Merge branch 'testing' of https://github.com/genenetwork/genenetwork2 into replace-bootstrap

34 files changed, 809 insertions, 544 deletions

diff --git a/wqflask/wqflask/correlation/correlation_functions.py b/wqflask/wqflask/correlation/correlation_functions.py
index b883e361..fd7691d4 100644
--- a/wqflask/wqflask/correlation/correlation_functions.py
+++ b/wqflask/wqflask/correlation/correlation_functions.py
@@ -71,34 +71,6 @@ def cal_zero_order_corr_for_tiss (primaryValue=[], targetValue=[], method='pears
     return corr_result
 
 
-###########################################################################
-#Input: cursor, symbolList (list), dataIdDict(Dict)
-#output: symbolValuepairDict (dictionary):one dictionary of Symbol and Value Pair,
-#        key is symbol, value is one list of expression values of one probeSet;
-#function: get one dictionary whose key is gene symbol and value is tissue expression data (list type).
-#Attention! All keys are lower case!
-###########################################################################
-def get_symbol_value_pairs(tissue_data):
-    id_list = [tissue_data[symbol.lower()].data_id for item in tissue_data]
-
-    symbol_value_pairs = {}
-    value_list=[]
-
-    query = """SELECT value, id
-               FROM TissueProbeSetData
-               WHERE Id IN {}""".format(create_in_clause(id_list))
-
-    try :
-        results = g.db.execute(query).fetchall()
-        for result in results:
-            value_list.append(result.value)
-        symbol_value_pairs[symbol] = value_list
-    except:
-        symbol_value_pairs[symbol] = None
-
-    return symbol_value_pairs
-
-
 ########################################################################################################
 #input: cursor, symbolList (list), dataIdDict(Dict): key is symbol
 #output: SymbolValuePairDict(dictionary):one dictionary of Symbol and Value Pair.
diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py
index 7d3b9b9f..fb4dc4f4 100644
--- a/wqflask/wqflask/correlation/show_corr_results.py
+++ b/wqflask/wqflask/correlation/show_corr_results.py
@@ -71,7 +71,6 @@ class CorrelationResults(object):
         assert('corr_sample_method' in start_vars)
         assert('corr_samples_group' in start_vars)
         assert('corr_dataset' in start_vars)
-        #assert('min_expr' in start_vars)
         assert('corr_return_results' in start_vars)
         if 'loc_chr' in start_vars:
             assert('min_loc_mb' in start_vars)
@@ -87,8 +86,6 @@ class CorrelationResults(object):
             else:
                 helper_functions.get_species_dataset_trait(self, start_vars)
 
-            #self.dataset.group.read_genotype_file()
-
             corr_samples_group = start_vars['corr_samples_group']
 
             self.sample_data = {}
@@ -102,11 +99,12 @@ class CorrelationResults(object):
                 'min_loc_mb' in start_vars and
                 'max_loc_mb' in start_vars):
 
+                self.location_type = get_string(start_vars, 'location_type')
                 self.location_chr = get_string(start_vars, 'loc_chr')
                 self.min_location_mb = get_int(start_vars, 'min_loc_mb')
                 self.max_location_mb = get_int(start_vars, 'max_loc_mb')
             else:
-                self.location_chr = self.min_location_mb = self.max_location_mb = None
+                self.location_type = self.location_chr = self.min_location_mb = self.max_location_mb = None
 
             self.get_formatted_corr_type()
             self.return_number = int(start_vars['corr_return_results'])
@@ -174,38 +172,46 @@ class CorrelationResults(object):
             self.correlation_data = collections.OrderedDict(sorted(list(self.correlation_data.items()),
                                                                    key=lambda t: -abs(t[1][0])))
 
-            if self.target_dataset.type == "ProbeSet" or self.target_dataset.type == "Geno":
-                #ZS: Convert min/max chromosome to an int for the location range option
-                range_chr_as_int = None
-                for order_id, chr_info in list(self.dataset.species.chromosomes.chromosomes.items()):
-                    if 'loc_chr' in start_vars:
-                        if chr_info.name == self.location_chr:
-                            range_chr_as_int = order_id
+
+            #ZS: Convert min/max chromosome to an int for the location range option
+            range_chr_as_int = None
+            for order_id, chr_info in list(self.dataset.species.chromosomes.chromosomes.items()):
+                if 'loc_chr' in start_vars:
+                    if chr_info.name == self.location_chr:
+                        range_chr_as_int = order_id
 
             for _trait_counter, trait in enumerate(list(self.correlation_data.keys())[:self.return_number]):
                 trait_object = create_trait(dataset=self.target_dataset, name=trait, get_qtl_info=True, get_sample_info=False)
                 if not trait_object:
                     continue
 
-                if self.target_dataset.type == "ProbeSet" or self.target_dataset.type == "Geno":
-                    #ZS: Convert trait chromosome to an int for the location range option
-                    chr_as_int = 0
-                    for order_id, chr_info in list(self.dataset.species.chromosomes.chromosomes.items()):
+                chr_as_int = 0
+                for order_id, chr_info in list(self.dataset.species.chromosomes.chromosomes.items()):
+                    if self.location_type == "highest_lod":
+                        if chr_info.name == trait_object.locus_chr:
+                            chr_as_int = order_id
+                    else:
                         if chr_info.name == trait_object.chr:
                             chr_as_int = order_id
 
                 if (float(self.correlation_data[trait][0]) >= self.p_range_lower and
                     float(self.correlation_data[trait][0]) <= self.p_range_upper):
 
-                    if self.target_dataset.type == "ProbeSet" or self.target_dataset.type == "Geno":
-
+                    if (self.target_dataset.type == "ProbeSet" or self.target_dataset.type == "Publish") and bool(trait_object.mean):
                         if (self.min_expr != None) and (float(trait_object.mean) < self.min_expr):
                             continue
-                        elif range_chr_as_int != None and (chr_as_int != range_chr_as_int):
+
+                    if range_chr_as_int != None and (chr_as_int != range_chr_as_int):
+                        continue
+                    if self.location_type == "highest_lod":
+                        if (self.min_location_mb != None) and (float(trait_object.locus_mb) < float(self.min_location_mb)):
+                            continue
+                        if (self.max_location_mb != None) and (float(trait_object.locus_mb) > float(self.max_location_mb)):
                             continue
-                        elif (self.min_location_mb != None) and (float(trait_object.mb) < float(self.min_location_mb)):
+                    else:
+                        if (self.min_location_mb != None) and (float(trait_object.mb) < float(self.min_location_mb)):
                             continue
-                        elif (self.max_location_mb != None) and (float(trait_object.mb) > float(self.max_location_mb)):
+                        if (self.max_location_mb != None) and (float(trait_object.mb) > float(self.max_location_mb)):
                             continue
 
                     (trait_object.sample_r,
@@ -454,13 +460,13 @@ class CorrelationResults(object):
         if not excluded_samples:
             excluded_samples = ()
 
+        sample_val_dict = json.loads(start_vars['sample_vals'])
         for sample in sample_names:
             if sample not in excluded_samples:
-                # print("Looking for",sample,"in",start_vars)
-                value = start_vars.get('value:' + sample)
-                if value:
-                    if not value.strip().lower() == 'x':
-                        self.sample_data[str(sample)] = float(value)
+                value = sample_val_dict[sample]
+                if not value.strip().lower() == 'x':
+                    self.sample_data[str(sample)] = float(value)
+
 
 def do_bicor(this_trait_vals, target_trait_vals):
     r_library = ro.r["library"]             # Map the library function
@@ -519,6 +525,7 @@ def generate_corr_json(corr_results, this_trait, dataset, target_dataset, for_ap
         elif target_dataset.type == "Publish":
             results_dict['abbreviation_display'] = "N/A"
             results_dict['description'] = "N/A"
+            results_dict['mean'] = "N/A"
             results_dict['authors_display'] = "N/A"
             results_dict['additive'] = "N/A"
             if for_api:
@@ -532,6 +539,8 @@ def generate_corr_json(corr_results, this_trait, dataset, target_dataset, for_ap
                 results_dict['abbreviation_display'] = trait.abbreviation
             if bool(trait.description_display):
                 results_dict['description'] = trait.description_display
+            if bool(trait.mean):
+                results_dict['mean'] = f"{float(trait.mean):.3f}"
             if bool(trait.authors):
                 authors_list = trait.authors.split(',')
                 if len(authors_list) > 6:
@@ -605,6 +614,7 @@ def get_header_fields(data_type, corr_method):
                             'Record',
                             'Abbreviation',
                             'Description',
+                            'Mean',
                             'Authors',
                             'Year',
                             'Sample rho',
@@ -618,6 +628,7 @@ def get_header_fields(data_type, corr_method):
                             'Record',
                             'Abbreviation',
                             'Description',
+                            'Mean',
                             'Authors',
                             'Year',
                             'Sample r',
diff --git a/wqflask/wqflask/gsearch.py b/wqflask/wqflask/gsearch.py
index 9e46c0c5..2b8d4bc1 100644
--- a/wqflask/wqflask/gsearch.py
+++ b/wqflask/wqflask/gsearch.py
@@ -1,4 +1,6 @@
 import json
+import datetime as dt
+from types import SimpleNamespace
 
 from flask import Flask, g
 from base.data_set import create_dataset
@@ -9,8 +11,9 @@ from base import webqtlConfig
 
 from utility import hmac
 
-from utility.type_checking import is_float, is_int, is_str, get_float, get_int, get_string
 from utility.benchmark import Bench
+from utility.authentication_tools import check_resource_availability
+from utility.type_checking import is_float, is_int, is_str, get_float, get_int, get_string
 
 from utility.logger import getLogger
 logger = getLogger(__name__)
@@ -42,15 +45,19 @@ class GSearch(object):
                 ProbeSetXRef.LRS AS lrs,
                 ProbeSetXRef.`Locus` AS locus,
                 ProbeSetXRef.`pValue` AS pvalue,
-                ProbeSetXRef.`additive` AS additive
-                FROM Species, InbredSet, ProbeSetXRef, ProbeSet, ProbeFreeze, ProbeSetFreeze, Tissue
-                WHERE InbredSet.`SpeciesId`=Species.`Id`
-                AND ProbeFreeze.InbredSetId=InbredSet.`Id`
-                AND ProbeFreeze.`TissueId`=Tissue.`Id`
-                AND ProbeSetFreeze.ProbeFreezeId=ProbeFreeze.Id
-                AND ( MATCH (ProbeSet.Name,ProbeSet.description,ProbeSet.symbol,alias,GenbankId, UniGeneId, Probe_Target_Description) AGAINST ('%s' IN BOOLEAN MODE) )
-                AND ProbeSet.Id = ProbeSetXRef.ProbeSetId
-                AND ProbeSetXRef.ProbeSetFreezeId=ProbeSetFreeze.Id
+                ProbeSetXRef.`additive` AS additive,
+                ProbeSetFreeze.Id AS probesetfreeze_id,
+                Geno.Chr as geno_chr,
+                Geno.Mb as geno_mb
+                FROM Species 
+                INNER JOIN InbredSet ON InbredSet.`SpeciesId`=Species.`Id` 
+                INNER JOIN ProbeFreeze ON ProbeFreeze.InbredSetId=InbredSet.`Id` 
+                INNER JOIN Tissue ON ProbeFreeze.`TissueId`=Tissue.`Id` 
+                INNER JOIN ProbeSetFreeze ON ProbeSetFreeze.ProbeFreezeId=ProbeFreeze.Id 
+                INNER JOIN ProbeSetXRef ON ProbeSetXRef.ProbeSetFreezeId=ProbeSetFreeze.Id 
+                INNER JOIN ProbeSet ON ProbeSet.Id = ProbeSetXRef.ProbeSetId 
+                LEFT JOIN Geno ON ProbeSetXRef.Locus = Geno.Name AND Geno.SpeciesId = Species.Id
+                WHERE ( MATCH (ProbeSet.Name,ProbeSet.description,ProbeSet.symbol,ProbeSet.alias,ProbeSet.GenbankId, ProbeSet.UniGeneId, ProbeSet.Probe_Target_Description) AGAINST ('%s' IN BOOLEAN MODE) )
                 AND ProbeSetFreeze.confidentiality < 1
                 AND ProbeSetFreeze.public > 0
                 ORDER BY species_name, inbredset_name, tissue_name, probesetfreeze_name, probeset_name
@@ -61,6 +68,7 @@ class GSearch(object):
                 re = g.db.execute(sql).fetchall()
 
             trait_list = []
+            dataset_to_permissions = {}
             with Bench("Creating trait objects"):
                 for i, line in enumerate(re):
                     this_trait = {}
@@ -90,16 +98,22 @@ class GSearch(object):
                     this_trait['additive'] = "N/A"
                     if line[14] != "" and line[14] != None:
                         this_trait['additive'] = '%.3f' % line[14]
-
-                    #dataset = create_dataset(line[3], "ProbeSet", get_samplelist=False)
-                    #trait_id = line[4]
-                    #with Bench("Building trait object"):
-                    trait_ob = create_trait(dataset_name=this_trait['dataset'], name=this_trait['name'], get_qtl_info=True, get_sample_info=False)
-                    if not trait_ob:
+                    this_trait['dataset_id'] = line[15]
+                    this_trait['locus_chr'] = line[16]
+                    this_trait['locus_mb'] = line[17]
+
+                    dataset_ob = SimpleNamespace(id=this_trait["dataset_id"], type="ProbeSet",species=this_trait["species"])
+                    if dataset_ob.id not in dataset_to_permissions:
+                        permissions = check_resource_availability(dataset_ob)
+                        dataset_to_permissions[dataset_ob.id] = permissions
+                    else:
+                        pemissions = dataset_to_permissions[dataset_ob.id]
+                    if "view" not in permissions['data']:
                         continue
+
                     max_lrs_text = "N/A"
-                    if trait_ob.locus_chr != "" and trait_ob.locus_mb != "":
-                        max_lrs_text = "Chr" + str(trait_ob.locus_chr) + ": " + str(trait_ob.locus_mb)
+                    if this_trait['locus_chr'] != None and this_trait['locus_mb'] != None:
+                        max_lrs_text = "Chr" + str(this_trait['locus_chr']) + ": " + str(this_trait['locus_mb'])
                     this_trait['max_lrs_text'] = max_lrs_text
 
                     trait_list.append(this_trait)
diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py
index 08c2d750..4df56190 100644
--- a/wqflask/wqflask/marker_regression/display_mapping_results.py
+++ b/wqflask/wqflask/marker_regression/display_mapping_results.py
@@ -270,8 +270,9 @@ class DisplayMappingResults(object):
 
         # Needing for form submission when doing single chr
         # mapping or remapping after changing options
-        self.samples = start_vars['samples']
-        self.vals = start_vars['vals']
+        self.sample_vals = start_vars['sample_vals']
+        self.sample_vals_dict = json.loads(self.sample_vals)
+
         self.transform = start_vars['transform']
         self.mapping_method = start_vars['mapping_method']
         self.mapping_results_path = start_vars['mapping_results_path']
@@ -492,11 +493,10 @@ class DisplayMappingResults(object):
 ## count the amount of individuals to be plotted, and increase self.graphHeight
         if self.haplotypeAnalystChecked and self.selectedChr > -1:
             thisTrait = self.this_trait
-            _strains, _vals, _vars, _aliases = thisTrait.export_informative()
             smd=[]
-            for ii, _val in enumerate(self.vals):
-                if _val != "x":
-                    temp = GeneralObject(name=self.samples[ii], value=float(_val))
+            for sample in self.sample_vals_dict.keys():
+                if self.sample_vals_dict[sample] != "x":
+                    temp = GeneralObject(name=sample, value=float(self.sample_vals_dict[sample]))
                     smd.append(temp)
                 else:
                     continue
@@ -636,7 +636,7 @@ class DisplayMappingResults(object):
             btminfo.append(HtmlGenWrapper.create_br_tag())
             btminfo.append('Mapping using genotype data as a trait will result in infinity LRS at one locus. In order to display the result properly, all LRSs higher than 100 are capped at 100.')
 
