Merge branch 'testing' into build/python3-migration

23 files changed, 539 insertions, 217 deletions

diff --git a/test/requests/link_checker.py b/test/requests/link_checker.py
index fa70747d..5e16a5cd 100644
--- a/test/requests/link_checker.py
+++ b/test/requests/link_checker.py
@@ -76,3 +76,26 @@ def check_links(args_obj, parser):
     check_page(
         host,
         host+"/show_trait?trait_id=1435395_s_at&dataset=HC_M2_0606_P")
+
+
+def check_packaged_js_files(args_obj, parser):
+    host = args_obj.host
+    js_files = [
+        # Datatables Extensions:
+        "/DataTablesExtensions/buttonsBootstrap/css/buttons.bootstrap.css",
+        "/DataTablesExtensions/buttons/js/dataTables.buttons.min.js",
+        "/DataTablesExtensions/buttonStyles/css/buttons.dataTables.min.css",
+        "/DataTablesExtensions/buttons/js/dataTables.buttons.min.js",
+        "/DataTablesExtensions/colResize/dataTables.colResize.js",
+        "/DataTablesExtensions/colReorder/js/dataTables.colReorder.js",
+        "/DataTablesExtensions/buttons/js/buttons.colVis.min.js",
+        "/DataTables/js/jquery.dataTables.js",
+        "/DataTablesExtensions/scroller/css/scroller.dataTables.min.css",
+        # Datatables plugins:
+        "/DataTablesExtensions/plugins/sorting/natural.js",
+        "/DataTablesExtensions/plugins/sorting/scientific.js",
+    ]
+
+    print("Checking links")
+    for link in js_files:
+        verify_link(host+link)
diff --git a/test/requests/test-website.py b/test/requests/test-website.py
index 74057e7f..f90d1843 100755
--- a/test/requests/test-website.py
+++ b/test/requests/test-website.py
@@ -6,6 +6,7 @@
 from __future__ import print_function
 import argparse
 from link_checker import check_links
+from link_checker import check_packaged_js_files
 from mapping_tests import check_mapping
 from navigation_tests import check_navigation
 from main_web_functionality import check_main_web_functionality
@@ -30,6 +31,7 @@ def run_all(args_obj, parser):
     link_checker.DO_FAIL = args_obj.fail
     check_main_web_functionality(args_obj, parser)
     check_links(args_obj, parser)
+    check_packaged_js_files(args_obj, parser)
     check_mapping(args_obj, parser)
     # TODO: Add other functions as they are created.
 
diff --git a/wqflask/tests/wqflask/api/test_gen_menu.py b/wqflask/tests/wqflask/api/test_gen_menu.py
index 79c77fec..239484aa 100644
--- a/wqflask/tests/wqflask/api/test_gen_menu.py
+++ b/wqflask/tests/wqflask/api/test_gen_menu.py
@@ -255,9 +255,9 @@ class TestGenMenu(unittest.TestCase):
             ('Mouse Tissue'), ('Human Tissue'), ('Rat Tissue')
         )
         self.assertEqual(build_types('mouse', 'random group'),
-                         [['M', 'M', 'Molecular Trait Datasets'],
-                          ['H', 'H', 'Molecular Trait Datasets'],
-                          ['R', 'R', 'Molecular Trait Datasets']])
+                         [['M', 'M', 'Molecular Traits'],
+                          ['H', 'H', 'Molecular Traits'],
+                          ['R', 'R', 'Molecular Traits']])
         db_mock.db.execute.assert_called_once_with(
             "SELECT DISTINCT Tissue.Name " +
             "FROM ProbeFreeze, ProbeSetFreeze, InbredSet, " +
diff --git a/wqflask/tests/wqflask/marker_regression/test_display_mapping_results.py b/wqflask/tests/wqflask/marker_regression/test_display_mapping_results.py
new file mode 100644
index 00000000..6f791df1
--- /dev/null
+++ b/wqflask/tests/wqflask/marker_regression/test_display_mapping_results.py
@@ -0,0 +1,151 @@
+import unittest
+
+from htmlgen import HTMLgen2 as HT
+from wqflask.marker_regression.display_mapping_results import (
+    DisplayMappingResults,
+    HtmlGenWrapper
+)
+
+
+class TestDisplayMappingResults(unittest.TestCase):
+    """Basic Methods to test Mapping Results"""
+    def test_pil_colors(self):
+        """Test that colors use PILLOW color format"""
+        self.assertEqual(DisplayMappingResults.CLICKABLE_WEBQTL_REGION_COLOR,
+                         (245, 211, 211))
+
+
+class TestHtmlGenWrapper(unittest.TestCase):
+    """Test Wrapper around HTMLGen"""
+    def test_create_image(self):
+        """Test HT.Image method"""
+        self.assertEqual(
+            str(HtmlGenWrapper.create_image_tag(src="test.png",
+                                                alt="random",
+                                                border="0",
+                                                width="10",
+                                                height="13",
+                                                usemap="#webqtlmap")),
+            ("""<IMG src="test.png" height="13" width="10" """
+             """alt="random" border="0" """
+             """usemap="#webqtlmap">""")
+        )
+
+    def test_create_form(self):
+        """Test HT.Form method"""
+        test_form = HtmlGenWrapper.create_form_tag(
+            cgi="/testing/",
+            enctype='multipart/form-data',
+            name="formName",
+            submit=HT.Input(type='hidden')
+        )
+        test_image = HtmlGenWrapper.create_image_tag(
+            src="test.png",
+            alt="random",
+            border="0",
+            width="10",
+            height="13",
+            usemap="#webqtlmap"
+        )
+        self.assertEqual(
+            str(test_form).replace("\n", ""),
+            ("""<FORM METHOD="POST" ACTION="/testing/" """
+             """ENCTYPE="multipart/form-data" """
+             """NAME="formName"><INPUT TYPE="hidden" """
+             """NAME="Default_Name"></FORM>"""))
+        hddn = {
+            'FormID': 'showDatabase',
+            'ProbeSetID': '_',
+            'database': "TestGeno",
+            'CellID': '_',
+            'RISet': "Test",
+            'incparentsf1': 'ON'
+        }
+        for key in hddn.keys():
+            test_form.append(HT.Input(name=key, value=hddn[key],
+                                      type='hidden'))
+        test_form.append(test_image)
+        self.assertEqual(str(test_form).replace("\n", ""), (
+            """<FORM METHOD="POST" ACTION="/testing/" """
+            """ENCTYPE="multipart/form-data" NAME="formName">"""
+            """<INPUT TYPE="hidden" NAME="database" VALUE="TestGeno">"""
+            """<INPUT TYPE="hidden" NAME="incparentsf1" VALUE="ON">"""
+            """<INPUT TYPE="hidden" NAME="FormID" VALUE="showDatabase">"""
+            """<INPUT TYPE="hidden" NAME="ProbeSetID" VALUE="_">"""
+            """<INPUT TYPE="hidden" NAME="RISet" VALUE="Test">"""
+            """<INPUT TYPE="hidden" NAME="CellID" VALUE="_">"""
+            """<IMG src="test.png" height="13" width="10" alt="random" """
+            """border="0" usemap="#webqtlmap">"""
+            """<INPUT TYPE="hidden" NAME="Default_Name"></FORM>"""))
+
+    def test_create_paragraph(self):
+        """Test HT.Paragraph method"""
+        test_p_element = HtmlGenWrapper.create_p_tag(id="smallSize")
+        par_text = (
+            "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."
+        )
+        self.assertEqual(
+            str(test_p_element),
+            """<P id="smallSize"></P>"""
+        )
+        test_p_element.append(HT.BR())
+        test_p_element.append(par_text)
+        self.assertEqual(
+            str(test_p_element),
+            """<P id="smallSize"><BR>{}</P>""".format(par_text)
+        )
+
+    def test_create_br_tag(self):
+        """Test HT.BR() method"""
+        self.assertEqual(str(HtmlGenWrapper.create_br_tag()),
+                         "<BR>")
+
+    def test_create_input_tag(self):
+        """Test HT.Input method"""
+        self.assertEqual(
+            str(HtmlGenWrapper.create_input_tag(
+                type="hidden",
+                name="name",
+                value="key",
+                Class="trait trait_")).replace("\n", ""),
+            ("""<INPUT TYPE="hidden" NAME="name" """
+             """class="trait trait_" VALUE="key">"""))
+
+    def test_create_map_tag(self):
+        """Test HT.Map method"""
+        self.assertEqual(str(HtmlGenWrapper.create_map_tag(
+            name="WebqTLImageMap")).replace("\n", ""),
+            """<MAP NAME="WebqTLImageMap"></MAP>""")
+        gifmap = HtmlGenWrapper.create_map_tag(areas=[])
+        gifmap.areas.append(HT.Area(shape="rect",
+                                    coords='1 2 3', href='#area1'))
+        gifmap.areas.append(HT.Area(shape="rect",
+                                    coords='1 2 3', href='#area2'))
+        self.assertEqual(
+            str(gifmap).replace("\n", ""),
+            ("""<MAP NAME="">"""
+             """<AREA coords="1 2 3" """
+             """href="#area1" shape="rect">"""
+             """<AREA coords="1 2 3" href="#area2" shape="rect">"""
+             """</MAP>"""))
+
+    def test_create_area_tag(self):
+        """Test HT.Area method"""
+        self.assertEqual(
+            str(HtmlGenWrapper.create_area_tag(
+                shape="rect",
+                coords="1 2",
+                href="http://test.com",
+                title="Some Title")).replace("\n", ""),
+            ("""<AREA coords="1 2" href="http://test.com" """
+             """shape="rect" title="Some Title">"""))
+
+    def test_create_link_tag(self):
+        """Test HT.HREF method"""
+        self.assertEqual(
+            str(HtmlGenWrapper.create_link_tag(
+                "www.test.com", "test", target="_blank")).replace("\n", ""),
+            """<A HREF="www.test.com" TARGET="_blank">test</A>""")
diff --git a/wqflask/tests/wqflask/marker_regression/test_display_marking_results.py b/wqflask/tests/wqflask/marker_regression/test_display_marking_results.py
deleted file mode 100644
index 67da508b..00000000
--- a/wqflask/tests/wqflask/marker_regression/test_display_marking_results.py
+++ /dev/null
@@ -1,9 +0,0 @@
-import unittest
-
-from wqflask.marker_regression.display_mapping_results import DisplayMappingResults
-
-class TestDisplayMappingResults(unittest.TestCase):
-    def test_pil_colors(self):
-        """Test that colors use PILLOW color format"""
-        self.assertEqual(DisplayMappingResults.CLICKABLE_WEBQTL_REGION_COLOR,
-                         (245, 211, 211))
diff --git a/wqflask/utility/Plot.py b/wqflask/utility/Plot.py
index 4f6e694e..7d9d7649 100644
--- a/wqflask/utility/Plot.py
+++ b/wqflask/utility/Plot.py
@@ -26,16 +26,12 @@
 
