type(mock_dataset).display_fields = mock.PropertyMock(
+            return_value=["a", "b", "c", "d"])
+        type(mock_dataset).type = 'Publish'
+
+        mock_trait = MockTrait(
+            dataset=mock_dataset,
+            pre_publication_description=utf_8_string
+        )
+        trait_attrs = {
+            "group_code": "test_code",
+            "pre_publication_description": "test_pre_pub",
+            "pre_publication_abbreviation": "ファイルを画面毎に見て行くには、次のコマンドを使います。",
+            "post_publication_description": None,
+            "pubmed_id": None,
+            'year': "2020",
+            "authors": "Jane Doe かいと",
+        }
+        for key, val in list(trait_attrs.items()):
+            setattr(mock_trait, key, val)
+        test_trait = retrieve_trait_info(trait=mock_trait,
+                                         dataset=mock_dataset)
+        self.assertEqual(test_trait.abbreviation,
+                         "ファイルを画面毎に見て行くには、次のコマンドを使います。".decode('utf-8'))
+        self.assertEqual(test_trait.authors,
+                         "Jane Doe かいと".decode('utf-8'))
+
+    @mock.patch('base.trait.requests.get')
+    @mock.patch('base.trait.g')
+    @mock.patch('base.trait.get_resource_id')
+    def test_retrieve_trait_info_with_non_empty_lrs(self,
+                                                    resource_id_mock,
+                                                    g_mock,
+                                                    requests_mock):
+        """Test """
+        resource_id_mock.return_value = 1
+        g_mock.db.execute.return_value.fetchone = mock.Mock()
+        g_mock.db.execute.return_value.fetchone.side_effect = [
+            [1, 2, 3, 4],  # trait_info = g.db.execute(query).fetchone()
+            [1, 2.37, 3, 4, 5],  # trait_qtl = g.db.execute(query).fetchone()
+            [2.7333, 2.1204]  # trait_info = g.db.execute(query).fetchone()
+        ]
+        requests_mock.return_value = None
+
+        mock_dataset = mock.MagicMock()
+        type(mock_dataset).display_fields = mock.PropertyMock(
+            return_value=["a", "b", "c", "d"])
+        type(mock_dataset).type = "ProbeSet"
+        type(mock_dataset).name = "RandomName"
+
+        mock_trait = MockTrait(
+            dataset=mock_dataset,
+            pre_publication_description="test_string"
+        )
+        trait_attrs = {
+            "description": "some description",
+            "probe_target_description": "some description",
+            "cellid": False,
+            "chr": 2.733,
+            "mb": 2.1204
+        }
+
+        for key, val in list(trait_attrs.items()):
+            setattr(mock_trait, key, val)
+        test_trait = retrieve_trait_info(trait=mock_trait,
+                                         dataset=mock_dataset,
+                                         get_qtl_info=True)
+        self.assertEqual(test_trait.LRS_score_repr,
+                         "2.4")
+
+    @mock.patch('base.trait.requests.get')
+    @mock.patch('base.trait.g')
+    @mock.patch('base.trait.get_resource_id')
+    def test_retrieve_trait_info_with_empty_lrs_field(self,
+                                                      resource_id_mock,
+                                                      g_mock,
+                                                      requests_mock):
+        """Test retrieve trait info with empty lrs field"""
+        resource_id_mock.return_value = 1
+        g_mock.db.execute.return_value.fetchone = mock.Mock()
+        g_mock.db.execute.return_value.fetchone.side_effect = [
+            [1, 2, 3, 4],  # trait_info = g.db.execute(query).fetchone()
+            [1, None, 3, 4, 5],  # trait_qtl = g.db.execute(query).fetchone()
+            [2, 3]  # trait_info = g.db.execute(query).fetchone()
+        ]
+        requests_mock.return_value = None
+
+        mock_dataset = mock.MagicMock()
+        type(mock_dataset).display_fields = mock.PropertyMock(
+            return_value=["a", "b", "c", "d"])
+        type(mock_dataset).type = "ProbeSet"
+        type(mock_dataset).name = "RandomName"
+
+        mock_trait = MockTrait(
+            dataset=mock_dataset,
+            pre_publication_description="test_string"
+        )
+        trait_attrs = {
+            "description": "some description",
+            "probe_target_description": "some description",
+            "cellid": False,
+            "chr": 2.733,
+            "mb": 2.1204
+        }
+
+        for key, val in list(trait_attrs.items()):
+            setattr(mock_trait, key, val)
+        test_trait = retrieve_trait_info(trait=mock_trait,
+                                         dataset=mock_dataset,
+                                         get_qtl_info=True)
+        self.assertEqual(test_trait.LRS_score_repr,
+                         "N/A")
+        self.assertEqual(test_trait.LRS_location_repr,
+                         "Chr2: 3.000000")
+
+    @mock.patch('base.trait.requests.get')
+    @mock.patch('base.trait.g')
+    @mock.patch('base.trait.get_resource_id')
+    def test_retrieve_trait_info_with_empty_chr_field(self,
+                                                      resource_id_mock,
+                                                      g_mock,
+                                                      requests_mock):
+        """Test retrieve trait info with empty chr field"""
+        resource_id_mock.return_value = 1
+        g_mock.db.execute.return_value.fetchone = mock.Mock()
+        g_mock.db.execute.return_value.fetchone.side_effect = [
+            [1, 2, 3, 4],  # trait_info = g.db.execute(query).fetchone()
+            [1, 2, 3, 4, 5],  # trait_qtl = g.db.execute(query).fetchone()
+            [None, 3]  # trait_info = g.db.execute(query).fetchone()
+        ]
+
+        requests_mock.return_value = None
+
+        mock_dataset = mock.MagicMock()
+        type(mock_dataset).display_fields = mock.PropertyMock(
+            return_value=["a", "b", "c", "d"])
+        type(mock_dataset).type = "ProbeSet"
+        type(mock_dataset).name = "RandomName"
+
+        mock_trait = MockTrait(
+            dataset=mock_dataset,
+            pre_publication_description="test_string"
+        )
+        trait_attrs = {
+            "description": "some description",
+            "probe_target_description": "some description",
+            "cellid": False,
+            "chr": 2.733,
+            "mb": 2.1204
+        }
+
+        for key, val in list(trait_attrs.items()):
+            setattr(mock_trait, key, val)
+        test_trait = retrieve_trait_info(trait=mock_trait,
+                                         dataset=mock_dataset,
+                                         get_qtl_info=True)
+        self.assertEqual(test_trait.LRS_score_repr,
+                         "N/A")
+        self.assertEqual(test_trait.LRS_location_repr,
+                         "N/A")
diff --git a/wqflask/tests/utility/test_authentication_tools.py b/wqflask/tests/utility/test_authentication_tools.py
new file mode 100644
index 00000000..99c74245
--- /dev/null
+++ b/wqflask/tests/utility/test_authentication_tools.py
@@ -0,0 +1,193 @@
+"""Tests for authentication tools"""
+import unittest
+import mock
+
+from utility.authentication_tools import check_resource_availability
+from utility.authentication_tools import add_new_resource
+
+
+class TestResponse:
+    """Mock Test Response after a request"""
+    @property
+    def content(self):
+        """Mock the content from Requests.get(params).content"""
+        return '["foo"]'
+
+
+class TestUser:
+    """Mock user"""
+    @property
+    def user_id(self):
+        """Mockes user id. Used in Flask.g.user_session.user_id"""
+        return "Jane"
+
+
+class TestUserSession:
+    """Mock user session"""
+    @property
+    def user_session(self):
+        """Mock user session. Mocks Flask.g.user_session object"""
+        return TestUser()
+
+
+def mock_add_resource(resource_ob, update=False):
+    return resource_ob
+
+
+class TestCheckResourceAvailability(unittest.TestCase):
+    """Test methods related to checking the resource availability"""
+    @mock.patch('utility.authentication_tools.add_new_resource')
+    @mock.patch('utility.authentication_tools.Redis')
+    @mock.patch('utility.authentication_tools.g')
+    @mock.patch('utility.authentication_tools.get_resource_id')
+    def test_check_resource_availability_default_mask(
+            self,
+            resource_id_mock,
+            g_mock,
+            redis_mock,
+            add_new_resource_mock):
+        """Test the resource availability with default mask"""
+        resource_id_mock.return_value = 1
+        g_mock.return_value = mock.Mock()
+        redis_mock.smembers.return_value = []
+        test_dataset = mock.MagicMock()
+        type(test_dataset).type = mock.PropertyMock(return_value="Test")
+        add_new_resource_mock.return_value = {"default_mask": 2}
+        self.assertEqual(check_resource_availability(test_dataset), 2)
+
+    @mock.patch('utility.authentication_tools.requests.get')
+    @mock.patch('utility.authentication_tools.add_new_resource')
+    @mock.patch('utility.authentication_tools.Redis')
+    @mock.patch('utility.authentication_tools.g')
+    @mock.patch('utility.authentication_tools.get_resource_id')
+    def test_check_resource_availability_non_default_mask(
+            self,
+            resource_id_mock,
+            g_mock,
+            redis_mock,
+            add_new_resource_mock,
+            requests_mock):
+        """Test the resource availability with default mask"""
+        resource_id_mock.return_value = 1
+        g_mock.return_value = mock.Mock()
+        redis_mock.smembers.return_value = []
+        add_new_resource_mock.return_value = {"default_mask": 2}
+        requests_mock.return_value = TestResponse()
+        test_dataset = mock.MagicMock()
+        type(test_dataset).type = mock.PropertyMock(return_value="Test")
+        self.assertEqual(check_resource_availability(test_dataset),
+                         ['foo'])
+
+    @mock.patch('utility.authentication_tools.webqtlConfig.SUPER_PRIVILEGES',
+                "SUPERUSER")
+    @mock.patch('utility.authentication_tools.requests.get')
+    @mock.patch('utility.authentication_tools.add_new_resource')
+    @mock.patch('utility.authentication_tools.Redis')
+    @mock.patch('utility.authentication_tools.g', TestUserSession())
+    @mock.patch('utility.authentication_tools.get_resource_id')
+    def test_check_resource_availability_of_super_user(
+            self,
+            resource_id_mock,
+            redis_mock,
+            add_new_resource_mock,
+            requests_mock):
+        """Test the resource availability if the user is the super user"""
+        resource_id_mock.return_value = 1
+        redis_mock.smembers.return_value = ["Jane"]
+        add_new_resource_mock.return_value = {"default_mask": 2}
+        requests_mock.return_value = TestResponse()
+        test_dataset = mock.MagicMock()
+        type(test_dataset).type = mock.PropertyMock(return_value="Test")
+        self.assertEqual(check_resource_availability(test_dataset),
+                         "SUPERUSER")
+
+    @mock.patch('utility.authentication_tools.webqtlConfig.DEFAULT_PRIVILEGES',
+                "John Doe")
+    def test_check_resource_availability_string_dataset(self):
+        """Test the resource availability if the dataset is a string"""
+        self.assertEqual(check_resource_availability("Test"),
+                         "John Doe")
+
+    @mock.patch('utility.authentication_tools.webqtlConfig.DEFAULT_PRIVILEGES',
+                "John Doe")
+    def test_check_resource_availability_temp(self):
+        """Test the resource availability if the dataset is a string"""
+        test_dataset = mock.MagicMock()
+        type(test_dataset).type = mock.PropertyMock(return_value="Temp")
+        self.assertEqual(check_resource_availability(test_dataset),
+                         "John Doe")
+
+
+class TestAddNewResource(unittest.TestCase):
+    """Test cases for add_new_resource method"""
+    @mock.patch('utility.authentication_tools.webqtlConfig.DEFAULT_PRIVILEGES',
+                "John Doe")
+    @mock.patch('utility.authentication_tools.add_resource', mock_add_resource)
+    @mock.patch('utility.authentication_tools.get_group_code')
+    def test_add_new_resource_if_publish_datatype(self, group_code_mock):
+        """Test add_new_resource if dataset type is 'publish'"""
+        group_code_mock.return_value = "Test"
+        test_dataset = mock.MagicMock()
+        type(test_dataset).type = mock.PropertyMock(return_value="Publish")
+        type(test_dataset).id = mock.PropertyMock(return_value=10)
+        expected_value = {
+            "owner_id": "none",
+            "default_mask": "John Doe",
+            "group_masks": {},
+            "name": "Test_None",
+            "data": {
+                "dataset": 10,
+                "trait": None
+            },
+            "type": "dataset-publish"
+        }
+        self.assertEqual(add_new_resource(test_dataset),
+                         expected_value)
+
+    @mock.patch('utility.authentication_tools.webqtlConfig.DEFAULT_PRIVILEGES',
+                "John Doe")
+    @mock.patch('utility.authentication_tools.add_resource', mock_add_resource)
+    @mock.patch('utility.authentication_tools.get_group_code')
+    def test_add_new_resource_if_geno_datatype(self, group_code_mock):
+        """Test add_new_resource if dataset type is 'geno'"""
+        group_code_mock.return_value = "Test"
+        test_dataset = mock.MagicMock()
+        type(test_dataset).name = mock.PropertyMock(return_value="Geno")
+        type(test_dataset).type = mock.PropertyMock(return_value="Geno")
+        type(test_dataset).id = mock.PropertyMock(return_value=20)
+        expected_value = {
+            "owner_id": "none",
+            "default_mask": "John Doe",
+            "group_masks": {},
+            "name": "Geno",
+            "data": {
+                "dataset": 20,
+            },
+            "type": "dataset-geno"
+        }
+        self.assertEqual(add_new_resource(test_dataset),
+                         expected_value)
+
+    @mock.patch('utility.authentication_tools.webqtlConfig.DEFAULT_PRIVILEGES',
+                "John Doe")
+    @mock.patch('utility.authentication_tools.add_resource', mock_add_resource)
+    @mock.patch('utility.authentication_tools.get_group_code')
+    def test_add_new_resource_if_other_datatype(self, group_code_mock):
+        """Test add_new_resource if dataset type is not 'geno' or 'publish'"""
+        group_code_mock.return_value = "Test"
+        test_dataset = mock.MagicMock()
+        type(test_dataset).name = mock.PropertyMock(return_value="Geno")
+        type(test_dataset).type = mock.PropertyMock(return_value="other")
+        type(test_dataset).id = mock.PropertyMock(return_value=20)
+        expected_value = {
+            "owner_id": "none",
+            "default_mask": "John Doe",
+            "group_masks": {},
+            "name": "Geno",
+            "data": {
+                "dataset": 20,
+            },
+            "type": "dataset-probeset"
+        }
+        self.assertEqual(add_new_resource(test_dataset),
+                         expected_value)
diff --git a/wqflask/tests/utility/test_hmac.py b/wqflask/tests/utility/test_hmac.py
new file mode 100644
index 00000000..16b50771
--- /dev/null
+++ b/wqflask/tests/utility/test_hmac.py
@@ -0,0 +1,39 @@
+# -*- coding: utf-8 -*-
+"""Test hmac utility functions"""
+
+import unittest
+import mock
+
+from utility.hmac import data_hmac
+from utility.hmac import url_for_hmac
+from utility.hmac import hmac_creation
+
+
+class TestHmacUtil(unittest.TestCase):
+    """Test Utility method for hmac creation"""
+
+    @mock.patch("utility.hmac.app.config", {'SECRET_HMAC_CODE': "secret"})
+    def test_hmac_creation(self):
+        """Test hmac creation with a utf-8 string"""
+        self.assertEqual(hmac_creation("ファイ"), "7410466338cfe109e946")
+
+    @mock.patch("utility.hmac.app.config", {'SECRET_HMAC_CODE': "secret"})
+    def test_data_hmac(self):
+        """Test data_hmac fn with a utf-8 string"""
+        self.assertEqual(data_hmac("ファイ"), "ファイ:7410466338cfe109e946")
+
+    @mock.patch("utility.hmac.app.config", {'SECRET_HMAC_CODE': "secret"})
+    @mock.patch("utility.hmac.url_for")
+    def test_url_for_hmac_with_plain_url(self, mock_url):
+        """Test url_for_hmac without params"""
+        mock_url.return_value = "https://mock_url.com/ファイ/"
+        self.assertEqual(url_for_hmac("ファイ"),
+                         "https://mock_url.com/ファイ/?hm=05bc39e659b1948f41e7")
+
+    @mock.patch("utility.hmac.app.config", {'SECRET_HMAC_CODE': "secret"})
+    @mock.patch("utility.hmac.url_for")
+    def test_url_for_hmac_with_param_in_url(self, mock_url):
+        """Test url_for_hmac with params"""
+        mock_url.return_value = "https://mock_url.com/?ファイ=1"
+        self.assertEqual(url_for_hmac("ファイ"),
+                         "https://mock_url.com/?ファイ=1&hm=4709c1708270644aed79")
diff --git a/wqflask/tests/wqflask/test_collect.py b/wqflask/tests/wqflask/test_collect.py
new file mode 100644
index 00000000..6b8d7931
--- /dev/null
+++ b/wqflask/tests/wqflask/test_collect.py
@@ -0,0 +1,57 @@
+"""Test cases for some methods in collect.py"""
+
+import unittest
+import mock
+
+from flask import Flask
+from wqflask.collect import process_traits
+
+app = Flask(__name__)
+
+
+class MockSession:
+    """Helper class for mocking wqflask.collect.g.user_session.logged_in"""
+    def __init__(self, is_logged_in=False):
+        self.is_logged_in = is_logged_in
+
+    @property
+    def logged_in(self):
+        return self.is_logged_in
+
+
+class MockFlaskG:
+    """Helper class for mocking wqflask.collect.g.user_session"""
+    def __init__(self, is_logged_in=False):
+        self.is_logged_in = is_logged_in
+
+    @property
+    def user_session(self):
+        if self.is_logged_in:
+            return MockSession(is_logged_in=True)
+        return MockSession()
+
+
+class TestCollect(unittest.TestCase):
+
+    def setUp(self):
+        self.app_context = app.app_context()
+        self.app_context.push()
+
+    def tearDown(self):
+        self.app_context.pop()
+
+    @mock.patch("wqflask.collect.g", MockFlaskG())
+    def test_process_traits_when_user_is_logged_out(self):
+        """
+        Test that the correct traits are returned when the user is logged
+        out
+        """
+        self.assertEqual(process_traits(
+            b'1452452_at:HC_M2_0606_P:163d04f7db7c9e110de6,'
+            b'1452447_at:HC_M2_0606_P:eeece8fceb67072debea,'
+            b'1451401_a_at:HC_M2_0606_P:a043d23b3b3906d8318e,'
+            b'1429252_at:HC_M2_0606_P:6fa378b349bc9180e8f5'),
+            set(['1429252_at:HC_M2_0606_P',
+                 '1451401_a_at:HC_M2_0606_P',
+                 '1452447_at:HC_M2_0606_P',
+                 '1452452_at:HC_M2_0606_P']))
diff --git a/wqflask/utility/authentication_tools.py b/wqflask/utility/authentication_tools.py
index 3553b92b..239b08e3 100644
--- a/wqflask/utility/authentication_tools.py
+++ b/wqflask/utility/authentication_tools.py
@@ -1,4 +1,6 @@
 from __future__ import absolute_import, print_function, division
+import logging
+from flask import Flask, g, redirect, url_for
 