-    def plotIntMapping(self, canvas, offset= (80, 120, 20, 100), zoom = 1, startMb = None, endMb = None, showLocusForm = ""):
+    def plotIntMapping(self, canvas, offset= (80, 120, 90, 100), zoom = 1, startMb = None, endMb = None, showLocusForm = ""):
         im_drawer = ImageDraw.Draw(canvas)
         #calculating margins
         xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset
@@ -644,10 +644,11 @@ class DisplayMappingResults(object):
             yTopOffset = max(90, yTopOffset)
         else:
             if self.legendChecked:
+                yTopOffset += 10
                 if self.covariates != "" and self.controlLocus and self.doControl != "false":
-                    yTopOffset = max(120, yTopOffset)
-                else:
-                    yTopOffset = max(100, yTopOffset)
+                    yTopOffset += 20
+                if len(self.transform) > 0:
+                    yTopOffset += 5
             else:
                 pass
 
@@ -858,14 +859,16 @@ class DisplayMappingResults(object):
                            text='%2.1f'%item, font=bootScaleFont, fill=BLACK)
 
         if self.legendChecked:
-            startPosY = 30
-            nCol = 2
+            if hasattr(self.traitList[0], 'chr') and hasattr(self.traitList[0], 'mb'):
+                startPosY = 30
+            else:
+                startPosY = 15
             smallLabelFont = ImageFont.truetype(font=TREBUC_FILE, size=12*fontZoom)
-            leftOffset = xLeftOffset+(nCol-1)*200
+            leftOffset = canvas.size[0] - xRightOffset - 190
             im_drawer.rectangle(
                 xy=((leftOffset, startPosY-6), (leftOffset+12, startPosY+6)),
                 fill=YELLOW, outline=BLACK)
-            im_drawer.text(xy=(leftOffset+ 20, startPosY+TEXT_Y_DISPLACEMENT),
+            im_drawer.text(xy=(canvas.size[0] - xRightOffset - 170, startPosY+TEXT_Y_DISPLACEMENT),
                            text='Frequency of the Peak LRS',
                            font=smallLabelFont, fill=BLACK)
 
@@ -941,28 +944,6 @@ class DisplayMappingResults(object):
             draw_open_polygon(canvas, xy=traitPixel, outline=BLACK,
                               fill=self.TRANSCRIPT_LOCATION_COLOR)
 
-        if self.legendChecked:
-            startPosY = 15
-            nCol = 2
-            smallLabelFont = ImageFont.truetype(font=TREBUC_FILE, size=12*fontZoom)
-            if self.manhattan_plot:
-                leftOffset = xLeftOffset
-            else:
-                leftOffset = xLeftOffset+(nCol-1)*200*fontZoom
-            draw_open_polygon(
-                canvas,
-                xy=(
-                    (leftOffset+7, startPosY-7),
-                    (leftOffset, startPosY+7),
-                    (leftOffset+14, startPosY+7)),
-                outline=BLACK, fill=self.TRANSCRIPT_LOCATION_COLOR
-            )
-            TEXT_Y_DISPLACEMENT = -8
-            im_drawer.text(
-                text="Sequence Site",
-                xy=(leftOffset+15, startPosY+TEXT_Y_DISPLACEMENT), font=smallLabelFont,
-                fill=self.TOP_RIGHT_INFO_COLOR)
-
     def drawSNPTrackNew(self, canvas, offset= (40, 120, 80, 10), zoom = 1, startMb = None, endMb = None):
         im_drawer = ImageDraw.Draw(canvas)
         if self.plotScale != 'physic' or self.selectedChr == -1 or not self.diffCol:
@@ -1059,17 +1040,38 @@ class DisplayMappingResults(object):
         labelFont=ImageFont.truetype(font=TREBUC_FILE, size=12*fontZoom)
         startPosY = 15
         stepPosY = 12*fontZoom
+
+        startPosX = canvas.size[0] - xRightOffset - 415
+        if hasattr(self.traitList[0], 'chr') and hasattr(self.traitList[0], 'mb'):
+            startPosY = 15
+            nCol = 2
+            smallLabelFont = ImageFont.truetype(font=TREBUC_FILE, size=12*fontZoom)
+
+            leftOffset = canvas.size[0] - xRightOffset - 190
+            draw_open_polygon(
+                canvas,
+                xy=(
+                    (leftOffset + 6, startPosY-7),
+                    (leftOffset - 1, startPosY+7),
+                    (leftOffset + 13, startPosY+7)),
+                outline=BLACK, fill=self.TRANSCRIPT_LOCATION_COLOR
+            )
+            TEXT_Y_DISPLACEMENT = -8
+            im_drawer.text(
+                text="Sequence Site",
+                xy=(leftOffset + 20, startPosY+TEXT_Y_DISPLACEMENT), font=smallLabelFont,
+                fill=self.TOP_RIGHT_INFO_COLOR)
+
         if self.manhattan_plot != True:
             im_drawer.line(
-                xy=((xLeftOffset, startPosY), (xLeftOffset+32, startPosY)),
+                xy=((startPosX, startPosY), (startPosX+32, startPosY)),
                 fill=self.LRS_COLOR, width=2)
             im_drawer.text(
-                text=self.LRS_LOD, xy=(xLeftOffset+40, startPosY+TEXT_Y_DISPLACEMENT),
+                text=self.LRS_LOD, xy=(startPosX+40, startPosY+TEXT_Y_DISPLACEMENT),
                 font=labelFont, fill=BLACK)
             startPosY += stepPosY
 
         if self.additiveChecked:
-            startPosX = xLeftOffset
             im_drawer.line(
                 xy=((startPosX, startPosY), (startPosX+17, startPosY)),
                 fill=self.ADDITIVE_COLOR_POSITIVE, width=2)
@@ -1079,10 +1081,9 @@ class DisplayMappingResults(object):
             im_drawer.text(
                 text='Additive Effect', xy=(startPosX+40, startPosY+TEXT_Y_DISPLACEMENT),
                 font=labelFont, fill=BLACK)
+            startPosY += stepPosY
 
         if self.genotype.type == 'intercross' and self.dominanceChecked:
-            startPosX = xLeftOffset
-            startPosY += stepPosY
             im_drawer.line(
                 xy=((startPosX, startPosY), (startPosX+17, startPosY)),
                 fill=self.DOMINANCE_COLOR_POSITIVE, width=4)
@@ -1092,45 +1093,47 @@ class DisplayMappingResults(object):
             im_drawer.text(
                 text='Dominance Effect', xy=(startPosX+42, startPosY+5),
                 font=labelFont, fill=BLACK)
+            startPosY += stepPosY
 
         if self.haplotypeAnalystChecked:
-            startPosY += stepPosY
-            startPosX = xLeftOffset
             im_drawer.line(
-                xy=((startPosX, startPosY), (startPosX+17, startPosY)),
+                xy=((startPosX-34, startPosY), (startPosX-17, startPosY)),
                 fill=self.HAPLOTYPE_POSITIVE, width=4)
             im_drawer.line(
-                xy=((startPosX+18, startPosY), (startPosX+35, startPosY)),
+                xy=((startPosX-17, startPosY), (startPosX, startPosY)),
                 fill=self.HAPLOTYPE_NEGATIVE, width=4)
             im_drawer.line(
-                xy=((startPosX+36, startPosY), (startPosX+53, startPosY)),
+                xy=((startPosX, startPosY), (startPosX+17, startPosY)),
                 fill=self.HAPLOTYPE_HETEROZYGOUS, width=4)
             im_drawer.line(
-                xy=((startPosX+54, startPosY), (startPosX+67, startPosY)),
+                xy=((startPosX+17, startPosY), (startPosX+34, startPosY)),
                 fill=self.HAPLOTYPE_RECOMBINATION, width=4)
             im_drawer.text(
                 text='Haplotypes (Pat, Mat, Het, Unk)',
-                xy=(startPosX+76, startPosY+5), font=labelFont, fill=BLACK)
+                xy=(startPosX+41, startPosY+TEXT_Y_DISPLACEMENT), font=labelFont, fill=BLACK)
+            startPosY += stepPosY
 
         if self.permChecked and self.nperm > 0:
-            startPosY += stepPosY
-            startPosX = xLeftOffset
+            thisStartX = startPosX
+            if self.multipleInterval and not self.bootChecked:
+                thisStartX = canvas.size[0] - xRightOffset - 205
             im_drawer.line(
-                xy=((startPosX, startPosY), ( startPosX + 32, startPosY)),
+                xy=((thisStartX, startPosY), ( startPosX + 32, startPosY)),
                 fill=self.SIGNIFICANT_COLOR, width=self.SIGNIFICANT_WIDTH)
             im_drawer.line(
-                xy=((startPosX, startPosY + stepPosY), ( startPosX + 32, startPosY + stepPosY)),
+                xy=((thisStartX, startPosY + stepPosY), ( startPosX + 32, startPosY + stepPosY)),
                 fill=self.SUGGESTIVE_COLOR, width=self.SUGGESTIVE_WIDTH)
             im_drawer.text(
                 text='Significant %s = %2.2f' % (self.LRS_LOD, self.significant),
-                xy=(xLeftOffset+42, startPosY+TEXT_Y_DISPLACEMENT), font=labelFont, fill=BLACK)
+                xy=(thisStartX+40, startPosY+TEXT_Y_DISPLACEMENT), font=labelFont, fill=BLACK)
             im_drawer.text(
                 text='Suggestive %s = %2.2f' % (self.LRS_LOD, self.suggestive),
-                xy=(xLeftOffset+42, startPosY + TEXT_Y_DISPLACEMENT +stepPosY), font=labelFont,
+                xy=(thisStartX+40, startPosY + TEXT_Y_DISPLACEMENT +stepPosY), font=labelFont,
                 fill=BLACK)
 
         labelFont = ImageFont.truetype(font=VERDANA_FILE, size=12*fontZoom)
         labelColor = BLACK
+
         if self.dataset.type == "Publish" or self.dataset.type == "Geno":
             dataset_label = self.dataset.fullname
         else:
@@ -1172,6 +1175,7 @@ class DisplayMappingResults(object):
             else:
                 string3 += 'no control for other QTLs'
 
+        y_constant = 10
         if self.this_trait.name:
             if self.selectedChr == -1:
                 identification = "Mapping on All Chromosomes for "
@@ -1197,23 +1201,48 @@ class DisplayMappingResults(object):
                 im_drawer.textsize(string2, font=labelFont)[0])
             im_drawer.text(
                 text=identification,
-                xy=(canvas.size[0] - xRightOffset-d, 20*fontZoom), font=labelFont,
+                xy=(xLeftOffset, y_constant*fontZoom), font=labelFont,
                 fill=labelColor)
+            y_constant += 15
         else:
             d = 4+ max(
                 im_drawer.textsize(string1, font=labelFont)[0],
                 im_drawer.textsize(string2, font=labelFont)[0])
+
+        if len(self.transform) > 0:
+            transform_text = "Transform - "
+            if self.transform == "qnorm":
+                transform_text += "Quantile Normalized"
+            elif self.transform == "log2" or self.transform == "log10":
+                transform_text += self.transform.capitalize()
+            elif self.transform == "sqrt":
+                transform_text += "Square Root"
+            elif self.transform == "zscore":
+                transform_text += "Z-Score"
+            elif self.transform == "invert":
+                transform_text += "Invert +/-"
+
+            im_drawer.text(
+                text=transform_text, xy=(xLeftOffset, y_constant*fontZoom),
+                font=labelFont, fill=labelColor)
+            y_constant += 15
         im_drawer.text(
-            text=string1, xy=(canvas.size[0] - xRightOffset-d, 35*fontZoom),
+            text=string1, xy=(xLeftOffset, y_constant*fontZoom),
             font=labelFont, fill=labelColor)
+        y_constant += 15
         im_drawer.text(
-            text=string2, xy=(canvas.size[0] - xRightOffset-d, 50*fontZoom),
+            text=string2, xy=(xLeftOffset, y_constant*fontZoom),
             font=labelFont, fill=labelColor)
+        y_constant += 15
         if string3 != '':
             im_drawer.text(
-                text=string3, xy=(canvas.size[0] - xRightOffset-d, 65*fontZoom),
+                text=string3, xy=(xLeftOffset, y_constant*fontZoom),
                 font=labelFont, fill=labelColor)
-
+            y_constant += 15
+            if string4 != '':
+                im_drawer.text(
+                    text=string4, xy=(xLeftOffset, y_constant*fontZoom),
+                    font=labelFont, fill=labelColor)
 
     def drawGeneBand(self, canvas, gifmap, plotXScale, offset= (40, 120, 80, 10), zoom = 1, startMb = None, endMb = None):
         im_drawer = ImageDraw.Draw(canvas)
@@ -1464,12 +1493,11 @@ class DisplayMappingResults(object):
         yPaddingTop = yTopOffset
 
         thisTrait = self.this_trait
-        _strains, _vals, _vars, _aliases = thisTrait.export_informative()
 
         smd=[]
-        for ii, _val in enumerate(self.vals):
-            if _val != "x":
-                temp = GeneralObject(name=self.samples[ii], value=float(_val))
+        for sample in self.sample_vals_dict.keys():
+            if self.sample_vals_dict[sample] != "x":
+                temp = GeneralObject(name=sample, value=float(self.sample_vals_dict[sample]))
                 smd.append(temp)
             else:
                 continue
@@ -2244,6 +2272,7 @@ class DisplayMappingResults(object):
                 )
                 sugg_coords = "%d, %d, %d, %d" % (start_pos_x, suggestiveY-2, rightEdge + 2*zoom, suggestiveY+2)
                 sig_coords = "%d, %d, %d, %d" % (start_pos_x, significantY-2, rightEdge + 2*zoom, significantY+2)
+
                 if self.LRS_LOD == 'LRS':
                     sugg_title = "Suggestive LRS = %0.2f" % self.suggestive
                     sig_title = "Significant LRS = %0.2f" % self.significant
diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py
index 61e4897c..ab3a7278 100644
--- a/wqflask/wqflask/marker_regression/gemma_mapping.py
+++ b/wqflask/wqflask/marker_regression/gemma_mapping.py
@@ -54,7 +54,7 @@ def run_gemma(this_trait, this_dataset, samples, vals, covariates, use_loco, maf
                                                                                           TEMPDIR,
                                                                                           trait_filename)
           if covariates != "":
-              gemma_command += ' -c %s/%s_covariates.txt -a %s/%s_snps.txt -lmm 2 -maf %s > %s/gn2/%s.json' % (flat_files('mapping'),
+              gemma_command += ' -c %s/%s_covariates.txt -a %s/%s_snps.txt -lmm 9 -maf %s > %s/gn2/%s.json' % (flat_files('mapping'),
                                                                                                                 this_dataset.group.name,
                                                                                                                 flat_files('genotype/bimbam'),
                                                                                                                 genofile_name,
@@ -62,7 +62,7 @@ def run_gemma(this_trait, this_dataset, samples, vals, covariates, use_loco, maf
                                                                                                                 TEMPDIR,
                                                                                                                 gwa_output_filename)
           else:
-              gemma_command += ' -a %s/%s_snps.txt -lmm 2 -maf %s > %s/gn2/%s.json' % (flat_files('genotype/bimbam'),
+              gemma_command += ' -a %s/%s_snps.txt -lmm 9 -maf %s > %s/gn2/%s.json' % (flat_files('genotype/bimbam'),
                                                                                                                genofile_name,
                                                                                                                maf,
                                                                                                                TEMPDIR,
@@ -80,7 +80,7 @@ def run_gemma(this_trait, this_dataset, samples, vals, covariates, use_loco, maf
 
           os.system(generate_k_command)
 
