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

22 files changed, 333 insertions, 200 deletions

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 4c8db1c4..2fd9a886 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -14,18 +14,35 @@ jobs:
     container: bonfacekilz/python2-genenetwork2:latest
 
     steps:
+    # First start with mariadb set then checkout. The checkout gives
+    # the mysqld enough time to start
+    - name: Set up mariadb
+      run: |
+        mysql_install_db --user=mysql --datadir=/usr/local/mysql
+        # Wait for the mysqld_safe process to start
+        mysqld_safe --user=mysql --datadir=/usr/local/mysql &
+
     # Use v1 of checkout since v2 fails
     - name: Checkout Project
       uses: actions/checkout@v1
 
-    # Redis is required by some of the tests
+    # Redis is required by some of the tests 6379
     - name: Start Redis
       run: |
-        redis-server --daemonize yes
+        /gn2-profile/bin/screen -dmLS redisconn /gn2-profile/bin/redis-server
+
+    # Redis is required by some of the tests 6379
+    - name: Bootstrap tables
+      run: |
+        mysql -u root -e "SHOW DATABASES;"
+        mysql -u root -e "CREATE DATABASE db_webqtl_s;"
+        mysql -u root -e "CREATE USER 'gn2'@'localhost' IDENTIFIED BY 'mysql_password';"
+        mysql -u root -e "GRANT ALL PRIVILEGES ON *.* TO 'gn2'@'localhost';FLUSH PRIVILEGES;"
 
     - name: Run the unit tests
       run: |
-        mkdir -p /genotype_files/genotype/json
-        env GN2_PROFILE=/usr/gn2-profile TMPDIR=/tmp SERVER_PORT=5004 \
-        GENENETWORK_FILES=/genotype_files/ bash bin/genenetwork2 \
+        env GN2_PROFILE=/gn2-profile \
+        TMPDIR=/tmp SERVER_PORT=5004 \
+        WEBSERVER_MODE=DEBUG LOG_LEVEL=DEBUG \
+        GENENETWORK_FILES=/genotype_files/ bin/genenetwork2 \
         etc/default_settings.py -c -m unittest discover -v
diff --git a/doc/docker-container.org b/doc/docker-container.org
index 3c9864c5..ec91824a 100644
--- a/doc/docker-container.org
+++ b/doc/docker-container.org
@@ -15,57 +15,60 @@ are ran from.
 
 Find instructions on how to set docker up inside GUIX [[https://github.com/pjotrp/guix-notes/blob/master/CONTAINERS.org#run-docker][here]]. This
 document will not get into that. It's assumed that you have a working
-dockec setup.
+docker setup.
 
 The rest of this document outlines how the docker container used in
-the CI builds were created.
+the CI builds was created.
 
 * Creating the Docker Images
 
-First create the image by running:
+The general idea is that GUIX is used to generate a set of binaries,
+which will be added to a base mariaDB image.
+
+First create the gn2 tar archive by running:
 
 #+begin_src sh
 # For the Python 2 version:
-env GUIX_PACKAGE_PATH="/home/bonface/projects/guix-bioinformatics::/home/bonface/projects/guix-past/modules" \
-    ./pre-inst-env guix pack -f docker --no-grafts \
-    -S /usr/bin=/bin -S /etc/profile=/etc/profile \
-    -S /share/genenetwork2=/share/genenetwork2 \
-    -S /share/javascript=/share/javascript \
-    -S /lib=/lib \
-    -S /usr/gn2-profile=/ \
-    coreutils bash genenetwork2
+env GUIX_PACKAGE_PATH="/home/bonface/projects/guix-bioinformatics:/home/bonface/projects/guix-past/modules" \
+    ./pre-inst-env guix pack --no-grafts\
+    -S /gn2-profile=/ \
+    screen genenetwork2
 
 # For the Python 3 version:
-env GUIX_PACKAGE_PATH="/home/bonface/projects/guix-bioinformatics::/home/bonface/projects/guix-past/modules" \
-    ./pre-inst-env guix pack -f docker --no-grafts \
-    -S /usr/bin=/bin -S /etc/profile=/etc/profile \
-    -S /share/genenetwork2=/share/genenetwork2 \
-    -S /share/javascript=/share/javascript \
-    -S /lib=/lib \
-    -S /usr/gn2-profile=/ \
-    coreutils bash python3-genenetwork2
+env GUIX_PACKAGE_PATH="/home/bonface/projects/guix-bioinformatics:/home/bonface/projects/guix-past/modules" \
+    ./pre-inst-env guix pack --no-grafts\
+    -S /gn2-profile=/ \
+    screen python3-genenetwork2
   #+end_src
 
 The output will look something similar to:
 
-: /gnu/store/dj1xh19jq1l9vwq24w3nay2954x0wabb-docker-pack.tar.gz
+: /gnu/store/x3m77vwaqcwba24p5s4lrb7w2ii16lj9-tarball-pack.tar.gz
+
+Now create a folder from which will host the following dockerfile. You
+can name this file Dockerfile. Note that mariadb is the base image
+since it already has mariadb installed for us.
+
+#+begin_src conf :mkdirp yes :tangle ~/docker/Dockerfile
+FROM mariadb:latest
 
-Load the docker image by running:
+COPY ./gn2.tar.gz /tmp/gn2.tar.gz
+RUN tar -xzf /tmp/gn2.tar.gz -C / && rm -f /tmp/gn2.tar.gz && \
+    mkdir -p /usr/local/mysql /genotype_files/genotype/json
+#+end_src
 
-: docker load --input /gnu/store/dj1xh19jq1l9vwq24w3nay2954x0wabb-docker-pack.tar.gz
+Build the image(Note the fullstop at the end):
 
-Results look something similar to:
+: sudo docker build -t python2-genenetwork2:latest -f Dockerfile .
 
-#+begin_export ascii
-a93f52b7f565: Loading layer  3.174GB/3.174GB
-Loaded image: coreutils-genenetwork2:latest
-#+end_export
+To load the image interactively you've just created:
+
+: docker run -ti "python2-genenetwork2:latest" bash
 
 Assuming you have a docker instance running, you could always run
 commands in it e.g:
 
-: docker run "coreutils-genenetwork2:latest" python --version 
-
+: docker run "python2-genenetwork2:latest" python --version 
 
 * Pushing to DockerHub
 
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index afffe780..e0ef559c 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -1173,40 +1173,6 @@ class TempDataSet(DataSet):
         self.fullname = 'Temporary Storage'
         self.shortname = 'Temp'
 
-    @staticmethod
-    def handle_pca(desc):
-        if 'PCA' in desc:
-            # Todo: Modernize below lines
-            desc = desc[desc.rindex(':')+1:].strip()
-        else:
-            desc = desc[:desc.index('entered')].strip()
-        return desc
-
-    def get_desc(self):
-        query = 'SELECT description FROM Temp WHERE Name=%s' % self.name
-        logger.sql(query)
-        g.db.execute(query)
-        desc = g.db.fetchone()[0]
-        desc = self.handle_pca(desc)
-        return desc
-
-    def retrieve_sample_data(self, trait):
-        query = """
-                SELECT
-                        Strain.Name, TempData.value, TempData.SE, TempData.NStrain, TempData.Id
-                FROM
-                        TempData, Temp, Strain
-                WHERE
-                        TempData.StrainId = Strain.Id AND
-                        TempData.Id = Temp.DataId AND
-                        Temp.name = '%s'
-                Order BY
-                        Strain.Name
-                """ % escape(trait.name)
-
-        logger.sql(query)
-        results = g.db.execute(query).fetchall()
-
 
 def geno_mrna_confidentiality(ob):
     dataset_table = ob.type + "Freeze"
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index 7666348e..8f8b5b70 100644
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -507,13 +507,14 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
             description_string = unicode(str(trait.description).strip(codecs.BOM_UTF8), 'utf-8')
             target_string = unicode(str(trait.probe_target_description).strip(codecs.BOM_UTF8), 'utf-8')
 