 import json
 import requests
@@ -9,33 +11,31 @@ from utility import hmac
 from utility.redis_tools import get_redis_conn, get_resource_info, get_resource_id, add_resource
 Redis = get_redis_conn()
 
-from flask import Flask, g, redirect, url_for
 
-import logging
-logger = logging.getLogger(__name__ )
+logger = logging.getLogger(__name__)
+
 
 def check_resource_availability(dataset, trait_id=None):
 
-    #At least for now assume temporary entered traits are accessible
-    if type(dataset) == str:
-        return webqtlConfig.DEFAULT_PRIVILEGES
-    if dataset.type == "Temp":
+    # At least for now assume temporary entered traits are accessible
+    if type(dataset) == str or dataset.type == "Temp":
         return webqtlConfig.DEFAULT_PRIVILEGES
 
     resource_id = get_resource_id(dataset, trait_id)
 
-    if resource_id: #ZS: This should never be false, but it's technically possible if a non-Temp dataset somehow had a type other than Publish/ProbeSet/Geno
+    if resource_id:  # ZS: This should never be false, but it's technically possible if a non-Temp dataset somehow had a type other than Publish/ProbeSet/Geno
         resource_info = get_resource_info(resource_id)
-        if not resource_info: #ZS: If resource isn't already in redis, add it with default privileges
+        if not resource_info:  # ZS: If resource isn't already in redis, add it with default privileges
             resource_info = add_new_resource(dataset, trait_id)
 
-    #ZS: Check if super-user - we should probably come up with some way to integrate this into the proxy
+    # ZS: Check if super-user - we should probably come up with some way to integrate this into the proxy
     if g.user_session.user_id in Redis.smembers("super_users"):
-       return webqtlConfig.SUPER_PRIVILEGES
+        return webqtlConfig.SUPER_PRIVILEGES
 
     response = None
 
-    the_url = "http://localhost:8080/available?resource={}&user={}".format(resource_id, g.user_session.user_id)
+    the_url = "http://localhost:8080/available?resource={}&user={}".format(
+        resource_id, g.user_session.user_id)
     try:
         response = json.loads(requests.get(the_url).content)
     except:
@@ -43,18 +43,19 @@ def check_resource_availability(dataset, trait_id=None):
 
     return response
 
+
 def add_new_resource(dataset, trait_id=None):
     resource_ob = {
-        'owner_id'    : "none", # webqtlConfig.DEFAULT_OWNER_ID,
+        'owner_id': "none",  # webqtlConfig.DEFAULT_OWNER_ID,
         'default_mask': webqtlConfig.DEFAULT_PRIVILEGES,
-        'group_masks' : {}
+        'group_masks': {}
     }
 
     if dataset.type == "Publish":
         resource_ob['name'] = get_group_code(dataset) + "_" + str(trait_id)
         resource_ob['data'] = {
             'dataset': dataset.id,
-            'trait'  : trait_id
+            'trait': trait_id
         }
         resource_ob['type'] = 'dataset-publish'
     elif dataset.type == "Geno":
@@ -74,15 +75,19 @@ def add_new_resource(dataset, trait_id=None):
 
     return resource_info
 
+
 def get_group_code(dataset):
-    results = g.db.execute("SELECT InbredSetCode from InbredSet where Name='{}'".format(dataset.group.name)).fetchone()
+    results = g.db.execute("SELECT InbredSetCode from InbredSet where Name='{}'".format(
+        dataset.group.name)).fetchone()
     if results[0]:
         return results[0]
     else:
         return ""
 
+
 def check_admin(resource_id=None):
-    the_url = "http://localhost:8080/available?resource={}&user={}".format(resource_id, g.user_session.user_id)
+    the_url = "http://localhost:8080/available?resource={}&user={}".format(
+        resource_id, g.user_session.user_id)
     try:
         response = json.loads(requests.get(the_url).content)['admin']
     except:
@@ -96,6 +101,7 @@ def check_admin(resource_id=None):
     else:
         return "not-admin"
 
+
 def check_owner(dataset=None, trait_id=None, resource_id=None):
     if resource_id:
         resource_info = get_resource_info(resource_id)
@@ -110,6 +116,7 @@ def check_owner(dataset=None, trait_id=None, resource_id=None):
 
     return False
 
+
 def check_owner_or_admin(dataset=None, trait_id=None, resource_id=None):
     if not resource_id:
         if dataset.type == "Temp":
diff --git a/wqflask/utility/hmac.py b/wqflask/utility/hmac.py
index b08be97e..fd75803e 100644
--- a/wqflask/utility/hmac.py
+++ b/wqflask/utility/hmac.py
@@ -7,11 +7,11 @@ from flask import url_for
 
 from wqflask import app
 
+
 def hmac_creation(stringy):
     """Helper function to create the actual hmac"""
 
     secret = app.config['SECRET_HMAC_CODE']
-
     hmaced = hmac.new(secret, stringy, hashlib.sha1)
     hm = hmaced.hexdigest()
     # ZS: Leaving the below comment here to ask Pjotr about
@@ -20,10 +20,12 @@ def hmac_creation(stringy):
     hm = hm[:20]
     return hm
 
+
 def data_hmac(stringy):
-    """Takes arbitray data string and appends :hmac so we know data hasn't been tampered with"""
+    """Takes arbitrary data string and appends :hmac so we know data hasn't been tampered with"""
     return stringy + ":" + hmac_creation(stringy)
 
+
 def url_for_hmac(endpoint, **values):
     """Like url_for but adds an hmac at the end to insure the url hasn't been tampered with"""
 
@@ -36,5 +38,6 @@ def url_for_hmac(endpoint, **values):
         combiner = "?"
     return url + combiner + "hm=" + hm
 
+
 app.jinja_env.globals.update(url_for_hmac=url_for_hmac,
-                             data_hmac=data_hmac)
\ No newline at end of file
+                             data_hmac=data_hmac)
diff --git a/wqflask/utility/redis_tools.py b/wqflask/utility/redis_tools.py
index 81ba04ea..ef02268e 100644
--- a/wqflask/utility/redis_tools.py
+++ b/wqflask/utility/redis_tools.py
@@ -4,23 +4,21 @@ import uuid
 import simplejson as json
 import datetime
 
-import redis # used for collections
-
-import logging
-
-from flask import (render_template, flash)
-
-from utility import hmac
+import redis  # used for collections
 
+from utility.hmac import hmac_creation
 from utility.logger import getLogger
 logger = getLogger(__name__)
 
+
 def get_redis_conn():
     Redis = redis.StrictRedis(port=6379)
     return Redis
 
+
 Redis = get_redis_conn()
 
+
 def is_redis_available():
     try:
         Redis.ping()
@@ -28,6 +26,7 @@ def is_redis_available():
         return False
     return True
 
+
 def get_user_id(column_name, column_value):
     user_list = Redis.hgetall("users")
     key_list = []
@@ -38,6 +37,7 @@ def get_user_id(column_name, column_value):
 
     return None
 
+
 def get_user_by_unique_column(column_name, column_value):
     item_details = None
 
@@ -52,9 +52,11 @@ def get_user_by_unique_column(column_name, column_value):
 
     return item_details
 
+
 def get_users_like_unique_column(column_name, column_value):
-    """
-    Like previous function, but this only checks if the input is a subset of a field and can return multiple results
+    """Like previous function, but this only checks if the input is a
+    subset of a field and can return multiple results
+
     """
     matched_users = []
 
@@ -74,7 +76,6 @@ def get_users_like_unique_column(column_name, column_value):
 
     return matched_users
 
-# def search_users_by_unique_column(column_name, column_value):
 
 def set_user_attribute(user_id, column_name, column_value):
     user_info = json.loads(Redis.hget("users", user_id))
@@ -82,6 +83,7 @@ def set_user_attribute(user_id, column_name, column_value):
 
     Redis.hset("users", user_id, json.dumps(user_info))
 
+
 def get_user_collections(user_id):
     collections = None
     collections = Redis.hget("collections", user_id)
@@ -91,22 +93,27 @@ def get_user_collections(user_id):
     else:
         return []
 
+
 def save_user(user, user_id):
     Redis.hset("users", user_id, json.dumps(user))
 
+
 def save_collections(user_id, collections_ob):
     Redis.hset("collections", user_id, collections_ob)
 
+
 def save_verification_code(user_email, code):
     Redis.hset("verification_codes", code, user_email)
 
+
 def check_verification_code(code):
     email_address = None
     user_details = None
     email_address = Redis.hget("verification_codes", code)
 
     if email_address:
-        user_details = get_user_by_unique_column('email_address', email_address)
+        user_details = get_user_by_unique_column(
+            'email_address', email_address)
         if user_details:
             return user_details
         else:
@@ -114,10 +121,12 @@ def check_verification_code(code):
     else:
         return None
 
+
 def get_user_groups(user_id):
-    #ZS: Get the groups where a user is an admin or a member and return lists corresponding to those two sets of groups
-    admin_group_ids = []  #ZS: Group IDs where user is an admin
-    user_group_ids = []   #ZS: Group IDs where user is a regular user
+    # ZS: Get the groups where a user is an admin or a member and
+    # return lists corresponding to those two sets of groups
+    admin_group_ids = []  # ZS: Group IDs where user is an admin
+    user_group_ids = []  # ZS: Group IDs where user is a regular user
     groups_list = Redis.hgetall("groups")
     for key in groups_list:
         try:
@@ -142,6 +151,7 @@ def get_user_groups(user_id):
 
     return admin_groups, user_groups
 
+
 def get_group_info(group_id):
     group_json = Redis.hget("groups", group_id)
     group_info = None
@@ -150,6 +160,7 @@ def get_group_info(group_id):
 
     return group_info
 
+
 def get_group_by_unique_column(column_name, column_value):
     """ Get group by column; not sure if there's a faster way to do this """
 
@@ -158,7 +169,8 @@ def get_group_by_unique_column(column_name, column_value):
     all_group_list = Redis.hgetall("groups")
     for key in all_group_list:
         group_info = json.loads(all_group_list[key])
-        if column_name == "admins" or column_name == "members": #ZS: Since these fields are lists, search in the list
+        # ZS: Since these fields are lists, search in the list
+        if column_name == "admins" or column_name == "members":
             if column_value in group_info[column_name]:
                 matched_groups.append(group_info)
         else:
@@ -167,9 +179,11 @@ def get_group_by_unique_column(column_name, column_value):
 
     return matched_groups
 
+
 def get_groups_like_unique_column(column_name, column_value):
-    """
-    Like previous function, but this only checks if the input is a subset of a field and can return multiple results
+    """Like previous function, but this only checks if the input is a
+    subset of a field and can return multiple results
+
     """
     matched_groups = []
 
@@ -178,7 +192,8 @@ def get_groups_like_unique_column(column_name, column_value):
         if column_name != "group_id":
             for key in group_list:
                 group_info = json.loads(group_list[key])
-                if column_name == "admins" or column_name == "members": #ZS: Since these fields are lists, search in the list
+                # ZS: Since these fields are lists, search in the list
+                if column_name == "admins" or column_name == "members":
                     if column_value in group_info[column_name]:
                         matched_groups.append(group_info)
                 else:
@@ -190,13 +205,15 @@ def get_groups_like_unique_column(column_name, column_value):
 
     return matched_groups
 
-def create_group(admin_user_ids, member_user_ids = [], group_name = "Default Group Name"):
+
+def create_group(admin_user_ids, member_user_ids=[],
+                 group_name="Default Group Name"):
     group_id = str(uuid.uuid4())
     new_group = {
-        "id"    : group_id,
+        "id": group_id,
         "admins": admin_user_ids,
-        "members" : member_user_ids,
-        "name"  : group_name,
+        "members": member_user_ids,
+        "name": group_name,
         "created_timestamp": datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p'),
         "changed_timestamp": datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p')
     }
@@ -205,8 +222,9 @@ def create_group(admin_user_ids, member_user_ids = [], group_name = "Default Gro
 
     return new_group
 
+
 def delete_group(user_id, group_id):
-    #ZS: If user is an admin of a group, remove it from the groups hash
+    # ZS: If user is an admin of a group, remove it from the groups hash
     group_info = get_group_info(group_id)
     if user_id in group_info["admins"]:
         Redis.hdel("groups", group_id)
@@ -214,9 +232,15 @@ def delete_group(user_id, group_id):
     else:
         None
 
-def add_users_to_group(user_id, group_id, user_emails = [], admins = False): #ZS "admins" is just to indicate whether the users should be added to the groups admins or regular users set
+
+# ZS "admins" is just to indicate whether the users should be added to
+# the groups admins or regular users set
+def add_users_to_group(user_id, group_id, user_emails=[], admins=False):
     group_info = get_group_info(group_id)
-    if user_id in group_info["admins"]: #ZS: Just to make sure that the user is an admin for the group, even though they shouldn't be able to reach this point unless they are
+    # ZS: Just to make sure that the user is an admin for the group,
+    # even though they shouldn't be able to reach this point unless
+    # they are
+    if user_id in group_info["admins"]:
         if admins:
             group_users = set(group_info["admins"])
         else:
@@ -231,25 +255,36 @@ def add_users_to_group(user_id, group_id, user_emails = [], admins = False): #ZS
         else:
             group_info["members"] = list(group_users)
 
-        group_info["changed_timestamp"] = datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p')
+        group_info["changed_timestamp"] = datetime.datetime.utcnow().strftime(
+            '%b %d %Y %I:%M%p')
         Redis.hset("groups", group_id, json.dumps(group_info))
         return group_info
     else:
         return None
 