-          gemma_command = GEMMA_WRAPPER_COMMAND + ' --json --input %s/gn2/%s.json -- ' % (TEMPDIR, k_output_filename) + GEMMAOPTS + ' -a %s/%s_snps.txt -lmm 2 -g %s/%s_geno.txt -p %s/gn2/%s.txt' % (flat_files('genotype/bimbam'),
+          gemma_command = GEMMA_WRAPPER_COMMAND + ' --json --input %s/gn2/%s.json -- ' % (TEMPDIR, k_output_filename) + GEMMAOPTS + ' -a %s/%s_snps.txt -lmm 9 -g %s/%s_geno.txt -p %s/gn2/%s.txt' % (flat_files('genotype/bimbam'),
                                                                                          genofile_name,
                                                                                          flat_files('genotype/bimbam'),
                                                                                          genofile_name,
@@ -101,7 +101,7 @@ def run_gemma(this_trait, this_dataset, samples, vals, covariates, use_loco, maf
         marker_obs = parse_loco_output(this_dataset, gwa_output_filename)
         return marker_obs, gwa_output_filename
     else:
-        marker_obs = parse_loco_output(this_dataset, gwa_output_filename)
+        marker_obs = parse_loco_output(this_dataset, gwa_output_filename, use_loco)
         return marker_obs, gwa_output_filename
 
 def gen_pheno_txt_file(this_dataset, genofile_name, vals, trait_filename):
@@ -145,41 +145,7 @@ def gen_covariates_file(this_dataset, covariates, samples):
                 outfile.write(str(this_covariate[i]) + "\t")
             outfile.write("\n")
 
-def parse_gemma_output(genofile_name):
-    included_markers = []
-    p_values = []
-    marker_obs = []
-
-    with open("{}{}_output.assoc.txt".format(webqtlConfig.GENERATED_IMAGE_DIR, genofile_name)) as output_file:
-        for line in output_file:
-            if line.startswith("chr\t"):
-                continue
-            else:
-                marker = {}
-                marker['name'] = line.split("\t")[1]
-                if line.split("\t")[0] != "X" and line.split("\t")[0] != "X/Y":
-                    if "chr" in line.split("\t")[0]:
-                        marker['chr'] = int(line.split("\t")[0][3:])
-                    else:
-                        marker['chr'] = int(line.split("\t")[0])
-                else:
-                    marker['chr'] = line.split("\t")[0]
-                marker['Mb'] = float(line.split("\t")[2]) / 1000000
-                marker['p_value'] = float(line.split("\t")[9])
-                if math.isnan(marker['p_value']) or (marker['p_value'] <= 0):
-                    marker['lod_score'] = 0
-                    #marker['lrs_value'] = 0
-                else:
-                    marker['lod_score'] = -math.log10(marker['p_value'])
-                    #marker['lrs_value'] = -math.log10(marker['p_value']) * 4.61
-                marker_obs.append(marker)
-
-                included_markers.append(line.split("\t")[1])
-                p_values.append(float(line.split("\t")[9]))
-
-    return marker_obs
-
-def parse_loco_output(this_dataset, gwa_output_filename):
+def parse_loco_output(this_dataset, gwa_output_filename, loco="True"):
 
     output_filelist = []
     with open("{}/gn2/".format(TEMPDIR) + gwa_output_filename + ".json") as data_file:
@@ -218,7 +184,8 @@ def parse_loco_output(this_dataset, gwa_output_filename):
                     else:
                         marker['chr'] = line.split("\t")[0]
                     marker['Mb'] = float(line.split("\t")[2]) / 1000000
-                    marker['p_value'] = float(line.split("\t")[9])
+                    marker['p_value'] = float(line.split("\t")[10])
+                    marker['additive'] = float(line.split("\t")[7])
                     if math.isnan(marker['p_value']) or (marker['p_value'] <= 0):
                         marker['lod_score'] = 0
                         #marker['lrs_value'] = 0
diff --git a/wqflask/wqflask/marker_regression/rqtl_mapping.py b/wqflask/wqflask/marker_regression/rqtl_mapping.py
index 0a5758af..4117a0e5 100644
--- a/wqflask/wqflask/marker_regression/rqtl_mapping.py
+++ b/wqflask/wqflask/marker_regression/rqtl_mapping.py
@@ -94,9 +94,6 @@ def run_rqtl_geno(vals, samples, dataset, mapping_scale, method, model, permChec
         ro.r('all_covars <- cbind(marker_covars, trait_covars)')
     else:
         ro.r('all_covars <- marker_covars')
-    #logger.info("Saving");
-    #ro.r('save.image(file = "/home/dannya/gn2-danny/cross.RData")')
-    #logger.info("Saving Done");
     covars = ro.r['all_covars']
     #DEBUG to save the session object to file
     if pair_scan:
@@ -159,7 +156,7 @@ def generate_cross_from_geno(dataset, scale_units):        # TODO: Need to figur
          toskip = which(unlist(lapply(header, function(x){ length(grep("Chr\t", x)) })) == 1)-1                            # Major hack to skip the geno headers
          type <- getGenoCode(header, 'type')
          if(type == '4-way'){
-            genocodes <- c('1','2','3','4')
+            genocodes <- NULL
          } else {
             genocodes <- c(getGenoCode(header, 'mat'), getGenoCode(header, 'het'), getGenoCode(header, 'pat'))             # Get the genotype codes
          }
@@ -174,7 +171,7 @@ def generate_cross_from_geno(dataset, scale_units):        # TODO: Need to figur
          require(qtl)
          if(type == '4-way'){
            cat('Loading in as 4-WAY\n')
-           cross = read.cross(file=out, 'csvr', genotypes=genocodes, crosstype="4way", convertXdata=FALSE)                 # Load the created cross file using R/qtl read.cross
+           cross = read.cross(file=out, 'csvr', genotypes=NULL, crosstype="4way")                                         # Load the created cross file using R/qtl read.cross
          }else if(type == 'f2'){
            cat('Loading in as F2\n')
            cross = read.cross(file=out, 'csvr', genotypes=genocodes, crosstype="f2")                                       # Load the created cross file using R/qtl read.cross
@@ -332,8 +329,6 @@ def add_cofactors(cross, this_dataset, covariates, samples):
                         covar_name_string += '"' + col_name + '", '
                     else:
                         covar_name_string += '"' + col_name + '"'
-
-                logger.info("covar_name_string:" + covar_name_string)
         else:
             col_name = "covar_" + str(i)
             cross = add_phenotype(cross, covar_as_string, col_name)
@@ -343,7 +338,6 @@ def add_cofactors(cross, this_dataset, covariates, samples):
                 covar_name_string += '"' + col_name + '"'
 
     covar_name_string += ")"
-    logger.info("covar_name_string:" + covar_name_string); 
     covars_ob = pull_var("trait_covars", cross, covar_name_string)
     return cross, covars_ob
 
diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py
index 891fcc66..72844903 100644
--- a/wqflask/wqflask/marker_regression/run_mapping.py
+++ b/wqflask/wqflask/marker_regression/run_mapping.py
@@ -71,56 +71,22 @@ class RunMapping(object):
         all_samples_ordered = self.dataset.group.all_samples_ordered()
 
         self.vals = []
-        if 'samples' in start_vars:
-            self.samples = start_vars['samples'].split(",")
-            if (len(genofile_samplelist) != 0):
-                for sample in genofile_samplelist:
-                    if sample in self.samples:
-                        value = start_vars.get('value:' + sample)
-                        if value:
-                            self.vals.append(value)
-                    else:
-                        self.vals.append("x")
-            else:
-                for sample in self.samples:
-                    value = start_vars.get('value:' + sample)
-                    if value:
-                        self.vals.append(value)
+        self.samples = []
+        self.sample_vals = start_vars['sample_vals']
+        sample_val_dict = json.loads(self.sample_vals)
+        samples = sample_val_dict.keys()
+        if (len(genofile_samplelist) != 0):
+            for sample in genofile_samplelist:
+                self.samples.append(sample)
+                if sample in samples:
+                    self.vals.append(sample_val_dict[sample])
+                else:
+                    self.vals.append("x")
         else:
-            self.samples = []
-            if (len(genofile_samplelist) != 0):
-                for sample in genofile_samplelist:
-                    if sample in self.dataset.group.samplelist:
-                        in_trait_data = False
-                        for item in self.this_trait.data:
-                            if self.this_trait.data[item].name == sample:
-                                value = start_vars['value:' + self.this_trait.data[item].name]
-                                self.samples.append(self.this_trait.data[item].name)
-                                self.vals.append(value)
-                                in_trait_data = True
-                                break
-                        if not in_trait_data:
-                            value = start_vars.get('value:' + sample)
-                            if value:
-                                self.samples.append(sample)
-                                self.vals.append(value)
-                    else:
-                        self.vals.append("x")
-            else:
-                for sample in self.dataset.group.samplelist: # sample is actually the name of an individual
-                    in_trait_data = False
-                    for item in self.this_trait.data:
-                        if self.this_trait.data[item].name == sample:
-                            value = start_vars['value:' + self.this_trait.data[item].name]
-                            self.samples.append(self.this_trait.data[item].name)
-                            self.vals.append(value)
-                            in_trait_data = True
-                            break
-                    if not in_trait_data:
-                        value = start_vars.get('value:' + sample)
-                        if value:
-                            self.samples.append(sample)
-                            self.vals.append(value)
+            for sample in self.dataset.group.samplelist:
+                if sample in samples:
+                    self.vals.append(sample_val_dict[sample])
+                    self.samples.append(sample)
 
         if 'n_samples' in start_vars:
             self.n_samples = start_vars['n_samples']
@@ -138,15 +104,15 @@ class RunMapping(object):
             mapping_results_filename = self.dataset.group.name + "_" + ''.join(random.choice(string.ascii_uppercase + string.digits) for _ in range(6))
             self.mapping_results_path = "{}{}.csv".format(webqtlConfig.GENERATED_IMAGE_DIR, mapping_results_filename)
 
-        if start_vars['manhattan_plot']:
-            self.color_scheme = "alternating"
-            if "color_scheme" in start_vars:
-                self.color_scheme = start_vars['color_scheme']
-                if self.color_scheme == "single":
-                    self.manhattan_single_color = start_vars['manhattan_single_color']
-            self.manhattan_plot = True
-        else:
-            self.manhattan_plot = False
+        self.manhattan_plot = False
+        if 'manhattan_plot' in start_vars:
+            if start_vars['manhattan_plot'].lower() != "false":
+                self.color_scheme = "alternating"
+                if "color_scheme" in start_vars:
+                    self.color_scheme = start_vars['color_scheme']
+                    if self.color_scheme == "single":
+                        self.manhattan_single_color = start_vars['manhattan_single_color']
+                self.manhattan_plot = True
 
         self.maf = start_vars['maf'] # Minor allele frequency
         if "use_loco" in start_vars:
diff --git a/wqflask/wqflask/pbkdf2.py b/wqflask/wqflask/pbkdf2.py
index aea5b06c..6346df03 100644
--- a/wqflask/wqflask/pbkdf2.py
+++ b/wqflask/wqflask/pbkdf2.py
@@ -2,15 +2,15 @@ import hashlib
 
 from werkzeug.security import safe_str_cmp as ssc
 
-
 # Replace this because it just wraps around Python3's internal
 # functions. Added this during migration.
 def pbkdf2_hex(data, salt, iterations=1000, keylen=24, hashfunc="sha1"):
     """Wrapper function of python's hashlib.pbkdf2_hmac.
     """
+
     dk = hashlib.pbkdf2_hmac(hashfunc,
                              bytes(data, "utf-8"),  # password
-                             bytes(salt, "utf-8"),  # salt
+                             salt,
                              iterations,
                              keylen)
     return dk.hex()
diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py
index 0d0894a4..9e8001cf 100644
--- a/wqflask/wqflask/search_results.py
+++ b/wqflask/wqflask/search_results.py
@@ -28,9 +28,9 @@ class SearchResultPage(object):
     #maxReturn = 3000
 
     def __init__(self, kw):
-        """This class gets invoked after hitting submit on the main menu (in
-views.py).
-
+        """
+            This class gets invoked after hitting submit on the main menu (in
+            views.py).
         """
 
         ###########################################
@@ -86,7 +86,6 @@ views.py).
             else:
                 self.gen_search_result()
 
-
     def gen_search_result(self):
         """
         Get the info displayed in the search result table from the set of results computed in
@@ -121,7 +120,9 @@ views.py).
                 trait_dict['hmac'] = hmac.data_hmac('{}:{}'.format(this_trait.name, this_trait.dataset.name))
                 if this_trait.dataset.type == "ProbeSet":
                     trait_dict['symbol'] = this_trait.symbol
-                    trait_dict['description'] = this_trait.description_display
+                    trait_dict['description'] = "N/A"
+                    if this_trait.description_display:
+                        trait_dict['description'] = this_trait.description_display
                     trait_dict['location'] = this_trait.location_repr
                     trait_dict['mean'] = "N/A"
                     trait_dict['additive'] = "N/A"
@@ -137,7 +138,9 @@ views.py).
                 elif this_trait.dataset.type == "Geno":
                     trait_dict['location'] = this_trait.location_repr
                 elif this_trait.dataset.type == "Publish":
-                    trait_dict['description'] = this_trait.description_display
+                    trait_dict['description'] = "N/A"
+                    if this_trait.description_display:
+                        trait_dict['description'] = this_trait.description_display
                     trait_dict['authors'] = this_trait.authors
                     trait_dict['pubmed_id'] = "N/A"
                     if this_trait.pubmed_id:
@@ -161,7 +164,14 @@ views.py).
                         trait_dict[key] = trait_dict[key].decode('utf-8')
                 trait_list.append(trait_dict)
 