-            if len(description_string) > 1 and description_string != 'None':
+            if str(description_string or "") != "" and description_string != 'None':
                 description_display = description_string
             else:
                 description_display = trait.symbol
 
-            if (len(description_display) > 1 and description_display != 'N/A' and
-                    len(target_string) > 1 and target_string != 'None'):
+            if (str(description_display or "") != "" and
+                description_display != 'N/A' and
+                str(target_string or "") != "" and target_string != 'None'):
                 description_display = description_display + '; ' + target_string.strip()
 
             # Save it for the jinja2 template
@@ -599,12 +600,11 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
                         trait.locus = trait.locus_chr = trait.locus_mb = trait.additive = ""
                 else:
                     trait.locus = trait.lrs = trait.additive = ""
-
-            if (dataset.type == 'Publish' or dataset.type == "ProbeSet") and trait.locus_chr != "" and trait.locus_mb != "":
+            if (dataset.type == 'Publish' or dataset.type == "ProbeSet") and str(trait.locus_chr or "") != "" and str(trait.locus_mb or "") != "":
                 trait.LRS_location_repr = LRS_location_repr = 'Chr%s: %.6f' % (trait.locus_chr, float(trait.locus_mb))
-                if trait.lrs != "":
+                if str(trait.lrs or "") != "":
                     trait.LRS_score_repr = LRS_score_repr = '%3.1f' % trait.lrs
     else:
         raise KeyError, `trait.name`+' information is not found in the database.'
         
-    return trait
\ No newline at end of file
+    return trait
diff --git a/wqflask/tests/base/test_trait.py b/wqflask/tests/base/test_trait.py
index 53b0d440..1a3820f2 100644
--- a/wqflask/tests/base/test_trait.py
+++ b/wqflask/tests/base/test_trait.py
@@ -96,6 +96,140 @@ class TestRetrieveTraitInfo(unittest.TestCase):
         test_trait = retrieve_trait_info(trait=mock_trait,
                                          dataset=mock_dataset)
         self.assertEqual(test_trait.abbreviation,
-                         "ファイルを画面毎に見て行くには、次のコマンドを使います。")
+                         "ファイルを画面毎に見て行くには、次のコマンドを使います。".decode('utf-8'))
         self.assertEqual(test_trait.authors,
-                         "Jane Doe かいと")
+                         "Jane Doe かいと".decode('utf-8'))
+
+    @mock.patch('base.trait.requests.get')
+    @mock.patch('base.trait.g')
+    @mock.patch('base.trait.get_resource_id')
+    def test_retrieve_trait_info_with_non_empty_lrs(self,
+                                                    resource_id_mock,
+                                                    g_mock,
+                                                    requests_mock):
+        """Test """
+        resource_id_mock.return_value = 1
+        g_mock.db.execute.return_value.fetchone = mock.Mock()
+        g_mock.db.execute.return_value.fetchone.side_effect = [
+            [1, 2, 3, 4],  # trait_info = g.db.execute(query).fetchone()
+            [1, 2.37, 3, 4, 5],  # trait_qtl = g.db.execute(query).fetchone()
+            [2.7333, 2.1204]  # trait_info = g.db.execute(query).fetchone()
+        ]
+        requests_mock.return_value = None
+
+        mock_dataset = mock.MagicMock()
+        type(mock_dataset).display_fields = mock.PropertyMock(
+            return_value=["a", "b", "c", "d"])
+        type(mock_dataset).type = "ProbeSet"
+        type(mock_dataset).name = "RandomName"
+
+        mock_trait = MockTrait(
+            dataset=mock_dataset,
+            pre_publication_description="test_string"
+        )
+        trait_attrs = {
+            "description": "some description",
+            "probe_target_description": "some description",
+            "cellid": False,
+            "chr": 2.733,
+            "mb": 2.1204
+        }
+
+        for key, val in list(trait_attrs.items()):
+            setattr(mock_trait, key, val)
+        test_trait = retrieve_trait_info(trait=mock_trait,
+                                         dataset=mock_dataset,
+                                         get_qtl_info=True)
+        self.assertEqual(test_trait.LRS_score_repr,
+                         "2.4")
+
+    @mock.patch('base.trait.requests.get')
+    @mock.patch('base.trait.g')
+    @mock.patch('base.trait.get_resource_id')
+    def test_retrieve_trait_info_with_empty_lrs_field(self,
+                                                      resource_id_mock,
+                                                      g_mock,
+                                                      requests_mock):
+        """Test retrieve trait info with empty lrs field"""
+        resource_id_mock.return_value = 1
+        g_mock.db.execute.return_value.fetchone = mock.Mock()
+        g_mock.db.execute.return_value.fetchone.side_effect = [
+            [1, 2, 3, 4],  # trait_info = g.db.execute(query).fetchone()
+            [1, None, 3, 4, 5],  # trait_qtl = g.db.execute(query).fetchone()
+            [2, 3]  # trait_info = g.db.execute(query).fetchone()
+        ]
+        requests_mock.return_value = None
+
+        mock_dataset = mock.MagicMock()
+        type(mock_dataset).display_fields = mock.PropertyMock(
+            return_value=["a", "b", "c", "d"])
+        type(mock_dataset).type = "ProbeSet"
+        type(mock_dataset).name = "RandomName"
+
+        mock_trait = MockTrait(
+            dataset=mock_dataset,
+            pre_publication_description="test_string"
+        )
+        trait_attrs = {
+            "description": "some description",
+            "probe_target_description": "some description",
+            "cellid": False,
+            "chr": 2.733,
+            "mb": 2.1204
+        }
+
+        for key, val in list(trait_attrs.items()):
+            setattr(mock_trait, key, val)
+        test_trait = retrieve_trait_info(trait=mock_trait,
+                                         dataset=mock_dataset,
+                                         get_qtl_info=True)
+        self.assertEqual(test_trait.LRS_score_repr,
+                         "N/A")
+        self.assertEqual(test_trait.LRS_location_repr,
+                         "Chr2: 3.000000")
+
+    @mock.patch('base.trait.requests.get')
+    @mock.patch('base.trait.g')
+    @mock.patch('base.trait.get_resource_id')
+    def test_retrieve_trait_info_with_empty_chr_field(self,
+                                                      resource_id_mock,
+                                                      g_mock,
+                                                      requests_mock):
+        """Test retrieve trait info with empty chr field"""
+        resource_id_mock.return_value = 1
+        g_mock.db.execute.return_value.fetchone = mock.Mock()
+        g_mock.db.execute.return_value.fetchone.side_effect = [
+            [1, 2, 3, 4],  # trait_info = g.db.execute(query).fetchone()
+            [1, 2, 3, 4, 5],  # trait_qtl = g.db.execute(query).fetchone()
+            [None, 3]  # trait_info = g.db.execute(query).fetchone()
+        ]
+
+        requests_mock.return_value = None
+
+        mock_dataset = mock.MagicMock()
+        type(mock_dataset).display_fields = mock.PropertyMock(
+            return_value=["a", "b", "c", "d"])
+        type(mock_dataset).type = "ProbeSet"
+        type(mock_dataset).name = "RandomName"
+
+        mock_trait = MockTrait(
+            dataset=mock_dataset,
+            pre_publication_description="test_string"
+        )
+        trait_attrs = {
+            "description": "some description",
+            "probe_target_description": "some description",
+            "cellid": False,
+            "chr": 2.733,
+            "mb": 2.1204
+        }
+
+        for key, val in list(trait_attrs.items()):
+            setattr(mock_trait, key, val)
+        test_trait = retrieve_trait_info(trait=mock_trait,
+                                         dataset=mock_dataset,
+                                         get_qtl_info=True)
+        self.assertEqual(test_trait.LRS_score_repr,
+                         "N/A")
+        self.assertEqual(test_trait.LRS_location_repr,
+                         "N/A")
diff --git a/wqflask/wqflask/__init__.py b/wqflask/wqflask/__init__.py
index d729aef5..7ed9c7b8 100644
--- a/wqflask/wqflask/__init__.py
+++ b/wqflask/wqflask/__init__.py
@@ -12,13 +12,24 @@ logging.basicConfig(level=logging.INFO)
 
 app = Flask(__name__)
 