-def remove_users_from_group(user_id, users_to_remove_ids, group_id, user_type = "members"): #ZS: User type is because I assume admins can remove other admins
+
+# ZS: User type is because I assume admins can remove other admins
+def remove_users_from_group(user_id,
+                            users_to_remove_ids,
+                            group_id,
+                            user_type="members"):
     group_info = get_group_info(group_id)
 
     if user_id in group_info["admins"]:
         users_to_remove_set = set(users_to_remove_ids)
-        if user_type == "admins" and user_id in users_to_remove_set: #ZS: Make sure an admin can't remove themselves from a group, since I imagine we don't want groups to be able to become admin-less
+        # ZS: Make sure an admin can't remove themselves from a group,
+        # since I imagine we don't want groups to be able to become
+        # admin-less
+        if user_type == "admins" and user_id in users_to_remove_set:
             users_to_remove_set.remove(user_id)
         group_users = set(group_info[user_type])
         group_users -= users_to_remove_set
         group_info[user_type] = list(group_users)
-        group_info["changed_timestamp"] = datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p')
+        group_info["changed_timestamp"] = datetime.datetime.utcnow().strftime(
+            '%b %d %Y %I:%M%p')
         Redis.hset("groups", group_id, json.dumps(group_info))
 
+
 def change_group_name(user_id, group_id, new_name):
     group_info = get_group_info(group_id)
     if user_id in group_info["admins"]:
@@ -259,22 +294,28 @@ def change_group_name(user_id, group_id, new_name):
     else:
         return None
 
+
 def get_resources():
     resource_list = Redis.hgetall("resources")
     return resource_list
 
+
 def get_resource_id(dataset, trait_id=None):
     resource_id = False
     if dataset.type == "Publish":
         if trait_id:
-            resource_id = hmac.hmac_creation("{}:{}:{}".format('dataset-publish', dataset.id, trait_id))
+            resource_id = hmac_creation("{}:{}:{}".format(
+                'dataset-publish', dataset.id, trait_id))
     elif dataset.type == "ProbeSet":
-        resource_id = hmac.hmac_creation("{}:{}".format('dataset-probeset', dataset.id))
+        resource_id = hmac_creation(
+            "{}:{}".format('dataset-probeset', dataset.id))
     elif dataset.type == "Geno":
-        resource_id = hmac.hmac_creation("{}:{}".format('dataset-geno', dataset.id))
+        resource_id = hmac_creation(
+            "{}:{}".format('dataset-geno', dataset.id))
 
     return resource_id
 
+
 def get_resource_info(resource_id):
     resource_info = Redis.hget("resources", resource_id)
     if resource_info:
@@ -282,17 +323,23 @@ def get_resource_info(resource_id):
     else:
         return None
 
+
 def add_resource(resource_info, update=True):
     if 'trait' in resource_info['data']:
-        resource_id = hmac.hmac_creation('{}:{}:{}'.format(str(resource_info['type']), str(resource_info['data']['dataset']), str(resource_info['data']['trait'])))
+        resource_id = hmac_creation('{}:{}:{}'.format(
+            str(resource_info['type']), str(
+                resource_info['data']['dataset']),
+            str(resource_info['data']['trait'])))
     else:
-        resource_id = hmac.hmac_creation('{}:{}'.format(str(resource_info['type']), str(resource_info['data']['dataset'])))
+        resource_id = hmac_creation('{}:{}'.format(
+            str(resource_info['type']), str(resource_info['data']['dataset'])))
 
     if update or not Redis.hexists("resources", resource_id):
         Redis.hset("resources", resource_id, json.dumps(resource_info))
 
     return resource_info
 
+
 def add_access_mask(resource_id, group_id, access_mask):
     the_resource = get_resource_info(resource_id)
     the_resource['group_masks'][group_id] = access_mask
@@ -301,9 +348,10 @@ def add_access_mask(resource_id, group_id, access_mask):
 
     return the_resource
 
+
 def change_resource_owner(resource_id, new_owner_id):
-    the_resource= get_resource_info(resource_id)
+    the_resource = get_resource_info(resource_id)
     the_resource['owner_id'] = new_owner_id
 
     Redis.delete("resource")
-    Redis.hset("resources", resource_id, json.dumps(the_resource))
\ No newline at end of file
+    Redis.hset("resources", resource_id, json.dumps(the_resource))
diff --git a/wqflask/wqflask/__init__.py b/wqflask/wqflask/__init__.py
index d729aef5..7ed9c7b8 100644
--- a/wqflask/wqflask/__init__.py
+++ b/wqflask/wqflask/__init__.py
@@ -12,13 +12,24 @@ logging.basicConfig(level=logging.INFO)
 
 app = Flask(__name__)
 
-app.config.from_envvar('GN2_SETTINGS')       # See http://flask.pocoo.org/docs/config/#configuring-from-files
+# See http://flask.pocoo.org/docs/config/#configuring-from-files
 # Note no longer use the badly named WQFLASK_OVERRIDES (nyi)
-
+app.config.from_envvar('GN2_SETTINGS')
 app.jinja_env.globals.update(
-    undefined = jinja2.StrictUndefined,
-    numify = formatting.numify
-)
+    undefined=jinja2.StrictUndefined,
+    numify=formatting.numify)
 
 from wqflask.api import router
+from wqflask import group_manager
+from wqflask import resource_manager
+from wqflask import search_results
+from wqflask import export_traits
+from wqflask import gsearch
+from wqflask import update_search_results
+from wqflask import docs
+from wqflask import news
+from wqflask import db_info
+from wqflask import user_login
+from wqflask import user_session
+
 import wqflask.views
diff --git a/wqflask/wqflask/collect.py b/wqflask/wqflask/collect.py
index 42a09fed..4c558bfe 100644
--- a/wqflask/wqflask/collect.py
+++ b/wqflask/wqflask/collect.py
@@ -1,41 +1,30 @@
 from __future__ import print_function, division, absolute_import
 
-
-import os
-import hashlib
 import datetime
-import time
-
-import uuid
-import hashlib
-import base64
-
-import urlparse
-
 import simplejson as json
 
-from flask import (Flask, g, render_template, url_for, request, make_response,
-                   redirect, flash, jsonify)
+from flask import g
+from flask import render_template
+from flask import url_for
+from flask import request
+from flask import redirect
+from flask import flash
 
 from wqflask import app
-
-from pprint import pformat as pf
-
-from wqflask.database import db_session
-
-from wqflask import model
-
-from utility import Bunch, Struct, hmac
+from utility import hmac
 from utility.formatting import numify
 from utility.redis_tools import get_redis_conn
-Redis = get_redis_conn()
 
-from base.trait import create_trait, retrieve_trait_info, jsonable
+from base.trait import create_trait
+from base.trait import retrieve_trait_info
+from base.trait import jsonable
 from base.data_set import create_dataset
 
-import logging
 from utility.logger import getLogger
+
 logger = getLogger(__name__)
+Redis = get_redis_conn()
+
 
 def process_traits(unprocessed_traits):
     if isinstance(unprocessed_traits, basestring):
diff --git a/wqflask/wqflask/correlation/corr_scatter_plot.py b/wqflask/wqflask/correlation/corr_scatter_plot.py
index 819836b1..0f3d455c 100644
--- a/wqflask/wqflask/correlation/corr_scatter_plot.py
+++ b/wqflask/wqflask/correlation/corr_scatter_plot.py
@@ -17,8 +17,15 @@ class CorrScatterPlot(object):
     """Page that displays a correlation scatterplot with a line fitted to it"""
 
     def __init__(self, params):
-        self.dataset_1 = data_set.create_dataset(params['dataset_1'])
-        self.dataset_2 = data_set.create_dataset(params['dataset_2'])
+        if "Temp" in params['dataset_1']:
+            self.dataset_1 = data_set.create_dataset(dataset_name = "Temp", dataset_type = "Temp", group_name = params['dataset_1'].split("_")[1])
+        else:
+            self.dataset_1 = data_set.create_dataset(params['dataset_1'])
+        if "Temp" in params['dataset_2']:
+            self.dataset_2 = data_set.create_dataset(dataset_name = "Temp", dataset_type = "Temp", group_name = params['dataset_2'].split("_")[1])
+        else:
+            self.dataset_2 = data_set.create_dataset(params['dataset_2'])
+
         #self.dataset_3 = data_set.create_dataset(params['dataset_3'])
         self.trait_1 = create_trait(name=params['trait_1'], dataset=self.dataset_1)
         self.trait_2 = create_trait(name=params['trait_2'], dataset=self.dataset_2)
diff --git a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
index 0ac94139..3beee84f 100644
--- a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
+++ b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
@@ -147,7 +147,7 @@ class CorrelationMatrix(object):
 
                     if num_overlap < self.lowest_overlap:
                         self.lowest_overlap = num_overlap
-                    if num_overlap == 0:
+                    if num_overlap < 2:
                         corr_result_row.append([target_trait, 0, num_overlap])
                         pca_corr_result_row.append(0)
                     else:
diff --git a/wqflask/wqflask/db_info.py b/wqflask/wqflask/db_info.py
new file mode 100644
index 00000000..f04e38bf
--- /dev/null
+++ b/wqflask/wqflask/db_info.py
@@ -0,0 +1,127 @@
+import httplib, urllib2

+import re

+

+from flask import Flask, g

+

+from utility.logger import getLogger

+logger = getLogger(__name__ )

+

+class InfoPage(object):

+    def __init__(self, start_vars):

+        self.info = None

+        self.gn_accession_id = None

+        if 'gn_accession_id' in start_vars:

+            self.gn_accession_id = start_vars['gn_accession_id']

+        self.info_page_name = start_vars['info_page_name']

+

+        self.get_info()

+        self.get_datasets_list()

+

+    def get_info(self, create=False):

+        query_base = ("SELECT InfoPageName, GN_AccesionId, Species.MenuName, Species.TaxonomyId, Tissue.Name, InbredSet.Name, " +

+                      "GeneChip.GeneChipName, GeneChip.GeoPlatform, AvgMethod.Name, Datasets.DatasetName, Datasets.GeoSeries, " +

+                      "Datasets.PublicationTitle, DatasetStatus.DatasetStatusName, Datasets.Summary, Datasets.AboutCases, " +

+                      "Datasets.AboutTissue, Datasets.AboutDataProcessing, Datasets.Acknowledgment, Datasets.ExperimentDesign, " +

+                      "Datasets.Contributors, Datasets.Citation, Datasets.Notes, Investigators.FirstName, Investigators.LastName, " +

+                      "Investigators.Address, Investigators.City, Investigators.State, Investigators.ZipCode, Investigators.Country, " +

+                      "Investigators.Phone, Investigators.Email, Investigators.Url, Organizations.OrganizationName, " +

+                      "InvestigatorId, DatasetId, DatasetStatusId, Datasets.AboutPlatform, InfoFileTitle, Specifics " +

+                      "FROM InfoFiles " +

+                      "LEFT JOIN Species USING (SpeciesId) " +

+                      "LEFT JOIN Tissue USING (TissueId) " +

+                      "LEFT JOIN InbredSet USING (InbredSetId) " +

+                      "LEFT JOIN GeneChip USING (GeneChipId) " +

+                      "LEFT JOIN AvgMethod USING (AvgMethodId) " +

+                      "LEFT JOIN Datasets USING (DatasetId) " +

+                      "LEFT JOIN Investigators USING (InvestigatorId) " +

+                      "LEFT JOIN Organizations USING (OrganizationId) " +

+                      "LEFT JOIN DatasetStatus USING (DatasetStatusId) WHERE ")

+

+        if self.gn_accession_id:

+            final_query = query_base + "GN_AccesionId = {}".format(self.gn_accession_id)

+            results = g.db.execute(final_query).fetchone()

+            if self.info_page_name and not results:

+				final_query = query_base + "InfoPageName={}".format(self.info_page_name)

+        elif self.info_page_name:

+            final_query = query_base + "InfoPageName={}".format(self.info_page_name)

+            results = g.db.execute(final_query).fetchone()

+        else:

+            raise 'No correct parameter found'

+

+        if results:

+            self.info = process_query_results(results)

+

+        if (not results or len(results) < 1) and self.info_page_name and create:

+            insert_sql = "INSERT INTO InfoFiles SET InfoFiles.InfoPageName={}".format(self.info_page_name)

+            return self.get_info()

+

+        if not self.gn_accession_id and self.info:

+            self.gn_accession_id = self.info['accession_id']

+        if not self.info_page_name and self.info:

+            self.info_page_name = self.info['info_page_name'] 

+

+    def get_datasets_list(self):

+        self.filelist = []

+        try:

+            response = urllib2.urlopen("http://datafiles.genenetwork.org/download/GN%s" % self.gn_accession_id)

+            data = response.read()

+

+            matches = re.findall(r"<tr>.+?</tr>", data, re.DOTALL)

+            for i, match in enumerate(matches):

+                if i == 0:

+                    continue

+                cells = re.findall(r"<td.+?>.+?</td>", match, re.DOTALL)

+                full_filename = re.search(r"<a href=\"(.+?)\"", cells[1], re.DOTALL).group(1).strip()

+                filename = full_filename.split("/")[-1]

+                filesize = re.search(r">(.+?)<", cells[2]).group(1).strip()

+                filedate = "N/A" #ZS: Since we can't get it for now

+

+                self.filelist.append([filename, filedate, filesize])

+        except Exception, e:

+            pass

+

+def process_query_results(results):

+    info_ob = {

+        'info_page_name': results[0],

+        'accession_id': results[1],

+        'menu_name': results[2],

+        'taxonomy_id': results[3],

+        'tissue_name': results[4],

+        'group_name': results[5],

+        'gene_chip_name': results[6],

+        'geo_platform': results[7],

+        'avg_method_name': results[8],

+        'dataset_name': results[9],

+        'geo_series': results[10],

+        'publication_title': results[11],

+        'dataset_status_name': results[12],

+        'dataset_summary': results[13],

+        'about_cases': results[14],

+        'about_tissue': results[15],

+        'about_data_processing': results[16],

+        'acknowledgement': results[17],

+        'experiment_design': results[18],

+        'contributors': results[19],

+        'citation': results[20],

+        'notes': results[21],

+        'investigator_firstname': results[22],

+        'investigator_lastname': results[23],

+        'investigator_address': results[24],

+        'investigator_city': results[25],

+        'investigator_state': results[26],

+        'investigator_zipcode': results[27],

+        'investigator_country': results[28],

+        'investigator_phone': results[29],

+        'investigator_email': results[30],

+        'investigator_url': results[31],

+        'organization_name': results[32],

+        'investigator_id': results[33],

+        'dataset_id': results[34],

+        'dataset_status_is': results[35],

+        'about_platform': results[36],

+        'info_file_title': results[37],

+        'specifics': results[38]