-        self.trait_list = json.dumps(trait_list)
+        self.trait_list = trait_list
+
+        if this_trait.dataset.type == "ProbeSet":
+            self.header_data_names = ['index', 'display_name', 'symbol', 'description', 'location', 'mean', 'lrs_score', 'lrs_location', 'additive']
+        elif this_trait.dataset.type == "Publish":
+            self.header_data_names = ['index', 'display_name', 'description', 'mean', 'authors', 'pubmed_text', 'lrs_score', 'lrs_location', 'additive']
+        elif this_trait.dataset.type == "Geno":
+            self.header_data_names = ['index', 'display_name', 'location']
 
     def search(self):
         """
diff --git a/wqflask/wqflask/server_side.py b/wqflask/wqflask/server_side.py
new file mode 100644
index 00000000..5f764767
--- /dev/null
+++ b/wqflask/wqflask/server_side.py
@@ -0,0 +1,93 @@
+# handles server side table processing
+
+
+
+class ServerSideTable(object):
+    """
+        This class is used to do server-side processing
+        on the DataTables table such as paginating, sorting,
+        filtering(not implemented) etc. This takes the load off
+        the client-side and reduces the size of data interchanged.
+
+        Usage:
+            ServerSideTable(table_data, request_values)
+        where,
+            `table_data` must have data members
+            `rows_count` as number of rows in the table,
+            `table_rows` as data rows of the table,
+            `header_data_names` as headers names of the table.
+
+            `request_values` must have request arguments values
+            including the DataTables server-side processing arguments.
+
+        Have a look at snp_browser_table() function in 
+        wqflask/wqflask/views.py for reference use.
+    """
+
+    def __init__(self, rows_count, table_rows, header_data_names, request_values):
+        self.request_values = request_values
+        self.sEcho = self.request_values['sEcho']
+
+        self.rows_count = rows_count
+        self.table_rows = table_rows
+        self.header_data_names = header_data_names
+        
+        self.sort_rows()
+        self.paginate_rows()
+
+    def sort_rows(self):
+        """
+        Sorts the rows taking in to account the column (or columns) that the
+        user has selected.
+        """
+        def is_reverse(str_direction):
+            """ Maps the 'desc' and 'asc' words to True or False. """
+            return True if str_direction == 'desc' else False
+
+        if (self.request_values['iSortCol_0'] != "") and (int(self.request_values['iSortingCols']) > 0):
+            for i in range(0, int(self.request_values['iSortingCols'])):
+                column_number = int(self.request_values['iSortCol_' + str(i)])
+                column_name = self.header_data_names[column_number - 1]
+                sort_direction = self.request_values['sSortDir_' + str(i)]
+                self.table_rows = sorted(self.table_rows,
+                              key=lambda x: x[column_name],
+                              reverse=is_reverse(sort_direction))
+
+    def paginate_rows(self):
+        """
+        Selects a subset of the filtered and sorted data based on if the table
+        has pagination, the current page and the size of each page.
+        """
+        def requires_pagination():
+            """ Check if the table is going to be paginated """
+            if self.request_values['iDisplayStart'] != "":
+                if int(self.request_values['iDisplayLength']) != -1:
+                    return True
+            return False
+
+        if not requires_pagination():
+            return
+
+        start = int(self.request_values['iDisplayStart'])
+        length = int(self.request_values['iDisplayLength'])
+
+        # if search returns only one page
+        if len(self.table_rows) <= length:
+            # display only one page
+            self.table_rows = self.table_rows[start:]
+        else:
+            limit = -len(self.table_rows) + start + length
+            if limit < 0:
+                # display pagination
+                self.table_rows = self.table_rows[start:limit]
+            else:
+                # display last page of pagination
+                self.table_rows = self.table_rows[start:]
+
+    def get_page(self):
+        output = {}
+        output['sEcho'] = str(self.sEcho)
+        output['iTotalRecords'] = str(float('Nan'))
+        output['iTotalDisplayRecords'] = str(self.rows_count)
+        output['data'] = self.table_rows
+        return output
diff --git a/wqflask/wqflask/show_trait/SampleList.py b/wqflask/wqflask/show_trait/SampleList.py
index 00495377..ece485ae 100644
--- a/wqflask/wqflask/show_trait/SampleList.py
+++ b/wqflask/wqflask/show_trait/SampleList.py
@@ -108,7 +108,7 @@ class SampleList(object):
                         FROM CaseAttribute, CaseAttributeXRefNew
                         WHERE CaseAttributeXRefNew.CaseAttributeId = CaseAttribute.Id
                         AND CaseAttributeXRefNew.InbredSetId = %s
-                        ORDER BY CaseAttribute.Name''', (str(self.dataset.group.id),))
+                        ORDER BY lower(CaseAttribute.Name)''', (str(self.dataset.group.id),))
 
         self.attributes = {}
         for attr, values in itertools.groupby(results.fetchall(), lambda row: (row.Id, row.Name)):
@@ -157,7 +157,7 @@ class SampleList(object):
                     except ValueError:
                         pass
 
-                    attribute_values[self.attributes[item.Id].name] = attribute_value
+                    attribute_values[self.attributes[item.Id].name.lower()] = attribute_value
                 self.sample_attribute_values[sample_name] = attribute_values
 
     def get_first_attr_col(self):
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index 0c6ae198..9b4a8fa4 100644
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -186,8 +186,6 @@ class ShowTrait(object):
 
         self.has_num_cases = has_num_cases(self.this_trait)
 
-        self.stats_table_width, self.trait_table_width = get_table_widths(self.sample_groups, self.has_num_cases)
-
         #ZS: Needed to know whether to display bar chart + get max sample name length in order to set table column width
         self.num_values = 0
         self.binary = "true" #ZS: So it knows whether to display the Binary R/qtl mapping method, which doesn't work unless all values are 0 or 1
@@ -206,6 +204,8 @@ class ShowTrait(object):
 
         sample_column_width = max_samplename_width * 8
 
+        self.stats_table_width, self.trait_table_width = get_table_widths(self.sample_groups, sample_column_width, self.has_num_cases)
+
         if self.num_values >= 5000:
             self.maf = 0.01
         else:
@@ -372,7 +372,7 @@ class ShowTrait(object):
 
         # We're checking a string here!
         assert isinstance(this_group, str), "We need a string type thing here"
-        if this_group[:3] == 'BXD' and this_group != "BXD-Longevity":
+        if this_group[:3] == 'BXD' and this_group != "BXD-Longevity" and this_group != "BXD-AE":
             this_group = 'BXD'
 
         if this_group:
@@ -547,12 +547,12 @@ def get_nearest_marker(this_trait, this_db):
         return result[0][0]
 
 
-def get_table_widths(sample_groups, has_num_cases=False):
+def get_table_widths(sample_groups, sample_column_width, has_num_cases=False):
     stats_table_width = 250
     if len(sample_groups) > 1:
         stats_table_width = 450
 
-    trait_table_width = 380
+    trait_table_width = 300 + sample_column_width
     if sample_groups[0].se_exists:
         trait_table_width += 80
     if has_num_cases:
diff --git a/wqflask/wqflask/snp_browser/snp_browser.py b/wqflask/wqflask/snp_browser/snp_browser.py
index 6c3fcf53..a52399a2 100644
--- a/wqflask/wqflask/snp_browser/snp_browser.py
+++ b/wqflask/wqflask/snp_browser/snp_browser.py
@@ -4,7 +4,7 @@ import string
 from PIL import (Image)
 
 from utility.logger import getLogger
-logger = getLogger(__name__ )
+logger = getLogger(__name__)
 
 from base import species
 from base import webqtlConfig
@@ -14,21 +14,21 @@ class SnpBrowser(object):
     def __init__(self, start_vars):
         self.strain_lists = get_browser_sample_lists()
         self.initialize_parameters(start_vars)
-        self.limit_number = 10000
 
         if self.first_run == "false":
             self.filtered_results = self.get_browser_results()
+            self.table_rows = self.get_table_rows()
+            self.rows_count = len(self.table_rows)
 
-            if len(self.filtered_results) <= self.limit_number:
-                self.table_rows = self.get_table_rows()
-            else:
-                self.empty_columns = None
+            del self.filtered_results
+
+            if 'sEcho' not in start_vars:
                 self.table_rows = []
 
             if self.limit_strains == "true":
-                self.header_fields, self.empty_field_count = get_header_list(variant_type = self.variant_type, strains = self.chosen_strains, empty_columns = self.empty_columns)
+                self.header_fields, self.empty_field_count, self.header_data_names = get_header_list(variant_type = self.variant_type, strains = self.chosen_strains, empty_columns = self.empty_columns)
             else:
-                self.header_fields, self.empty_field_count = get_header_list(variant_type = self.variant_type, strains = self.strain_lists, species = self.species_name, empty_columns = self.empty_columns)
+                self.header_fields, self.empty_field_count, self.header_data_names = get_header_list(variant_type = self.variant_type, strains = self.strain_lists, species = self.species_name, empty_columns = self.empty_columns)
 
     def initialize_parameters(self, start_vars):
         if 'first_run' in start_vars:
@@ -368,19 +368,19 @@ class SnpBrowser(object):
 
         #ZS: list of booleans representing which columns are entirely empty, so they aren't displayed on the page; only including ones that are sometimes empty (since there's always a location, etc)
         self.empty_columns = {
-                    "snp_source": "false",
-                    "conservation_score": "false",
-                    "gene_name": "false",
-                    "transcript": "false",
-                    "exon": "false",
-                    "domain_2": "false",
-                    "function": "false", 
-                    "function_details": "false"
-            }
+            "snp_source": "false",
+            "conservation_score": "false",
+            "gene_name": "false",
+            "transcript": "false",
+            "exon": "false",
+            "domain_2": "false",
+            "function": "false",
+            "function_details": "false"
+        }
 
         the_rows = []
         for i, result in enumerate(self.filtered_results):
-            this_row = []
+            this_row = {}
             if self.variant_type == "SNP":
                 snp_name, rs, chr, mb, alleles, gene, transcript, exon, domain, function, function_details, snp_source, conservation_score, snp_id = result[:14]
                 allele_value_list = result[14:]
@@ -520,13 +520,10 @@ class SnpBrowser(object):
                     "source_name": str(source_name)
                 }
                 #this_row = [indel_name, indel_chr, indel_mb_s, indel_mb_e, indel_strand, indel_type, indel_size, indel_sequence, source_name]
-            else:
-                this_row = {}
 
             the_rows.append(this_row)
 
         return the_rows
-                
 
     def include_record(self, domain, function, snp_source, conservation_score):
         """ Decide whether to add this record """
@@ -674,9 +671,13 @@ def get_header_list(variant_type, strains, species = None, empty_columns = None)
     empty_field_count = 0 #ZS: This is an awkward way of letting the javascript know the index where the allele value columns start; there's probably a better way of doing this
 
     header_fields = []
+    header_data_names = []
     if variant_type == "SNP":
         header_fields.append(['Index', 'SNP ID', 'Chr', 'Mb', 'Alleles', 'Source', 'ConScore', 'Gene', 'Transcript', 'Exon', 'Domain 1', 'Domain 2', 'Function', 'Details'])
+        header_data_names = ['index', 'snp_name', 'chr', 'mb_formatted', 'alleles', 'snp_source', 'conservation_score', 'gene_name', 'transcript', 'exon', 'domain_1', 'domain_2', 'function', 'function_details']
+
         header_fields.append(strain_list)
+        header_data_names += strain_list
 
         if empty_columns != None:
             if empty_columns['snp_source'] == "false":
@@ -703,11 +704,16 @@ def get_header_list(variant_type, strains, species = None, empty_columns = None)
             if empty_columns['function_details'] == "false":
                 empty_field_count += 1
                 header_fields[0].remove('Details')
+        
+        for col in empty_columns.keys():
+            if empty_columns[col] == "false":
+                header_data_names.remove(col)
 
     elif variant_type == "InDel":
         header_fields = ['Index', 'ID', 'Type', 'InDel Chr', 'Mb Start', 'Mb End', 'Strand', 'Size', 'Sequence', 'Source']
+        header_data_names = ['index', 'indel_name', 'indel_type', 'indel_chr', 'indel_mb_s', 'indel_mb_e', 'indel_strand', 'indel_size', 'indel_sequence', 'source_name']
 
-    return header_fields, empty_field_count
+    return header_fields, empty_field_count, header_data_names
 
 def get_effect_details_by_category(effect_name = None, effect_value = None):
     gene_list = []
@@ -868,8 +874,6 @@ def get_gene_id_name_dict(species_id, gene_name_list):
     if len(results) > 0:
         for item in results:
             gene_id_name_dict[item[1]] = item[0]
-    else:
-        pass
 
     return gene_id_name_dict
 
@@ -883,7 +887,7 @@ def check_if_in_gene(species_id, chr, mb):
         query = """SELECT geneId,geneSymbol
                    FROM GeneList
                    WHERE chromosome = '{0}' AND
-                        (txStart < {1} AND txEnd > {1}); """.format(species_id, chr, mb)
+                        (txStart < {1} AND txEnd > {1}); """.format(chr, mb)
 
     result = g.db.execute(query).fetchone()
 
diff --git a/wqflask/wqflask/static/new/css/snp_browser.css b/wqflask/wqflask/static/new/css/snp_browser.css
index 30fe9a59..a7942d2a 100644
--- a/wqflask/wqflask/static/new/css/snp_browser.css
+++ b/wqflask/wqflask/static/new/css/snp_browser.css
@@ -6,6 +6,10 @@ table.dataTable thead th {
   vertical-align: bottom;
 }
 
+table.dataTable tbody tr.selected {
+  background-color: #ffee99;
+}
+
 table.dataTable thead .sorting,
 table.dataTable thead .sorting_asc,
 table.dataTable thead .sorting_desc,
@@ -18,7 +22,7 @@ table.dataTable thead .sorting_desc_disabled {
 table.dataTable thead th{
   border-right: 1px solid white;
   color: white;
-  background-color: royalblue;
+  background-color: #369;
 }
 
 table.dataTable tbody td {
diff --git a/wqflask/wqflask/static/new/css/trait_list.css b/wqflask/wqflask/static/new/css/trait_list.css
index b83655da..c7249721 100644
--- a/wqflask/wqflask/static/new/css/trait_list.css
+++ b/wqflask/wqflask/static/new/css/trait_list.css
@@ -12,9 +12,43 @@ div.show-hide-container {
 }
 
 button.active {
-    background: #e5e5e5;
+    background: #BEBEBE;
     -webkit-box-shadow: inset 0px 0px 5px #c1c1c1;
        -moz-box-shadow: inset 0px 0px 5px #c1c1c1;
             box-shadow: inset 0px 0px 5px #c1c1c1;
      outline: none;
-  }
\ No newline at end of file
+}
+
+div.dts {
+    display:block !important
+}
+
+div.dts div.dts_loading {
+    z-index:1
+}
+
+div.dts div.dts_label {
+    position:absolute;
+    right:10px;
+    background:rgba(0,0,0,0.8);
+    color:white;
+    box-shadow:3px 3px 10px rgba(0,0,0,0.5);
+    text-align:right;
+    border-radius:3px;
+    padding:0.4em;
+    z-index:2;
+    display:none
+}
+
+div.dts div.dataTables_scrollBody {
+    background:repeating-linear-gradient(45deg, #edeeff, #edeeff 10px, #fff 10px, #fff 20px)
+}
+
+div.dts div.dataTables_scrollBody table {
+    z-index:2
+}
+
+div.dts div.dataTables_paginate,div.dts div.dataTables_length{
+    display:none
+}
+
diff --git a/wqflask/wqflask/static/new/javascript/draw_probability_plot.js b/wqflask/wqflask/static/new/javascript/draw_probability_plot.js
index 3d756303..1b944d4f 100644
--- a/wqflask/wqflask/static/new/javascript/draw_probability_plot.js
+++ b/wqflask/wqflask/static/new/javascript/draw_probability_plot.js
@@ -118,7 +118,6 @@
           };
         };
         data = [make_data('samples_primary'), make_data('samples_other')];
-        console.log("THE DATA IS:", data);
         d3.select("#prob_plot_container svg").datum(data).call(chart);
         if (js_data.trait_symbol != null) {
             $("#prob_plot_title").html("<h3>" + js_data.trait_symbol + ": " + js_data.trait_id + "</h3>");
diff --git a/wqflask/wqflask/static/new/javascript/init_genome_browser.js b/wqflask/wqflask/static/new/javascript/init_genome_browser.js
index 2552fb04..508f5bf2 100644
--- a/wqflask/wqflask/static/new/javascript/init_genome_browser.js
+++ b/wqflask/wqflask/static/new/javascript/init_genome_browser.js
@@ -1,5 +1,3 @@
-console.log("THE FILES:", js_data.browser_files)
-
 snps_filename = "/browser_input?filename=" + js_data.browser_files[0]
 annot_filename = "/browser_input?filename=" + js_data.browser_files[1]
 
diff --git a/wqflask/wqflask/static/new/javascript/initialize_show_trait_tables.js b/wqflask/wqflask/static/new/javascript/initialize_show_trait_tables.js
index 5a4f151c..4362a75e 100644
--- a/wqflask/wqflask/static/new/javascript/initialize_show_trait_tables.js
+++ b/wqflask/wqflask/static/new/javascript/initialize_show_trait_tables.js
@@ -93,7 +93,7 @@ build_columns = function() {
     );
   }
 