-app.config.from_envvar('GN2_SETTINGS')       # See http://flask.pocoo.org/docs/config/#configuring-from-files
+# See http://flask.pocoo.org/docs/config/#configuring-from-files
 # Note no longer use the badly named WQFLASK_OVERRIDES (nyi)
-
+app.config.from_envvar('GN2_SETTINGS')
 app.jinja_env.globals.update(
-    undefined = jinja2.StrictUndefined,
-    numify = formatting.numify
-)
+    undefined=jinja2.StrictUndefined,
+    numify=formatting.numify)
 
 from wqflask.api import router
+from wqflask import group_manager
+from wqflask import resource_manager
+from wqflask import search_results
+from wqflask import export_traits
+from wqflask import gsearch
+from wqflask import update_search_results
+from wqflask import docs
+from wqflask import news
+from wqflask import db_info
+from wqflask import user_login
+from wqflask import user_session
+
 import wqflask.views
diff --git a/wqflask/wqflask/correlation/corr_scatter_plot.py b/wqflask/wqflask/correlation/corr_scatter_plot.py
index 819836b1..0f3d455c 100644
--- a/wqflask/wqflask/correlation/corr_scatter_plot.py
+++ b/wqflask/wqflask/correlation/corr_scatter_plot.py
@@ -17,8 +17,15 @@ class CorrScatterPlot(object):
     """Page that displays a correlation scatterplot with a line fitted to it"""
 
     def __init__(self, params):
-        self.dataset_1 = data_set.create_dataset(params['dataset_1'])
-        self.dataset_2 = data_set.create_dataset(params['dataset_2'])
+        if "Temp" in params['dataset_1']:
+            self.dataset_1 = data_set.create_dataset(dataset_name = "Temp", dataset_type = "Temp", group_name = params['dataset_1'].split("_")[1])
+        else:
+            self.dataset_1 = data_set.create_dataset(params['dataset_1'])
+        if "Temp" in params['dataset_2']:
+            self.dataset_2 = data_set.create_dataset(dataset_name = "Temp", dataset_type = "Temp", group_name = params['dataset_2'].split("_")[1])
+        else:
+            self.dataset_2 = data_set.create_dataset(params['dataset_2'])
+
         #self.dataset_3 = data_set.create_dataset(params['dataset_3'])
         self.trait_1 = create_trait(name=params['trait_1'], dataset=self.dataset_1)
         self.trait_2 = create_trait(name=params['trait_2'], dataset=self.dataset_2)
diff --git a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
index 0ac94139..3beee84f 100644
--- a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
+++ b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
@@ -147,7 +147,7 @@ class CorrelationMatrix(object):
 
                     if num_overlap < self.lowest_overlap:
                         self.lowest_overlap = num_overlap
-                    if num_overlap == 0:
+                    if num_overlap < 2:
                         corr_result_row.append([target_trait, 0, num_overlap])
                         pca_corr_result_row.append(0)
                     else:
diff --git a/wqflask/wqflask/docs.py b/wqflask/wqflask/docs.py
index 78407e22..9fad1cf1 100644
--- a/wqflask/wqflask/docs.py
+++ b/wqflask/wqflask/docs.py
@@ -11,7 +11,7 @@ class Docs(object):
 
     def __init__(self, entry, start_vars={}):
         sql = """
-            SELECT Docs.title, Docs.content
+            SELECT Docs.title, CAST(Docs.content AS BINARY)
             FROM Docs
             WHERE Docs.entry LIKE %s
             """
@@ -22,7 +22,7 @@ class Docs(object):
             self.content = ""
         else:
             self.title = result[0]
-            self.content = result[1].encode("latin1")
+            self.content = result[1]
 
         self.editable = "false"
         # ZS: Removing option to edit to see if text still gets vandalized
diff --git a/wqflask/wqflask/static/new/css/show_trait.css b/wqflask/wqflask/static/new/css/show_trait.css
index 338302af..92deab20 100644
--- a/wqflask/wqflask/static/new/css/show_trait.css
+++ b/wqflask/wqflask/static/new/css/show_trait.css
@@ -46,4 +46,9 @@ table.dataTable.cell-border tbody th, table.dataTable.cell-border tbody td {
 table.dataTable.cell-border tbody tr th:first-child,
 table.dataTable.cell-border tbody tr td:first-child {
   border-left: 1px solid #ccc;
+}
+
+.glyphicon {
+  position: relative;
+  top: 2px;
 }
\ No newline at end of file
diff --git a/wqflask/wqflask/static/new/javascript/search_results.js b/wqflask/wqflask/static/new/javascript/search_results.js
index 685d6291..86660126 100644
--- a/wqflask/wqflask/static/new/javascript/search_results.js
+++ b/wqflask/wqflask/static/new/javascript/search_results.js
@@ -93,7 +93,7 @@ $(function() {
 
   });
 
-  add = function() {
+  add_to_collection = function() {
     var traits;
     traits = $("#trait_table input:checked").map(function() {
       return $(this).val();
@@ -250,7 +250,7 @@ $(function() {
   $("#select_all").click(select_all);
   $("#deselect_all").click(deselect_all);
   $("#invert").click(invert);
-  $("#add").click(add);
+  $("#add").click(add_to_collection);
   $("#submit_bnw").click(submit_bnw);
   $("#export_traits").click(export_traits);
   $('.trait_checkbox, .btn').click(change_buttons);
@@ -261,6 +261,12 @@ $(function() {
 
   let na_equivalent_vals = ["N/A", "--", ""]; //ZS: Since there are multiple values that should be treated the same as N/A
 
+  function extract_inner_text(the_string){
+    var span = document.createElement('span');
+    span.innerHTML = the_string;
+    return span.textContent || span.innerText;
+  }
+
   function sort_NAs(a, b, sort_function){
     if ( na_equivalent_vals.includes(a) && na_equivalent_vals.includes(b)) {
       return 0;
@@ -276,10 +282,10 @@ $(function() {
 
   $.extend( $.fn.dataTableExt.oSort, {
     "natural-minus-na-asc": function (a, b) {
-      return sort_NAs(a, b, naturalAsc)
+      return sort_NAs(extract_inner_text(a), extract_inner_text(b), naturalAsc)
     },
     "natural-minus-na-desc": function (a, b) {
-      return sort_NAs(a, b, naturalDesc)
+      return sort_NAs(extract_inner_text(a), extract_inner_text(b), naturalDesc)
     }
   });
 
diff --git a/wqflask/wqflask/templates/base.html b/wqflask/wqflask/templates/base.html
index e6802cc4..b44538cf 100644
--- a/wqflask/wqflask/templates/base.html
+++ b/wqflask/wqflask/templates/base.html
@@ -21,6 +21,14 @@
     {% block css %}
     {% endblock %}
 