+    }

+

+    return info_ob

+        
\ No newline at end of file
diff --git a/wqflask/wqflask/docs.py b/wqflask/wqflask/docs.py
index 78407e22..9fad1cf1 100644
--- a/wqflask/wqflask/docs.py
+++ b/wqflask/wqflask/docs.py
@@ -11,7 +11,7 @@ class Docs(object):
 
     def __init__(self, entry, start_vars={}):
         sql = """
-            SELECT Docs.title, Docs.content
+            SELECT Docs.title, CAST(Docs.content AS BINARY)
             FROM Docs
             WHERE Docs.entry LIKE %s
             """
@@ -22,7 +22,7 @@ class Docs(object):
             self.content = ""
         else:
             self.title = result[0]
-            self.content = result[1].encode("latin1")
+            self.content = result[1]
 
         self.editable = "false"
         # ZS: Removing option to edit to see if text still gets vandalized
diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py
index 9bde343c..8a44b3fd 100644
--- a/wqflask/wqflask/marker_regression/run_mapping.py
+++ b/wqflask/wqflask/marker_regression/run_mapping.py
@@ -401,9 +401,7 @@ class RunMapping(object):
                           rs  = marker['name'],
                           pos  = this_ps
                       )
-                  #if 'p_value' in marker:
-                  #    logger.debug("P EXISTS:", marker['p_value'])
-                  #else:
+
                   if 'lrs_value' in marker and marker['lrs_value'] > 0:
                       browser_marker['p_wald'] = 10**-(marker['lrs_value']/4.61)
                   elif 'lod_score' in marker and marker['lod_score'] > 0:
@@ -417,6 +415,12 @@ class RunMapping(object):
                       if marker['chr'] > highest_chr or marker['chr'] == "X" or marker['chr'] == "X/Y":
                           highest_chr = marker['chr']
                       if ('lod_score' in marker.keys()) or ('lrs_value' in marker.keys()):
+                          if 'Mb' in marker.keys():
+                              marker['display_pos'] = "Chr" + str(marker['chr']) + ": " + "{:.3f}".format(marker['Mb'])
+                          elif 'cM' in marker.keys():
+                              marker['display_pos'] = "Chr" + str(marker['chr']) + ": " + "{:.3f}".format(marker['cM'])
+                          else:
+                              marker['display_pos'] = "N/A"
                           self.qtl_results.append(marker)
 
               with Bench("Exporting Results"):
diff --git a/wqflask/wqflask/resource_manager.py b/wqflask/wqflask/resource_manager.py
index 39a07310..14ff2183 100644
--- a/wqflask/wqflask/resource_manager.py
+++ b/wqflask/wqflask/resource_manager.py
@@ -25,16 +25,16 @@ def manage_resource():
         group_masks_with_names = get_group_names(group_masks)
         default_mask = resource_info['default_mask']['data']
         owner_id = resource_info['owner_id']
-        owner_info = get_user_by_unique_column("user_id", owner_id)
-
-        if 'name' in owner_info:
-            owner_display_name = owner_info['full_name']
-        elif 'user_name' in owner_info:
-            owner_display_name = owner_info['user_name']
-        elif 'email_address' in owner_info:
-            owner_display_name = owner_info['email_address']
-        else:
-            owner_display_name = None
+
+        owner_display_name = None
+        if owner_id != "none":
+            owner_info = get_user_by_unique_column("user_id", owner_id)
+            if 'name' in owner_info:
+                owner_display_name = owner_info['full_name']
+            elif 'user_name' in owner_info:
+                owner_display_name = owner_info['user_name']
+            elif 'email_address' in owner_info:
+                owner_display_name = owner_info['email_address']
 
         return render_template("admin/manage_resource.html", owner_name = owner_display_name, resource_id = resource_id, resource_info=resource_info, default_mask=default_mask, group_masks=group_masks_with_names, admin_status=admin_status)
 
diff --git a/wqflask/wqflask/static/new/css/marker_regression.css b/wqflask/wqflask/static/new/css/marker_regression.css
index f1a26a83..e0a5ceea 100644
--- a/wqflask/wqflask/static/new/css/marker_regression.css
+++ b/wqflask/wqflask/static/new/css/marker_regression.css
@@ -62,6 +62,10 @@ table.dataTable tbody td {
   padding: 4px 20px 2px 10px;
 }
 
+table.dataTable tbody tr.selected {
+  background-color: #ffee99;
+}
+
 table.dataTable.cell-border tbody th, table.dataTable.cell-border tbody td {
   border-top: 1px solid #ccc;
   border-right: 1px solid #ccc;
diff --git a/wqflask/wqflask/static/new/css/show_trait.css b/wqflask/wqflask/static/new/css/show_trait.css
index 853819ea..7a7f5455 100644
--- a/wqflask/wqflask/static/new/css/show_trait.css
+++ b/wqflask/wqflask/static/new/css/show_trait.css
@@ -54,4 +54,8 @@ table.dataTable.cell-border tbody tr td:first-child {
 
 .trait_value_input {
   text-align: right;
+
+.glyphicon {
+  position: relative;
+  top: 2px;
 }
\ No newline at end of file
diff --git a/wqflask/wqflask/static/new/javascript/search_results.js b/wqflask/wqflask/static/new/javascript/search_results.js
index 4e87d67a..86660126 100644
--- a/wqflask/wqflask/static/new/javascript/search_results.js
+++ b/wqflask/wqflask/static/new/javascript/search_results.js
@@ -93,7 +93,7 @@ $(function() {
 
   });
 
-  add = function() {
+  add_to_collection = function() {
     var traits;
     traits = $("#trait_table input:checked").map(function() {
       return $(this).val();
@@ -250,7 +250,7 @@ $(function() {
   $("#select_all").click(select_all);
   $("#deselect_all").click(deselect_all);
   $("#invert").click(invert);
-  $("#add").click(add);
+  $("#add").click(add_to_collection);
   $("#submit_bnw").click(submit_bnw);
   $("#export_traits").click(export_traits);
   $('.trait_checkbox, .btn').click(change_buttons);
@@ -259,14 +259,22 @@ $(function() {
   let naturalAsc = $.fn.dataTableExt.oSort["natural-ci-asc"]
   let naturalDesc = $.fn.dataTableExt.oSort["natural-ci-desc"]
 
+  let na_equivalent_vals = ["N/A", "--", ""]; //ZS: Since there are multiple values that should be treated the same as N/A
+
+  function extract_inner_text(the_string){
+    var span = document.createElement('span');
+    span.innerHTML = the_string;
+    return span.textContent || span.innerText;
+  }
+
   function sort_NAs(a, b, sort_function){
-    if (a === "N/A" && b === "N/A") {
+    if ( na_equivalent_vals.includes(a) && na_equivalent_vals.includes(b)) {
       return 0;
     }
-    if (a === "N/A"){
+    if (na_equivalent_vals.includes(a)){
       return 1
     }
-    if (b === "N/A") {
+    if (na_equivalent_vals.includes(b)) {
       return -1;
     }
     return sort_function(a, b)
@@ -274,11 +282,25 @@ $(function() {
 
   $.extend( $.fn.dataTableExt.oSort, {
     "natural-minus-na-asc": function (a, b) {
-      return sort_NAs(a, b, naturalAsc)
+      return sort_NAs(extract_inner_text(a), extract_inner_text(b), naturalAsc)
     },
     "natural-minus-na-desc": function (a, b) {
-      return sort_NAs(a, b, naturalDesc)
+      return sort_NAs(extract_inner_text(a), extract_inner_text(b), naturalDesc)
     }
   });
 
+  $.fn.dataTable.ext.order['dom-checkbox'] = function  ( settings, col )
+  {
+      return this.api().column( col, {order:'index'} ).nodes().map( function ( td, i ) {
+          return $('input', td).prop('checked') ? '1' : '0';
+      } );
+  };
+
+  $.fn.dataTable.ext.order['dom-inner-text'] = function  ( settings, col )
+  {
+      return this.api().column( col, {order:'index'} ).nodes().map( function ( td, i ) {
+          return $(td).text();
+      } );
+  }
+
 });
\ No newline at end of file
diff --git a/wqflask/wqflask/templates/base.html b/wqflask/wqflask/templates/base.html
index 50562200..b44538cf 100644
--- a/wqflask/wqflask/templates/base.html
+++ b/wqflask/wqflask/templates/base.html
@@ -4,7 +4,9 @@
 
 <head>
     <meta charset="utf-8">
-    <title>{% block title %}{% endblock %}</title>
+
+    <title>{% block title %}{% endblock %} GeneNetwork 2</title>
+
     <meta name="description" content="">
     <meta name="author" content="">
     <link rel="icon" type="image/png" sizes="64x64" href="/static/new/images/CITGLogo.png">
@@ -19,6 +21,14 @@
     {% block css %}
     {% endblock %}
 
+    <style>
+        table.dataTable thead .sorting_asc {
+            background-image: url({{ url_for("js", filename="DataTables/images/sort_asc_disabled.png") }});
+        }
+        table.dataTable thead .sorting_desc {
+            background-image: url({{ url_for("js", filename="DataTables/images/sort_desc_disabled.png") }});
+        }
+    </style>
 </head>
 
 <body style="width: 100%">
diff --git a/wqflask/wqflask/templates/collections/add.html b/wqflask/wqflask/templates/collections/add.html
index 825dfb84..62b6abb5 100644
--- a/wqflask/wqflask/templates/collections/add.html
+++ b/wqflask/wqflask/templates/collections/add.html
@@ -5,7 +5,7 @@
         or add to an existing collection.</p>
     </div>
     <div class="modal-body" style="margin-left: 20px;">
-        <form action="/collections/new" data-validate="parsley" id="add_form">
+        <form action="/collections/new" target="_blank" data-validate="parsley" id="add_form">
             {% if traits is defined %}
             <input type="hidden" name="traits" value="{{ traits }}" />
             {% else %}
diff --git a/wqflask/wqflask/templates/collections/view.html b/wqflask/wqflask/templates/collections/view.html
index dce814dd..d1a97310 100644
--- a/wqflask/wqflask/templates/collections/view.html
+++ b/wqflask/wqflask/templates/collections/view.html
@@ -8,7 +8,7 @@
 {% block content %}
 <!-- Start of body -->
 
-    <div class="container" style="min-width: 2050px;">
+    <div class="container">
         <h1>
             <span id="collection_name">{{ uc.name }}</span>
             <input type="text" name="new_collection_name" style="font-size: 20px; display: none; width: 500px;" class="form-control" placeholder="{{ uc.name }}"> 
@@ -16,8 +16,6 @@
         </h1>
         <h3>This collection has {{ '{}'.format(numify(trait_obs|count, "record", "records")) }}</h3>
 
-        <!--<hr style="height: 1px; background-color: #A9A9A9;">-->
-
         <div>
           <form id="collection_form" action="/delete" method="post">
             <input type="hidden" name="uc_id" id="uc_id" value="{{ uc.id }}" />
@@ -77,7 +75,7 @@
             <input type="hidden" name="database_name" id="database_name" value="None">
             <input type="hidden" name="export_data" id="export_data" value="">
             <input type="hidden" name="file_name" id="file_name" value="collection_table">
-            <button class="btn btn-default" id="export_traits">Download CSV</button>
+            <button class="btn btn-default" id="export_traits">Download</button>
             <input type="text" id="searchbox" class="form-control" style="width: 200px; display: inline; padding-bottom: 9px;" placeholder="Search Table For ...">
             <input type="text" id="select_top" class="form-control" style="width: 200px; display: inline; padding-bottom: 9px;" placeholder="Select Top ...">
             <button class="btn btn-default" id="deselect_all" type="button"><span class="glyphicon glyphicon-remove"></span> Deselect</button>
@@ -87,7 +85,7 @@
             <div style="margin-top: 10px; margin-bottom: 5px;">
                 <b>Show/Hide Columns:</b>
             </div>
-            <div>
+            <div style="min-width: 1500px;">
                 <table class="table-hover table-striped cell-border" id='trait_table' style="float: left;">
                     <thead>
                         <tr>
@@ -99,9 +97,9 @@
                             <th data-export="Description">Description</th>
                             <th data-export="Location">Location</th>
                             <th data-export="Mean">Mean</th>
-                            <th data-export="Max LRS">Max LRS <a href="http://genenetwork.org//glossary.html#L" target="_blank"><sup>?</sup></a></th>
-                            <th data-export="Max LRS Location">Max LRS Location</th>
-                            <th data-export="Add. Eff.">Additive Effect <a href="http://genenetwork.org//glossary.html#A" target="_blank"><sup>?</sup></a></th>
+                            <th data-export="Max LRS">High P <a href="http://genenetwork.org//glossary.html#L" target="_blank"><sup style="font-size: small; color: #FF0000;"> ?</sup></a></th>
+                            <th data-export="Peak Location">Peak Location</th>
+                            <th data-export="Add. Eff.">Effect Size <a href="http://genenetwork.org//glossary.html#A" target="_blank"><sup style="font-size: small; color: #FF0000;"> ?</sup></a></th>
                         </tr>
                     </thead>
 
@@ -144,7 +142,7 @@
                             <TD data-export="{{ this_trait.LRS_score_repr }}" align="right">N/A</TD>
                             {% endif %}
                             <TD data-export="{{ this_trait.LRS_location_repr }}">{{ this_trait.LRS_location_repr }}</TD>
-                            {% if this_trait.additive|float > 0 %}
+                            {% if this_trait.additive|float != 0 %}
                             <TD data-export="{{ this_trait.additive }}" align="right">{{ '%0.3f' % this_trait.additive|float }}</TD>
                             {% else %}
                             <TD data-export="{{ this_trait.additive }}" align="right">N/A</TD>
@@ -166,13 +164,13 @@
 {% block js %}
     <script language="javascript" type="text/javascript" src="/static/new/js_external/jszip.min.js"></script>
     <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='js_alt/md5.min.js') }}"></script>
-    <script type="text/javascript" src="/static/new/javascript/search_results.js"></script>
     <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.dataTables.min.js') }}"></script>
     <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/plugins/sorting/natural.js') }}"></script>
     <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/colResize/dataTables.colResize.js') }}"></script>
     <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/colReorder/js/dataTables.colReorder.js') }}"></script>
     <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/buttons/js/dataTables.buttons.min.js') }}"></script>
     <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/buttons/js/buttons.colVis.min.js') }}"></script>
+    <script type="text/javascript" src="/static/new/javascript/search_results.js"></script>
 