-  attr_keys = Object.keys(js_data.attributes).sort((a, b) => (js_data.attributes[a].name > js_data.attributes[b].name) ? 1 : -1)
+  attr_keys = Object.keys(js_data.attributes).sort((a, b) => (js_data.attributes[a].name.toLowerCase() > js_data.attributes[b].name.toLowerCase()) ? 1 : -1)
   for (i = 0; i < attr_keys.length; i++){
     column_list.push(
       {
diff --git a/wqflask/wqflask/static/new/javascript/search_results.js b/wqflask/wqflask/static/new/javascript/search_results.js
index 9ffef4f8..ecb1220d 100644
--- a/wqflask/wqflask/static/new/javascript/search_results.js
+++ b/wqflask/wqflask/static/new/javascript/search_results.js
@@ -1,4 +1,4 @@
-change_buttons = function() {
+change_buttons = function(check_node = 0) {
   var button, buttons, item, num_checked, text, _i, _j, _k, _l, _len, _len2, _len3, _len4, _results, _results2;
   buttons = ["#add", "#remove"];
 
@@ -6,7 +6,7 @@ change_buttons = function() {
   table_api = $('#trait_table').DataTable();
   check_cells = table_api.column(0).nodes().to$();
   for (let i = 0; i < check_cells.length; i++) {
-    if (check_cells[i].childNodes[0].checked){
+    if (check_cells[i].childNodes[check_node].checked){
       num_checked += 1
     }
   }
@@ -95,29 +95,37 @@ $(function() {
 
   $('#select_top').keyup(function(){
       num_rows = $(this).val()
+
       if (num_rows = parseInt(num_rows)){
-          i = 0
-          $('#trait_table > tbody > tr').each(function(){
-              if (i < num_rows) {
-                  $(this).find('.trait_checkbox').prop("checked", true)
-                  if (!$(this).closest('tr').hasClass('selected')) {
-                      $(this).closest('tr').addClass('selected')
-                  }
-              }
-              else {
-                  if ($(this).closest('tr').hasClass('selected')) {
-                      $(this).closest('tr').removeClass('selected')
-                      $(this).find('.trait_checkbox').prop("checked", false)
-                  }
-              }
-              i += 1
-          });
+          table_api = $('#trait_table').DataTable();
+
+          check_cells = table_api.column(0).nodes().to$();
+          for (let i = 0; i < num_rows; i++) {
+            check_cells[i].childNodes[0].checked = true;
+          }
+
+          check_rows = table_api.rows().nodes();
+          for (let i=0; i < num_rows; i++) {
+            if (check_rows[i].classList.contains("selected")){
+              continue
+            } else {
+              check_rows[i].classList.add("selected")
+            }
+          }
+          for (let i = num_rows; i < check_rows.length; i++){
+            check_cells[i].childNodes[0].checked = false;
+            if (check_rows[i].classList.contains("selected")){
+              check_rows[i].classList.remove("selected")
+            }
+          }
       }
       else {
-          $('#trait_table > tbody > tr').each(function(){
-              $(this).closest('tr').removeClass('selected')
-              $(this).find('.trait_checkbox').prop("checked", false)
-          });
+        for (let i = 0; i < check_rows.length; i++){
+          check_cells[i].childNodes[0].checked = false;
+          if (check_rows[i].classList.contains("selected")){
+            check_rows[i].classList.remove("selected")
+          }
+        }
       }
       change_buttons();
   });
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index 5dc9e456..1c8e328d 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -94,21 +94,7 @@ add = function() {
 $('#add_to_collection').click(add);
 sample_lists = js_data.sample_lists;
 sample_group_types = js_data.sample_group_types;
-d3.select("#select_compare_trait").on("click", (function(_this) {
-  return function() {
-    $('.scatter-matrix-container').remove();
-    return open_trait_selection();
-  };
-})(this));
-d3.select("#select_covariates").on("click", (function(_this) {
-  return function() {
-    return open_covariate_selection();
-  };
-})(this));
-$("#remove_covariates").click(function () {
-    $("input[name=covariates]").val("")
-    $(".selected-covariates").val("")
-});
+
 $(".select_covariates").click(function () {
   open_covariate_selection();
 });
@@ -116,11 +102,7 @@ $(".remove_covariates").click(function () {
   $("input[name=covariates]").val("")
   $(".selected-covariates").val("")
 });
-d3.select("#clear_compare_trait").on("click", (function(_this) {
-  return function() {
-    return $('.scatter-matrix-container').remove();
-  };
-})(this));
+
 open_trait_selection = function() {
   return $('#collections_holder').load('/collections/list?color_by_trait #collections_list', (function(_this) {
     return function() {
@@ -233,6 +215,8 @@ update_histogram = function() {
 
   if ($('input[name="transform"]').val() != ""){
     root.histogram_layout['xaxis']['title'] = "<b>" + js_data.unit_type +  " (" + $('input[name="transform"]').val() + ")</b>"
+  } else {
+    root.histogram_layout['xaxis']['title'] = "<b>" + js_data.unit_type + "</b>"
   }
 
   Plotly.newPlot('histogram', root.histogram_data, root.histogram_layout, root.modebar_options);
@@ -281,6 +265,8 @@ update_bar_chart = function() {
 
   if ($('input[name="transform"]').val() != ""){
     root.bar_layout['yaxis']['title'] = "<b>" + js_data.unit_type +  " (" + $('input[name="transform"]').val() + ")</b>"
+  } else {
+    root.bar_layout['yaxis']['title'] = "<b>" + js_data.unit_type + "</b>"
   }
 
   root.bar_data[0]['y'] = trait_vals
@@ -322,6 +308,8 @@ update_box_plot = function() {
 
   if ($('input[name="transform"]').val() != ""){
     root.box_layout['yaxis']['title'] = "<b>" + js_data.unit_type +  " (" + $('input[name="transform"]').val() + ")</b>"
+  } else {
+    root.box_layout['yaxis']['title'] = "<b>" + js_data.unit_type + "</b>"
   }
 
   Plotly.newPlot('box_plot', root.box_data, root.box_layout, root.modebar_options)
@@ -353,6 +341,8 @@ update_violin_plot = function() {
 
   if ($('input[name="transform"]').val() != ""){
     root.violin_layout['yaxis']['title'] = "<b>" + js_data.unit_type +  " (" + $('input[name="transform"]').val() + ")</b>"
+  } else {
+    root.violin_layout['yaxis']['title'] = "<b>" + js_data.unit_type + "</b>"
   }
 
   Plotly.newPlot('violin_plot', root.violin_data, root.violin_layout, root.modebar_options)
@@ -427,6 +417,25 @@ process_id = function() {
   }
   return processed;
 };
+
+fetch_sample_values = function() {
+  // This is meant to fetch all sample values using DataTables API, since they can't all be submitted with the form when using Scroller (and this should also be faster)
+  sample_val_dict = {};
+
+  table = 'samples_primary';
+  if ($('#' + table).length){
+    table_api = $('#' + table).DataTable();
+    val_nodes = table_api.column(3).nodes().to$();
+    for (_j = 0; _j < val_nodes.length; _j++){
+      sample_name = val_nodes[_j].childNodes[0].name.split(":")[1]
+      sample_val = val_nodes[_j].childNodes[0].value
+      sample_val_dict[sample_name] = sample_val
+    }
+  }
+
+  return sample_val_dict;
+}
+
 edit_data_change = function() {
   var already_seen, checkbox, name, real_dict, real_value, real_variance, row, rows, sample_sets, table, tables, _i, _j, _len, _len1;
   already_seen = {};
@@ -456,15 +465,15 @@ edit_data_change = function() {
         if (is_number(sample_val) && sample_val !== "") {
           sample_val = parseFloat(sample_val);
           sample_sets[table].add_value(sample_val);
-          if (typeof var_nodes !== 'undefined'){
-            sample_var = null;
-          } else {
+          try {
             sample_var = var_nodes[_j].childNodes[0].value
             if (is_number(sample_var)) {
               sample_var = parseFloat(sample_var)
             } else {
               sample_var = null;
             }
+          } catch {
+            sample_var = null;
           }
           sample_dict = {
             value: sample_val,
@@ -479,6 +488,7 @@ edit_data_change = function() {
         }
       }
     }
+
   }
 
   update_stat_values(sample_sets);
@@ -524,8 +534,31 @@ on_corr_method_change = function() {
 };
 $('select[name=corr_type]').change(on_corr_method_change);
 
+on_dataset_change = function() {
+  let dataset_type = $('select[name=corr_dataset] option:selected').data('type');
+  let location_type = $('select[name=location_type] option:selected').val();
+
+  if (dataset_type == "mrna_assay"){
+    $('#min_expr_filter').show();
+    $('select[name=location_type] option:disabled').prop('disabled', false)
+  }
+  else if (dataset_type == "pheno"){
+    $('#min_expr_filter').show();
+    $('select[name=location_type]>option:eq(0)').prop('disabled', true).attr('selected', false);
+    $('select[name=location_type]>option:eq(1)').prop('disabled', false).attr('selected', true);
+  }
+  else {
+    $('#min_expr_filter').hide();
+    $('select[name=location_type]>option:eq(0)').prop('disabled', false).attr('selected', true);
+    $('select[name=location_type]>option:eq(1)').prop('disabled', true).attr('selected', false);
+  }
+}
+
+$('select[name=corr_dataset]').change(on_dataset_change);
+$('select[name=location_type]').change(on_dataset_change);
+
 submit_special = function(url) {
-  get_table_contents_for_form_submit("trait_data_form");
+  $("input[name=sample_vals]").val(JSON.stringify(fetch_sample_values()))
   $("#trait_data_form").attr("action", url);
   $("#trait_data_form").submit();
 };
@@ -549,8 +582,8 @@ get_table_contents_for_form_submit = function(form_id) {
  });
 }
 
-var corr_input_list = ['corr_type', 'primary_samples', 'trait_id', 'dataset', 'group', 'tool_used', 'form_url', 'corr_sample_method', 'corr_samples_group', 'corr_dataset', 'min_expr',
-                        'corr_return_results', 'loc_chr', 'min_loc_mb', 'max_loc_mb', 'p_range_lower', 'p_range_upper']
+var corr_input_list = ['sample_vals', 'corr_type', 'primary_samples', 'trait_id', 'dataset', 'group', 'tool_used', 'form_url', 'corr_sample_method', 'corr_samples_group', 'corr_dataset', 'min_expr',
+                        'corr_return_results', 'location_type', 'loc_chr', 'min_loc_mb', 'max_loc_mb', 'p_range_lower', 'p_range_upper']
 
 $(".corr_compute").on("click", (function(_this) {
   return function() {
@@ -571,7 +604,7 @@ populate_sample_attributes_values_dropdown = function() {
   sample_attributes = [];
 
   var attributes_as_list = Object.keys(js_data.attributes).map(function(key) {
-    return [key, js_data.attributes[key].name];
+    return [key, js_data.attributes[key].name.toLowerCase()];
   });
 
   attributes_as_list.sort(function(first, second) {
@@ -631,6 +664,8 @@ block_by_attribute_value = function() {
       this_val_node.value = "x";
     }
   }
+
+  edit_data_change();
 };
 $('#exclude_by_attr').click(block_by_attribute_value);
 
@@ -800,6 +835,7 @@ reset_samples_table = function() {
 };
 $('.reset').click(function() {
   reset_samples_table();
+  $('input[name="transform"]').val("");
   edit_data_change();
 });
 
@@ -1289,7 +1325,7 @@ if (js_data.num_values < 256) {
     margin: {
         l: left_margin,
         r: 30,
-        t: 30,
+        t: 100,
         b: bottom_margin
     }
   };
diff --git a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
index 34582f21..3ae52975 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
@@ -141,7 +141,7 @@ $('input[name=display_all]').change((function(_this) {
 })(this));
 
 //ZS: This is a list of inputs to be passed to the loading page, since not all inputs on the trait page are relevant to mapping
-var mapping_input_list = ['temp_uuid', 'trait_id', 'dataset', 'tool_used', 'form_url', 'method', 'transform', 'trimmed_markers', 'selected_chr', 'chromosomes', 'mapping_scale',
+var mapping_input_list = ['temp_uuid', 'trait_id', 'dataset', 'tool_used', 'form_url', 'method', 'transform', 'trimmed_markers', 'selected_chr', 'chromosomes', 'mapping_scale', 'sample_vals',
                           'score_type', 'suggestive', 'significant', 'num_perm', 'permCheck', 'perm_output', 'perm_strata', 'categorical_vars', 'num_bootstrap', 'bootCheck', 'bootstrap_results',
                           'LRSCheck', 'covariates', 'maf', 'use_loco', 'manhattan_plot', 'control_marker', 'control_marker_db', 'do_control', 'genofile', 
                           'pair_scan', 'startMb', 'endMb', 'graphWidth', 'lrsMax', 'additiveCheck', 'showSNP', 'showGenes', 'viewLegend', 'haplotypeAnalystCheck', 
diff --git a/wqflask/wqflask/static/new/javascript/stats.js b/wqflask/wqflask/static/new/javascript/stats.js
index 4df03412..6c443ab3 100644
--- a/wqflask/wqflask/static/new/javascript/stats.js
+++ b/wqflask/wqflask/static/new/javascript/stats.js
@@ -91,8 +91,6 @@ Stats = (function() {
   Stats.prototype.interquartile = function() {
     var iq, length, q1, q3;
     length = this.the_values.length;
-    console.log("in interquartile the_values are:", this.the_values);
-    console.log("length is:", length);
     if (js_data.dataset_type == "ProbeSet" && js_data.data_scale == "linear_positive") {
       q1 = Math.log2(this.the_values[Math.floor(length * .25)]);
       q3 = Math.log2(this.the_values[Math.floor(length * .75)]);
diff --git a/wqflask/wqflask/templates/base.html b/wqflask/wqflask/templates/base.html
index a86b9ea9..38161851 100644
--- a/wqflask/wqflask/templates/base.html
+++ b/wqflask/wqflask/templates/base.html
@@ -265,7 +265,7 @@
     {% endblock %}
 