+    <style>
+        table.dataTable thead .sorting_asc {
+            background-image: url({{ url_for("js", filename="DataTables/images/sort_asc_disabled.png") }});
+        }
+        table.dataTable thead .sorting_desc {
+            background-image: url({{ url_for("js", filename="DataTables/images/sort_desc_disabled.png") }});
+        }
+    </style>
 </head>
 
 <body style="width: 100%">
diff --git a/wqflask/wqflask/templates/collections/add.html b/wqflask/wqflask/templates/collections/add.html
index 825dfb84..62b6abb5 100644
--- a/wqflask/wqflask/templates/collections/add.html
+++ b/wqflask/wqflask/templates/collections/add.html
@@ -5,7 +5,7 @@
         or add to an existing collection.</p>
     </div>
     <div class="modal-body" style="margin-left: 20px;">
-        <form action="/collections/new" data-validate="parsley" id="add_form">
+        <form action="/collections/new" target="_blank" data-validate="parsley" id="add_form">
             {% if traits is defined %}
             <input type="hidden" name="traits" value="{{ traits }}" />
             {% else %}
diff --git a/wqflask/wqflask/templates/collections/view.html b/wqflask/wqflask/templates/collections/view.html
index dce814dd..bc487a59 100644
--- a/wqflask/wqflask/templates/collections/view.html
+++ b/wqflask/wqflask/templates/collections/view.html
@@ -16,8 +16,6 @@
         </h1>
         <h3>This collection has {{ '{}'.format(numify(trait_obs|count, "record", "records")) }}</h3>
 
-        <!--<hr style="height: 1px; background-color: #A9A9A9;">-->
-
         <div>
           <form id="collection_form" action="/delete" method="post">
             <input type="hidden" name="uc_id" id="uc_id" value="{{ uc.id }}" />
@@ -77,7 +75,7 @@
             <input type="hidden" name="database_name" id="database_name" value="None">
             <input type="hidden" name="export_data" id="export_data" value="">
             <input type="hidden" name="file_name" id="file_name" value="collection_table">
-            <button class="btn btn-default" id="export_traits">Download CSV</button>
+            <button class="btn btn-default" id="export_traits">Download</button>
             <input type="text" id="searchbox" class="form-control" style="width: 200px; display: inline; padding-bottom: 9px;" placeholder="Search Table For ...">
             <input type="text" id="select_top" class="form-control" style="width: 200px; display: inline; padding-bottom: 9px;" placeholder="Select Top ...">
             <button class="btn btn-default" id="deselect_all" type="button"><span class="glyphicon glyphicon-remove"></span> Deselect</button>
@@ -99,9 +97,9 @@
                             <th data-export="Description">Description</th>
                             <th data-export="Location">Location</th>
                             <th data-export="Mean">Mean</th>
-                            <th data-export="Max LRS">Max LRS <a href="http://genenetwork.org//glossary.html#L" target="_blank"><sup>?</sup></a></th>
-                            <th data-export="Max LRS Location">Max LRS Location</th>
-                            <th data-export="Add. Eff.">Additive Effect <a href="http://genenetwork.org//glossary.html#A" target="_blank"><sup>?</sup></a></th>
+                            <th data-export="Max LRS">Max LRS <a href="http://genenetwork.org//glossary.html#L" target="_blank"><sup style="font-size: small; color: #FF0000;"> ?</sup></a></th>
+                            <th data-export="Peak Location">Peak Location</th>
+                            <th data-export="Add. Eff.">Effect Size <a href="http://genenetwork.org//glossary.html#A" target="_blank"><sup style="font-size: small; color: #FF0000;"> ?</sup></a></th>
                         </tr>
                     </thead>
 
@@ -144,7 +142,7 @@
                             <TD data-export="{{ this_trait.LRS_score_repr }}" align="right">N/A</TD>
                             {% endif %}
                             <TD data-export="{{ this_trait.LRS_location_repr }}">{{ this_trait.LRS_location_repr }}</TD>
-                            {% if this_trait.additive|float > 0 %}
+                            {% if this_trait.additive|float != 0 %}
                             <TD data-export="{{ this_trait.additive }}" align="right">{{ '%0.3f' % this_trait.additive|float }}</TD>
                             {% else %}
                             <TD data-export="{{ this_trait.additive }}" align="right">N/A</TD>
@@ -166,13 +164,13 @@
 {% block js %}
     <script language="javascript" type="text/javascript" src="/static/new/js_external/jszip.min.js"></script>
     <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='js_alt/md5.min.js') }}"></script>
-    <script type="text/javascript" src="/static/new/javascript/search_results.js"></script>
     <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.dataTables.min.js') }}"></script>
     <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/plugins/sorting/natural.js') }}"></script>
     <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/colResize/dataTables.colResize.js') }}"></script>
     <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/colReorder/js/dataTables.colReorder.js') }}"></script>
     <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/buttons/js/dataTables.buttons.min.js') }}"></script>
     <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/buttons/js/buttons.colVis.min.js') }}"></script>
+    <script type="text/javascript" src="/static/new/javascript/search_results.js"></script>
 