 
     <script language="javascript" type="text/javascript">
@@ -187,22 +185,22 @@
             console.time("Creating table");
             $('#trait_table').dataTable( {
                 "columns": [
-                    { "type": "natural", "width": 10 },
+                    {
+                        "orderDataType": "dom-checkbox",
+                        "orderSequence": [ "desc", "asc"],
+                        "width": 10
+                    },
                     { "type": "natural", "width": 50 },
                     { "type": "natural" },
-                    { "type": "natural", "width": 120 },
+                    { 'type': "natural-minus-na", "width": 120 },
                     { "type": "natural" },
                     { "type": "natural"  },
-                    { "type": "natural", "width": 130 },
-                    { "type": "natural", "width": 35 },
-                    { "type": "natural", "width": 35 },
-                    { "type": "natural", "width": 130 },
-                    { "type": "natural" }
+                    { "type": "natural", "width": 125 },
+                    { "type": "natural", "width": 60 },
+                    { "type": "natural", "width": 60 },
+                    { "type": "natural", "width": 125 },
+                    { "type": "natural", "width": 85 }
                 ],
-                "columnDefs": [ {
-                    "targets": 0,
-                    "orderable": false
-                } ],
                 "order": [[1, "asc" ]],
                 buttons: [
                     {
diff --git a/wqflask/wqflask/templates/correlation_matrix.html b/wqflask/wqflask/templates/correlation_matrix.html
index 9b96de1c..d556f31a 100644
--- a/wqflask/wqflask/templates/correlation_matrix.html
+++ b/wqflask/wqflask/templates/correlation_matrix.html
@@ -51,7 +51,7 @@
       {% if result[0].name == trait.name and result[0].dataset == trait.dataset %}
       <td nowrap="ON" align="center" bgcolor="#cccccc" style="padding: 3px; line-height: 1.1;"><a href="/show_trait?trait_id={{ trait.name }}&dataset={{ trait.dataset.name }}"><font style="font-size: 12px; color: #3071a9; font-weight: bold;" ><em>n</em><br>{{ result[2] }}</font></a></td>
       {% else %}
-      <td nowrap="ON" align="middle" class="corr_cell" style="padding: 3px; line-height: 1.1;"><a href="/corr_scatter_plot?dataset_1={{ trait.dataset.name }}&dataset_2={{ result[0].dataset.name }}&trait_1={{ trait.name }}&trait_2={{ result[0].name }}"><font style="font-size: 12px; color: #3071a9; font-weight: bold;" ><span class="corr_value">{{ '%0.2f' % result[1] }}</span><br>{{ result[2] }}</font></a></td>
+      <td nowrap="ON" align="middle" class="corr_cell" style="padding: 3px; line-height: 1.1;"><a href="/corr_scatter_plot?dataset_1={% if trait.dataset.name == 'Temp' %}Temp_{{ trait.dataset.group.name }}{% else %}{{ trait.dataset.name }}{% endif %}&dataset_2={% if result[0].dataset.name == 'Temp' %}Temp_{{ result[0].dataset.group.name }}{% else %}{{ result[0].dataset.name }}{% endif %}&trait_1={{ trait.name }}&trait_2={{ result[0].name }}"><font style="font-size: 12px; color: #3071a9; font-weight: bold;" ><span class="corr_value">{{ '%0.2f' % result[1] }}</span><br>{{ result[2] }}</font></a></td>
       {% endif %}
       {% endfor %}
     </tr>
diff --git a/wqflask/wqflask/templates/correlation_page.html b/wqflask/wqflask/templates/correlation_page.html
index e597bea9..fb218e29 100644
--- a/wqflask/wqflask/templates/correlation_page.html
+++ b/wqflask/wqflask/templates/correlation_page.html
@@ -144,7 +144,7 @@
                         <td data-export="{{ trait.description_display }}">{{ trait.description_display }}</TD>
                         <td data-export="{{ trait.location_repr }}" style="white-space: nowrap;">{{ trait.location_repr }}</td>
                         <td data-export="{{ '%0.3f' % trait.mean|float }}" align="right">{{ '%0.3f' % trait.mean|float }}</td>
-                        <td data-export="{{ '%0.3f'|format(trait.sample_r) }}"" align="right"><a target="_blank" href="corr_scatter_plot?dataset_1={{dataset.name}}&dataset_2={{trait.dataset.name}}&trait_1={{this_trait.name}}&trait_2={{trait.name}}">{{ '%0.3f'|format(trait.sample_r) }}</a></td>
+                        <td data-export="{{ '%0.3f'|format(trait.sample_r) }}"" align="right"><a target="_blank" href="corr_scatter_plot?dataset_1={% if dataset.name == 'Temp' %}Temp_{{ dataset.group.name }}{% else %}{{ dataset.name }}{% endif %}&dataset_2={% if trait.dataset.name == 'Temp' %}Temp_{{ trait.dataset.group.name }}{% else %}{{ trait.dataset.name }}{% endif %}&trait_1={{ this_trait.name }}&trait_2={{ trait.name }}">{{ '%0.3f'|format(trait.sample_r) }}</a></td>
                         <td data-export="{{ trait.num_overlap }}" align="right">{{ trait.num_overlap }}</td>
                         <td data-export="{{ '%0.3e'|format(trait.sample_p) }}" align="right">{{ '%0.3e'|format(trait.sample_p) }}</td>
                         {% if trait.lit_corr == "" or trait.lit_corr == 0.000 %}
@@ -164,22 +164,26 @@
                         <td data-export={% if trait.additive != "" %}"{{ '%0.3f' % trait.additive|float }}"{% else %}"N/A"{% endif %} align="right">{% if trait.additive != "" %}{{ '%0.3f' % trait.additive|float }}{% else %}N/A{% endif %}</td>
                       {% elif target_dataset.type == "Publish" %}
                         {% if trait.abbreviation %}
-                        <TD title="{{ trait.abbreviation }}" data-export="{{ trait.abbreviation }}">{% if trait.abbreviation|length > 20 %}{{ trait.abbreviation[:20] }}...{% else %}{{ trait.abbreviation }}{% endif %}</TD>
+                        <td title="{{ trait.abbreviation }}" data-export="{{ trait.abbreviation }}">{% if trait.abbreviation|length > 20 %}{{ trait.abbreviation[:20] }}...{% else %}{{ trait.abbreviation }}{% endif %}</td>
                         {% else %}
-                        <TD data-export="N/A">N/A</TD>
+                        <td data-export="N/A">N/A</td>
                         {% endif %}
                         <td data-export="{{ trait.description_display }}">{% if trait.description_display|length > 70 %}{{ trait.description_display[:70] }}...{% else %}{{ trait.description_display }}{% endif %}</td>
                         {% if trait.authors %}
                         <td data-export="{{ trait.authors }}">{% if trait.authors.split(',') > 6 %}{{ trait.authors.split(',')[:6]|join(', ') }}, et al.{% else %}{{ trait.authors }}{% endif %}</td>
                         {% else %}
-                        <TD data-export="N/A">N/A</TD>
+                        <td data-export="N/A">N/A</td>
                         {% endif %}
                         <td data-export="{{ trait.pubmed_text }}">
+                            {% if trait.pubmed_text != "N/A" %}
                             <a href="{{ trait.pubmed_link }}">
                                 {{ trait.pubmed_text }}
                             </a>
+                            {% else %}
+                            {{ trait.pubmed_text }}
+                            {% endif %}
                         </td>
-                        <td data-export="{{ '%0.3f'|format(trait.sample_r) }}" align="right"><a target="_blank" href="corr_scatter_plot?dataset_1={{dataset.name}}&dataset_2={{trait.dataset.name}}&trait_1={{this_trait.name}}&trait_2={{trait.name}}">{{ '%0.3f'|format(trait.sample_r) }}</a></td>
+                        <td data-export="{{ '%0.3f'|format(trait.sample_r) }}"" align="right"><a target="_blank" href="corr_scatter_plot?dataset_1={% if dataset.name == 'Temp' %}Temp_{{ dataset.group.name }}{% else %}{{ dataset.name }}{% endif %}&dataset_2={{ trait.dataset.name }}&trait_1={{ this_trait.name }}&trait_2={{ trait.name }}">{{ '%0.3f'|format(trait.sample_r) }}</a></td>
                         <td data-export="{{ trait.num_overlap }}" align="right">{{ trait.num_overlap }}</td>
                         <td data-export="{{ '%0.3e'|format(trait.sample_p) }}" align="right">{{ '%0.3e'|format(trait.sample_p) }}</td>
                         <td data-export="{{ trait.LRS_score_repr }}" align="right">{{ trait.LRS_score_repr }}</td>
@@ -187,7 +191,7 @@
                         <td data-export={% if trait.additive != "" %}"{{ '%0.3f' % trait.additive|float }}"{% else %}"N/A"{% endif %} align="right">{% if trait.additive != "" %}{{ '%0.3f' % trait.additive|float }}{% else %}N/A{% endif %}</td>
                       {% elif target_dataset.type == "Geno" %}
                         <td data-export="{{ trait.location_repr }}" align="right">{{ trait.location_repr }}</TD>
-                        <td data-export="{{ '%0.3f'|format(trait.sample_r) }}" align="right"><a target="_blank" href="corr_scatter_plot?dataset_1={{dataset.name}}&dataset_2={{trait.dataset.name}}&trait_1={{this_trait.name}}&trait_2={{trait.name}}">{{ '%0.3f'|format(trait.sample_r) }}</a></td>
+                        <td data-export="{{ '%0.3f'|format(trait.sample_r) }}"" align="right"><a target="_blank" href="corr_scatter_plot?dataset_1={% if dataset.name == 'Temp' %}Temp_{{ dataset.group.name }}{% else %}{{ dataset.name }}{% endif %}&dataset_2={{ trait.dataset.name }}&trait_1={{ this_trait.name }}&trait_2={{ trait.name }}">{{ '%0.3f'|format(trait.sample_r) }}</a></td>
                         <td data-export="{{ trait.num_overlap }}" align="right">{{ trait.num_overlap }}</td>
                         <td data-export="{{ '%0.3e'|format(trait.sample_p) }}" align="right">{{ '%0.3e'|format(trait.sample_p) }}</td>
                       {% endif %}
@@ -365,9 +369,9 @@
                     { "type": "numeric-html", 'orderSequence': [ "desc", "asc"] },
                     { "type": "numeric-html", 'orderSequence': [ "desc", "asc"] },
                     { "type": "scientific" },
-                    { "type": "natural" },
-                    { "type": "natural" },
-                    { "type": "natural" }
+                    { "type": "natural-minus-na" },
+                    { "type": "natural-minus-na" },
+                    { "type": "natural-minus-na" }
                 ],
                 "createdRow": function ( row, data, index ) {
                     $('td', row).eq(4).attr('title', $('td', row).eq(4).text());
@@ -419,13 +423,13 @@
                     { "type": "natural" },
                     { "type": "natural", "width": "20%" },
                     { "type": "natural", "width": "12%" },
-                    { "orderDataType": "dom-innertext" },
+                    { "type": "natural-minus-na" },
                     { "orderDataType": "dom-innertext", 'orderSequence': [ "desc", "asc"] },
                     { "type": "natural" },
                     { "type": "scientific" },
-                    { "type": "natural" },
-                    { "type": "natural" },
-                    { "type": "natural" }
+                    { "type": "natural-minus-na" },
+                    { "type": "natural-minus-na" },
+                    { "type": "natural-minus-na" }
                 ],
                 "order": [[9, "asc" ]],
                 "sDom": "Btir",
@@ -461,7 +465,7 @@
                     { "type": "natural" },
                     { "type": "natural" },
                     { "orderDataType": "dom-innertext", 'orderSequence': [ "desc", "asc"] },
-                    { "type": "natural" },
+                    { "type": "natural-minus-na" },
                     { "type": "scientific" }
                 ],
                 "order": [[6, "asc" ]],
diff --git a/wqflask/wqflask/templates/gsearch_gene.html b/wqflask/wqflask/templates/gsearch_gene.html
index 478d6f5f..d2c78d65 100644
--- a/wqflask/wqflask/templates/gsearch_gene.html
+++ b/wqflask/wqflask/templates/gsearch_gene.html
@@ -59,20 +59,6 @@
     </script>
 
     <script type="text/javascript" charset="utf-8">
-        $.fn.dataTable.ext.order['dom-checkbox'] = function  ( settings, col )
-        {
-            return this.api().column( col, {order:'index'} ).nodes().map( function ( td, i ) {
-                return $('input', td).prop('checked') ? '1' : '0';
-            } );
-        };
-
-        $.fn.dataTable.ext.order['dom-inner-text'] = function  ( settings, col )
-        {
-            return this.api().column( col, {order:'index'} ).nodes().map( function ( td, i ) {
-                return $(td).text();
-            } );
-        }
-
         $(document).ready( function () {
             
             $('#trait_table tr').click(function(event) {
@@ -252,7 +238,7 @@
                 'sDom': "pitirp",
                 'autoWidth': true,
                 'iDisplayLength': 500,
-                'deferRender': true,
+                'deferRender': false,
                 'paging': true,
                 'orderClasses': true,
                 'processing': true,
diff --git a/wqflask/wqflask/templates/gsearch_pheno.html b/wqflask/wqflask/templates/gsearch_pheno.html
index eb998d15..c44231f3 100644
--- a/wqflask/wqflask/templates/gsearch_pheno.html
+++ b/wqflask/wqflask/templates/gsearch_pheno.html
@@ -59,20 +59,6 @@
     </script>
 
     <script type="text/javascript" charset="utf-8">
-        $.fn.dataTable.ext.order['dom-checkbox'] = function  ( settings, col )
-        {
-            return this.api().column( col, {order:'index'} ).nodes().map( function ( td, i ) {
-                return $('input', td).prop('checked') ? '1' : '0';
-            } );
-        };
-
-        $.fn.dataTable.ext.order['dom-inner-text'] = function  ( settings, col )
-        {
-            return this.api().column( col, {order:'index'} ).nodes().map( function ( td, i ) {
-                return $(td).text();
-            } );
-        }
-
         $(document).ready( function () {
 
             $('#trait_table tr').click(function(event) {
@@ -172,6 +158,7 @@
                       'title': "Record",
                       'type': "natural",
                       'data': null,
+                      'orderDataType': "dom-inner-text",
                       'render': function(data, type, row, meta) {
                         return '<a target="_blank" href="/show_trait?trait_id=' + data.name + '&dataset=' + data.dataset + '">' + data.display_name + '</a>'
                       }
@@ -252,7 +239,7 @@
                 'order': [[1, "asc" ]],
                 'sDom': "pitirp",
                 'autoWidth': false,
-                'deferRender': true,
+                'deferRender': false,
                 'iDisplayLength': 500,
                 'paging': true,
                 'orderClasses': true,
diff --git a/wqflask/wqflask/templates/index_page_orig.html b/wqflask/wqflask/templates/index_page_orig.html
index 06b71f53..6b3bec9a 100755
--- a/wqflask/wqflask/templates/index_page_orig.html
+++ b/wqflask/wqflask/templates/index_page_orig.html
@@ -17,13 +17,13 @@
     </header>
 -->
 
-    <div class="container-fluid" style="min-width: 1200px;">
+    <div class="container-fluid" style="min-width: 1210px;">
 
         {{ flash_me() }}
 
         <div class="row" style="width: 100%;">
 
-            <div class="col-xs-5" style="min-width: 530px; max-width: 550px;">
+            <div class="col-xs-4" style="margin-right:50px; min-width: 530px; max-width: 550px;">
                 <section id="search">
                     <div>
                         <h1>Select and search</h1>
@@ -84,7 +84,7 @@
                                     <label for="or_search" class="col-xs-1 control-label" style="padding-left: 0px; padding-right: 0px; width: 65px !important;">Get Any:</label>
                                     <div class="col-xs-10 controls" style="padding-left: 20px;">
                                         <div class="col-8">
-                                          <textarea onkeydown="pressed(event)" name="search_terms_or" rows="1" class="form-control search-query" style="max-width: 550px; width: 450px !important;" id="or_search"></textarea>
+                                          <textarea onkeydown="pressed(event)" name="search_terms_or" rows="1" class="form-control search-query" style="resize: vertical; max-width: 550px; width: 450px !important;" id="or_search"></textarea>
                                         </div>
                                     </div>
                                 </div>
@@ -105,7 +105,7 @@
                                     <label for="and_search" class="col-xs-1 control-label" style="padding-left: 0px; padding-right: 0px; width: 65px !important;">Combined:</label>
                                     <div class="col-xs-10 controls" style="padding-left: 20px;">
                                         <div class="col-8">
-                                          <textarea onkeydown="pressed(event)" name="search_terms_and" rows="1" class="form-control search-query" style="max-width: 550px; width: 450px !important;" id="and_search"></textarea>
+                                          <textarea onkeydown="pressed(event)" name="search_terms_and" rows="1" class="form-control search-query" style="resize: vertical; max-width: 550px; width: 450px !important;" id="and_search"></textarea>
                                         </div>
                                     </div>
                                 </div>
@@ -184,7 +184,7 @@
                 </section>
             </div>
 
-            <div style="padding-left:80px" class="col-xs-4" style="width: 600px !important;">
+            <div class="col-xs-4" style="width: 600px !important;">
 	        <section id="affiliates">
 	            <div class="page-header">
                         <h1>Affiliates</h1>
diff --git a/wqflask/wqflask/templates/info_page.html b/wqflask/wqflask/templates/info_page.html
new file mode 100644
index 00000000..d8b7d74c
--- /dev/null
+++ b/wqflask/wqflask/templates/info_page.html
@@ -0,0 +1,92 @@
+{% extends "base.html" %}

+{% block title %}Policies{% endblock %}

+{% block content %}

+

+<h1 id="parent-fieldname-title">Data Set Group: {{ info.dataset_name }}

+<!--<a href="/infoshare/manager/member-studies-edit.html?DatasetId=%s"><img src="/images/modify.gif" alt="modify this page" border="0" valign="middle"></a>-->

+<span style="color:red;">{{ info.info_page_name }}</span>

+</h1>

+<table border="0" width="100%">

+<tr>

+<td valign="top" width="50%">

+<table name="info_table" cellSpacing=0 cellPadding=5 width=100% border=0>

+    <tr><td><b>Data Set:</b>  {{ info.info_file_title }} <!--<a href="/infoshare/manager/member-infofile-edit.html?GN_AccesionId=%s"><img src="/images/modify.gif" alt="modify this page" border="0" valign="middle"></a>--></td></tr>

+    <tr><td><b>GN Accession:</b> GN{{ gn_accession_id }}</td></tr>

+    <tr><td><b>GEO Series:</b> <a href="http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc={{ info.geo_series }}" target="_blank">{{ info.geo_series }}</a></td></tr>

+    <tr><td><b>Title:</b> {{ info.publication_title }}</td></tr>

+    <tr><td><b>Organism:</b> <a href="http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id={{ info.taxonomy_id }}" target="_blank">{{ info.menu_name }}</a></td></tr>

+    <tr><td><b>Group:</b> {{ info.group_name }}</td></tr>

+    <tr><td><b>Tissue:</b> {{ info.tissue_name }}</td></tr>

+    <tr><td><b>Dataset Status:</b> {{ info.dataset_status_name }}</td></tr>

+    <tr><td><b>Platforms:</b> <a href="http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc={{ info.geo_platform }}" target="_blank">{{ info.gene_chip_name }}</a></td></tr>

+    <tr><td><b>Normalization:</b> {{ info.avg_method_name }}</td></tr>

+</table>

+</td>

+<td valign="top" width="50%">

+<table border="0" width="100%">

+    <tr>

+        <td><b>Contact Information</b></td>

+    </tr>

+    <tr>

+        <td>

+            {{ info.investigator_first_name }} {{ info.inveestigator_last_name }}<br>

+            {{ info.organization_name }} <br>

+            {{ info.investigator_address }}<br>

+            {{ info.investigator_city }}, {{ info.investigator_state }} {{ info.investigator_zipcode }} {{ info.investigator_country }}<br>