     <script type="text/javascript">
-     $(window).load(function() {
+     document.addEventListener('DOMContentLoaded', function() {
          let timeToLoad = document.createElement("p");
          timeToLoad.innerHTML = "It took your browser " + ((Date.now() - pageLoadStart)/1000) + " second(s) to render this page";
          document.querySelector("footer .row .col-xs-6").appendChild(timeToLoad);
diff --git a/wqflask/wqflask/templates/correlation_page.html b/wqflask/wqflask/templates/correlation_page.html
index 8e2a23fd..6188c0e7 100644
--- a/wqflask/wqflask/templates/correlation_page.html
+++ b/wqflask/wqflask/templates/correlation_page.html
@@ -95,14 +95,15 @@
           {% elif target_dataset.type == 'Publish' %}
           <button class="toggle-vis" data-column="3">Abbreviation</button>
           <button class="toggle-vis" data-column="4">Description</button>
-          <button class="toggle-vis" data-column="5">Authors</button>
-          <button class="toggle-vis" data-column="6">Year</button>
-          <button class="toggle-vis" data-column="7">Sample {% if corr_method == 'pearson' %}r{% else %}rho{% endif %}</button>
-          <button class="toggle-vis" data-column="8">N</button>
-          <button class="toggle-vis" data-column="9">Sample p({% if corr_method == 'pearson' %}r{% else %}rho{% endif %})</button>
-          <button class="toggle-vis" data-column="10">Peak LOD</button>
-          <button class="toggle-vis" data-column="11">Peak Location</button>
-          <button class="toggle-vis" data-column="12">Effect Size</button>
+          <button class="toggle-vis" data-column="5">Mean</button>
+          <button class="toggle-vis" data-column="6">Authors</button>
+          <button class="toggle-vis" data-column="7">Year</button>
+          <button class="toggle-vis" data-column="8">Sample {% if corr_method == 'pearson' %}r{% else %}rho{% endif %}</button>
+          <button class="toggle-vis" data-column="9">N</button>
+          <button class="toggle-vis" data-column="10">Sample p({% if corr_method == 'pearson' %}r{% else %}rho{% endif %})</button>
+          <button class="toggle-vis" data-column="11">Peak LOD</button>
+          <button class="toggle-vis" data-column="12">Peak Location</button>
+          <button class="toggle-vis" data-column="13">Effect Size</button>
           {% else %}
           <button class="toggle-vis" data-column="3">Location</button>
           <button class="toggle-vis" data-column="4">Sample {% if corr_method == 'pearson' %}r{% else %}rho{% endif %}</button>
@@ -399,6 +400,13 @@
                       }
                     },
                     {
+                      'title': "Mean",
+                      'type': "natural-minus-na",
+                      'width': "40px",
+                      'data': "mean",
+                      'orderSequence': [ "desc", "asc"]
+                    },
+                    {
                       'title': "Authors",
                       'type': "natural",
                       'width': "400px",
@@ -514,6 +522,8 @@
                 } ],
                 {% if target_dataset.type == 'Geno' %}
                 "order": [[6, "asc" ]],
+                {% elif target_dataset.type == 'Publish' %}
+                "order": [[10, "asc" ]],
                 {% else %}
                 "order": [[9, "asc" ]],
                 {% endif %}
diff --git a/wqflask/wqflask/templates/mapping_results.html b/wqflask/wqflask/templates/mapping_results.html
index 1a601bef..cfdebde5 100644
--- a/wqflask/wqflask/templates/mapping_results.html
+++ b/wqflask/wqflask/templates/mapping_results.html
@@ -31,10 +31,7 @@
         {% endif %}
         <input type="hidden" name="results_path" value="{{ mapping_results_path }}">
         <input type="hidden" name="method" value="{{ mapping_method }}">
-        <input type="hidden" name="samples" value="{{ samples|join(",") }}">
-        {% for sample in samples %}
-        <input type="hidden" name="value:{{ sample }}" value="{{ vals[loop.index - 1] }}">
-        {% endfor %}
+        <input type="hidden" name="sample_vals" value="{{ sample_vals }}">
         <input type="hidden" name="n_samples" value="{{ n_samples }}">
         <input type="hidden" name="maf" value="{{ maf }}">
         <input type="hidden" name="use_loco" value="{{ use_loco }}">
@@ -248,7 +245,7 @@
         <button class="btn btn-default" id="select_all"><span class="glyphicon glyphicon-ok"></span> Select All</button>
         <button class="btn btn-default" id="deselect_all"><span class="glyphicon glyphicon-remove"></span> Deselect All</button>
         <button class="btn btn-default" id="invert"><span class="glyphicon glyphicon-resize-vertical"></span> Invert</button>
-        <button class="btn btn-success" id="add" disabled><span class="glyphicon glyphicon-plus-sign"></span> Add</button>
+        {% if geno_db_exists == "True" %}<button class="btn btn-success" id="add" disabled><span class="glyphicon glyphicon-plus-sign"></span> Add</button>{% endif %}
         <br />
         <br />
           <div id="table_container" style="width:{% if 'additive' in trimmed_markers[0] %}600{% else %}550{% endif %}px;">
@@ -375,6 +372,20 @@
             console.time("Creating table");
             {% if selectedChr == -1 %}
             $('#trait_table').DataTable( {
+                "drawCallback": function( settings ) {
+                  $('#trait_table tr').off().on("click", function(event) {
+                    if (event.target.type !== 'checkbox' && event.target.tagName.toLowerCase() !== 'a') {
+                      var obj =$(this).find('input');
+                      obj.prop('checked', !obj.is(':checked'));
+                    }
+                    if ($(this).hasClass("selected")){
+                      $(this).removeClass("selected")
+                    } else {
+                      $(this).addClass("selected")
+                    }
+                    {% if geno_db_exists == "True" %}change_buttons(check_node=1){% endif %}
+                  });
+                },
                 "columns": [
                     { "type": "natural", "width": "5%" },
                     { "type": "natural", "width": "8%" },
@@ -389,7 +400,7 @@
                     "orderable": false
                 } ],
                 "language": {
-                  "info": "Showing1 from _START_ to _END_ of " + js_data.total_markers + " records",
+                  "info": "Showing from _START_ to _END_ of " + js_data.total_markers + " records",
                 },
                 "order": [[1, "asc" ]],
                 "sDom": "iRZtir",
@@ -450,7 +461,7 @@
 
         });
 
-        var mapping_input_list = ['temp_uuid', 'trait_id', 'dataset', 'tool_used', 'form_url', 'method', 'transform', 'trimmed_markers', 'selected_chr', 'chromosomes', 'mapping_scale',
+        var mapping_input_list = ['temp_uuid', 'trait_id', 'dataset', 'tool_used', 'form_url', 'method', 'transform', 'trimmed_markers', 'selected_chr', 'chromosomes', 'mapping_scale', 'sample_vals',
                             'score_type', 'suggestive', 'significant', 'num_perm', 'permCheck', 'perm_output', 'perm_strata', 'categorical_vars', 'num_bootstrap', 'bootCheck', 'bootstrap_results',
                             'LRSCheck', 'covariates', 'maf', 'use_loco', 'manhattan_plot', 'color_scheme', 'manhattan_single_color', 'control_marker', 'control_marker_db', 'do_control', 'genofile',
                             'pair_scan', 'startMb', 'endMb', 'graphWidth', 'lrsMax', 'additiveCheck', 'showSNP', 'showGenes', 'viewLegend', 'haplotypeAnalystCheck', 
diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html
index f2334512..9b36568c 100644
--- a/wqflask/wqflask/templates/search_result_page.html
+++ b/wqflask/wqflask/templates/search_result_page.html
@@ -3,7 +3,6 @@
 {% block css %}
     <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='DataTables/css/jquery.dataTables.css') }}" />
     <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='fontawesome/css/font-awesome.min.css') }}" />
-    <link rel="stylesheet" type="text/css" href="{{ url_for('js', filename='DataTablesExtensions/scroller/css/scroller.dataTables.min.css') }}">
     <link rel="stylesheet" type="text/css" href="{{ url_for('js', filename='DataTablesExtensions/buttonStyles/css/buttons.dataTables.min.css') }}">
     <link rel="stylesheet" type="text/css" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.1/css/all.min.css">
     <link rel="stylesheet" type="text/css" href="/static/new/css/show_trait.css" />
@@ -125,7 +124,7 @@
             {% endif %}
           </div>
           {% endif %}
-          <div id="table_container" {% if dataset.type == 'ProbeSet' or dataset.type == 'Publish' %}style="min-width: 1500px;"{% endif %}>
+          <div id="table_container" {% if dataset.type == 'ProbeSet' or dataset.type == 'Publish' %}style="min-width: 1500px; max-width:100%;"{% 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>
                  <td colspan="100%" align="center"><br><b><font size="15">Loading...</font></b><br></td>
@@ -146,6 +145,7 @@
     <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='js_alt/md5.min.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="https://cdn.datatables.net/scroller/2.0.2/js/dataTables.scroller.min.js"></script>
     <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='jszip/jszip.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/buttons/js/dataTables.buttons.min.js') }}"></script>
@@ -160,6 +160,16 @@
 
     <script type="text/javascript" charset="utf-8">
         $(document).ready( function () {
+
+            var getParams = function(url) {
+                let parser = document.createElement('a');
+                parser.href = url;
+                let params = parser.search.substring(1);
+                if(params.length > 0) {
+                    return ('?'+params);
+                }
+                return params;
+            };
             
             $('#trait_table tr').click(function(event) {
                 if (event.target.type !== 'checkbox') {
@@ -225,7 +235,7 @@
                       'data': null,
                       'width': "25px",
                       'orderDataType': "dom-checkbox",
-                      'orderSequence': [ "desc", "asc"],
+                      'orderable': false,
                       'render': function(data, type, row, meta) {
                         return '<input type="checkbox" name="searchResult" class="checkbox trait_checkbox" value="' + data.hmac + '">'
                       }
@@ -264,36 +274,36 @@
                       }
                     },
                     {
-                      'title': "Location",
+                      'title': "<div style='text-align: right;'>Location</div>",
                       'type': "natural-minus-na",
                       'width': "125px",
                       'data': "location"
                     },
                     {
-                      'title': "Mean",
+                      'title': "<div style='text-align: right;'>Mean</div>",
                       'type': "natural-minus-na",
-                      'width': "40px",
+                      'width': "30px",
                       'data': "mean",
                       'orderSequence': [ "desc", "asc"]
                     },
                     {
-                      'title': "Peak <a href=\"{{ url_for('glossary_blueprint.glossary') }}#LRS\" target=\"_blank\" style=\"color: white;\">&nbsp;<i class=\"fa fa-info-circle\" aria-hidden=\"true\"></i></a>LOD",
+                      'title': "<div style='text-align: right;'>Peak <a href=\"{{ url_for('glossary_blueprint.glossary') }}#LRS\" target=\"_blank\" style=\"color: white;\">&nbsp;<i class=\"fa fa-info-circle\" aria-hidden=\"true\"></i></a></div><div style='text-align: right;'>LOD&ensp;&emsp;</div>",
                       'type': "natural-minus-na",
                       'data': "lod_score",
                       'width': "60px",
                       'orderSequence': [ "desc", "asc"]
                     },
                     {
-                      'title': "Peak Location",
+                      'title': "<div style='text-align: right;'>Peak Location</div>",
                       'type': "natural-minus-na",
                       'width': "125px",
                       'data': "lrs_location"
                     },
                     {
-                      'title': "Effect Size<a href=\"{{ url_for('glossary_blueprint.glossary') }}#A\" target=\"_blank\" style=\"color: white;\">&nbsp;<i class=\"fa fa-info-circle\" aria-hidden=\"true\"></i></a>",
+                      'title': "<div style='text-align: right;'>Effect <a href=\"{{ url_for('glossary_blueprint.glossary') }}#A\" target=\"_blank\" style=\"color: white;\">&nbsp;<i class=\"fa fa-info-circle\" aria-hidden=\"true\"></i></a></div><div style='text-align: right;'>Size&ensp;&emsp;</div>",
                       'type': "natural-minus-na",
                       'data': "additive",
-                      'width': "90px",
+                      'width': "60px",
                       'orderSequence': [ "desc", "asc"]
                     }{% elif dataset.type == 'Publish' %},
                     {
@@ -310,16 +320,16 @@
                       }
                     },
                     {
-                      'title': "Mean",
+                      'title': "<div style='text-align: right;'>Mean</div>",
                       'type': "natural-minus-na",
-                      'width': "110px",
+                      'width': "30px",
                       'data': "mean",
                       'orderSequence': [ "desc", "asc"]
                     },
                     {
                       'title': "Authors",
                       'type': "natural",
-                      'width': "500px",
+                      'width': "300px",
                       'data': null,
                       'render': function(data, type, row, meta) {
                         author_list = data.authors.split(",")
@@ -332,10 +342,10 @@
                       }
                     },
                     {
-                      'title': "Year",
+                      'title': "<div style='text-align: right;'>Year</div>",
                       'type': "natural-minus-na",
                       'data': null,
-                      'width': "80px",
+                      'width': "25px",
                       'render': function(data, type, row, meta) {
                         if (data.pubmed_id != "N/A"){
                           return '<a href="' + data.pubmed_link + '">' + data.pubmed_text + '</a>'
@@ -346,45 +356,43 @@
                       'orderSequence': [ "desc", "asc"]
                     },
                     {
-                      'title': "Peak <a href=\"{{ url_for('glossary_blueprint.glossary') }}#LRS\" target=\"_blank\" style=\"color: white;\">&nbsp;<i class=\"fa fa-info-circle\" aria-hidden=\"true\"></i></a>LOD",
+                      'title': "<div style='text-align: right;'>Peak <a href=\"{{ url_for('glossary_blueprint.glossary') }}#LRS\" target=\"_blank\" style=\"color: white;\">&nbsp;<i class=\"fa fa-info-circle\" aria-hidden=\"true\"></i></a></div><div style='text-align: right;'>LOD&ensp;&emsp;</div>",
                       'type': "natural-minus-na",
                       'data': "lod_score",
                       'width': "60px",
                       'orderSequence': [ "desc", "asc"]
                     },
                     {
-                      'title': "Peak Location",
+                      'title': "<div style='text-align: right;'>Peak Location</div>",
                       'type': "natural-minus-na",
                       'width': "120px",
                       'data': "lrs_location"
                     },
                     {
-                      'title': "Effect Size<a href=\"{{ url_for('glossary_blueprint.glossary') }}#A\" target=\"_blank\" style=\"color: white;\">&nbsp;<i class=\"fa fa-info-circle\" aria-hidden=\"true\"></i></a>",
+                      'title': "<div style='text-align: right;'>Effect <a href=\"{{ url_for('glossary_blueprint.glossary') }}#A\" target=\"_blank\" style=\"color: white;\">&nbsp;<i class=\"fa fa-info-circle\" aria-hidden=\"true\"></i></a></div><div style='text-align: right;'>Size&ensp;&emsp;</div>",
                       'type': "natural-minus-na",
-                      'width': "120px",
+                      'width': "60px",
                       'data': "additive",
                       'orderSequence': [ "desc", "asc"]
                     }{% elif dataset.type == 'Geno' %},
                     {
-                      'title': "Location",
+                      'title': "<div style='text-align: right;'>Location</div>",
                       'type': "natural-minus-na",
                       'width': "120px",
                       'data': "location"
                     }{% endif %}
                 ],
                 "order": [[1, "asc" ]],
-                'sDom': "itirp",
-                'iDisplayLength': 500,
-                'deferRender': true,
-                'paging': true,
-                'orderClasses': true,
-                'processing': true,
-                'language': {
-                  'loadingRecords': '&nbsp;',
-                  'processing': 'Loading...'
-                }
+                'sDom': "iti",
+                "autoWidth": true,
+                "bSortClasses": false,
+                "scrollY": "100vh",
+                "scroller":  true,
+                "scrollCollapse": true
             } );
             