 from __future__ import print_function
 
-from PIL import (Image, ImageColor, ImageDraw, ImageFont)
-from pprint import pformat as pf
+from PIL import ImageColor
+from PIL import ImageDraw
+from PIL import ImageFont
 
 from math import *
-import random
-import sys, os
-from numarray import linear_algebra as la
-from numarray import ones, array, dot, swapaxes
 
-import webqtlUtil
 import corestats
 from base import webqtlConfig
 from utility.pillow_utils import draw_rotated_text
diff --git a/wqflask/utility/pillow_utils.py b/wqflask/utility/pillow_utils.py
index 1e2ed075..c486abba 100644
--- a/wqflask/utility/pillow_utils.py
+++ b/wqflask/utility/pillow_utils.py
@@ -1,5 +1,7 @@
 from PIL import Image, ImageColor, ImageDraw, ImageFont
 
+from utility.tools import TEMPDIR
+
 import utility.logger
 logger = utility.logger.getLogger(__name__ )
 
@@ -14,7 +16,7 @@ def draw_rotated_text(canvas, text, font, xy, fill=BLACK, angle=-90):
     draw_text = ImageDraw.Draw(tmp_img)
     draw_text.text(text=text, xy=(0, 0), font=font, fill=fill)
     tmp_img2 = tmp_img.rotate(angle, expand=1)
-    tmp_img2.save("/tmp/{}.png".format(text), format="png")
+    tmp_img2.save("/{0}/{1}.png".format(TEMPDIR, text), format="png")
     canvas.paste(im=tmp_img2, box=tuple([int(i) for i in xy]))
 
 # def draw_open_polygon(canvas: Image, xy: tuple, fill: ImageColor=WHITE, outline: ImageColor=BLACK):
diff --git a/wqflask/wqflask/api/gen_menu.py b/wqflask/wqflask/api/gen_menu.py
index 71d9ee03..41966f78 100644
--- a/wqflask/wqflask/api/gen_menu.py
+++ b/wqflask/wqflask/api/gen_menu.py
@@ -128,7 +128,7 @@ def build_types(species, group):
             these_datasets = build_datasets(species, group, result[0])
             if len(these_datasets) > 0:
                 results.append([str(result[0]), str(result[0]),
-                                "Molecular Trait Datasets"])
+                                "Molecular Traits"])
 
     return results
 
diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py
index f06db5d5..255e3b74 100644
--- a/wqflask/wqflask/marker_regression/display_mapping_results.py
+++ b/wqflask/wqflask/marker_regression/display_mapping_results.py
@@ -24,13 +24,13 @@
 #
 # Last updated by Zach 12/14/2010
 
-import datetime
 import string
 from math import *
-from PIL import (Image, ImageDraw, ImageFont, ImageColor)
-import sys, os
-import pickle
-import http.client
+from PIL import Image
+from PIL import ImageDraw
+from PIL import ImageFont
+from PIL import ImageColor
+import os
 import json
 
 from flask import Flask, g
@@ -40,11 +40,10 @@ from htmlgen import HTMLgen2 as HT
 from base import webqtlConfig
 from base.GeneralObject import GeneralObject
 from utility import webqtlUtil
-from utility import helper_functions
 from utility import Plot
 from utility.benchmark import Bench
 from wqflask.interval_analyst import GeneUtil
-from base.webqtlConfig import TMPDIR, GENERATED_TEXT_DIR, GENERATED_IMAGE_DIR
+from base.webqtlConfig import GENERATED_IMAGE_DIR
 from utility.pillow_utils import draw_rotated_text, draw_open_polygon
 
 import utility.logger
@@ -84,22 +83,53 @@ ARIAL_FILE = "./wqflask/static/fonts/arial.ttf"
 
 assert(os.path.isfile(VERDANA_FILE))
 
-# ---- END: FONT FILES ---- #
 
-#########################################
-#      Inteval Mapping Plot Page
-#########################################
+class HtmlGenWrapper:
+    """Wrapper Methods for HTML gen"""
+    @staticmethod
+    def create_image_tag(**kwargs):
+        return HT.Image(**kwargs)
+
+    @staticmethod
+    def create_form_tag(**kwargs):
+        return HT.Form(**kwargs)
+
+    @staticmethod
+    def create_p_tag(**kwargs):
+        return HT.Paragraph(**kwargs)
+
+    @staticmethod
+    def create_br_tag():
+        return HT.BR()
+
+    @staticmethod
+    def create_input_tag(**kwargs):
+        return HT.Input(**kwargs)
+
+    @staticmethod
+    def create_area_tag(**kwargs):
+        return HT.Area(**kwargs)
+
+    @staticmethod
+    def create_link_tag(href, content, **kwargs):
+        return HT.Href(href, content, **kwargs)
+
+    @staticmethod
+    def create_map_tag(**kwargs):
+        return HT.Map(**kwargs)
+
+
 class DisplayMappingResults(object):
+    """Inteval Mapping Plot Page"""
     cMGraphInterval = 5
     GRAPH_MIN_WIDTH = 900
-    GRAPH_MAX_WIDTH = 10000 # Don't set this too high
+    GRAPH_MAX_WIDTH = 10000  # Don't set this too high
     GRAPH_DEFAULT_WIDTH = 1280
     MULT_GRAPH_DEFAULT_WIDTH = 2000
     MULT_GRAPH_MIN_WIDTH = 1400
     MULT_GRAPH_DEFAULT_WIDTH = 1600
     GRAPH_DEFAULT_HEIGHT = 600
 
-
     # Display order:
     # UCSC BAND =========
     # ENSEMBL BAND -=-=-=
@@ -110,22 +140,27 @@ class DisplayMappingResults(object):
     BAND_HEIGHT = 10
     BAND_HEIGHT = 10
 
-    NUM_GENE_ROWS       = 10
-    EACH_GENE_HEIGHT    = 6  # number of pixels tall, for each gene to display
+    NUM_GENE_ROWS = 10
+    EACH_GENE_HEIGHT = 6  # number of pixels tall, for each gene to display
     EACH_GENE_ARROW_WIDTH = 5
     EACH_GENE_ARROW_SPACING = 14
     DRAW_DETAIL_MB = 4
     DRAW_UTR_LABELS_MB = 4
 
-    qmarkImg = HT.Image('/images/qmarkBoxBlue.gif', width=10, height=13, border=0, alt='Glossary')
-    # Note that "qmark.gif" is a similar, smaller, rounded-edges question mark. It doesn't look
-    # like the ones on the image, though, which is why we don't use it here.
+    qmarkImg = HtmlGenWrapper.create_image_tag(
+        src='/images/qmarkBoxBlue.gif',
+        width="10", height="13", border="0", alt='Glossary'
+    )
+
+    # Note that "qmark.gif" is a similar, smaller, rounded-edges
+    # question mark. It doesn't look like the ones on the image,
+    # though, which is why we don't use it here.
 