 
     <script language="javascript" type="text/javascript">
@@ -187,10 +185,14 @@
             console.time("Creating table");
             $('#trait_table').dataTable( {
                 "columns": [
-                    { "type": "natural", "width": 10 },
+                    {
+                        "orderDataType": "dom-checkbox",
+                        "orderSequence": [ "desc", "asc"],
+                        "width": 10
+                    },
                     { "type": "natural", "width": 50 },
                     { "type": "natural" },
-                    { "type": "natural", "width": 120 },
+                    { 'type': "natural-minus-na", "width": 120 },
                     { "type": "natural" },
                     { "type": "natural"  },
                     { "type": "natural", "width": 130 },
@@ -199,10 +201,6 @@
                     { "type": "natural", "width": 130 },
                     { "type": "natural" }
                 ],
-                "columnDefs": [ {
-                    "targets": 0,
-                    "orderable": false
-                } ],
                 "order": [[1, "asc" ]],
                 buttons: [
                     {
diff --git a/wqflask/wqflask/templates/correlation_matrix.html b/wqflask/wqflask/templates/correlation_matrix.html
index 9b96de1c..d556f31a 100644
--- a/wqflask/wqflask/templates/correlation_matrix.html
+++ b/wqflask/wqflask/templates/correlation_matrix.html
@@ -51,7 +51,7 @@
       {% if result[0].name == trait.name and result[0].dataset == trait.dataset %}
       <td nowrap="ON" align="center" bgcolor="#cccccc" style="padding: 3px; line-height: 1.1;"><a href="/show_trait?trait_id={{ trait.name }}&dataset={{ trait.dataset.name }}"><font style="font-size: 12px; color: #3071a9; font-weight: bold;" ><em>n</em><br>{{ result[2] }}</font></a></td>
       {% else %}
-      <td nowrap="ON" align="middle" class="corr_cell" style="padding: 3px; line-height: 1.1;"><a href="/corr_scatter_plot?dataset_1={{ trait.dataset.name }}&dataset_2={{ result[0].dataset.name }}&trait_1={{ trait.name }}&trait_2={{ result[0].name }}"><font style="font-size: 12px; color: #3071a9; font-weight: bold;" ><span class="corr_value">{{ '%0.2f' % result[1] }}</span><br>{{ result[2] }}</font></a></td>
+      <td nowrap="ON" align="middle" class="corr_cell" style="padding: 3px; line-height: 1.1;"><a href="/corr_scatter_plot?dataset_1={% if trait.dataset.name == 'Temp' %}Temp_{{ trait.dataset.group.name }}{% else %}{{ trait.dataset.name }}{% endif %}&dataset_2={% if result[0].dataset.name == 'Temp' %}Temp_{{ result[0].dataset.group.name }}{% else %}{{ result[0].dataset.name }}{% endif %}&trait_1={{ trait.name }}&trait_2={{ result[0].name }}"><font style="font-size: 12px; color: #3071a9; font-weight: bold;" ><span class="corr_value">{{ '%0.2f' % result[1] }}</span><br>{{ result[2] }}</font></a></td>
       {% endif %}
       {% endfor %}
     </tr>
diff --git a/wqflask/wqflask/templates/correlation_page.html b/wqflask/wqflask/templates/correlation_page.html
index e597bea9..fb218e29 100644
--- a/wqflask/wqflask/templates/correlation_page.html
+++ b/wqflask/wqflask/templates/correlation_page.html
@@ -144,7 +144,7 @@
                         <td data-export="{{ trait.description_display }}">{{ trait.description_display }}</TD>
                         <td data-export="{{ trait.location_repr }}" style="white-space: nowrap;">{{ trait.location_repr }}</td>
                         <td data-export="{{ '%0.3f' % trait.mean|float }}" align="right">{{ '%0.3f' % trait.mean|float }}</td>
-                        <td data-export="{{ '%0.3f'|format(trait.sample_r) }}"" align="right"><a target="_blank" href="corr_scatter_plot?dataset_1={{dataset.name}}&dataset_2={{trait.dataset.name}}&trait_1={{this_trait.name}}&trait_2={{trait.name}}">{{ '%0.3f'|format(trait.sample_r) }}</a></td>
+                        <td data-export="{{ '%0.3f'|format(trait.sample_r) }}"" align="right"><a target="_blank" href="corr_scatter_plot?dataset_1={% if dataset.name == 'Temp' %}Temp_{{ dataset.group.name }}{% else %}{{ dataset.name }}{% endif %}&dataset_2={% if trait.dataset.name == 'Temp' %}Temp_{{ trait.dataset.group.name }}{% else %}{{ trait.dataset.name }}{% endif %}&trait_1={{ this_trait.name }}&trait_2={{ trait.name }}">{{ '%0.3f'|format(trait.sample_r) }}</a></td>
                         <td data-export="{{ trait.num_overlap }}" align="right">{{ trait.num_overlap }}</td>
                         <td data-export="{{ '%0.3e'|format(trait.sample_p) }}" align="right">{{ '%0.3e'|format(trait.sample_p) }}</td>
                         {% if trait.lit_corr == "" or trait.lit_corr == 0.000 %}
@@ -164,22 +164,26 @@
                         <td data-export={% if trait.additive != "" %}"{{ '%0.3f' % trait.additive|float }}"{% else %}"N/A"{% endif %} align="right">{% if trait.additive != "" %}{{ '%0.3f' % trait.additive|float }}{% else %}N/A{% endif %}</td>
                       {% elif target_dataset.type == "Publish" %}
                         {% if trait.abbreviation %}
-                        <TD title="{{ trait.abbreviation }}" data-export="{{ trait.abbreviation }}">{% if trait.abbreviation|length > 20 %}{{ trait.abbreviation[:20] }}...{% else %}{{ trait.abbreviation }}{% endif %}</TD>
+                        <td title="{{ trait.abbreviation }}" data-export="{{ trait.abbreviation }}">{% if trait.abbreviation|length > 20 %}{{ trait.abbreviation[:20] }}...{% else %}{{ trait.abbreviation }}{% endif %}</td>
                         {% else %}
-                        <TD data-export="N/A">N/A</TD>
+                        <td data-export="N/A">N/A</td>
                         {% endif %}
                         <td data-export="{{ trait.description_display }}">{% if trait.description_display|length > 70 %}{{ trait.description_display[:70] }}...{% else %}{{ trait.description_display }}{% endif %}</td>
                         {% if trait.authors %}
                         <td data-export="{{ trait.authors }}">{% if trait.authors.split(',') > 6 %}{{ trait.authors.split(',')[:6]|join(', ') }}, et al.{% else %}{{ trait.authors }}{% endif %}</td>
                         {% else %}
-                        <TD data-export="N/A">N/A</TD>
+                        <td data-export="N/A">N/A</td>
                         {% endif %}
                         <td data-export="{{ trait.pubmed_text }}">
+                            {% if trait.pubmed_text != "N/A" %}
                             <a href="{{ trait.pubmed_link }}">
                                 {{ trait.pubmed_text }}
                             </a>
+                            {% else %}
+                            {{ trait.pubmed_text }}
+                            {% endif %}
                         </td>
-                        <td data-export="{{ '%0.3f'|format(trait.sample_r) }}" align="right"><a target="_blank" href="corr_scatter_plot?dataset_1={{dataset.name}}&dataset_2={{trait.dataset.name}}&trait_1={{this_trait.name}}&trait_2={{trait.name}}">{{ '%0.3f'|format(trait.sample_r) }}</a></td>
+                        <td data-export="{{ '%0.3f'|format(trait.sample_r) }}"" align="right"><a target="_blank" href="corr_scatter_plot?dataset_1={% if dataset.name == 'Temp' %}Temp_{{ dataset.group.name }}{% else %}{{ dataset.name }}{% endif %}&dataset_2={{ trait.dataset.name }}&trait_1={{ this_trait.name }}&trait_2={{ trait.name }}">{{ '%0.3f'|format(trait.sample_r) }}</a></td>
                         <td data-export="{{ trait.num_overlap }}" align="right">{{ trait.num_overlap }}</td>
                         <td data-export="{{ '%0.3e'|format(trait.sample_p) }}" align="right">{{ '%0.3e'|format(trait.sample_p) }}</td>
                         <td data-export="{{ trait.LRS_score_repr }}" align="right">{{ trait.LRS_score_repr }}</td>
@@ -187,7 +191,7 @@
                         <td data-export={% if trait.additive != "" %}"{{ '%0.3f' % trait.additive|float }}"{% else %}"N/A"{% endif %} align="right">{% if trait.additive != "" %}{{ '%0.3f' % trait.additive|float }}{% else %}N/A{% endif %}</td>
                       {% elif target_dataset.type == "Geno" %}
                         <td data-export="{{ trait.location_repr }}" align="right">{{ trait.location_repr }}</TD>
-                        <td data-export="{{ '%0.3f'|format(trait.sample_r) }}" align="right"><a target="_blank" href="corr_scatter_plot?dataset_1={{dataset.name}}&dataset_2={{trait.dataset.name}}&trait_1={{this_trait.name}}&trait_2={{trait.name}}">{{ '%0.3f'|format(trait.sample_r) }}</a></td>
+                        <td data-export="{{ '%0.3f'|format(trait.sample_r) }}"" align="right"><a target="_blank" href="corr_scatter_plot?dataset_1={% if dataset.name == 'Temp' %}Temp_{{ dataset.group.name }}{% else %}{{ dataset.name }}{% endif %}&dataset_2={{ trait.dataset.name }}&trait_1={{ this_trait.name }}&trait_2={{ trait.name }}">{{ '%0.3f'|format(trait.sample_r) }}</a></td>
                         <td data-export="{{ trait.num_overlap }}" align="right">{{ trait.num_overlap }}</td>
                         <td data-export="{{ '%0.3e'|format(trait.sample_p) }}" align="right">{{ '%0.3e'|format(trait.sample_p) }}</td>
                       {% endif %}
@@ -365,9 +369,9 @@
                     { "type": "numeric-html", 'orderSequence': [ "desc", "asc"] },
                     { "type": "numeric-html", 'orderSequence': [ "desc", "asc"] },
                     { "type": "scientific" },
-                    { "type": "natural" },
-                    { "type": "natural" },
-                    { "type": "natural" }
+                    { "type": "natural-minus-na" },
+                    { "type": "natural-minus-na" },
+                    { "type": "natural-minus-na" }
                 ],
                 "createdRow": function ( row, data, index ) {
                     $('td', row).eq(4).attr('title', $('td', row).eq(4).text());
@@ -419,13 +423,13 @@
                     { "type": "natural" },
                     { "type": "natural", "width": "20%" },
                     { "type": "natural", "width": "12%" },
-                    { "orderDataType": "dom-innertext" },
+                    { "type": "natural-minus-na" },
                     { "orderDataType": "dom-innertext", 'orderSequence': [ "desc", "asc"] },
                     { "type": "natural" },
                     { "type": "scientific" },
-                    { "type": "natural" },
-                    { "type": "natural" },
-                    { "type": "natural" }
+                    { "type": "natural-minus-na" },
+                    { "type": "natural-minus-na" },
+                    { "type": "natural-minus-na" }
                 ],
                 "order": [[9, "asc" ]],
                 "sDom": "Btir",
@@ -461,7 +465,7 @@
                     { "type": "natural" },
                     { "type": "natural" },
                     { "orderDataType": "dom-innertext", 'orderSequence': [ "desc", "asc"] },
-                    { "type": "natural" },
+                    { "type": "natural-minus-na" },
                     { "type": "scientific" }
                 ],
                 "order": [[6, "asc" ]],
diff --git a/wqflask/wqflask/templates/index_page_orig.html b/wqflask/wqflask/templates/index_page_orig.html
index 06b71f53..6b3bec9a 100755
--- a/wqflask/wqflask/templates/index_page_orig.html
+++ b/wqflask/wqflask/templates/index_page_orig.html
@@ -17,13 +17,13 @@
     </header>
 -->
 