+            Tel. {{ info.investigator_phone }}<br>

+            {{ info.investigator_email }}<br>

+            <a href="{{ info.investigator_url }}" target="_blank">Website</a>

+        </td>

+    </tr>

+

+<tr>

+    <td><b>Download datasets and supplementary data files</b></td>

+</tr>

+<tr>

+    <td>

+        <ul style="line-height: 160%">

+            {% for file in filelist %}

+            <li><a href="http://datafiles.genenetwork.org/download/GN{{ gn_accession_id }}/{{ file[0] }}">{{ file[0] }} ({{ file[2] }})</a></li>

+            {% endfor %}

+        </ul>

+    </td>

+</tr>

+

+<tr><td>

+</td></tr>

+

+</table>

+</td>

+</tr>

+</table>

+<HR>

+<p>

+<table name="info_table" width="100%" border="0" cellpadding="5" cellspacing="0">

+<tr><td><span style="font-size:115%%;font-weight:bold;">Specifics of this Data Set:</span></td></tr>

+    <tr><td> {{ info.specifics|safe }}<br><br></td></tr>

+<tr><td><span style="font-size:115%%;font-weight:bold;">Summary:</span></td></tr>

+    <tr><td> {{ info.dataset_summary|safe }}<br><br></td></tr>

+<tr><td><span style="font-size:115%; font-weight:bold;">About the cases used to generate this set of data:</span></td></tr>

+    <tr><td> {{ info.about_cases|safe }}<br><br></td></tr>

+<tr><td><span style="font-size:115%; font-weight:bold;">About the tissue used to generate this set of data:</span></td></tr>

+    <tr><td> {{ info.about_tissue|safe }}<br><br></td></tr>

+    <tr><td><span style="font-size:115%; font-weight:bold;">About the array platform:</span></td></tr>

+    <tr><td> {{ info.about_platform|safe }}<br><br></td></tr>

+<tr><td><span style="font-size:115%; font-weight:bold;">About data values and data processing:</span></td></tr>

+    <tr><td> {{ info.about_data_processing|safe }}<br><br></td></tr>

+<tr><td><span style="font-size:115%; font-weight:bold;">Notes:</span></td></tr>

+    <tr><td> {{ info.notes|safe }}<br><br></td></tr>

+<tr><td><span style="font-size:115%; font-weight:bold;">Experiment Type:</span></td></tr>

+    <tr><td> {{ info.experiment_design|safe }}<br><br></td></tr>

+<tr><td><span style="font-size:115%; font-weight:bold;">Contributor:</span></td></tr>

+    <tr><td> {{ info.contributors|safe }}<br><br></td></tr>

+<tr><td><span style="font-size:115%; font-weight:bold;">Citation:</span></td></tr>

+    <tr><td> {{ info.citation|safe }}<br><br></td></tr>

+<tr><td><span style="font-size:115%; font-weight:bold;">Data source acknowledgment:</span></td></tr>

+    <tr><td> {{ info.acknowledgement|safe }}<br><br></td></tr>

+<tr><td><span style="font-size:115%; font-weight:bold;">Study Id:</span></td></tr>

+    <tr><td> {{ info.dataset_id }}<br><br></td></tr>

+</table>

+</p>

+ 

+{% endblock %}
\ No newline at end of file
diff --git a/wqflask/wqflask/templates/mapping_results.html b/wqflask/wqflask/templates/mapping_results.html
index 8edda548..41d760c0 100644
--- a/wqflask/wqflask/templates/mapping_results.html
+++ b/wqflask/wqflask/templates/mapping_results.html
@@ -228,71 +228,61 @@
         <button class="btn btn-success" id="add" disabled><span class="glyphicon glyphicon-plus-sign"></span> Add</button>
         <br />
         <br />
-          <div id="table_container" style="width:{% if 'additive' in trimmed_markers[0] %}500{% else %}470{% endif %}px;">
-          <table id="trait_table" class="table-hover table-striped cell-border dataTable no-footer">
-            <thead>
-              <tr>
-                <th></th>
-                <th>Row</th>
-                <th>Marker</th>
-                <th>{{ LRS_LOD }}</th>
-                <th>Chr</th>
-                {% if plotScale != "physic" %}
-                <th>cM</th>
-                {% else %}
-                <th align="right">Mb</th>
-                {% endif %}
-                {% if 'additive' in trimmed_markers[0] %}
-                <th>Add Eff</th>
-                {% endif %}
-                {% if 'dominance' in trimmed_markers[0] and dataset.group.genetic_type != "riset" %}
-                <th>Dom Eff</th>
-                {% endif %}
-              </tr>
-            </thead>
-            <tbody>
-              {% for marker in trimmed_markers %}
-              <tr>
-                <td align="center" style="padding: 1px 0px 1px 0px;">
-                  <input type="checkbox" name="selectCheck"
-                         class="checkbox trait_checkbox"
-                         value="{{ data_hmac('{}:{}Geno'.format(marker.name, dataset.group.name)) }}">
-                </td>
-                <td align="right">{{ loop.index }}</td>
-                <td>{% if geno_db_exists == "True" %}<a href="/show_trait?trait_id={{ marker.name }}&dataset={{ dataset.group.name }}Geno">{{ marker.name }}</a>{% else %}{{ marker.name }}{% endif %}</td>
-                {% if LRS_LOD == "LOD" or LRS_LOD == "-log(p)" %}
-                {% if 'lod_score' in marker %}
-                <td align="right">{{ '%0.2f' | format(marker.lod_score|float) }}</td>
-                {% else %}
-                <td align="right">{{ '%0.2f' | format(marker.lrs_value|float / 4.61) }}</td>
-                {% endif %}
-                {% else %}
-                {% if 'lod_score' in marker %}
-                <td align="right">{{ '%0.2f' | format(marker.lod_score|float * 4.61) }}</td>
-                {% else %}
-                <td align="right">{{ '%0.2f' | format(marker.lrs_value|float) }}</td>
-                {% endif %}
-                {% endif %}
-                <td align="right">{{marker.chr}}</td>
-                {% if plotScale != "physic" %}
-                {% if 'cM' in marker %}
-                <td align="right">{{ '%0.3f' | format(marker.cM|float) }}</td>
-                {% else %}
-                <td align="right">{{ '%0.3f' | format(marker.Mb|float) }}</td>
-                {% endif %}
-                {% else %}
-                <td align="right">{{ '%0.6f' | format(marker.Mb|float) }}</td>
-                {% endif %}
-                {% if 'additive' in marker %}
-                <td align="right">{{ '%0.3f' | format(marker.additive|float) }}</td>
-                {% endif %}
-                {% if 'dominance' in marker and dataset.group.genetic_type != "riset" %}
-                <td align="right">{{ '%0.2f' | format(marker.dominance|float) }}</td>
-                {% endif %}
-              </tr>
-              {% endfor %}
-            </tbody>
-          </table>
+          <div id="table_container" style="width:{% if 'additive' in trimmed_markers[0] %}600{% else %}550{% endif %}px;">
+            <table id="trait_table" class="table-hover table-striped cell-border dataTable no-footer">
+              <thead>
+                <tr>
+                  <th></th>
+                  <th>Row</th>
+                  <th>Marker</th>
+                  {% if LRS_LOD == "-log(p)" %}
+                  <th>–log(p)</th>
+                  {% else %}
+                  <th>{{ LRS_LOD }}</th>
+                  {% endif %}
+                  <th>Position ({% if plotScale == "physic" %}Mb{% else %}cM{% endif %})</th>
+                  {% if 'additive' in trimmed_markers[0] %}
+                  <th>Add Eff</th>
+                  {% endif %}
+                  {% if 'dominance' in trimmed_markers[0] and dataset.group.genetic_type != "riset" %}
+                  <th>Dom Eff</th>
+                  {% endif %}
+                </tr>
+              </thead>
+              <tbody>
+                {% for marker in trimmed_markers %}
+                <tr>
+                  <td align="center" style="padding: 1px 0px 1px 0px;">
+                    <input type="checkbox" name="selectCheck"
+                           class="checkbox trait_checkbox"
+                           value="{{ data_hmac('{}:{}Geno'.format(marker.name, dataset.group.name)) }}">
+                  </td>
+                  <td align="right">{{ loop.index }}</td>
+                  <td>{% if geno_db_exists == "True" %}<a href="/show_trait?trait_id={{ marker.name }}&dataset={{ dataset.group.name }}Geno">{{ marker.name }}</a>{% else %}{{ marker.name }}{% endif %}</td>
+                  {% if LRS_LOD == "LOD" or LRS_LOD == "-log(p)" %}
+                  {% if 'lod_score' in marker %}
+                  <td align="right">{{ '%0.2f' | format(marker.lod_score|float) }}</td>
+                  {% else %}
+                  <td align="right">{{ '%0.2f' | format(marker.lrs_value|float / 4.61) }}</td>
+                  {% endif %}
+                  {% else %}
+                  {% if 'lod_score' in marker %}
+                  <td align="right">{{ '%0.2f' | format(marker.lod_score|float * 4.61) }}</td>
+                  {% else %}
+                  <td align="right">{{ '%0.2f' | format(marker.lrs_value|float) }}</td>
+                  {% endif %}
+                  {% endif %}
+                  <td align="right">{{ marker.display_pos }}</td>
+                  {% if 'additive' in marker %}
+                  <td align="right">{{ '%0.3f' | format(marker.additive|float) }}</td>
+                  {% endif %}
+                  {% if 'dominance' in marker and dataset.group.genetic_type != "riset" %}
+                  <td align="right">{{ '%0.2f' | format(marker.dominance|float) }}</td>
+                  {% endif %}
+                </tr>
+                {% endfor %}
+              </tbody>
+            </table>
           </div>
         </div>
         {% elif selectedChr != -1 and plotScale =="physic" and (dataset.group.species == 'mouse' or dataset.group.species == 'rat') %}
@@ -362,8 +352,7 @@
                 "columns": [
                     { "type": "natural", "width": "5%" },
                     { "type": "natural", "width": "8%" },
-                    { "type": "natural", "width": "25%" },
-                    { "type": "natural" },
+                    { "type": "natural", "width": "20%" },
                     { "type": "natural" },
                     { "type": "natural" }{% if 'additive' in qtlresults[0] %},
                     { "type": "natural" }{% endif %}{% if 'dominance' in qtlresults[0] and dataset.group.genetic_type != "riset" %},
@@ -395,16 +384,16 @@
                   $('td', row).eq(9).attr("align", "right");
                 },
                 "columns": [
-                    { "bSortable": false},
-                    { "type": "natural" },
-                    { "type": "natural" },
-                    { "type": "natural" },
-                    { "type": "natural" },
-                    { "type": "natural" },
-                    { "type": "natural" },
-                    { "type": "natural" },
+                    { "orderDataType": "dom-checkbox" },
+                    { "type": "natural"},
+                    { "type": "natural" , "orderDataType": "dom-inner-text" },
+                    { "type": "natural" , "orderDataType": "dom-inner-text" },
+                    { "type": "natural" , "orderDataType": "dom-inner-text" },
                     { "type": "natural" },
                     { "type": "natural" },
+                    { "type": "natural-minus-na" },
+                    { "type": "natural-minus-na" },
+                    { "type": "natural-minus-na" , "orderDataType": "dom-inner-text" },
                     { "type": "natural" }
                 ],
                 "columnDefs": [ {
diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html
index 53373b41..2318bfb8 100644
--- a/wqflask/wqflask/templates/search_result_page.html
+++ b/wqflask/wqflask/templates/search_result_page.html
@@ -127,7 +127,7 @@
               <input type="hidden" name="export_data" id="export_data" value="">
               <button class="btn btn-default" id="select_all" type="button"><span class="glyphicon glyphicon-ok"></span> Select</button>
               <button class="btn btn-success" id="add" type="button" disabled><span class="glyphicon glyphicon-plus-sign"></span> Add</button>
-              <button class="btn btn-default" id="export_traits">Download CSV</button>
+              <button class="btn btn-default" id="export_traits">Download <span class="glyphicon glyphicon-download"></span></button>
               <input type="text" id="searchbox" class="form-control" style="width: 200px; display: inline;" placeholder="Search This Table For ...">
               <input type="text" id="select_top" class="form-control" style="width: 200px; display: inline;" placeholder="Select Top ...">
               <button class="btn btn-default" id="deselect_all" type="button"><span class="glyphicon glyphicon-remove"></span> Deselect</button>
@@ -140,7 +140,6 @@
             <b>Show/Hide Columns:</b>
           </div>
           {% endif %}
-          <!--<div id="table_container" style="min-width: {% if dataset.type == 'ProbeSet' or dataset.type == 'Publish' %}2000{% else %}380{% endif %}px;">-->
           <div id="table_container" {% if dataset.type == 'ProbeSet' or dataset.type == 'Publish' %}style="min-width: 1500px;"{% endif %}>
             <table class="table-hover table-striped cell-border" id='trait_table' style="float: left; width: {% if dataset.type == 'Geno' %}380px{% else %}100%{% endif %};">
                 <tbody>
@@ -174,21 +173,6 @@
     </script>
 
     <script type="text/javascript" charset="utf-8">
-
-        $.fn.dataTable.ext.order['dom-checkbox'] = function  ( settings, col )
-        {
-            return this.api().column( col, {order:'index'} ).nodes().map( function ( td, i ) {
-                return $('input', td).prop('checked') ? '1' : '0';
-            } );
-        };
-
-        $.fn.dataTable.ext.order['dom-inner-text'] = function  ( settings, col )
-        {
-            return this.api().column( col, {order:'index'} ).nodes().map( function ( td, i ) {
-                return $(td).text();
-            } );
-        }
-
         $(document).ready( function () {
             
             $('#trait_table tr').click(function(event) {
@@ -289,10 +273,9 @@
                     },
                     {
                       'title': "Record",
-                      'type': "natural",
+                      'type': "natural-minus-na",
                       'data': null,
                       'width': "60px",
-                      'orderDataType': "dom-inner-text",
                       'render': function(data, type, row, meta) {
                         return '<a target="_blank" href="/show_trait?trait_id=' + data.name + '&dataset=' + data.dataset + '">' + data.display_name + '</a>'
                       }
@@ -306,7 +289,6 @@
                     {
                       'title': "Description",
                       'type': "natural",
-                      'width': "500px",
                       'data': null,
                       'render': function(data, type, row, meta) {
                         try {
@@ -319,7 +301,7 @@
                     {
                       'title': "Location",
                       'type': "natural-minus-na",
-                      'width': "120px",
+                      'width': "125px",
                       'data': "location"
                     },
                     {
@@ -330,23 +312,23 @@
                       'orderSequence': [ "desc", "asc"]
                     },
                     {
-                      'title': "Max LRS<a href=\"http://genenetwork.org//glossary.html#LRS\" target=\"_blank\" style=\"color: white;\"><sup>?</sup></a>",
+                      'title': "High P<a href=\"http://genenetwork.org//glossary.html#LRS\" target=\"_blank\" style=\"color: white;\"><sup style=\"font-size: small; color: #FF0000;\"> ?</sup></a>",
                       'type': "natural-minus-na",
                       'data': "lrs_score",
-                      'width': "80px",
+                      'width': "60px",
                       'orderSequence': [ "desc", "asc"]
                     },
                     {
-                      'title': "Max LRS Location",
+                      'title': "Peak Location",
                       'type': "natural-minus-na",
-                      'width': "150px",
+                      'width': "125px",
                       'data': "lrs_location"
                     },
                     {
-                      'title': "Additive Effect<a href=\"http://genenetwork.org//glossary.html#A\" target=\"_blank\" style=\"color: white;\"><sup>?</sup></a>",
+                      'title': "Effect Size<a href=\"http://genenetwork.org//glossary.html#A\" target=\"_blank\" style=\"color: white;\"><sup style=\"font-size: small; color: #FF0000;\"> ?</sup></a>",
                       'type': "natural-minus-na",
                       'data': "additive",
-                      'width': "120px",
+                      'width': "85px",
                       'orderSequence': [ "desc", "asc"]
                     }{% elif dataset.type == 'Publish' %},
                     {
@@ -382,17 +364,11 @@
                           author_string = data.authors
                         }
                         return author_string
-                        // try {
-                        //   return decodeURIComponent(escape(author_string))
-                        // } catch(err){
-                        //   return author_string
-                        // }
                       }
                     },
                     {
                       'title': "Year",
                       'type': "natural-minus-na",
-                      'orderDataType': "dom-inner-text",
                       'data': null,
                       'width': "80px",
                       'render': function(data, type, row, meta) {
@@ -405,20 +381,20 @@
                       'orderSequence': [ "desc", "asc"]
                     },
                     {
-                      'title': "Max LRS<a href=\"http://genenetwork.org//glossary.html#LRS\" target=\"_blank\" style=\"color: white;\"><sup>?</sup></a>",
+                      'title': "Max LRS<a href=\"http://genenetwork.org//glossary.html#LRS\" target=\"_blank\" style=\"color: white;\"><sup style=\"font-size: small; color: #FF0000;\"> ?</sup></a>",
                       'type': "natural-minus-na",
                       'data': "lrs_score",
                       'width': "80px",
                       'orderSequence': [ "desc", "asc"]
                     },
                     {
-                      'title': "Max LRS Location",
+                      'title': "Peak Location",
                       'type': "natural-minus-na",
-                      'width': "150px",
+                      'width': "120px",
                       'data': "lrs_location"
                     },
                     {
-                      'title': "Additive Effect<a href=\"http://genenetwork.org//glossary.html#A\" target=\"_blank\" style=\"color: white;\"><sup>?</sup></a>",
+                      'title': "Effect Size<a href=\"http://genenetwork.org//glossary.html#A\" target=\"_blank\" style=\"color: white;\"><sup style=\"font-size: small; color: #FF0000;\"> ?</sup></a>",
                       'type': "natural-minus-na",
                       'width': "120px",
                       'data': "additive",
@@ -427,7 +403,7 @@
                     {
                       'title': "Location",
                       'type': "natural-minus-na",
-                      'width': "140px",
+                      'width': "120px",
                       'data': "location"
                     }{% endif %}
                 ],
diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index 2d65f008..5ed7a90b 100644
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -37,7 +37,7 @@
         <input type="hidden" name="covariates" value="">
         <input type="hidden" name="transform" value="">
 