     HELP_WINDOW_NAME = 'helpWind'
 
-    ## BEGIN HaplotypeAnalyst
+    # BEGIN HaplotypeAnalyst
     NR_INDIVIDUALS = 0
-    ## END HaplotypeAnalyst
+    # END HaplotypeAnalyst
 
     ALEX_DEBUG_BOOL_PRINT_GENE_LIST = 1
 
@@ -133,13 +168,13 @@ class DisplayMappingResults(object):
 
     LODFACTOR = 4.61
 
-    SNP_COLOR           = ORANGE # Color for the SNP "seismograph"
+    SNP_COLOR = ORANGE  # Color for the SNP "seismograph"
     TRANSCRIPT_LOCATION_COLOR = MEDIUMPURPLE
 
     BOOTSTRAP_BOX_COLOR = YELLOW
-    LRS_COLOR           = ImageColor.getrgb("#0000FF")
-    SIGNIFICANT_COLOR   = ImageColor.getrgb("#EBC7C7")
-    SUGGESTIVE_COLOR    = GAINSBORO
+    LRS_COLOR = ImageColor.getrgb("#0000FF")
+    SIGNIFICANT_COLOR = ImageColor.getrgb("#EBC7C7")
+    SUGGESTIVE_COLOR = GAINSBORO
     SIGNIFICANT_WIDTH = 5
     SUGGESTIVE_WIDTH = 5
     ADDITIVE_COLOR_POSITIVE = GREEN
@@ -147,33 +182,33 @@ class DisplayMappingResults(object):
     DOMINANCE_COLOR_POSITIVE = DARKVIOLET
     DOMINANCE_COLOR_NEGATIVE = RED
 
-    ## BEGIN HaplotypeAnalyst
+    # BEGIN HaplotypeAnalyst
     HAPLOTYPE_POSITIVE = GREEN
     HAPLOTYPE_NEGATIVE = RED
     HAPLOTYPE_HETEROZYGOUS = BLUE
     HAPLOTYPE_RECOMBINATION = DARKGRAY
-    ## END HaplotypeAnalyst
+    # END HaplotypeAnalyst
 
     TOP_RIGHT_INFO_COLOR = BLACK
 
-    CLICKABLE_WEBQTL_REGION_COLOR     = ImageColor.getrgb("#F5D3D3")
+    CLICKABLE_WEBQTL_REGION_COLOR = ImageColor.getrgb("#F5D3D3")
     CLICKABLE_WEBQTL_REGION_OUTLINE_COLOR = ImageColor.getrgb("#FCE9E9")
-    CLICKABLE_WEBQTL_TEXT_COLOR       = ImageColor.getrgb("#912828")
+    CLICKABLE_WEBQTL_TEXT_COLOR = ImageColor.getrgb("#912828")
 
-    CLICKABLE_PHENOGEN_REGION_COLOR   = ImageColor.getrgb("#A2FB94")
+    CLICKABLE_PHENOGEN_REGION_COLOR = ImageColor.getrgb("#A2FB94")
     CLICKABLE_PHENOGEN_REGION_OUTLINE_COLOR = ImageColor.getrgb("#CEFEC7")
-    CLICKABLE_PHENOGEN_TEXT_COLOR     = ImageColor.getrgb("#1FD504")
+    CLICKABLE_PHENOGEN_TEXT_COLOR = ImageColor.getrgb("#1FD504")
 
-    CLICKABLE_UCSC_REGION_COLOR     = ImageColor.getrgb("#DDDDEE")
+    CLICKABLE_UCSC_REGION_COLOR = ImageColor.getrgb("#DDDDEE")
     CLICKABLE_UCSC_REGION_OUTLINE_COLOR = ImageColor.getrgb("#EDEDFF")
-    CLICKABLE_UCSC_TEXT_COLOR       = ImageColor.getrgb("#333366")
+    CLICKABLE_UCSC_TEXT_COLOR = ImageColor.getrgb("#333366")
 
-    CLICKABLE_ENSEMBL_REGION_COLOR  = ImageColor.getrgb("#EEEEDD")
+    CLICKABLE_ENSEMBL_REGION_COLOR = ImageColor.getrgb("#EEEEDD")
     CLICKABLE_ENSEMBL_REGION_OUTLINE_COLOR = ImageColor.getrgb("#FEFEEE")
-    CLICKABLE_ENSEMBL_TEXT_COLOR    = ImageColor.getrgb("#555500")
+    CLICKABLE_ENSEMBL_TEXT_COLOR = ImageColor.getrgb("#555500")
 
     GRAPH_BACK_LIGHT_COLOR = ImageColor.getrgb("#FBFBFF")
-    GRAPH_BACK_DARK_COLOR  = ImageColor.getrgb("#F1F1F9")
+    GRAPH_BACK_DARK_COLOR = ImageColor.getrgb("#F1F1F9")
 
     HELP_PAGE_REF = '/glossary.html'
 
@@ -200,7 +235,8 @@ class DisplayMappingResults(object):
             self.temp_trait = "True"
             self.group = start_vars['group']
 
-        #Needing for form submission when doing single chr mapping or remapping after changing options
+        # 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.transform = start_vars['transform']
@@ -211,9 +247,9 @@ class DisplayMappingResults(object):
             self.mapmodel_rqtl_geno = start_vars['model']
             self.pair_scan = start_vars['pair_scan']
 
-        #if self.mapping_method != "gemma" and self.mapping_method != "plink":
         self.js_data = start_vars['js_data']
-        self.trimmed_markers = start_vars['trimmed_markers'] #Top markers to display in table
+        # Top markers to display in table
+        self.trimmed_markers = start_vars['trimmed_markers']
 
         if self.dataset.group.species == "rat":
             self._ucscDb = "rn6"
@@ -225,7 +261,7 @@ class DisplayMappingResults(object):
         #####################################
         # Options
         #####################################
-        #Mapping options
+        # Mapping options
         if start_vars['mapping_scale'] != "":
             self.plotScale = start_vars['mapping_scale']
         else:
@@ -514,7 +550,11 @@ class DisplayMappingResults(object):
             "{}.png".format(
                 os.path.join(webqtlConfig.GENERATED_IMAGE_DIR, self.filename)),
             format='png')
-        intImg=HT.Image('/image/'+self.filename+'.png', border=0, usemap='#WebQTLImageMap')
+        intImg = HtmlGenWrapper.create_image_tag(
+            src="/image/{}.png".format(self.filename),
+            border="0", usemap='#WebQTLImageMap'
+        )
+        self.intImg = intImg
 
         #Scales plot differently for high resolution
         if self.draw2X:
@@ -531,11 +571,16 @@ class DisplayMappingResults(object):
         ################################################################
         #this form is used for opening Locus page or trait page, only available for genetic mapping
         if showLocusForm:
-            showLocusForm = HT.Form(cgi= os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), enctype='multipart/form-data',
-                name=showLocusForm, submit=HT.Input(type='hidden'))
+            showLocusForm = HtmlGenWrapper.create_form_tag(
+                cgi=os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE),
+                enctype='multipart/form-data',
+                name=showLocusForm,
+                submit=HtmlGenWrapper.create_input_tag(type='hidden'))
+
             hddn = {'FormID':'showDatabase', 'ProbeSetID':'_','database':fd.RISet+"Geno",'CellID':'_', 'RISet':fd.RISet, 'incparentsf1':'ON'}
-            for key in list(hddn.keys()):
-                showLocusForm.append(HT.Input(name=key, value=hddn[key], type='hidden'))
+            for key in hddn.keys():
+                showLocusForm.append(HtmlGenWrapper.create_input_tag(
+                    name=key, value=hddn[key], type='hidden'))
             showLocusForm.append(intImg)
         else:
             showLocusForm = intImg
@@ -546,10 +591,12 @@ class DisplayMappingResults(object):
         ################################################################
         # footnote goes here
         ################################################################
-        btminfo = HT.Paragraph(Id="smallsize") #Small('More information about this graph is available here.')
+        # Small('More information about this graph is available here.')
+        btminfo = HtmlGenWrapper.create_p_tag(id="smallsize")
 
         if self.traitList and self.traitList[0].dataset and self.traitList[0].dataset.type == 'Geno':
-            btminfo.append(HT.BR(), '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.')
+            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 = ""):
         im_drawer = ImageDraw.Draw(canvas)
@@ -605,8 +652,8 @@ class DisplayMappingResults(object):
         if zoom == 2:
             drawAreaHeight -= 60
 