-    <div class="container-fluid" style="min-width: 1200px;">
+    <div class="container-fluid" style="min-width: 1210px;">
 
         {{ flash_me() }}
 
         <div class="row" style="width: 100%;">
 
-            <div class="col-xs-5" style="min-width: 530px; max-width: 550px;">
+            <div class="col-xs-4" style="margin-right:50px; min-width: 530px; max-width: 550px;">
                 <section id="search">
                     <div>
                         <h1>Select and search</h1>
@@ -84,7 +84,7 @@
                                     <label for="or_search" class="col-xs-1 control-label" style="padding-left: 0px; padding-right: 0px; width: 65px !important;">Get Any:</label>
                                     <div class="col-xs-10 controls" style="padding-left: 20px;">
                                         <div class="col-8">
-                                          <textarea onkeydown="pressed(event)" name="search_terms_or" rows="1" class="form-control search-query" style="max-width: 550px; width: 450px !important;" id="or_search"></textarea>
+                                          <textarea onkeydown="pressed(event)" name="search_terms_or" rows="1" class="form-control search-query" style="resize: vertical; max-width: 550px; width: 450px !important;" id="or_search"></textarea>
                                         </div>
                                     </div>
                                 </div>
@@ -105,7 +105,7 @@
                                     <label for="and_search" class="col-xs-1 control-label" style="padding-left: 0px; padding-right: 0px; width: 65px !important;">Combined:</label>
                                     <div class="col-xs-10 controls" style="padding-left: 20px;">
                                         <div class="col-8">
-                                          <textarea onkeydown="pressed(event)" name="search_terms_and" rows="1" class="form-control search-query" style="max-width: 550px; width: 450px !important;" id="and_search"></textarea>
+                                          <textarea onkeydown="pressed(event)" name="search_terms_and" rows="1" class="form-control search-query" style="resize: vertical; max-width: 550px; width: 450px !important;" id="and_search"></textarea>
                                         </div>
                                     </div>
                                 </div>
@@ -184,7 +184,7 @@
                 </section>
             </div>
 
-            <div style="padding-left:80px" class="col-xs-4" style="width: 600px !important;">
+            <div class="col-xs-4" style="width: 600px !important;">
 	        <section id="affiliates">
 	            <div class="page-header">
                         <h1>Affiliates</h1>
diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html
index 282e752d..e2e1aa46 100644
--- a/wqflask/wqflask/templates/search_result_page.html
+++ b/wqflask/wqflask/templates/search_result_page.html
@@ -127,7 +127,7 @@
               <input type="hidden" name="export_data" id="export_data" value="">
               <button class="btn btn-default" id="select_all" type="button"><span class="glyphicon glyphicon-ok"></span> Select</button>
               <button class="btn btn-success" id="add" type="button" disabled><span class="glyphicon glyphicon-plus-sign"></span> Add</button>
-              <button class="btn btn-default" id="export_traits">Download CSV</button>
+              <button class="btn btn-default" id="export_traits">Download <span class="glyphicon glyphicon-download"></span></button>
               <input type="text" id="searchbox" class="form-control" style="width: 200px; display: inline;" placeholder="Search This Table For ...">
               <input type="text" id="select_top" class="form-control" style="width: 200px; display: inline;" placeholder="Select Top ...">
               <button class="btn btn-default" id="deselect_all" type="button"><span class="glyphicon glyphicon-remove"></span> Deselect</button>
@@ -274,10 +274,9 @@
                     },
                     {
                       'title': "Record",
-                      'type': "natural",
+                      'type': "natural-minus-na",
                       'data': null,
                       'width': "60px",
-                      'orderDataType': "dom-inner-text",
                       'render': function(data, type, row, meta) {
                         return '<a target="_blank" href="/show_trait?trait_id=' + data.name + '&dataset=' + data.dataset + '">' + data.display_name + '</a>'
                       }
@@ -315,20 +314,20 @@
                       'orderSequence': [ "desc", "asc"]
                     },
                     {
-                      'title': "Max LRS<a href=\"http://genenetwork.org//glossary.html#LRS\" target=\"_blank\" style=\"color: white;\"><sup>?</sup></a>",
+                      'title': "Max LRS<a href=\"http://genenetwork.org//glossary.html#LRS\" target=\"_blank\" style=\"color: white;\"><sup style=\"font-size: small; color: #FF0000;\"> ?</sup></a>",
                       'type': "natural-minus-na",
                       'data': "lrs_score",
                       'width': "80px",
                       'orderSequence': [ "desc", "asc"]
                     },
                     {
-                      'title': "Max LRS Location",
+                      'title': "Peak Location",
                       'type': "natural-minus-na",
-                      'width': "150px",
+                      'width': "120px",
                       'data': "lrs_location"
                     },
                     {
-                      'title': "Additive Effect<a href=\"http://genenetwork.org//glossary.html#A\" target=\"_blank\" style=\"color: white;\"><sup>?</sup></a>",
+                      'title': "Effect Size<a href=\"http://genenetwork.org//glossary.html#A\" target=\"_blank\" style=\"color: white;\"><sup style=\"font-size: small; color: #FF0000;\"> ?</sup></a>",
                       'type': "natural-minus-na",
                       'data': "additive",
                       'width': "120px",
@@ -367,17 +366,11 @@
                           author_string = data.authors
                         }
                         return author_string
-                        // try {
-                        //   return decodeURIComponent(escape(author_string))
-                        // } catch(err){
-                        //   return author_string
-                        // }
                       }
                     },
                     {
                       'title': "Year",
                       'type': "natural-minus-na",
-                      'orderDataType': "dom-inner-text",
                       'data': null,
                       'width': "80px",
                       'render': function(data, type, row, meta) {
@@ -390,20 +383,20 @@
                       'orderSequence': [ "desc", "asc"]
                     },
                     {
-                      'title': "Max LRS<a href=\"http://genenetwork.org//glossary.html#LRS\" target=\"_blank\" style=\"color: white;\"><sup>?</sup></a>",
+                      'title': "Max LRS<a href=\"http://genenetwork.org//glossary.html#LRS\" target=\"_blank\" style=\"color: white;\"><sup style=\"font-size: small; color: #FF0000;\"> ?</sup></a>",
                       'type': "natural-minus-na",
                       'data': "lrs_score",
                       'width': "80px",
                       'orderSequence': [ "desc", "asc"]
                     },
                     {
-                      'title': "Max LRS Location",
+                      'title': "Peak Location",
                       'type': "natural-minus-na",
-                      'width': "150px",
+                      'width': "120px",
                       'data': "lrs_location"
                     },
                     {
-                      'title': "Additive Effect<a href=\"http://genenetwork.org//glossary.html#A\" target=\"_blank\" style=\"color: white;\"><sup>?</sup></a>",
+                      'title': "Effect Size<a href=\"http://genenetwork.org//glossary.html#A\" target=\"_blank\" style=\"color: white;\"><sup style=\"font-size: small; color: #FF0000;\"> ?</sup></a>",
                       'type': "natural-minus-na",
                       'width': "120px",
                       'data': "additive",
@@ -412,7 +405,7 @@
                     {
                       'title': "Location",
                       'type': "natural-minus-na",
-                      'width': "140px",
+                      'width': "120px",
                       'data': "location"
                     }{% endif %}
                 ],
diff --git a/wqflask/wqflask/templates/show_trait_details.html b/wqflask/wqflask/templates/show_trait_details.html
index 8b3e4907..4aced50c 100644
--- a/wqflask/wqflask/templates/show_trait_details.html
+++ b/wqflask/wqflask/templates/show_trait_details.html
@@ -215,43 +215,27 @@
 