+            trait_table.draw(); //ZS: This makes the table adjust its height properly on initial load
+
             $('.toggle-vis').on( 'click', function (e) {
               e.preventDefault();
 
diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index c881eb76..77fc9342 100644
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -35,6 +35,7 @@
         <input type="hidden" name="genofile" value="">
         <input type="hidden" name="covariates" value="">
         <input type="hidden" name="transform" value="">
+        <input type="hidden" name="sample_vals" value="">
 
         <div class="container showtrait-main-div">
             <div class="panel-group" id="accordion">
diff --git a/wqflask/wqflask/templates/show_trait_calculate_correlations.html b/wqflask/wqflask/templates/show_trait_calculate_correlations.html
index ba72ff27..cba977ac 100644
--- a/wqflask/wqflask/templates/show_trait_calculate_correlations.html
+++ b/wqflask/wqflask/templates/show_trait_calculate_correlations.html
@@ -2,86 +2,94 @@
     <div class="col-xs-3 correlation-options">
       <div class="form-horizontal section-form-div">
 
-          <div class="form-group">
-              <label for="corr_type" class="col-xs-2 control-label">Method</label>
-              <div class="col-xs-3 controls">
-                  <select name="corr_type" class="form-control">
-                      <option value="sample">Sample r</option>
-                      <option value="lit">Literature r</option>
-                      <option value="tissue">Tissue r</option>
-                  </select>
-              </div>
-          </div>
+        <div class="form-group">
+            <label for="corr_type" class="col-xs-2 control-label">Method</label>
+            <div class="col-xs-3 controls">
+                <select name="corr_type" class="form-control">
+                    <option value="sample">Sample r</option>
+                    <option value="lit">Literature r</option>
+                    <option value="tissue">Tissue r</option>
+                </select>
+            </div>
+        </div>
 
-          <div class="form-group">
-              <label for="corr_dataset" class="col-xs-2 control-label">Database</label>
-              <div class="col-xs-10 controls">
-                  <select name="corr_dataset" class="form-control">
-                      {% for tissue in corr_tools.dataset_menu %}
-                          {% if tissue.tissue %}
-                              <optgroup label="{{ tissue.tissue }} ------">
-                          {% endif %}
-                          {% for dataset in tissue.datasets %}
-                              <option value="{{ dataset[1] }}"
-                              {% if corr_tools.dataset_menu_selected == dataset[1] %}
-                                  selected
-                              {% endif %}>
-                                {{ dataset[0] }}
-                              </option>
-                          {% endfor %}
-                          {% if tissue.tissue %}
-                              </optgroup>
-                          {% endif %}
-                      {% endfor %}
-                  </select>
-              </div>
-          </div>
+        <div class="form-group">
+            <label for="corr_dataset" class="col-xs-2 control-label">Database</label>
+            <div class="col-xs-10 controls">
+                <select name="corr_dataset" class="form-control">
+                    {% for tissue in corr_tools.dataset_menu %}
+                        {% if tissue.tissue %}
+                        <optgroup label="{{ tissue.tissue }} ------">
+                        {% endif %}
+                        {% for dataset in tissue.datasets %}
+                        <option data-type="{% if tissue.tissue %}mrna_assay{% elif dataset[1][-4:] == 'Geno' %}geno{% else %}pheno{% endif %}" value="{{ dataset[1] }}"
+                        {% if corr_tools.dataset_menu_selected == dataset[1] %}
+                            selected
+                        {% endif %}>
+                        {{ dataset[0] }}
+                        </option>
+                        {% endfor %}
+                        {% if tissue.tissue %}
+                        </optgroup>
+                        {% endif %}
+                    {% endfor %}
+                </select>
+            </div>
+        </div>
 
-          <div class="form-group">
-              <label for="corr_return_results" class="col-xs-2 control-label">Limit to</label>
-              <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 }}"
-                          {% if corr_tools.return_results_menu_selected == return_result %}
-                              selected
-                          {% endif %}>
-                          Top {{ return_result }}
-                          </option>
-                      {% endfor %}
-                  </select>
-              </div>
-          </div>
+        <div class="form-group">
+            <label for="corr_return_results" class="col-xs-2 control-label">Limit to</label>
+            <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 }}"
+                        {% if corr_tools.return_results_menu_selected == return_result %}
+                            selected
+                        {% endif %}>
+                        Top {{ return_result }}
+                        </option>
+                    {% endfor %}
+                </select>
+            </div>
+        </div>
 
-          <div class="form-group">
-              <label for="corr_samples_group" class="col-xs-2 control-label">Samples</label>
-              <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>
-                      {% endfor %}
-                  </select>
-              </div>
-          </div>
+        <div class="form-group">
+            <label for="corr_samples_group" class="col-xs-2 control-label">Samples</label>
+            <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>
+                    {% endfor %}
+                </select>
+            </div>
+        </div>
 
-          <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-4 controls">
-                  <select name="corr_sample_method" class="form-control">
-                      <option value="pearson">Pearson</option>
-                      <option value="spearman">Spearman Rank</option>
-                      <option value="bicor">Biweight Midcorrelation</option>
-                  </select>
-              </div>
-          </div>
-          {% if dataset.type != "Publish" %}
-          <div class="form-group">
-              <label class="col-xs-2 control-label">Min Expr</label>
-              <div class="col-xs-4 controls">
-                  <input name="min_expr" value="" type="text" class="form-control min-expr-field">
-              </div>
-          </div>
-          <div class="form-group">
+        <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-4 controls">
+                <select name="corr_sample_method" class="form-control">
+                    <option value="pearson">Pearson</option>
+                    <option value="spearman">Spearman Rank</option>
+                    <option value="bicor">Biweight Midcorrelation</option>
+                </select>
+            </div>
+        </div>
+        <div id="min_expr_filter" class="form-group" style="display: {% if dataset.type != 'Geno' %}block{% else %}none{% endif %};">
+            <label class="col-xs-2 control-label">Min Expr</label>
+            <div class="col-xs-4 controls">
+                <input name="min_expr" value="" type="text" class="form-control min-expr-field">
+            </div>
+        </div>
+        <div class="form-group">
+            <label for="location_type" class="col-xs-2 control-label">Location Type</label>
+            <div class="col-xs-4 controls">
+                <select name="location_type" class="form-control">
+                    <option value="gene" {% if dataset.type == 'Publish' %}disabled{% endif %}>Gene</option>
+                    <option value="highest_lod">Highest LOD</option>
+                </select>
+            </div>
+        </div>
+        <div id="location_filter" class="form-group">
               <label class="col-xs-2 control-label">Location</label>
               <div class="col-xs-6 controls">
                   <span>
@@ -91,7 +99,6 @@
                   <br>
               </div>
           </div>
-          {% endif %}
           <div class="form-group">
               <label class="col-xs-2 control-label">Range</label>
               <div class="col-xs-5 controls">
diff --git a/wqflask/wqflask/templates/show_trait_edit_data.html b/wqflask/wqflask/templates/show_trait_edit_data.html
index 4ad11a5e..0d34bebc 100644
--- a/wqflask/wqflask/templates/show_trait_edit_data.html
+++ b/wqflask/wqflask/templates/show_trait_edit_data.html
@@ -1,12 +1,9 @@
 <div>
     {% for sample_type in sample_groups %}
       <div class="sample-table-container">
-        {% if loop.index == 1 %}
+        {% if loop.index == 1 and (sample_groups[0].se_exists or has_num_cases or sample_groups[0].attributes|length > 0) %}
         <b>Show/Hide Columns:</b>
         <br>
-        <button class="toggle-vis" data-column="1">ID</button>
-        <button class="toggle-vis" data-column="2">Sample</button>
-        <button class="toggle-vis" data-column="3">Value</button>
         {% if sample_groups[0].se_exists %}
         <button class="toggle-vis" data-column="4,5">SE</button>
         {% if has_num_cases %}
diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html
index eca436c6..c42fe4aa 100755
--- a/wqflask/wqflask/templates/show_trait_mapping_tools.html
+++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html
@@ -74,8 +74,8 @@
                               No collections available. Please add traits to a collection to use them as covariates.
                               {% else %}
                               <div class="select-covar-div">
-                                <button type="button" id="select_covariates" class="btn btn-default select-covar-button">Select</button>
-                                <button type="button" id="remove_covariates" class="btn btn-default select-covar-button">Remove</button>
+                                <button type="button" class="btn btn-default select-covar-button select_covariates">Select</button>
+                                <button type="button" class="btn btn-default select-covar-button remove_covariates">Remove</button>
                               </div>
                               <textarea rows="3" cols="50" readonly placeholder="No covariates selected" class="selected-covariates"></textarea>
                               {% endif %}
@@ -317,8 +317,8 @@
                             No collections available. Please add traits to a collection to use them as covariates.
                             {% else %}
                             <div class="select-covar-div">
-                              <button type="button" id="select_covariates" class="btn btn-default select-covar-button">Select</button>
-                              <button type="button" id="remove_covariates" class="btn btn-default select-covar-button">Remove</button>
+                              <button type="button" class="btn btn-default select-covar-button select_covariates">Select</button>
+                              <button type="button" class="btn btn-default select-covar-button remove_covariates">Remove</button>
                             </div>
                             <textarea rows="3" cols="50" readonly placeholder="No covariates selected" class="selected-covariates"></textarea>
                             {% endif %}
diff --git a/wqflask/wqflask/templates/show_trait_statistics.html b/wqflask/wqflask/templates/show_trait_statistics.html
index 4f347d4e..865959b1 100644
--- a/wqflask/wqflask/templates/show_trait_statistics.html
+++ b/wqflask/wqflask/templates/show_trait_statistics.html
@@ -21,9 +21,6 @@
             <li>
                 <a href="#violin_plot_tab" class="violin_plot_tab" data-toggle="tab">Violin Plot</a>
             </li>
-            <li>
-                <a href="#scatterplot_matrix" data-toggle="tab">Scatterplot Matrix</a>
-            </li>
         </ul>
         <div class="tab-content">
             <div class="tab-pane active" id="stats_tab">
@@ -116,19 +113,6 @@
                     <div id="violin_plot"></div>
                 </div>
             </div>
-            <div class="tab-pane" id="scatterplot_matrix">
-                <div class="btn-group scatterplot-btn-div">
-                    <button type="button" class="btn btn-default" id="select_compare_trait">
-                        <i class="icon-th-large"></i> Select Traits
-                    </button>
-                    <button type="button" class="btn btn-default" id="clear_compare_trait">
-                        <i class="icon-trash"></i> Clear
-                    </button>
-                </div>
-                <div id="scatterplot_container">
-                    <div id="comparison_scatterplot" class="qtlcharts"></div>
-                </div>
-            </div>
         </div>
     </div>
     <div id="collections_holder_wrapper" style="display:none;">
diff --git a/wqflask/wqflask/templates/snp_browser.html b/wqflask/wqflask/templates/snp_browser.html
index a96b8e3b..b9aea570 100644
--- a/wqflask/wqflask/templates/snp_browser.html
+++ b/wqflask/wqflask/templates/snp_browser.html
@@ -15,7 +15,7 @@
         <input type="hidden" name="first_run" value="{{ first_run }}">
         <input type="hidden" name="chosen_strains_mouse" value="{{ chosen_strains_mouse|join(",") }}">
         <input type="hidden" name="chosen_strains_rat" value="{{ chosen_strains_rat|join(",") }}">
-        <div class="col-xs-4" style="padding-left: 0px;">
+        <div class="col-xs-4" style="width: 260px; padding-left: 30px; padding-right: 0px;">
           <div class="form-group row" style="margin-bottom: 5px;">
             <label for="snp_or_indel" style="text-align: right;" class="col-xs-4 col-form-label"><b>Type:</b></label>
             <div class="col-xs-8">
@@ -74,7 +74,7 @@
             </div>
           </div>
         </div>
-        <div class="col-xs-4" style="padding-left: 0px;">
+        <div class="col-xs-4" style="width: 310px; padding-left: 0px; padding-right: 20px;">
           <div class="form-group row" style="margin-bottom: 10px;">
             <label for="strains" style="text-align: right;" class="col-xs-4 col-form-label"><b>Strains:</b></label>
             <div class="col-xs-8">
@@ -107,8 +107,14 @@
               </div>
             </div>
           </div>
+          <div class="form-group row">
+            <label class="col-xs-4 col-form-label"></label>
+            <div class="col-xs-8" style="margin-top: 65px;">
+              <input class="btn btn-primary" type="button" name="export_csv" value="Export to CSV">
+            </div>
+          </div>
         </div>
-        <div class="col-xs-4" style="padding-left: 20px;">
+        <div class="col-xs-4" style="width: 310px; padding-left: 20px;">
           <div class="form-group row" style="margin-bottom: 5px;">
             <label for="domain" style="text-align: right;" class="col-xs-4 col-form-label"><b>Domain:</b></label>
             <div class="col-xs-8">
@@ -182,24 +188,21 @@
     </div>
 
     <div style="margin-top: 20px;">
-    {% if filtered_results is defined %}
-    {% if filtered_results|length > limit_number %}
-    There are more than 10000 results. Consider limiting your search to a smaller range.
-    {% else %}
+    {% if table_rows is defined %}
     <table class="dataTable cell-border nowrap" id="results_table" style="float: left;">
       <thead>
         <tr>
           <th></th>
           {% if header_fields|length == 2 %}
           {% for header in header_fields[0] %}
-          <th data-export="{{ header }}">{{ header }}</th>
+          <th data-export="{{ header }}" name="{{ header }}">{{ header }}</th>
           {% endfor %}
           {% for strain in header_fields[1] %}
-          <th data-export="{{ strain }}" style="align: center; text-align: center; line-height: 15px;">{% for letter in strain %}<div style="transform: rotate(90deg);">{{ letter }}</div>{% endfor %}</th>
+          <th data-export="{{ strain }}" name="{{ strain }}" style="align: center; text-align: center; line-height: 12px;">{% for letter in strain|reverse %}<div style="transform: rotate(270deg);">{{ letter }}</div>{% endfor %}</th>
           {% endfor %}
           {% else %}
           {% for header in header_fields %}
-          <th data-export="{{ header }}">{{ header }}</th>
+          <th data-export="{{ header }}" name="{{ header }}">{{ header }}</th>
           {% endfor %}
           {% endif %}
         </tr>
@@ -208,7 +211,6 @@
       <td colspan="100%" align="center"><br><b><font size="15">Loading...</font></b><br></td>
       </tbody>
     </table>
-    {% endif %}
     {% endif %}     
     </div>
   </div>
@@ -222,12 +224,24 @@
   <script language="javascript" type="text/javascript" src="/static/new/javascript/typeahead_rn6.json"></script>
 