-        #Image map
-        gifmap = HT.Map(name = "WebQTLImageMap")
+        # Image map
+        gifmap = HtmlGenWrapper.create_map_tag(name="WebQTLImageMap")
 
         newoffset = (xLeftOffset, xRightOffset, yTopOffset, yBottomOffset)
         # Draw the alternating-color background first and get plotXScale
@@ -954,8 +1001,8 @@ class DisplayMappingResults(object):
             if thisTrait.db:
                 COORDS = "%d,%d,%d,%d" %(rectWidth+2+rightShift, yPaddingTop+kstep*15, rectWidth+2+rightShift+nameWidth, yPaddingTop+10+kstep*15,)
                 HREF= "javascript:showDatabase3('%s','%s','%s','');" % (showLocusForm, thisTrait.db.name, thisTrait.name)
-                Areas = HT.Area(shape='rect', coords=COORDS, href=HREF)
-                gifmap.areas.append(Areas)
+                Areas = HtmlGenWrapper.create_area_tag(shape='rect', coords=COORDS, href=HREF)
+                gifmap.areas.append(Areas) ### TODO
 
     def drawLegendPanel(self, canvas, offset= (40, 120, 80, 10), zoom = 1):
         im_drawer = ImageDraw.Draw(canvas)
@@ -1357,7 +1404,13 @@ class DisplayMappingResults(object):
 
             COORDS = "%d, %d, %d, %d" %(geneStartPix, geneYLocation, geneEndPix, (geneYLocation + self.EACH_GENE_HEIGHT))
             # NL: 06-02-2011 Rob required to display NCBI info in a new window
-            gifmap.areas.append(HT.Area(shape='rect', coords=COORDS, href=HREF, title=TITLE, target="_blank"))
+            gifmap.areas.append(
+                HtmlGenWrapper.create_area_tag(
+                    shape='rect',
+                    coords=COORDS,
+                    href=HREF,
+                    title=TITLE,
+                    target="_blank"))
 
 ## BEGIN HaplotypeAnalyst
     def drawHaplotypeBand(self, canvas, gifmap, plotXScale, offset= (40, 120, 80, 10), zoom = 1, startMb = None, endMb = None):
@@ -1389,6 +1442,8 @@ class DisplayMappingResults(object):
         #Initializing plotRight, error before
         plotRight = xRightOffset
 
+        im_drawer = ImageDraw.Draw(canvas)
+
 #### find out PlotRight
         for _chr in self.genotype:
             if _chr.name == self.ChrList[self.selectedChr][0]:
@@ -1523,7 +1578,12 @@ class DisplayMappingResults(object):
                                     COORDS = "%d, %d, %d, %d" %(geneStartPix, geneYLocation+ind*self.EACH_GENE_HEIGHT, geneEndPix+1, (geneYLocation + ind*self.EACH_GENE_HEIGHT))
                                     TITLE = "Strain: %s, marker (%s) \n Position  %2.3f Mb." % (samplelist[k], _chr[j].name, float(txStart))
                                     HREF = ''
-                                    gifmap.areas.append(HT.Area(shape='rect', coords=COORDS, href=HREF, title=TITLE))
+                                    gifmap.areas.append(
+                                        HtmlGenWrapper.create_area_tag(
+                                            shape='rect',
+                                            coords=COORDS,
+                                            href=HREF,
+                                            title=TITLE))
 
                                     # if there are no more markers in a chromosome, the plotRight value calculated above will be before the plotWidth
                                     # resulting in some empty space on the right side of the plot area. This draws an "unknown" bar from plotRight to the edge.
@@ -1642,7 +1702,12 @@ class DisplayMappingResults(object):
                 WEBQTL_HREF = "javascript:rangeView('%s', %f, %f)" % (self.selectedChr - 1, max(0, (calBase-webqtlZoomWidth))/1000000.0, (calBase+webqtlZoomWidth)/1000000.0)
 
                 WEBQTL_TITLE = "Click to view this section of the genome in WebQTL"
-                gifmap.areas.append(HT.Area(shape='rect', coords=WEBQTL_COORDS, href=WEBQTL_HREF, title=WEBQTL_TITLE))
+                gifmap.areas.append(
+                    HtmlGenWrapper.create_area_tag(
+                        shape='rect',
+                        coords=WEBQTL_COORDS,
+                        href=WEBQTL_HREF,
+                        title=WEBQTL_TITLE))
                 im_drawer.rectangle(
                     xy=((xBrowse1, paddingTop),
                         (xBrowse2, (paddingTop + self.BAND_HEIGHT))),
@@ -1659,7 +1724,12 @@ class DisplayMappingResults(object):
                     else:
                         PHENOGEN_HREF = "https://phenogen.org/gene.jsp?speciesCB=Mm&auto=Y&geneTxt=chr%s:%d-%d&genomeVer=mm10" % (self.selectedChr, max(0, calBase-flankingWidthInBases), calBase+flankingWidthInBases)
                     PHENOGEN_TITLE = "Click to view this section of the genome in PhenoGen"
-                    gifmap.areas.append(HT.Area(shape='rect', coords=PHENOGEN_COORDS, href=PHENOGEN_HREF, title=PHENOGEN_TITLE))
+                    gifmap.areas.append(
+                        HtmlGenWrapper.create_area_tag(
+                            shape='rect',
+                            coords=PHENOGEN_COORDS,
+                            href=PHENOGEN_HREF,
+                            title=PHENOGEN_TITLE))
                     im_drawer.rectangle(
                         xy=((xBrowse1, phenogenPaddingTop),
                             (xBrowse2, (phenogenPaddingTop+self.BAND_HEIGHT))),
@@ -1675,7 +1745,12 @@ class DisplayMappingResults(object):
                 else:
                     UCSC_HREF = "http://genome.ucsc.edu/cgi-bin/hgTracks?db=%s&position=chr%s:%d-%d" % (self._ucscDb, self.selectedChr, max(0, calBase-flankingWidthInBases), calBase+flankingWidthInBases)
                 UCSC_TITLE = "Click to view this section of the genome in the UCSC Genome Browser"
-                gifmap.areas.append(HT.Area(shape='rect', coords=UCSC_COORDS, href=UCSC_HREF, title=UCSC_TITLE))
+                gifmap.areas.append(
+                    HtmlGenWrapper.create_area_tag(
+                        shape='rect',
+                        coords=UCSC_COORDS,
+                        href=UCSC_HREF,
+                        title=UCSC_TITLE))
                 im_drawer.rectangle(
                     xy=((xBrowse1, ucscPaddingTop),
                         (xBrowse2, (ucscPaddingTop+self.BAND_HEIGHT))),
@@ -1692,7 +1767,11 @@ class DisplayMappingResults(object):
                 else:
                     ENSEMBL_HREF = "http://www.ensembl.org/Rattus_norvegicus/contigview?chr=%s&start=%d&end=%d" % (self.selectedChr, max(0, calBase-flankingWidthInBases), calBase+flankingWidthInBases)
                 ENSEMBL_TITLE = "Click to view this section of the genome in the Ensembl Genome Browser"
-                gifmap.areas.append(HT.Area(shape='rect', coords=ENSEMBL_COORDS, href=ENSEMBL_HREF, title=ENSEMBL_TITLE))
+                gifmap.areas.append(HtmlGenWrapper.create_area_tag(
+                    shape='rect',
+                    coords=ENSEMBL_COORDS,
+                    href=ENSEMBL_HREF,
+                    title=ENSEMBL_TITLE))
                 im_drawer.rectangle(
                     xy=((xBrowse1, ensemblPaddingTop),
                         (xBrowse2, (ensemblPaddingTop+self.BAND_HEIGHT))),
@@ -1923,10 +2002,15 @@ class DisplayMappingResults(object):
                              yZero+40+Zorder*(LRectWidth+3)+LRectWidth)),
                         outline=rectColor, fill=rectColor, width = 0)
                     COORDS="%d,%d,%d,%d"%(xLeftOffset+offsetA-LRectHeight, yZero+40+Zorder*(LRectWidth+3),\
-                            xLeftOffset+offsetA, yZero+40+Zorder*(LRectWidth+3)+LRectWidth)
-                    HREF="/show_trait?trait_id=%s&dataset=%s" % (Lname, self.dataset.group.name+"Geno")
+                            xLeftOffset+offsetA,yZero+40+Zorder*(LRectWidth+3)+LRectWidth)
+                    HREF = "/show_trait?trait_id=%s&dataset=%s" % (Lname, self.dataset.group.name+"Geno")
                     #HREF="javascript:showDatabase3('%s','%s','%s','');" % (showLocusForm,fd.RISet+"Geno", Lname)
-                    Areas=HT.Area(shape='rect', coords=COORDS, href=HREF, target="_blank", title="Locus : " + Lname)
+                    Areas = HtmlGenWrapper.create_area_tag(
+                        shape='rect',
+                        coords=COORDS,
+                        href=HREF,
+                        target="_blank",
+                        title="Locus : {}".format(Lname))
                     gifmap.areas.append(Areas)
                 ##piddle bug
                 if j == 0:
@@ -2017,9 +2101,17 @@ class DisplayMappingResults(object):
         LRSLODFont=ImageFont.truetype(font=VERDANA_FILE, size=int(18*zoom*1.5))
 