 <div style="margin-bottom:15px;" class="btn-toolbar">
     <div class="btn-group">
-        <a href="#redirect">
-        <button type="button" id="add_to_collection" class="btn btn-primary" title="Add to collection">Add</button>
-        </a>
+        <button type="button" id="add_to_collection" class="btn btn-success" title="Add to Collection">Add</button>
         {% if this_trait.dataset.type == 'ProbeSet' or this_trait.dataset.type == 'Geno' %}
         {% if this_trait.symbol != None %}
-        <a target="_blank" href="http://gn1.genenetwork.org/webqtl/main.py?cmd=sch&amp;gene={{ this_trait.symbol }}&amp;alias=1&amp;species={{ dataset.group.species }}">
-        <button type="button" class="btn btn-default" title="Find similar expression data">Find</button>
-        </a>
+        <button type="button" class="btn btn-default" title="Find similar expression data" onclick="window.open('http://gn1.genenetwork.org/webqtl/main.py?cmd=sch&amp;gene={{ this_trait.symbol }}&amp;alias=1&amp;species={{ dataset.group.species }}', '_blank')">Find</button>
         {% endif %}
         {% if UCSC_BLAT_URL != "" %}
-        <a target="_blank" href="{{ UCSC_BLAT_URL }}">
-        <button type="button" class="btn btn-default" title="Check probe locations at UCSC">Verify</button>
-        </a>
+        <button type="button" class="btn btn-default" title="Check probe locations at UCSC" onclick="window.open('{{ UCSC_BLAT_URL }}', '_blank')">Verify</button>
         {% endif %}
         {% if this_trait.symbol != None %}
-        <a target="_blank" href="http://gn1.genenetwork.org/webqtl/main.py?FormID=geneWiki&symbol={{ this_trait.symbol }}">
-        <button type="button" class="btn btn-default" title="Write or review comments about this gene">GeneWiki</button>
-        </a>
+        <button type="button" class="btn btn-default" title="Write or review comments about this gene" onclick="window.open('http://gn1.genenetwork.org/webqtl/main.py?FormID=geneWiki&symbol={{ this_trait.symbol }}', '_blank')">GeneWiki</button>
         {% if dataset.group.species == "mouse" or dataset.group.species == "rat" %}
-        <a href="/snp_browser?first_run=true&species={{ dataset.group.species }}&gene_name={{ this_trait.symbol }}&limit_strains=on">
-        <button type="button" class="btn btn-default" title="View SNPs and Indels">SNPs</button>
-        </a>
+        <button type="button" class="btn btn-default" title="View SNPs and Indels" onclick="window.open('/snp_browser?first_run=true&species={{ dataset.group.species }}&gene_name={{ this_trait.symbol }}&limit_strains=on', '_blank')">SNPs</button>
         {% endif %}
         {% endif %}
         {% if show_probes == "True" %}
-        <a target="_blank" href="http://gn1.genenetwork.org/webqtl/main.py?FormID=showProbeInfo&database={{ this_trait.dataset.name }}&ProbeSetID={{ this_trait.name }}&CellID={{ this_trait.cellid }}&RISet={{ dataset.group.name }}&incparentsf1=ON">
-        <button type="button" class="btn btn-default" title="Check sequence of probes">Probes</button>
-        </a>
+        <button type="button" class="btn btn-default" title="Check sequence of probes" onclick="window.open('http://gn1.genenetwork.org/webqtl/main.py?FormID=showProbeInfo&database={{ this_trait.dataset.name }}&ProbeSetID={{ this_trait.name }}&CellID={{ this_trait.cellid }}&RISet={{ dataset.group.name }}&incparentsf1=ON', '_blank')">Probes</button>
         {% endif %}
         {% endif %}
-        <a target="_blank" href="http://gn1.genenetwork.org/webqtl/main.py?cmd=show&db={{ this_trait.dataset.name }}&probeset={{ this_trait.name }}">
-        <button type="button" id="view_in_gn1" class="btn btn-primary" title="View Trait in GN1">View in GN1</button>
-        </a>
+        <button type="button" id="view_in_gn1" class="btn btn-primary" title="View Trait in GN1" onclick="window.open('http://gn1.genenetwork.org/webqtl/main.py?cmd=show&db={{ this_trait.dataset.name }}&probeset={{ this_trait.name }}', '_blank')">Go to GN1</button>
         {% if admin_status == "owner" or admin_status == "edit-admins" or admin_status == "edit-access" %}
-        <a target="_blank" href="./resources/manage?resource_id={{ resource_id }}">
-            <button type="button" id="edit_resource" class="btn btn-success" title="Edit Resource">Edit</button>
-        </a>
+            <button type="button" id="edit_resource" class="btn btn-success" title="Edit Resource" onclick="window.open('./resources/manage?resource_id={{ resource_id }}', '_blank')">Edit</button>
         {% endif %}
     </div>
 </div>
diff --git a/wqflask/wqflask/templates/show_trait_edit_data.html b/wqflask/wqflask/templates/show_trait_edit_data.html
index 05a2be73..a8ed91b1 100644
--- a/wqflask/wqflask/templates/show_trait_edit_data.html
+++ b/wqflask/wqflask/templates/show_trait_edit_data.html
@@ -5,7 +5,7 @@
           <input type="text" id="{{ sample_type.sample_group_type }}_searchbox" class="form-control" style="width: 200px; display: inline; float: left; vertical-align: top;" placeholder="Search This Table For ...">
         </div>
         <div style="padding-left: 10px; display: inline;">
-          <input type="button" class="btn btn-default export" value="Export">
+          <button class="btn btn-default export">Export <span class="glyphicon glyphicon-download-alt"></span></button>
           <select class="select optional span2 export_format">
             <option value="excel">Excel</option>
             <option value="csv">CSV</option>
diff --git a/wqflask/wqflask/templates/show_trait_statistics.html b/wqflask/wqflask/templates/show_trait_statistics.html
index 974081d3..7bdb3ef9 100644
--- a/wqflask/wqflask/templates/show_trait_statistics.html
+++ b/wqflask/wqflask/templates/show_trait_statistics.html
@@ -76,11 +76,13 @@
                             <i class="icon-signal"></i> Sort By Value
                             </button>
                         </div>
+                        <!--
                         <div class="btn-group">
-                            <button type="button" class="btn btn-default" id="color_by_trait">
+                            <button type="button" class="btn btn-default" id="color_by_trait" style="margin-bottom: 5px;">
                                 <i class="icon-tint"></i> Color by Trait
                             </button>
                         </div>
+                        -->
                         <div id="bar_chart_container">
                             <div id="bar_chart"></div>
                         </div>
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 3d623736..94ec7137 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -29,15 +29,7 @@ import array
 import sqlalchemy
 from wqflask import app
 from flask import g, Response, request, make_response, render_template, send_from_directory, jsonify, redirect, url_for, send_file
-from wqflask import group_manager
-from wqflask import resource_manager
-from wqflask import search_results
-from wqflask import export_traits
-from wqflask import gsearch
-from wqflask import update_search_results
-from wqflask import docs
-from wqflask import news
-from wqflask import db_info
+
 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
@@ -54,6 +46,12 @@ from wqflask.correlation import corr_scatter_plot
 from wqflask.wgcna import wgcna_analysis
 from wqflask.ctl import ctl_analysis
 from wqflask.snp_browser import snp_browser
+from wqflask.search_results import SearchResultPage
+from wqflask.export_traits import export_search_results_csv
+from wqflask.gsearch import GSearch
+from wqflask.update_search_results import GSearch as UpdateGSearch
+from wqflask.docs import Docs, update_text
+from wqflask.db_info import InfoPage
 