-        <div class="container" style="min-width: 1450px;">
+        <div class="container" style="min-width: 700px;">
             <div class="panel-group" id="accordion">
                 <div class="panel panel-default">
                     <div class="panel-heading" data-toggle="collapse" data-parent="#accordion" data-target="#collapseOne" aria-expanded="true">
diff --git a/wqflask/wqflask/templates/show_trait_calculate_correlations.html b/wqflask/wqflask/templates/show_trait_calculate_correlations.html
index 1378b91b..9420c9c6 100644
--- a/wqflask/wqflask/templates/show_trait_calculate_correlations.html
+++ b/wqflask/wqflask/templates/show_trait_calculate_correlations.html
@@ -1,5 +1,5 @@
 <div>
-  <div class="col-xs-7">
+  <div class="col-xs-6" style="min-width: 800px;">
     <div style="padding: 20px" class="form-horizontal">
         
         <div class="form-group">
@@ -39,7 +39,7 @@
         
         <div class="form-group">
             <label for="corr_return_results" class="col-xs-2 control-label">Return</label>
-            <div class="col-xs-3 controls">
+            <div class="col-xs-4 controls">
                 <select name="corr_return_results" class="form-control">
                     {% for return_result in corr_tools.return_results_menu %}
                         <option value="{{ return_result }}" 
@@ -55,7 +55,7 @@
         
         <div class="form-group">
             <label for="corr_samples_group" class="col-xs-2 control-label">Samples</label>
-            <div class="col-xs-3 controls">
+            <div class="col-xs-4 controls">
                 <select name="corr_samples_group" class="form-control">
                     {% for group, pretty_group in sample_group_types.items() %}
                         <option value="{{ group }}">{{ pretty_group }}</option>
@@ -66,7 +66,7 @@
             
         <div id="corr_sample_method" class="form-group">
             <label for="corr_sample_method" class="col-xs-2 control-label">Type</label>
-            <div class="col-xs-3 controls">
+            <div class="col-xs-4 controls">
                 <select name="corr_sample_method" class="form-control">
                     <option value="pearson">Pearson</option>
                     <option value="spearman">Spearman Rank</option>
@@ -77,7 +77,7 @@
         {% if dataset.type != "Publish" %}
         <div class="form-group">
             <label class="col-xs-2 control-label">Min Expr</label>
-            <div class="col-xs-3 controls">
+            <div class="col-xs-4 controls">
                 <input name="min_expr" value="" type="text" class="form-control" style="width: 70px;">
             </div>
         </div>
@@ -114,7 +114,7 @@
         </div>
     </div>
   </div>
-  <div class="col-xs-5">
+  <div>
     <span id="sample_r_desc" class="correlation_desc fs12">
         The <a href="http://genenetwork.org/correlationAnnotation.html#genetic_r">Sample Correlation</a>
         is computed
diff --git a/wqflask/wqflask/templates/show_trait_details.html b/wqflask/wqflask/templates/show_trait_details.html
index 8b3e4907..4aced50c 100644
--- a/wqflask/wqflask/templates/show_trait_details.html
+++ b/wqflask/wqflask/templates/show_trait_details.html
@@ -215,43 +215,27 @@
 
 <div style="margin-bottom:15px;" class="btn-toolbar">
     <div class="btn-group">
-        <a href="#redirect">
-        <button type="button" id="add_to_collection" class="btn btn-primary" title="Add to collection">Add</button>
-        </a>
+        <button type="button" id="add_to_collection" class="btn btn-success" title="Add to Collection">Add</button>
         {% if this_trait.dataset.type == 'ProbeSet' or this_trait.dataset.type == 'Geno' %}
         {% if this_trait.symbol != None %}
-        <a target="_blank" href="http://gn1.genenetwork.org/webqtl/main.py?cmd=sch&amp;gene={{ this_trait.symbol }}&amp;alias=1&amp;species={{ dataset.group.species }}">
-        <button type="button" class="btn btn-default" title="Find similar expression data">Find</button>
-        </a>
+        <button type="button" class="btn btn-default" title="Find similar expression data" onclick="window.open('http://gn1.genenetwork.org/webqtl/main.py?cmd=sch&amp;gene={{ this_trait.symbol }}&amp;alias=1&amp;species={{ dataset.group.species }}', '_blank')">Find</button>
         {% endif %}
         {% if UCSC_BLAT_URL != "" %}
-        <a target="_blank" href="{{ UCSC_BLAT_URL }}">
-        <button type="button" class="btn btn-default" title="Check probe locations at UCSC">Verify</button>
-        </a>
+        <button type="button" class="btn btn-default" title="Check probe locations at UCSC" onclick="window.open('{{ UCSC_BLAT_URL }}', '_blank')">Verify</button>
         {% endif %}
         {% if this_trait.symbol != None %}
-        <a target="_blank" href="http://gn1.genenetwork.org/webqtl/main.py?FormID=geneWiki&symbol={{ this_trait.symbol }}">
-        <button type="button" class="btn btn-default" title="Write or review comments about this gene">GeneWiki</button>
-        </a>
+        <button type="button" class="btn btn-default" title="Write or review comments about this gene" onclick="window.open('http://gn1.genenetwork.org/webqtl/main.py?FormID=geneWiki&symbol={{ this_trait.symbol }}', '_blank')">GeneWiki</button>
         {% if dataset.group.species == "mouse" or dataset.group.species == "rat" %}
-        <a href="/snp_browser?first_run=true&species={{ dataset.group.species }}&gene_name={{ this_trait.symbol }}&limit_strains=on">
-        <button type="button" class="btn btn-default" title="View SNPs and Indels">SNPs</button>
-        </a>
+        <button type="button" class="btn btn-default" title="View SNPs and Indels" onclick="window.open('/snp_browser?first_run=true&species={{ dataset.group.species }}&gene_name={{ this_trait.symbol }}&limit_strains=on', '_blank')">SNPs</button>
         {% endif %}
         {% endif %}
         {% if show_probes == "True" %}
-        <a target="_blank" href="http://gn1.genenetwork.org/webqtl/main.py?FormID=showProbeInfo&database={{ this_trait.dataset.name }}&ProbeSetID={{ this_trait.name }}&CellID={{ this_trait.cellid }}&RISet={{ dataset.group.name }}&incparentsf1=ON">
-        <button type="button" class="btn btn-default" title="Check sequence of probes">Probes</button>
-        </a>
+        <button type="button" class="btn btn-default" title="Check sequence of probes" onclick="window.open('http://gn1.genenetwork.org/webqtl/main.py?FormID=showProbeInfo&database={{ this_trait.dataset.name }}&ProbeSetID={{ this_trait.name }}&CellID={{ this_trait.cellid }}&RISet={{ dataset.group.name }}&incparentsf1=ON', '_blank')">Probes</button>
         {% endif %}
         {% endif %}
-        <a target="_blank" href="http://gn1.genenetwork.org/webqtl/main.py?cmd=show&db={{ this_trait.dataset.name }}&probeset={{ this_trait.name }}">
-        <button type="button" id="view_in_gn1" class="btn btn-primary" title="View Trait in GN1">View in GN1</button>
-        </a>
+        <button type="button" id="view_in_gn1" class="btn btn-primary" title="View Trait in GN1" onclick="window.open('http://gn1.genenetwork.org/webqtl/main.py?cmd=show&db={{ this_trait.dataset.name }}&probeset={{ this_trait.name }}', '_blank')">Go to GN1</button>
         {% if admin_status == "owner" or admin_status == "edit-admins" or admin_status == "edit-access" %}
-        <a target="_blank" href="./resources/manage?resource_id={{ resource_id }}">
-            <button type="button" id="edit_resource" class="btn btn-success" title="Edit Resource">Edit</button>
-        </a>
+            <button type="button" id="edit_resource" class="btn btn-success" title="Edit Resource" onclick="window.open('./resources/manage?resource_id={{ resource_id }}', '_blank')">Edit</button>
         {% endif %}
     </div>
 </div>
diff --git a/wqflask/wqflask/templates/show_trait_edit_data.html b/wqflask/wqflask/templates/show_trait_edit_data.html
index 05a2be73..a8ed91b1 100644
--- a/wqflask/wqflask/templates/show_trait_edit_data.html
+++ b/wqflask/wqflask/templates/show_trait_edit_data.html
@@ -5,7 +5,7 @@
           <input type="text" id="{{ sample_type.sample_group_type }}_searchbox" class="form-control" style="width: 200px; display: inline; float: left; vertical-align: top;" placeholder="Search This Table For ...">
         </div>
         <div style="padding-left: 10px; display: inline;">
-          <input type="button" class="btn btn-default export" value="Export">
+          <button class="btn btn-default export">Export <span class="glyphicon glyphicon-download-alt"></span></button>
           <select class="select optional span2 export_format">
             <option value="excel">Excel</option>
             <option value="csv">CSV</option>
diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html
index 27040045..94388b2f 100755
--- a/wqflask/wqflask/templates/show_trait_mapping_tools.html
+++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html
@@ -397,8 +397,8 @@
             </div>
         </div>
     </div>
-    <div class="col-xs-7">
-        <dl style="width: 500px;">
+    <div>
+        <dl>
              {% for mapping_method in dataset.group.mapping_names %}
              {% if mapping_method == "GEMMA" %}
              <dt style="padding-top: 20px;">GEMMA</dt>
diff --git a/wqflask/wqflask/templates/show_trait_statistics.html b/wqflask/wqflask/templates/show_trait_statistics.html
index 974081d3..7bdb3ef9 100644
--- a/wqflask/wqflask/templates/show_trait_statistics.html
+++ b/wqflask/wqflask/templates/show_trait_statistics.html
@@ -76,11 +76,13 @@
                             <i class="icon-signal"></i> Sort By Value
                             </button>
                         </div>
+                        <!--
                         <div class="btn-group">
-                            <button type="button" class="btn btn-default" id="color_by_trait">
+                            <button type="button" class="btn btn-default" id="color_by_trait" style="margin-bottom: 5px;">
                                 <i class="icon-tint"></i> Color by Trait
                             </button>
                         </div>
+                        -->
                         <div id="bar_chart_container">
                             <div id="bar_chart"></div>
                         </div>
diff --git a/wqflask/wqflask/templates/tutorials.html b/wqflask/wqflask/templates/tutorials.html
index 3e6ef01c..f9d12ba5 100644
--- a/wqflask/wqflask/templates/tutorials.html
+++ b/wqflask/wqflask/templates/tutorials.html
@@ -15,3 +15,4 @@ and initial mapping results for Rat GWAS P50 as implemented in GeneNetwork.org</
 </TR></TABLE>
 
 {% endblock %}
+
diff --git a/wqflask/wqflask/user_login.py b/wqflask/wqflask/user_login.py
index 9331f369..077a799b 100644
--- a/wqflask/wqflask/user_login.py
+++ b/wqflask/wqflask/user_login.py
@@ -453,7 +453,9 @@ def register_user(params):
         user_details['confirmed'] = 1
 
         user_details['registration_info'] = basic_info()
-        save_user(user_details, user_details['user_id'])
+
+        if len(errors) == 0:
+            save_user(user_details, user_details['user_id'])
 
         return errors
 
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index fc9949a8..94ec7137 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -29,14 +29,7 @@ import array
 import sqlalchemy
 from wqflask import app
 from flask import g, Response, request, make_response, render_template, send_from_directory, jsonify, redirect, url_for, send_file
-from wqflask import group_manager
-from wqflask import resource_manager
-from wqflask import search_results
-from wqflask import export_traits
-from wqflask import gsearch
-from wqflask import update_search_results
-from wqflask import docs
-from wqflask import news
+
 from wqflask.submit_bnw import get_bnw_input
 from base.data_set import create_dataset, DataSet    # Used by YAML in marker_regression
 from wqflask.show_trait import show_trait
@@ -53,6 +46,12 @@ from wqflask.correlation import corr_scatter_plot
 from wqflask.wgcna import wgcna_analysis
 from wqflask.ctl import ctl_analysis
 from wqflask.snp_browser import snp_browser
+from wqflask.search_results import SearchResultPage
+from wqflask.export_traits import export_search_results_csv
+from wqflask.gsearch import GSearch
+from wqflask.update_search_results import GSearch as UpdateGSearch
+from wqflask.docs import Docs, update_text
+from wqflask.db_info import InfoPage
 
 from utility import temp_data
 from utility.tools import SQL_URI,TEMPDIR,USE_REDIS,USE_GN_SERVER,GN_SERVER_URL,GN_VERSION,JS_TWITTER_POST_FETCHER_PATH,JS_GUIX_PATH, CSS_PATH
@@ -66,9 +65,6 @@ from utility.benchmark import Bench
 
 from pprint import pformat as pf
 
-from wqflask import user_login
-from wqflask import user_session
-
 from wqflask import collect
 from wqflask.database import db_session
 
@@ -215,7 +211,7 @@ def search_page():
         logger.info("Skipping Redis cache (USE_REDIS=False)")
 
     logger.info("request.args is", request.args)
-    the_search = search_results.SearchResultPage(request.args)
+    the_search = SearchResultPage(request.args)
     result = the_search.__dict__
     valid_search = result['search_term_exists']
 
@@ -233,7 +229,7 @@ def search_page():
 @app.route("/gsearch", methods=('GET',))
 def gsearchact():
     logger.info(request.url)
-    result = gsearch.GSearch(request.args).__dict__
+    result = GSearch(request.args).__dict__
     type = request.args['type']
     if type == "gene":
         return render_template("gsearch_gene.html", **result)
@@ -244,7 +240,7 @@ def gsearchact():
 def gsearch_updating():
     logger.info("REQUEST ARGS:", request.values)
     logger.info(request.url)
-    result = update_search_results.GSearch(request.args).__dict__
+    result = UpdateGSearch(request.args).__dict__
     return result['results']
     # type = request.args['type']
     # if type == "gene":
@@ -257,7 +253,7 @@ def docedit():
     logger.info(request.url)
     try:
         if g.user_session.record['user_email_address'] == "zachary.a.sloan@gmail.com" or g.user_session.record['user_email_address'] == "labwilliams@gmail.com":
-            doc = docs.Docs(request.args['entry'], request.args)
+            doc = Docs(request.args['entry'], request.args)
             return render_template("docedit.html", **doc.__dict__)
         else:
             return "You shouldn't be here!"
@@ -273,7 +269,7 @@ def generated_file(filename):
 @app.route("/help")
 def help():
     logger.info(request.url)
-    doc = docs.Docs("help", request.args)
+    doc = Docs("help", request.args)
     return render_template("docs.html", **doc.__dict__)
 
 @app.route("/wgcna_setup", methods=('POST',))
@@ -308,54 +304,54 @@ def ctl_results():
 