         yZero = yTopOffset + plotHeight
-        LRSHeightThresh = drawAreaHeight
-        AdditiveHeightThresh = drawAreaHeight/2
-        DominanceHeightThresh = drawAreaHeight/2
+        # LRSHeightThresh = drawAreaHeight
+        # AdditiveHeightThresh = drawAreaHeight/2
+        # DominanceHeightThresh = drawAreaHeight/2
+        if self.selectedChr == 1:
+            LRSHeightThresh = drawAreaHeight - yTopOffset + 30*(zoom - 1)
+            AdditiveHeightThresh = LRSHeightThresh/2
+            DominanceHeightThresh = LRSHeightThresh/2
+        else:
+            LRSHeightThresh = drawAreaHeight
+            AdditiveHeightThresh = drawAreaHeight/2
+            DominanceHeightThresh = drawAreaHeight/2
         # LRSHeightThresh = (yZero - yTopOffset + 30*(zoom - 1))
         # AdditiveHeightThresh = LRSHeightThresh/2
         # DominanceHeightThresh = LRSHeightThresh/2
@@ -2127,8 +2219,14 @@ class DisplayMappingResults(object):
                 else:
                     sugg_title = "Suggestive LOD = %0.2f" % (self.suggestive/4.61)
                     sig_title = "Significant LOD = %0.2f" % (self.significant/4.61)
-                Areas1 = HT.Area(shape='rect', coords=sugg_coords, title=sugg_title)
-                Areas2 = HT.Area(shape='rect', coords=sig_coords, title=sig_title)
+                Areas1 = HtmlGenWrapper.create_area_tag(
+                    shape='rect',
+                    coords=sugg_coords,
+                    title=sugg_title)
+                Areas2 = HtmlGenWrapper.create_area_tag(
+                    shape='rect',
+                    coords=sig_coords,
+                    title=sig_title)
                 gifmap.areas.append(Areas1)
                 gifmap.areas.append(Areas2)
 
@@ -2255,7 +2353,7 @@ class DisplayMappingResults(object):
                     startPosX += newStartPosX
                     oldStartPosX = newStartPosX
 
-            #ZS: This is beause the chromosome value stored in qtlresult['chr'] can be (for example) either X or 20 depending upon the mapping method/scale used
+            #ZS: This is because the chromosome value stored in qtlresult['chr'] can be (for example) either X or 20 depending upon the mapping method/scale used
             this_chr = str(self.ChrList[self.selectedChr][0])
             if self.plotScale != "physic":
                 this_chr = str(self.ChrList[self.selectedChr][1]+1)
@@ -2580,7 +2678,10 @@ class DisplayMappingResults(object):
                 #add by NL 09-03-2010
                 HREF = "javascript:chrView(%d,%s);" % (i, self.ChrLengthMbList)
                 #HREF = "javascript:changeView(%d,%s);" % (i,self.ChrLengthMbList)
-                Areas = HT.Area(shape='rect', coords=COORDS, href=HREF)
+                Areas = HtmlGenWrapper.create_area_tag(
+                    shape='rect',
+                    coords=COORDS,
+                    href=HREF)
                 gifmap.areas.append(Areas)
                 startPosX +=  (self.ChrLengthDistList[i]+self.GraphInterval)*plotXScale
 
@@ -2666,7 +2767,11 @@ class DisplayMappingResults(object):
                 tableIterationsCnt = tableIterationsCnt + 1
 
                 this_row = [] #container for the cells of each row
-                selectCheck = HT.Input(type="checkbox", name="selectCheck", value=theGO["GeneSymbol"], Class="checkbox trait_checkbox") #checkbox for each row
+                selectCheck = HtmlGenWrapper.create_input_tag(
+                    type="checkbox",
+                    name="selectCheck",
+                    value=theGO["GeneSymbol"],
+                    Class="checkbox trait_checkbox")  # checkbox for each row
 
                 geneLength = (theGO["TxEnd"] - theGO["TxStart"])*1000.0
                 tenPercentLength = geneLength*0.0001
@@ -2724,41 +2829,77 @@ class DisplayMappingResults(object):
 
                         this_row = [selectCheck.__str__(),
                                     str(tableIterationsCnt),
-                                    HT.Href(geneIdString, theGO["GeneSymbol"], target="_blank").__str__(),
-                                    HT.Href(mouseStartString, "%0.6f" % txStart, target="_blank").__str__(),
-                                    HT.Href("javascript:rangeView('%s', %f, %f)" % (str(chr_as_int), txStart-tenPercentLength, txEnd+tenPercentLength), "%0.3f" % geneLength).__str__(),
+                                    str(HtmlGenWrapper.create_link_tag(
+                                        geneIdString,
+                                        theGO["GeneSymbol"],
+                                        target="_blank")
+                                    ),
+                                    str(HtmlGenWrapper.create_link_tag(
+                                        mouseStartString,
+                                        "{:.6f}".format(txStart),
+                                        target="_blank")
+                                    ),
+                                    str(HtmlGenWrapper.create_link_tag(
+                                        "javascript:rangeView('{}', {:f}, {:f})".format(
+                                            str(chr_as_int),
+                                            txStart-tenPercentLength,
+                                            txEnd+tenPercentLength),
+                                        "{:.3f}".format(geneLength))),
                                     snpString,
                                     snpDensityStr,
                                     avgExpr,
                                     humanChr,
-                                    HT.Href(humanStartString, humanStartDisplay, target="_blank").__str__(),
+                                    str(HtmlGenWrapper.create_link_tag(
+                                        humanStartString,
+                                        humanStartDisplay,
+                                        target="_blank")),
                                     literatureCorrelationString,
                                     geneDescription]
                     else:
                         this_row = [selectCheck.__str__(),
                                     str(tableIterationsCnt),
-                                    HT.Href(geneIdString, theGO["GeneSymbol"], target="_blank").__str__(),
-                                    HT.Href(mouseStartString, "%0.6f" % txStart, target="_blank").__str__(),
-                                    HT.Href("javascript:rangeView('%s', %f, %f)" % (str(chr_as_int), txStart-tenPercentLength, txEnd+tenPercentLength), "%0.3f" % geneLength).__str__(),
+                                    str(HtmlGenWrapper.create_link_tag(
+                                        geneIdString, theGO["GeneSymbol"],
+                                        target="_blank")),
+                                    str(HtmlGenWrapper.create_link_tag(
+                                        mouseStartString,
+                                        "{:.6f}".format(txStart),
+                                        target="_blank")),
+                                    str(HtmlGenWrapper.create_link_tag(
+                                        "javascript:rangeView('{}', {:f}, {:f})".format(
+                                            str(chr_as_int),
+                                            txStart-tenPercentLength,
+                                            txEnd+tenPercentLength),
+                                        "{:.3f}".format(geneLength))),
                                     snpString,
                                     snpDensityStr,
                                     avgExpr,
                                     humanChr,
-                                    HT.Href(humanStartString, humanStartDisplay, target="_blank").__str__(),
+                                    str(HtmlGenWrapper.create_link_tag(
+                                        humanStartString,
+                                        humanStartDisplay,
+                                        target="_blank")),
                                     geneDescription]
 
                 gene_table_body.append(this_row)
 
         elif self.dataset.group.species == 'rat':
             for gIndex, theGO in enumerate(geneCol):
-                this_row = [] #container for the cells of each row
-                selectCheck = HT.Input(type="checkbox", name="selectCheck", Class="checkbox trait_checkbox").__str__() #checkbox for each row
+                this_row = []  # container for the cells of each row
+                selectCheck = str(HtmlGenWrapper.create_input_tag(
+                    type="checkbox",
+                    name="selectCheck",
+                    Class="checkbox trait_checkbox"))  # checkbox for each row
 
                 #ZS: May want to get this working again later
                 #webqtlSearch = HT.Href(os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE)+"?cmd=sch&gene=%s&alias=1&species=rat" % theGO["GeneSymbol"], ">>", target="_blank").__str__()
 
                 if theGO["GeneID"] != "":
-                    geneSymbolNCBI = HT.Href("http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=Graphics&list_uids=%s" % theGO["GeneID"], theGO["GeneSymbol"], Class="normalsize", target="_blank").__str__()
+                    geneSymbolNCBI = str(HtmlGenWrapper.create_link_tag(
+                        "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=Graphics&list_uids={}".format(theGO["GeneID"]),
+                        theGO["GeneSymbol"],
+                        Class="normalsize",
+                        target="_blank"))
                 else:
                     geneSymbolNCBI = theGO["GeneSymbol"]
 