 from utility import temp_data
 from utility.tools import SQL_URI,TEMPDIR,USE_REDIS,USE_GN_SERVER,GN_SERVER_URL,GN_VERSION,JS_TWITTER_POST_FETCHER_PATH,JS_GUIX_PATH, CSS_PATH
@@ -67,9 +65,6 @@ from utility.benchmark import Bench
 
 from pprint import pformat as pf
 
-from wqflask import user_login
-from wqflask import user_session
-
 from wqflask import collect
 from wqflask.database import db_session
 
@@ -216,7 +211,7 @@ def search_page():
         logger.info("Skipping Redis cache (USE_REDIS=False)")
 
     logger.info("request.args is", request.args)
-    the_search = search_results.SearchResultPage(request.args)
+    the_search = SearchResultPage(request.args)
     result = the_search.__dict__
     valid_search = result['search_term_exists']
 
@@ -234,7 +229,7 @@ def search_page():
 @app.route("/gsearch", methods=('GET',))
 def gsearchact():
     logger.info(request.url)
-    result = gsearch.GSearch(request.args).__dict__
+    result = GSearch(request.args).__dict__
     type = request.args['type']
     if type == "gene":
         return render_template("gsearch_gene.html", **result)
@@ -245,7 +240,7 @@ def gsearchact():
 def gsearch_updating():
     logger.info("REQUEST ARGS:", request.values)
     logger.info(request.url)
-    result = update_search_results.GSearch(request.args).__dict__
+    result = UpdateGSearch(request.args).__dict__
     return result['results']
     # type = request.args['type']
     # if type == "gene":
@@ -258,7 +253,7 @@ def docedit():
     logger.info(request.url)
     try:
         if g.user_session.record['user_email_address'] == "zachary.a.sloan@gmail.com" or g.user_session.record['user_email_address'] == "labwilliams@gmail.com":
-            doc = docs.Docs(request.args['entry'], request.args)
+            doc = Docs(request.args['entry'], request.args)
             return render_template("docedit.html", **doc.__dict__)
         else:
             return "You shouldn't be here!"
@@ -274,7 +269,7 @@ def generated_file(filename):
 @app.route("/help")
 def help():
     logger.info(request.url)
-    doc = docs.Docs("help", request.args)
+    doc = Docs("help", request.args)
     return render_template("docs.html", **doc.__dict__)
 
 @app.route("/wgcna_setup", methods=('POST',))
@@ -309,54 +304,54 @@ def ctl_results():
 
 @app.route("/news")
 def news():
-    doc = docs.Docs("news", request.args)
+    doc = Docs("news", request.args)
     return render_template("docs.html", **doc.__dict__)
 
 @app.route("/references")
 def references():
-    doc = docs.Docs("references", request.args)
+    doc = Docs("references", request.args)
     return render_template("docs.html", **doc.__dict__)
     #return render_template("reference.html")
 
 @app.route("/intro")
 def intro():
-    doc = docs.Docs("intro", request.args)
+    doc = Docs("intro", request.args)
     return render_template("docs.html", **doc.__dict__)
 
 @app.route("/policies")
 def policies():
-    doc = docs.Docs("policies", request.args)
+    doc = Docs("policies", request.args)
     #return render_template("policies.html")
     return render_template("docs.html", **doc.__dict__)
 
 @app.route("/links")
 def links():
-    #doc = docs.Docs("links", request.args)
+    #doc = Docs("links", request.args)
     #return render_template("docs.html", **doc.__dict__)
     return render_template("links.html")
 
 @app.route("/tutorials")
 def tutorials():
-    #doc = docs.Docs("links", request.args)
+    #doc = Docs("links", request.args)
     #return render_template("docs.html", **doc.__dict__)
     return render_template("tutorials.html")
 
 @app.route("/credits")
 def credits():
-    #doc = docs.Docs("links", request.args)
+    #doc = Docs("links", request.args)
     #return render_template("docs.html", **doc.__dict__)
     return render_template("credits.html")
 
 @app.route("/environments")
 def environments():
-    doc = docs.Docs("environments", request.args)
+    doc = Docs("environments", request.args)
     return render_template("docs.html", **doc.__dict__)
     #return render_template("environments.html", **doc.__dict__)
 
 @app.route("/update_text", methods=('POST',))
 def update_page():
-    docs.update_text(request.form)
-    doc = docs.Docs(request.form['entry_type'], request.form)
+    update_text(request.form)
+    doc = Docs(request.form['entry_type'], request.form)
     return render_template("docs.html", **doc.__dict__)
 
 @app.route("/submit_trait")
@@ -371,7 +366,7 @@ def create_temp_trait():
 
     #template_vars = submit_trait.SubmitTrait(request.form)
 
-    doc = docs.Docs("links")
+    doc = Docs("links")
     return render_template("links.html", **doc.__dict__)
     #return render_template("show_trait.html", **template_vars.__dict__)
 
@@ -426,7 +421,7 @@ def export_traits_csv():
     logger.info("In export_traits_csv")
     logger.info("request.form:", request.form)
     logger.info(request.url)
-    file_list = export_traits.export_search_results_csv(request.form)
+    file_list = export_search_results_csv(request.form)
 
     if len(file_list) > 1:
         now = datetime.datetime.now()
@@ -911,7 +906,7 @@ def snp_browser_page():
 
 @app.route("/db_info", methods=('GET',))
 def db_info_page():
-    template_vars = db_info.InfoPage(request.args)
+    template_vars = InfoPage(request.args)
 
     return render_template("info_page.html", **template_vars.__dict__)