 @app.route("/news")
 def news():
-    doc = docs.Docs("news", request.args)
+    doc = Docs("news", request.args)
     return render_template("docs.html", **doc.__dict__)
 
 @app.route("/references")
 def references():
-    doc = docs.Docs("references", request.args)
+    doc = Docs("references", request.args)
     return render_template("docs.html", **doc.__dict__)
     #return render_template("reference.html")
 
 @app.route("/intro")
 def intro():
-    doc = docs.Docs("intro", request.args)
+    doc = Docs("intro", request.args)
     return render_template("docs.html", **doc.__dict__)
 
 @app.route("/policies")
 def policies():
-    doc = docs.Docs("policies", request.args)
+    doc = Docs("policies", request.args)
     #return render_template("policies.html")
     return render_template("docs.html", **doc.__dict__)
 
 @app.route("/links")
 def links():
-    #doc = docs.Docs("links", request.args)
+    #doc = Docs("links", request.args)
     #return render_template("docs.html", **doc.__dict__)
     return render_template("links.html")
 
 @app.route("/tutorials")
 def tutorials():
-    #doc = docs.Docs("links", request.args)
+    #doc = Docs("links", request.args)
     #return render_template("docs.html", **doc.__dict__)
     return render_template("tutorials.html")
 
 @app.route("/credits")
 def credits():
-    #doc = docs.Docs("links", request.args)
+    #doc = Docs("links", request.args)
     #return render_template("docs.html", **doc.__dict__)
     return render_template("credits.html")
 
 @app.route("/environments")
 def environments():
-    doc = docs.Docs("environments", request.args)
+    doc = Docs("environments", request.args)
     return render_template("docs.html", **doc.__dict__)
     #return render_template("environments.html", **doc.__dict__)
 
 @app.route("/update_text", methods=('POST',))
 def update_page():
-    docs.update_text(request.form)
-    doc = docs.Docs(request.form['entry_type'], request.form)
+    update_text(request.form)
+    doc = Docs(request.form['entry_type'], request.form)
     return render_template("docs.html", **doc.__dict__)
 
 @app.route("/submit_trait")
@@ -370,7 +366,7 @@ def create_temp_trait():
 
     #template_vars = submit_trait.SubmitTrait(request.form)
 
-    doc = docs.Docs("links")
+    doc = Docs("links")
     return render_template("links.html", **doc.__dict__)
     #return render_template("show_trait.html", **template_vars.__dict__)
 
@@ -425,7 +421,7 @@ def export_traits_csv():
     logger.info("In export_traits_csv")
     logger.info("request.form:", request.form)
     logger.info(request.url)
-    file_list = export_traits.export_search_results_csv(request.form)
+    file_list = export_search_results_csv(request.form)
 
     if len(file_list) > 1:
         now = datetime.datetime.now()
@@ -908,12 +904,24 @@ def snp_browser_page():
 
     return render_template("snp_browser.html", **template_vars.__dict__)
 
+@app.route("/db_info", methods=('GET',))
+def db_info_page():
+    template_vars = InfoPage(request.args)
+
+    return render_template("info_page.html", **template_vars.__dict__)
+
 @app.route("/tutorial/WebQTLTour", methods=('GET',))
 def tutorial_page():
     #ZS: Currently just links to GN1
     logger.info(request.url)
     return redirect("http://gn1.genenetwork.org/tutorial/WebQTLTour/")
 
+@app.route("/tutorial/security", methods=('GET',))
+def security_tutorial_page():
+    #ZS: Currently just links to GN1
+    logger.info(request.url)
+    return render_template("admin/security_help.html")
+
 @app.route("/submit_bnw", methods=('POST',))
 def submit_bnw():
     logger.info(request.url)
diff --git a/wqflask/wqflask/wgcna/wgcna_analysis.py b/wqflask/wqflask/wgcna/wgcna_analysis.py
index 880a1cb2..70077703 100644
--- a/wqflask/wqflask/wgcna/wgcna_analysis.py
+++ b/wqflask/wqflask/wgcna/wgcna_analysis.py
@@ -1,5 +1,8 @@
-# WGCNA analysis for GN2
-# Author / Maintainer: Danny Arends <Danny.Arends@gmail.com>
+"""
+WGCNA analysis for GN2
+
+Author / Maintainer: Danny Arends <Danny.Arends@gmail.com>
+"""
 import sys
 from numpy import *
 import scipy as sp                            # SciPy
@@ -17,106 +20,138 @@ from utility import helper_functions
 from rpy2.robjects.packages import importr
 utils = importr("utils")
 
-## Get pointers to some common R functions
-r_library       = ro.r["library"]             # Map the library function
-r_options       = ro.r["options"]             # Map the options function
-r_read_csv      = ro.r["read.csv"]            # Map the read.csv function
-r_dim           = ro.r["dim"]                 # Map the dim function
-r_c             = ro.r["c"]                   # Map the c function
-r_cat           = ro.r["cat"]                 # Map the cat function
-r_paste         = ro.r["paste"]               # Map the paste function
-r_unlist        = ro.r["unlist"]              # Map the unlist function
-r_unique        = ro.r["unique"]              # Map the unique function
-r_length        = ro.r["length"]              # Map the length function
-r_unlist        = ro.r["unlist"]              # Map the unlist function
-r_list          = ro.r.list                   # Map the list function
-r_matrix        = ro.r.matrix                 # Map the matrix function
-r_seq           = ro.r["seq"]                 # Map the seq function
-r_table         = ro.r["table"]               # Map the table function
-r_names         = ro.r["names"]               # Map the names function
-r_sink          = ro.r["sink"]                # Map the sink function
-r_is_NA         = ro.r["is.na"]               # Map the is.na function
-r_file          = ro.r["file"]                # Map the file function
-r_png           = ro.r["png"]                 # Map the png function for plotting
-r_dev_off       = ro.r["dev.off"]             # Map the dev.off function
+# Get pointers to some common R functions
+r_library = ro.r["library"]    # Map the library function
+r_options = ro.r["options"]    # Map the options function
+r_read_csv = ro.r["read.csv"]  # Map the read.csv function
+r_dim = ro.r["dim"]            # Map the dim function
+r_c = ro.r["c"]                # Map the c function
+r_cat = ro.r["cat"]            # Map the cat function
+r_paste = ro.r["paste"]        # Map the paste function
+r_unlist = ro.r["unlist"]      # Map the unlist function
+r_unique = ro.r["unique"]      # Map the unique function
+r_length = ro.r["length"]      # Map the length function
+r_unlist = ro.r["unlist"]      # Map the unlist function
+r_list = ro.r.list             # Map the list function
+r_matrix = ro.r.matrix         # Map the matrix function
+r_seq = ro.r["seq"]            # Map the seq function
+r_table = ro.r["table"]        # Map the table function
+r_names = ro.r["names"]        # Map the names function
+r_sink = ro.r["sink"]          # Map the sink function
+r_is_NA = ro.r["is.na"]        # Map the is.na function
+r_file = ro.r["file"]          # Map the file function
+r_png = ro.r["png"]            # Map the png function for plotting
+r_dev_off = ro.r["dev.off"]    # Map the dev.off function
+
 
 class WGCNA(object):
     def __init__(self):
+        # To log output from stdout/stderr to a file add `r_sink(log)`
         print("Initialization of WGCNA")
-        #log = r_file("/tmp/genenetwork_wcgna.log", open = "wt")
-        #r_sink(log)                                  # Uncomment the r_sink() commands to log output from stdout/stderr to a file
-        #r_sink(log, type = "message")
-        r_library("WGCNA")                            # Load WGCNA - Should only be done once, since it is quite expensive
-        r_options(stringsAsFactors = False)
+
+        # Load WGCNA - Should only be done once, since it is quite expensive
+        r_library("WGCNA")
+        r_options(stringsAsFactors=False)
         print("Initialization of WGCNA done, package loaded in R session")
-        self.r_enableWGCNAThreads    = ro.r["enableWGCNAThreads"]        # Map the enableWGCNAThreads function
-        self.r_pickSoftThreshold     = ro.r["pickSoftThreshold"]         # Map the pickSoftThreshold function
-        self.r_blockwiseModules      = ro.r["blockwiseModules"]          # Map the blockwiseModules function
-        self.r_labels2colors         = ro.r["labels2colors"]             # Map the labels2colors function
-        self.r_plotDendroAndColors   = ro.r["plotDendroAndColors"]       # Map the plotDendroAndColors function
+        # Map the enableWGCNAThreads function
+        self.r_enableWGCNAThreads = ro.r["enableWGCNAThreads"]
+        # Map the pickSoftThreshold function
+        self.r_pickSoftThreshold = ro.r["pickSoftThreshold"]
+        # Map the blockwiseModules function
+        self.r_blockwiseModules = ro.r["blockwiseModules"]
+        # Map the labels2colors function
+        self.r_labels2colors = ro.r["labels2colors"]
+        # Map the plotDendroAndColors function
+        self.r_plotDendroAndColors = ro.r["plotDendroAndColors"]
         print("Obtained pointers to WGCNA functions")
 
     def run_analysis(self, requestform):
         print("Starting WGCNA analysis on dataset")
-        self.r_enableWGCNAThreads()                                      # Enable multi threading
-        self.trait_db_list = [trait.strip() for trait in requestform['trait_list'].split(',')]
-        print("Retrieved phenotype data from database", requestform['trait_list'])
+        # Enable multi threading
+        self.r_enableWGCNAThreads()
+        self.trait_db_list = [trait.strip()
+                              for trait in requestform['trait_list'].split(',')]
+        print("Retrieved phenotype data from database",
+              requestform['trait_list'])
         helper_functions.get_trait_db_obs(self, self.trait_db_list)
 
-        self.input = {}           # self.input contains the phenotype values we need to send to R
-        strains = []              # All the strains we have data for (contains duplicates)
-        traits  = []              # All the traits we have data for (should not contain duplicates)
+        # self.input contains the phenotype values we need to send to R
+        self.input = {}
+        # All the strains we have data for (contains duplicates)
+        strains = []
+        # All the traits we have data for (should not contain duplicates)
+        traits = []
         for trait in self.trait_list:
             traits.append(trait[0].name)
             self.input[trait[0].name] = {}
             for strain in trait[0].data:
                 strains.append(strain)
-                self.input[trait[0].name][strain]  = trait[0].data[strain].value
+                self.input[trait[0].name][strain] = trait[0].data[strain].value
 
         # Transfer the load data from python to R
-        uStrainsR = r_unique(ro.Vector(strains))    # Unique strains in R vector
+        # Unique strains in R vector
+        uStrainsR = r_unique(ro.Vector(strains))
         uTraitsR = r_unique(ro.Vector(traits))      # Unique traits in R vector
 
         r_cat("The number of unique strains:", r_length(uStrainsR), "\n")
         r_cat("The number of unique traits:", r_length(uTraitsR), "\n")
 
-        # rM is the datamatrix holding all the data in R /rows = strains columns = traits
-        rM = ro.r.matrix(ri.NA_Real, nrow=r_length(uStrainsR), ncol=r_length(uTraitsR), dimnames = r_list(uStrainsR, uTraitsR))
+        # rM is the datamatrix holding all the data in
+        # R /rows = strains columns = traits
+        rM = ro.r.matrix(ri.NA_Real, nrow=r_length(uStrainsR), ncol=r_length(
+            uTraitsR), dimnames=r_list(uStrainsR, uTraitsR))
         for t in uTraitsR:
-            trait = t[0]                  # R uses vectors every single element is a vector
+            # R uses vectors every single element is a vector
+            trait = t[0]
             for s in uStrainsR:
-                strain = s[0]             # R uses vectors every single element is a vector
-                #DEBUG: print(trait, strain, " in python: ", self.input[trait].get(strain), "in R:", rM.rx(strain,trait)[0])
-                rM.rx[strain, trait] = self.input[trait].get(strain)  # Update the matrix location
+                # R uses vectors every single element is a vector
+                strain = s[0]
+                rM.rx[strain, trait] = self.input[trait].get(
+                    strain)  # Update the matrix location
                 sys.stdout.flush()
 
         self.results = {}
-        self.results['nphe'] = r_length(uTraitsR)[0]          # Number of phenotypes/traits
-        self.results['nstr'] = r_length(uStrainsR)[0]         # Number of strains
+        # Number of phenotypes/traits
+        self.results['nphe'] = r_length(uTraitsR)[0]
+        self.results['nstr'] = r_length(
+            uStrainsR)[0]         # Number of strains
         self.results['phenotypes'] = uTraitsR                 # Traits used
-        self.results['strains'] = uStrainsR                   # Strains used in the analysis
-        self.results['requestform'] = requestform             # Store the user specified parameters for the output page
+        # Strains used in the analysis
+        self.results['strains'] = uStrainsR
+        # Store the user specified parameters for the output page
+        self.results['requestform'] = requestform
 
-        # Calculate soft threshold if the user specified the SoftThreshold variable
+        # Calculate soft threshold if the user specified the
+        # SoftThreshold variable
         if requestform.get('SoftThresholds') is not None:
-          powers = [int(threshold.strip()) for threshold in requestform['SoftThresholds'].rstrip().split(",")]
-          rpow = r_unlist(r_c(powers))
-          print "SoftThresholds: {} == {}".format(powers, rpow)
-          self.sft    = self.r_pickSoftThreshold(rM, powerVector = rpow, verbose = 5)
-
-          print "PowerEstimate: {}".format(self.sft[0])
-          self.results['PowerEstimate'] = self.sft[0]
-          if self.sft[0][0] is ri.NA_Integer:
-            print "No power is suitable for the analysis, just use 1"
-            self.results['Power'] = 1                         # No power could be estimated
-          else:
-            self.results['Power'] = self.sft[0][0]            # Use the estimated power
+            powers = [int(threshold.strip())
+                      for threshold in requestform['SoftThresholds'].rstrip().split(",")]
+            rpow = r_unlist(r_c(powers))
+            print("SoftThresholds: {} == {}".format(powers, rpow))
+            self.sft = self.r_pickSoftThreshold(
+                rM, powerVector=rpow, verbose=5)
+
+            print("PowerEstimate: {}".format(self.sft[0]))
+            self.results['PowerEstimate'] = self.sft[0]
+            if self.sft[0][0] is ri.NA_Integer:
+                print "No power is suitable for the analysis, just use 1"
+                # No power could be estimated
+                self.results['Power'] = 1
+            else:
+                # Use the estimated power
+                self.results['Power'] = self.sft[0][0]
         else:
-          # The user clicked a button, so no soft threshold selection
-          self.results['Power'] = requestform.get('Power')    # Use the power value the user gives
+            # The user clicked a button, so no soft threshold selection
+            # Use the power value the user gives
+            self.results['Power'] = requestform.get('Power')
 
         # Create the block wise modules using WGCNA
-        network = self.r_blockwiseModules(rM, power = self.results['Power'], TOMType = requestform['TOMtype'], minModuleSize = requestform['MinModuleSize'], verbose = 3)
+        network = self.r_blockwiseModules(
+            rM,
+            power=self.results['Power'],
+            TOMType=requestform['TOMtype'],
+            minModuleSize=requestform['MinModuleSize'],
+            verbose=3)
 
         # Save the network for the GUI
         self.results['network'] = network
@@ -130,7 +165,9 @@ class WGCNA(object):
         self.results['imgloc'] = GENERATED_IMAGE_DIR + self.results['imgurl']
         r_png(self.results['imgloc'], width=1000, height=600, type='cairo-png')
         mergedColors = self.r_labels2colors(network[1])
-        self.r_plotDendroAndColors(network[5][0], mergedColors, "Module colors", dendroLabels = False, hang = 0.03, addGuide = True, guideHang = 0.05)
+        self.r_plotDendroAndColors(network[5][0], mergedColors,
+                                   "Module colors", dendroLabels=False,
+                                   hang=0.03, addGuide=True, guideHang=0.05)
         r_dev_off()
         sys.stdout.flush()
 
@@ -146,11 +183,9 @@ class WGCNA(object):
         print("Processing WGCNA output")
         template_vars = {}
         template_vars["input"] = self.input
-        template_vars["powers"] = self.sft[1:]                      # Results from the soft threshold analysis
+        # Results from the soft threshold analysis
+        template_vars["powers"] = self.sft[1:]
         template_vars["results"] = self.results
         self.render_image(results)
         sys.stdout.flush()
-        #r_sink(type = "message")                                   # This restores R output to the stdout/stderr
-        #r_sink()                                                   # We should end the Rpy session more or less
         return(dict(template_vars))
-