@@ -2798,7 +2939,9 @@ class DisplayMappingResults(object):
                             str(gIndex+1),
                             geneSymbolNCBI,
                             "%0.6f" % theGO["TxStart"],
-                            HT.Href(geneLengthURL, "%0.3f" % (geneLength*1000.0)).__str__(),
+                            str(HtmlGenWrapper.create_link_tag(
+                                geneLengthURL,
+                                "{:.3f}".format(geneLength*1000.0))),
                             avgExprVal,
                             mouseChr,
                             mouseTxStart,
diff --git a/wqflask/wqflask/static/new/javascript/search_results.js b/wqflask/wqflask/static/new/javascript/search_results.js
index b3ed06fc..16eff345 100644
--- a/wqflask/wqflask/static/new/javascript/search_results.js
+++ b/wqflask/wqflask/static/new/javascript/search_results.js
@@ -138,14 +138,14 @@ $(function() {
   };
 
   submit_bnw = function() {
-    trait_data = get_traits_from_table("trait_table", "submit_bnw")
+    trait_data = submit_traits_to_export_or_bnw("trait_table", "submit_bnw")
   }
 
   export_traits = function() {
-    trait_data = get_traits_from_table("trait_table", "export_csv")
+    trait_data = submit_traits_to_export_or_bnw("trait_table", "export_csv")
   };
 
-  get_traits_from_table = function(table_name, destination) {
+  submit_traits_to_export_or_bnw = function(table_name, destination) {
     trait_table = $('#'+table_name);
     table_dict = {};
 
@@ -181,55 +181,58 @@ $(function() {
     $('#export_form').submit();
   };
 
-  $("#corr_matrix").on("click", function() {
-      traits = $("#trait_table input:checked").map(function() {
+  get_traits_from_table = function(){
+    traits = $("#trait_table input:checked").map(function() {
+      return $(this).val();
+    }).get();
+    if (traits.length == 0){
+      num_traits = $("#trait_table input").length
+      if (num_traits <= 100){
+        traits = $("#trait_table input").map(function() {
           return $(this).val();
-      }).get();
+        }).get();
+      }
+    }
+    return traits
+  }
+
+  $("#corr_matrix").on("click", function() {
+      traits = get_traits_from_table()
       $("#trait_list").val(traits)
       $("input[name=tool_used]").val("Correlation Matrix")
       $("input[name=form_url]").val($(this).data("url"))
       return submit_special("/loading")
   });
   $("#network_graph").on("click", function() {
-      traits = $("#trait_table input:checked").map(function() {
-         return $(this).val();
-      }).get();
+      traits = get_traits_from_table()
       $("#trait_list").val(traits)
       $("input[name=tool_used]").val("Network Graph")
       $("input[name=form_url]").val($(this).data("url"))
       return submit_special("/loading")
   });
   $("#wgcna_setup").on("click", function() {
-      traits = $("#trait_table input:checked").map(function() {
-          return $(this).val();
-      }).get();
+      traits = get_traits_from_table()
       $("#trait_list").val(traits)
       $("input[name=tool_used]").val("WGCNA Setup")
       $("input[name=form_url]").val($(this).data("url"))
       return submit_special("/loading")
   });
   $("#ctl_setup").on("click", function() {
-      traits = $("#trait_table input:checked").map(function() {
-          return $(this).val();
-      }).get();
+      traits = get_traits_from_table()
       $("#trait_list").val(traits)
       $("input[name=tool_used]").val("CTL Setup")
       $("input[name=form_url]").val($(this).data("url"))
       return submit_special("/loading")
   });
   $("#heatmap").on("click", function() {
-      traits = $("#trait_table input:checked").map(function() {
-          return $(this).val();
-      }).get();
+      traits = get_traits_from_table()
       $("#trait_list").val(traits)
       $("input[name=tool_used]").val("Heatmap")
       $("input[name=form_url]").val($(this).data("url"))
       return submit_special("/loading")
   });
   $("#comp_bar_chart").on("click", function() {
-      traits = $("#trait_table input:checked").map(function() {
-          return $(this).val();
-      }).get();
+      traits = get_traits_from_table()
       $("#trait_list").val(traits)
       $("input[name=tool_used]").val("Comparison Bar Chart")
       $("input[name=form_url]").val($(this).data("url"))
@@ -237,9 +240,7 @@ $(function() {
   });
 
   $("#send_to_webgestalt, #send_to_bnw, #send_to_geneweaver").on("click", function() {
-      traits = $("#trait_table input:checked").map(function() {
-          return $(this).val();
-      }).get();
+      traits = get_traits_from_table()
       $("#trait_list").val(traits)
       url = $(this).data("url")
       return submit_special(url)
diff --git a/wqflask/wqflask/templates/collections/list.html b/wqflask/wqflask/templates/collections/list.html
index 94e22c4d..9e0c0f07 100644
--- a/wqflask/wqflask/templates/collections/list.html
+++ b/wqflask/wqflask/templates/collections/list.html
@@ -2,7 +2,7 @@
 {% block title %}Your Collections{% endblock %}
 {% 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="/static/new/packages/DataTables/extensions/buttons.bootstrap.css" />
+    <link rel="stylesheet" type="text/css" href="{{ url_for('js', filename='DataTablesExtensions/buttonsBootstrap/css/buttons.bootstrap.css') }}" />
     <link rel="stylesheet" type="text/css" href="/static/new/css/show_trait.css" />
 {% endblock %}
 {% block content %}
@@ -70,8 +70,8 @@
     <script type="text/javascript" src="/static/new/javascript/search_results.js"></script>
     <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.dataTables.min.js') }}"></script>
     <script language="javascript" type="text/javascript" src="/static/new/js_external/jszip.min.js"></script>
-    <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/dataTables.naturalSort.js"></script>
-    <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/extensions/dataTables.buttons.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>
     <script>
             $('#trait_table').dataTable( {
                 "drawCallback": function( settings ) {
diff --git a/wqflask/wqflask/templates/collections/view.html b/wqflask/wqflask/templates/collections/view.html
index b56a89da..5c8edab8 100644
--- a/wqflask/wqflask/templates/collections/view.html
+++ b/wqflask/wqflask/templates/collections/view.html
@@ -2,7 +2,7 @@
 {% block title %}View Collection{% endblock %}
 {% 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="/static/new/packages/DataTables/extensions/buttons.dataTables.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="/static/new/css/show_trait.css" />
 {% endblock %}
 {% block content %}
@@ -72,6 +72,7 @@
             <br />
             <form id="export_form" method="POST" action="/export_traits_csv">
             <button class="btn btn-default" id="select_all" type="button"><span class="glyphicon glyphicon-ok"></span> Select All</button>
+            <button class="btn btn-default" id="invert" type="button"><span class="glyphicon glyphicon-ok"></span> Invert</button>
             <button class="btn" id="add" disabled="disabled" type="button"><i class="icon-plus-sign"></i> Copy</button>
             <input type="hidden" name="database_name" id="database_name" value="None">
             <input type="hidden" name="export_data" id="export_data" value="">
@@ -167,11 +168,11 @@
     <script language="javascript" type="text/javascript" src="/static/new/js_external/md5.min.js"></script>
     <script type="text/javascript" src="/static/new/javascript/search_results.js"></script>
     <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.dataTables.min.js') }}"></script>
-    <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/dataTables.naturalSort.js"></script>
-    <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/extensions/dataTables.colResize.js"></script>
-    <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/extensions/dataTables.colReorder.js"></script>
-    <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/extensions/dataTables.buttons.min.js"></script>
-    <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/extensions/buttons.colVis.min.js"></script>
+    <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/plugins/sorting/natural.js') }}"></script>
+    <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/colResize/dataTables.colResize.js') }}"></script>
+    <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/colReorder/js/dataTables.colReorder.js') }}"></script>
+    <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/buttons/js/dataTables.buttons.min.js') }}"></script>
+    <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/buttons/js/buttons.colVis.min.js') }}"></script>
 