   <script type='text/javascript'>
-      var json_rows = {{ table_rows|safe }};
       var empty_columns = {{ empty_columns|safe }};
+
+      var remain_field_count = 15 - {{ empty_field_count|safe }};
+      var total_field_count = 15 - {{ empty_field_count|safe }} + {{ allele_list|safe|length }};
   </script>
 
   <script language="javascript">
 
+    var getParams = function(url) {
+      let parser = document.createElement('a');
+      parser.href = url;
+      let params = parser.search.substring(1);
+      if(params.length > 0) {
+        return ('?'+params);
+      }
+      return params;
+    };
+
     var substringMatcher = function(strs) {
       return function findMatches(q, cb) {
         var matches, substringRegex;
@@ -260,19 +274,20 @@
       source: substringMatcher(rat_genes)
     });
 
-    {% if filtered_results is defined %}
+    {% if table_rows is defined %}
     $("#results_table").DataTable( {
-      'data': json_rows,
       {% if variant_type == "SNP" %}
       'columns': [
         {
           'data': null,
+          'className': 'dt-body-center',
           'orderable': false,
           'render': function(data, type, row, meta) {
-            return '<input type="checkbox" name="trait_check">'
+            return '<input type="checkbox" class="checkbox" id="variant_checkbox" onchange="onVarinatCheck(this)" name="trait_check">'
           }
         }, {
-          'data': 'index'
+          'data': 'index',
+          'className': 'dt-body-right'
         }, {
           'data': null,
           'render': function(data, type, row, meta) {
@@ -283,27 +298,30 @@
             }
           }
         }, {
-          'data': 'chr'
+          'data': 'chr',
+          'className': 'dt-body-center'
         }, {
-          'data': 'mb_formatted'
+          'data': 'mb_formatted',
+          'className': 'dt-body-right'
         }, {
           'data': 'alleles'
         }, {% if empty_columns['snp_source'] == "true" %}{
           'data': null,
           'render': function(data, type, row, meta) {
             if (data.snp_source == "Sanger/UCLA") {
-              return '<a href="' + data.source_urls[0] + '">Sanger</a><a href="' + data.source_urls[1] + '">UCLA</a>'
+              return '<a href="' + data.source_urls[0] + '">Sanger</a>, <a href="' + data.source_urls[1] + '">UCLA</a>'
             } else {
               return data.snp_source
             }
           }
         }, {% endif %} {% if empty_columns['conservation_score'] == "true" %}{
-          'data': 'conservation_score'
+          'data': 'conservation_score',
+          'className': 'dt-body-right'
         }, {% endif %} {% if empty_columns['gene_name'] == "true" %}{
           'data': null,
           'render': function(data, type, row, meta) {
             if (data.gene_name != "") {
-              return '<i>' + data.gene_name + '</i><br><a href="' + data.gene_link + '">NCBI</a>'
+              return '<i>' + data.gene_name + '</i>, <a href="' + data.gene_link + '">NCBI</a>'
             } else {
               return data.gene_name
             }
@@ -330,6 +348,7 @@
         }, {% endif %} {% for item in allele_list %} {
           'data': null,
           'orderable': false,
+          'className': 'dt-body-center',
           'render': function(data, type, row, meta) {
             if (typeof data.allele_value_list[{{ loop.index - 1 }}][0] !== "undefined") {
               return data.allele_value_list[{{ loop.index - 1 }}][0]
@@ -339,12 +358,9 @@
           }
         }{% if loop.index < allele_list|length %},{% endif %}{% endfor %}
       ],
-      'createdRow': function( row, data, dataIndex) {
-        $('td', row).eq(0).attr("style", "text-align: center; padding: 4px 10px 2px 10px;");
-        $('td', row).eq(1).attr("align", "right");
-        for (i = {{ 15 - empty_field_count }}; i < ({{ 15 - empty_field_count }} + {{ allele_list|length }}); i++) {
+      'createdRow': function(row, data, dataIndex) {
+        for (i = remain_field_count; i < total_field_count; i++) {
           var this_allele = $('td', row).eq(i).text();
-          $('td', row).eq(i).attr("style", "text-align: center; padding: 4px 10px 2px 10px;");
           switch (this_allele) {
             case "A":
               $('td', row).eq(i).addClass('A_allele_color');
@@ -380,24 +396,29 @@
         {
           'data': null,
           'render': function(data, type, row, meta) {
-            return '<input type="checkbox" name="trait_check">'
+            return '<input type="checkbox" class="checkbox" id="variant_checkbox" onchange="onVarinatCheck(this)" name="trait_check">'
           }
         }, {
-          'data': 'index'
+          'data': 'index',
+          'className': 'dt-body-right'
         }, {
           'data': 'indel_name'
         }, {
           'data': 'indel_type'
         }, {
-          'data': 'indel_chr'
+          'data': 'indel_chr',
+          'className': 'dt-body-center'
         }, {
-          'data': 'indel_mb_s'
+          'data': 'indel_mb_s',
+          'className': 'dt-body-right'
         }, {
-          'data': 'indel_mb_e'
+          'data': 'indel_mb_e',
+          'className': 'dt-body-right'
         }, {
           'data': 'indel_strand'
         }, {
-          'data': 'indel_size'
+          'data': 'indel_size',
+          'className': 'dt-body-right'
         }, {
           'data': 'indel_sequence'
         }, {
@@ -407,15 +428,28 @@
       {% endif %}
       'order': [[1, "asc" ]],
       'sDom': "rtip",
-      'iDisplayLength': 500,
-      'processing': true,
-      'language': {
-        'loadingRecords': '&nbsp;',
-        'processing': 'Loading...'
+      'iDisplayLength': 100,
+      'bServerSide': true,
+      'sAjaxSource': '/snp_browser_table'+getParams(window.location.href),
+      'infoCallback': function(settings, start, end, max, total, pre) {
+        return "Showing " + start + " to " + (start + this.api().data().length - 1) + " of " + total + " entries";
       }
     });
     {% endif %}
 
+    function onVarinatCheck(checkboxElem) {
+        if (checkboxElem.checked) {
+            if (!checkboxElem.parentElement.parentElement.classList.contains('selected')) {
+                checkboxElem.parentElement.parentElement.classList.add('selected')
+            }
+        }
+        else {
+            if (checkboxElem.parentElement.parentElement.classList.contains('selected')) {
+                checkboxElem.parentElement.parentElement.classList.remove('selected')
+            }
+        }
+    }
+
     $("#species_select").change(function() {
         this_species = $(this).val();
         $("#strain_select").empty()
@@ -509,6 +543,40 @@
       });
       $("input[name=chosen_strains]").val(strain_list.join(","));
     });
+
+    
+
+    $("input[name=export_csv]").click(function() {
+      var csv = [];
+      var rows = document.querySelectorAll("table tr");
+
+      var headers = [];
+      var col_header = rows[0].querySelectorAll("th");
+      for(let i = 1; i < col_header.length; i++) {
+        headers.push(col_header[i].getAttribute("name"));
+      }
+      csv.push(headers.join(","));
+
+      for (let i = 1; i < rows.length; i++) {
+        var row = [], cols = rows[i].querySelectorAll("td");
+        var checkBox = rows[i].querySelector("input");
+
+        if(checkBox.checked == true) {
+          for (let j = 1; j < cols.length; j++)
+            row.push(cols[j].innerText);
+
+            csv.push(row.join(","));
+        }
+      }
+
+      var csvFile = new Blob([csv.join("\n")], {type: "text/csv"});
+      var downloadLink = document.createElement("a");
+      downloadLink.download = "variant_data.csv";
+      downloadLink.href = window.URL.createObjectURL(csvFile);
+      downloadLink.style.display = "none";
+      document.body.appendChild(downloadLink);
+      downloadLink.click();
+    });
   </script>
 {% endblock %}
 
diff --git a/wqflask/wqflask/user_login.py b/wqflask/wqflask/user_login.py
index f25ebc32..041f1f11 100644
--- a/wqflask/wqflask/user_login.py
+++ b/wqflask/wqflask/user_login.py
@@ -25,7 +25,7 @@ from utility.logger import getLogger
 logger = getLogger(__name__)
 
 from smtplib import SMTP
-from utility.tools import SMTP_CONNECT, SMTP_USERNAME, SMTP_PASSWORD, LOG_SQL_ALCHEMY
+from utility.tools import SMTP_CONNECT, SMTP_USERNAME, SMTP_PASSWORD, LOG_SQL_ALCHEMY, GN2_BRANCH_URL
 
 THREE_DAYS = 60 * 60 * 24 * 3
 
@@ -39,8 +39,12 @@ def basic_info():
 
 
 def encode_password(pass_gen_fields, unencrypted_password):
+    if isinstance(pass_gen_fields['salt'], bytes):
+        salt = pass_gen_fields['salt']
+    else:
+        salt = bytes(pass_gen_fields['salt'], "utf-8")
     encrypted_password = pbkdf2.pbkdf2_hex(str(unencrypted_password), 
-                                           pass_gen_fields['salt'], 
+                                           salt,
                                            pass_gen_fields['iterations'], 
                                            pass_gen_fields['keylength'], 
                                            pass_gen_fields['hashfunc'])
@@ -239,7 +243,7 @@ def github_oauth2():
     }
 
     result = requests.post("https://github.com/login/oauth/access_token", json=data)
-    result_dict = {arr[0]:arr[1] for arr in [tok.split("=") for tok in [token.encode("utf-8") for token in result.text.split("&")]]}
+    result_dict = {arr[0]:arr[1] for arr in [tok.split("=") for tok in result.text.split("&")]}
 
     github_user = get_github_user_details(result_dict["access_token"])
 
@@ -277,9 +281,11 @@ def orcid_oauth2():
         data = {
             "client_id": ORCID_CLIENT_ID, 
             "client_secret": ORCID_CLIENT_SECRET, 
-            "grant_type": "authorization_code", 
+            "grant_type": "authorization_code",
+            "redirect_uri": GN2_BRANCH_URL + "n/login/orcid_oauth2",
             "code": code
         }
+
         result = requests.post(ORCID_TOKEN_URL, data=data)
         result_dict = json.loads(result.text.encode("utf-8"))
 
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 25563e86..e4834d53 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -26,6 +26,15 @@ 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 import server_side
 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
@@ -220,6 +229,26 @@ def search_page():
     else:
         return render_template("search_error.html")
 
+@app.route("/search_table", methods=('GET',))
+def search_page_table():
+    logger.info("in search_page table")
+    logger.info(request.url)
+
+    logger.info("request.args is", request.args)
+    the_search = search_results.SearchResultPage(request.args)
+
+    logger.info(type(the_search.trait_list))
+    logger.info(the_search.trait_list)
+    
+    current_page = server_side.ServerSideTable(
+        len(the_search.trait_list),
+        the_search.trait_list,
+        the_search.header_data_names,
+        request.args,
+    ).get_page()
+
+    return flask.jsonify(current_page)
+
 @app.route("/gsearch", methods=('GET',))
 def gsearchact():
     logger.info(request.url)
@@ -621,12 +650,13 @@ def loading_page():
         wanted = initial_start_vars['wanted_inputs'].split(",")
         start_vars = {}
         for key, value in list(initial_start_vars.items()):
-            if key in wanted or key.startswith(('value:')):
+            if key in wanted:
                 start_vars[key] = value
 
         if 'n_samples' in start_vars:
             n_samples = int(start_vars['n_samples'])
         else:
+            sample_vals_dict = json.loads(start_vars['sample_vals'])
             if 'group' in start_vars:
                 dataset = create_dataset(start_vars['dataset'], group_name = start_vars['group'])
             else:
@@ -642,9 +672,9 @@ def loading_page():
                         samples = genofile_samples
 
             for sample in samples:
-                value = start_vars.get('value:' + sample)
-                if value != "x":
-                    n_samples += 1
+                if sample in sample_vals_dict:
+                    if sample_vals_dict[sample] != "x":
+                        n_samples += 1
 
         start_vars['n_samples'] = n_samples
         start_vars['wanted_inputs'] = initial_start_vars['wanted_inputs']
@@ -660,7 +690,6 @@ def loading_page():
 @app.route("/run_mapping", methods=('POST',))
 def mapping_results_page():
     initial_start_vars = request.form
-    #logger.debug("Mapping called with initial_start_vars:", initial_start_vars.items())
     logger.info(request.url)
     temp_uuid = initial_start_vars['temp_uuid']
     wanted = (
@@ -670,6 +699,7 @@ def mapping_results_page():
         'species',
         'samples',
         'vals',
+        'sample_vals',
         'first_run',
         'output_files',
         'geno_db_exists',
@@ -723,13 +753,11 @@ def mapping_results_page():
     )
     start_vars = {}
     for key, value in list(initial_start_vars.items()):
-        if key in wanted or key.startswith(('value:')):
+        if key in wanted:
             start_vars[key] = value
-    #logger.debug("Mapping called with start_vars:", start_vars)
 
     version = "v3"
     key = "mapping_results:{}:".format(version) + json.dumps(start_vars, sort_keys=True)
-    #logger.info("key is:", pf(key))
     with Bench("Loading cache"):
         result = None # Just for testing
         #result = Redis.get(key)
@@ -751,10 +779,9 @@ def mapping_results_page():
                     rendered_template = render_template("mapping_error.html")
                     return rendered_template
             except:
-                rendered_template = render_template("mapping_error.html")
-                return rendered_template
+               rendered_template = render_template("mapping_error.html")
+               return rendered_template
 
-            #if template_vars.mapping_method != "gemma" and template_vars.mapping_method != "plink":
             template_vars.js_data = json.dumps(template_vars.js_data,
                                                     default=json_default_handler,
                                                     indent="   ")
@@ -775,10 +802,6 @@ def mapping_results_page():
                     rendered_template = render_template("pair_scan_results.html", **result)
             else:
                 gn1_template_vars = display_mapping_results.DisplayMappingResults(result).__dict__
-                #pickled_result = pickle.dumps(result, pickle.HIGHEST_PROTOCOL)
-                #logger.info("pickled result length:", len(pickled_result))
-                #Redis.set(key, pickled_result)
-                #Redis.expire(key, 1*60)
 
                 with Bench("Rendering template"):
                     #if (gn1_template_vars['mapping_method'] == "gemma") or (gn1_template_vars['mapping_method'] == "plink"):
@@ -896,6 +919,19 @@ def db_info_page():
 
     return render_template("info_page.html", **template_vars.__dict__)
 
+@app.route("/snp_browser_table", methods=('GET',))
+def snp_browser_table():
+    logger.info(request.url)
+    snp_table_data = snp_browser.SnpBrowser(request.args)
+    current_page = server_side.ServerSideTable(
+        snp_table_data.rows_count,
+        snp_table_data.table_rows,
+        snp_table_data.header_data_names,
+        request.args,
+    ).get_page()
+
+    return flask.jsonify(current_page)
+
 @app.route("/tutorial/WebQTLTour", methods=('GET',))
 def tutorial_page():
     #ZS: Currently just links to GN1