 
     <script language="javascript" type="text/javascript">
diff --git a/wqflask/wqflask/templates/corr_scatterplot.html b/wqflask/wqflask/templates/corr_scatterplot.html
index 5877e367..4739b467 100644
--- a/wqflask/wqflask/templates/corr_scatterplot.html
+++ b/wqflask/wqflask/templates/corr_scatterplot.html
@@ -132,44 +132,8 @@
       <br>
       <div id="scatterplot2"></div>
       <br>
-      <div class="row" style="min-width: 700px; overflow: hidden;">
-      <div style="float: left;">
-      <table class="table table-hover table-striped table-bordered" style="width: 80%; margin-left: 60px; text-align: right;">
-        <thead>
-          <tr><th style="text-align: right;">Statistic</th><th style="text-align: right;">Value</th></tr>
-        </thead>
-        <tbody>
-          <tr>
-            <td>Number</td>
-            <td>{{jsdata.num_overlap}}</td>
-          </tr>
-          <tr>
-            <td>Slope</td>
-            <td>{{ jsdata.slope_string }}</td>
-          </tr>
-          <tr>
-            <td>Intercept</td>
-            <td>{{'%0.3f' % jsdata.intercept}}</td>
-          </tr>
-          <tr>
-            <td>r value</td>
-            <td>{{'%0.3f' % jsdata.r_value}}</td>
-          </tr>
-          <tr>
-            <td>P value</td>
-            <td>{% if jsdata.p_value < 0.001 %}{{'%0.3e' % jsdata.p_value}}{% else %}{{'%0.3f' % jsdata.p_value}}{% endif %}</td>
-          </tr>
-          <tr>
-            <td style="text-align: left;" colspan="2">
-              Regression Line
-              <br>
-              y = {{ jsdata.slope_string }} * x {% if jsdata.intercept < 0 %}- {{'%0.3f' % (jsdata.intercept * -1)}}{% else %}+ {{'%0.3f' % jsdata.intercept}}{% endif %}
-            </td>
-          </tr>
-        </tbody>
-      </table>
-      </div>
-      <div style="margin-left: 50px; min-width: 300px; float: left;">
+      <div style="min-width: 700px; overflow: hidden;">
+      <div style="margin-left: 50px; min-width: 300px;">
         {% if trait_1.dataset.type == "ProbeSet" %}
         <div>
           X axis:
@@ -240,15 +204,7 @@
         </div>
         {% endif %}
       </div>
-      </div>
-    </div>
-
-    <div class="tab-pane" id="tp2">
-      <br>
-      <div id="srscatterplot2"></div>
-      <br>
-      <div class="row" style="min-width: 700px; overflow: hidden;">
-      <div style="float: left;">
+      <div style="float: left; margin-top:30px;">
         <table class="table table-hover table-striped table-bordered" style="width: 80%; margin-left: 60px; text-align: right;">
           <thead>
             <tr><th style="text-align: right;">Statistic</th><th style="text-align: right;">Value</th></tr>
@@ -260,31 +216,39 @@
             </tr>
             <tr>
               <td>Slope</td>
-              <td>{{ jsdata.srslope_string }}</td>
+              <td>{{ jsdata.slope_string }}</td>
             </tr>
             <tr>
               <td>Intercept</td>
-              <td>{{'%0.3f' % jsdata.srintercept}}</td>
+              <td>{{'%0.3f' % jsdata.intercept}}</td>
             </tr>
             <tr>
               <td>r value</td>
-              <td>{{'%0.3f' % jsdata.srr_value}}</td>
+              <td>{{'%0.3f' % jsdata.r_value}}</td>
             </tr>
-	    <tr>
+            <tr>
               <td>P value</td>
-              <td>{% if jsdata.srp_value < 0.001 %}{{'%0.3e' % jsdata.srp_value}}{% else %}{{'%0.3f' % jsdata.srp_value}}{% endif %}</td>
+              <td>{% if jsdata.p_value < 0.001 %}{{'%0.3e' % jsdata.p_value}}{% else %}{{'%0.3f' % jsdata.p_value}}{% endif %}</td>
             </tr>
             <tr>
               <td style="text-align: left;" colspan="2">
                 Regression Line
                 <br>
-                y = {{ jsdata.srslope_string }} * x {% if jsdata.srintercept < 0 %}- {{'%0.3f' % (jsdata.srintercept * -1)}}{% else %}+ {{'%0.3f' % jsdata.srintercept}}{% endif %}
+                y = {{ jsdata.slope_string }} * x {% if jsdata.intercept < 0 %}- {{'%0.3f' % (jsdata.intercept * -1)}}{% else %}+ {{'%0.3f' % jsdata.intercept}}{% endif %}
               </td>
             </tr>
           </tbody>
         </table>
+        </div>
       </div>
-      <div style="margin-left: 50px; min-width: 300px; float: left;">
+    </div>
+
+    <div class="tab-pane" id="tp2">
+      <br>
+      <div id="srscatterplot2"></div>
+      <br>
+      <div class="row" style="min-width: 700px; overflow: hidden;">
+      <div style="margin-left: 50px; min-width: 300px;">
         {% if trait_1.dataset.type == "ProbeSet" %}
         <div>
           X axis:
@@ -335,6 +299,42 @@
         </div>
         {% endif %}
       </div>
+      <div style="float: left; margin-top: 30px;">
+        <table class="table table-hover table-striped table-bordered" style="width: 80%; margin-left: 60px; text-align: right;">
+          <thead>
+            <tr><th style="text-align: right;">Statistic</th><th style="text-align: right;">Value</th></tr>
+          </thead>
+          <tbody>
+            <tr>
+              <td>Number</td>
+              <td>{{jsdata.num_overlap}}</td>
+            </tr>
+            <tr>
+              <td>Slope</td>
+              <td>{{ jsdata.srslope_string }}</td>
+            </tr>
+            <tr>
+              <td>Intercept</td>
+              <td>{{'%0.3f' % jsdata.srintercept}}</td>
+            </tr>
+            <tr>
+              <td>r value</td>
+              <td>{{'%0.3f' % jsdata.srr_value}}</td>
+            </tr>
+	    <tr>
+              <td>P value</td>
+              <td>{% if jsdata.srp_value < 0.001 %}{{'%0.3e' % jsdata.srp_value}}{% else %}{{'%0.3f' % jsdata.srp_value}}{% endif %}</td>
+            </tr>
+            <tr>
+              <td style="text-align: left;" colspan="2">
+                Regression Line
+                <br>
+                y = {{ jsdata.srslope_string }} * x {% if jsdata.srintercept < 0 %}- {{'%0.3f' % (jsdata.srintercept * -1)}}{% else %}+ {{'%0.3f' % jsdata.srintercept}}{% endif %}
+              </td>
+            </tr>
+          </tbody>
+        </table>
+      </div>
       </div>
   </div>
 
@@ -351,8 +351,8 @@
     <script language="javascript" type="text/javascript" src="/static/new/js_external/d3-tip.min.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/js_external/jscolor.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/javascript/panelutil.js"></script>
-    <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.dataTables.js"></script>
-    <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/dataTables.naturalSort.js"></script>
+    <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.dataTables.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="/static/new/javascript/get_traits_from_collection.js"></script>-->
     <script type="text/javascript" src="/static/new/js_external/plotly-latest.min.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/javascript/draw_corr_scatterplot.js"></script>
diff --git a/wqflask/wqflask/templates/correlation_matrix.html b/wqflask/wqflask/templates/correlation_matrix.html
index cb9fb815..4e17a0b2 100644
--- a/wqflask/wqflask/templates/correlation_matrix.html
+++ b/wqflask/wqflask/templates/correlation_matrix.html
@@ -36,7 +36,7 @@
       <td align="center"><input type="checkbox" class="checkbox" style="margin-left: 3px; margin-right: 1px;"></td>
       <td align="right" style="padding-right: 4px;" >
         <a href="/show_trait?trait_id={{ trait.name }}&dataset={{ trait.dataset.name }}"><font style="font-size: 14px; font-style: Bold;"><b>Trait {{ loop.index }}: {{ trait.dataset.name }}&nbsp;&nbsp;{{ trait.name }}</b></font></a>
-        <div class="shortName" style="display:none">{% if trait.dataset.type == "ProbeSet" %}Gene Symbol: {{ trait.symbol }}{% elif trait.dataset.type == "Publish" %}Trait Symbol: {{ trait.post_publication_abbreviation }}{% elif trait.dataset.type == "Geno" %}Genotype{% endif %} </div>
+        <div class="shortName">{% if trait.dataset.type == "ProbeSet" %}Gene Symbol: {{ trait.symbol }}{% elif trait.dataset.type == "Publish" %}Trait Symbol: {{ trait.post_publication_abbreviation }}{% elif trait.dataset.type == "Geno" %}Genotype{% endif %} </div>
         <div class="verboseName" style="display: none;">
         {% if trait.dataset.type == "ProbeSet" %}
           <div>{{ trait.symbol }} on Chr {{ trait.chr }} @ {{ trait.mb }} Mb</div><div>{{ trait.description }}</div><div>{{ trait.probe_target_description }}</div>
diff --git a/wqflask/wqflask/templates/correlation_page.html b/wqflask/wqflask/templates/correlation_page.html
index df3e43f1..afa19c4a 100644
--- a/wqflask/wqflask/templates/correlation_page.html
+++ b/wqflask/wqflask/templates/correlation_page.html
@@ -2,9 +2,9 @@
 {% block title %}Correlation Results{% endblock %}
 {% 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="/static/new/packages/DataTables/extensions/buttons.bootstrap.css" />
-    <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/extensions/buttons.dataTables.css">
     <link rel="stylesheet" type="text/css" href="/static/new/css/show_trait.css" />
+    <link rel="stylesheet" type="text/css" href="{{ url_for('js', filename='DataTablesExtensions/buttonsBootstrap/css/buttons.bootstrap.css') }}" />
+    <link rel="stylesheet" type="text/css" href="{{ url_for('js', filename='DataTablesExtensions/buttonStyles/css/buttons.dataTables.min.css') }}">
 {% endblock %}
 {% block content %}
     <div class="container" style="min-width: 1250px;">
@@ -207,9 +207,9 @@
     <script language="javascript" type="text/javascript" src="/static/packages/underscore/underscore-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="/static/new/packages/DataTables/extensions/dataTables.buttons.min.js"></script>
-    <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/extensions/buttons.colVis.min.js"></script>
-    <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/dataTables.naturalSort.js"></script>
+    <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/buttons/js/dataTables.buttons.min.js') }}"></script>
+    <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/buttons/js/buttons.colVis.min.js') }}"></script>
+    <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/plugins/sorting/natural.js') }}"></script>
 
     <script type="text/javascript" charset="utf-8">
         var table_json = {{ json_results | safe }}
diff --git a/wqflask/wqflask/templates/gsearch_gene.html b/wqflask/wqflask/templates/gsearch_gene.html
index 62ef1a7b..617bdc0f 100644
--- a/wqflask/wqflask/templates/gsearch_gene.html
+++ b/wqflask/wqflask/templates/gsearch_gene.html
@@ -50,9 +50,9 @@
     <script language="javascript" type="text/javascript" src="/static/new/javascript/search_results.js"></script>
     <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.dataTables.min.js') }}"></script>
     <script language="javascript" type="text/javascript" src="/static/new/js_external/jszip.min.js"></script>
-    <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/dataTables.naturalSort.js"></script>
-    <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/extensions/dataTables.colReorder.js"></script>
-    <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/extensions/dataTables.colResize.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/colReorder/js/dataTables.colReorder.js') }}"></script>
+    <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/colResize/dataTables.colResize.js') }}"></script>
 
     <script type='text/javascript'>
       var the_rows = {{ trait_list|safe }};
diff --git a/wqflask/wqflask/templates/gsearch_pheno.html b/wqflask/wqflask/templates/gsearch_pheno.html
index f5058158..66995346 100644
--- a/wqflask/wqflask/templates/gsearch_pheno.html
+++ b/wqflask/wqflask/templates/gsearch_pheno.html
@@ -50,9 +50,9 @@
     <script language="javascript" type="text/javascript" src="/static/new/javascript/search_results.js"></script>
     <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.dataTables.min.js') }}"></script>
     <script language="javascript" type="text/javascript" src="/static/new/js_external/jszip.min.js"></script>
-    <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/dataTables.naturalSort.js"></script>
-    <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/extensions/dataTables.colReorder.js"></script>
-    <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/extensions/dataTables.colResize.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/colReorder/js/dataTables.colReorder.js') }}"></script>
+    <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/colResize/dataTables.colResize.js') }}"></script>
 
     <script type='text/javascript'>
       var the_rows = {{ trait_list|safe }};
diff --git a/wqflask/wqflask/templates/mapping_results.html b/wqflask/wqflask/templates/mapping_results.html
index 6348ca31..961c3b21 100644
--- a/wqflask/wqflask/templates/mapping_results.html
+++ b/wqflask/wqflask/templates/mapping_results.html
@@ -341,8 +341,8 @@
 
     <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/buttons/1.0.0/js/dataTables.buttons.min.js"></script>
-    <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/dataTables.scientific.js"></script>
-    <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/dataTables.naturalSort.js"></script>
+    <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/plugins/sorting/scientific.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="/static/packages/purescript_genome_browser/js/purescript-genetics-browser.js"></script>
 
     <script>
diff --git a/wqflask/wqflask/templates/pair_scan_results.html b/wqflask/wqflask/templates/pair_scan_results.html
index b13b393f..5c776fc1 100644
--- a/wqflask/wqflask/templates/pair_scan_results.html
+++ b/wqflask/wqflask/templates/pair_scan_results.html
@@ -66,7 +66,7 @@
     <script language="javascript" type="text/javascript" src="/static/new/js_external/d3-tip.min.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.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="/static/new/packages/DataTables/js/dataTables.scientific.js"></script>
+    <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/plugins/sorting/scientific.js') }}"></script>
     <script language="javascript" type="text/javascript" src="/static/packages/DT_bootstrap/DT_bootstrap.js"></script>
     <script language="javascript" type="text/javascript" src="/static/packages/TableTools/media/js/TableTools.min.js"></script>
     <script language="javascript" type="text/javascript" src="/static/packages/underscore/underscore-min.js"></script>
diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html
index 1f76ea82..dbdca9f8 100644
--- a/wqflask/wqflask/templates/search_result_page.html
+++ b/wqflask/wqflask/templates/search_result_page.html
@@ -2,8 +2,8 @@
 {% block title %}Search Results{% endblock %}
 {% 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="/static/new/packages/DataTables/extensions/scroller.dataTables.min.css">
-    <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/extensions/buttons.dataTables.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="/static/new/css/show_trait.css" />
 {% endblock %}
 {% block content %}
@@ -137,7 +137,7 @@
           </div>
           {% endif %}
           <!--<div id="table_container" style="min-width: {% if dataset.type == 'ProbeSet' or dataset.type == 'Publish' %}2000{% else %}380{% endif %}px;">-->
-          <div id="table_container">
+          <div id="table_container" {% if dataset.type == 'ProbeSet' or dataset.type == 'Publish' %}style="min-width: 1500px;"{% endif %}>
             <table class="table-hover table-striped cell-border" id='trait_table' style="float: left; width: {% if dataset.type == 'Geno' %}380px{% else %}100%{% endif %};">
                 <tbody>
                  <td colspan="100%" align="center"><br><b><font size="15">Loading...</font></b><br></td>
@@ -159,9 +159,9 @@
 
     <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="/static/new/js_external/jszip.min.js"></script>
-    <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/dataTables.naturalSort.js"></script>
-    <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/extensions/dataTables.buttons.min.js"></script>
-    <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/extensions/buttons.colVis.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>
+    <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/buttons/js/buttons.colVis.min.js') }}"></script>
 
     <script type='text/javascript'>
         var trait_list = {{ trait_list|safe }};
diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index acee6724..15442ca7 100644
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -147,9 +147,9 @@
     <script type="text/javascript" src="/static/new/javascript/show_trait.js"></script>
     <script type="text/javascript" src="/static/new/javascript/validation.js"></script>
 
-    <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.dataTables.js"></script>
-    <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/dataTables.scientific.js"></script>
-    <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/dataTables.naturalSort.js"></script>
+    <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.dataTables.js') }}"></script>
+    <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/plugins/sorting/scientific.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="/static/new/packages/noUiSlider/nouislider.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/javascript/get_covariates_from_collection.js"></script>
 
diff --git a/wqflask/wqflask/templates/snp_browser.html b/wqflask/wqflask/templates/snp_browser.html
index 4537cd06..fb564b28 100644
--- a/wqflask/wqflask/templates/snp_browser.html
+++ b/wqflask/wqflask/templates/snp_browser.html
@@ -1,7 +1,7 @@
 {% extends "base.html" %}
 {% 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="/static/new/packages/DataTables/extensions/buttons.bootstrap.css" />
+    <link rel="stylesheet" type="text/css" href="{{ url_for('js', filename='DataTablesExtensions/buttonsBootstrap/css/buttons.bootstrap.css') }}" />
     <link rel="stylesheet" type="text/css" href="/static/new/css/typeahead-bootstrap.css" />
     <link rel="stylesheet" type="text/css" href="/static/new/css/snp_browser.css" />
 {% endblock %}
@@ -215,8 +215,8 @@
 
 {% endblock %}
 {% block js %}
-  <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.dataTables.js"></script>
-  <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/dataTables.naturalSort.js"></script>
+  <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.dataTables.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="/static/new/js_external/typeahead.bundle.js"></script>
 
   <script language="javascript" type="text/javascript" src="/static/new/javascript/typeahead_rn6.json"></script>
diff --git a/wqflask/wqflask/user_session.py b/wqflask/wqflask/user_session.py
index ba659fe5..3aa2c151 100644
--- a/wqflask/wqflask/user_session.py
+++ b/wqflask/wqflask/user_session.py
@@ -13,7 +13,7 @@ from wqflask import app
 from utility import hmac
 
 #from utility.elasticsearch_tools import get_elasticsearch_connection
-from utility.redis_tools import get_redis_conn, get_user_id, get_user_collections, save_collections
+from utility.redis_tools import get_redis_conn, get_user_id, get_user_by_unique_column, set_user_attribute, get_user_collections, save_collections
 Redis = get_redis_conn()
 
 from utility.logger import getLogger
@@ -53,6 +53,18 @@ def create_signed_cookie():
     logger.debug("uuid_signed:", uuid_signed)
     return the_uuid, uuid_signed
 
+@app.route("/user/manage", methods=('GET','POST'))
+def manage_user():
+    params = request.form if request.form else request.args
+    if 'new_full_name' in params:
+        set_user_attribute(g.user_session.user_id, 'full_name', params['new_full_name'])
+    if 'new_organization' in params:
+        set_user_attribute(g.user_session.user_id, 'organization', params['new_organization'])
+
+    user_details = get_user_by_unique_column("user_id", g.user_session.user_id)
+
+    return render_template("admin/manage_user.html", user_details = user_details)
+
 class UserSession(object):
     """Logged in user handling"""