From 7438f3c45122f02c25155b42ede703ad2845649c Mon Sep 17 00:00:00 2001
From: zsloan
Date: Wed, 17 Jun 2020 13:40:10 -0500
Subject: Fixed issue caused by mapping scale sometimes being wrong + fixed
 Verify link

---
 wqflask/wqflask/marker_regression/gemma_mapping.py            |  2 --
 wqflask/wqflask/marker_regression/run_mapping.py              |  1 +
 wqflask/wqflask/show_trait/show_trait.py                      |  8 ++++----
 .../wqflask/static/new/javascript/show_trait_mapping_tools.js |  4 ++--
 wqflask/wqflask/templates/show_trait_mapping_tools.html       | 11 +++++++++++
 5 files changed, 18 insertions(+), 8 deletions(-)

diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py
index 88d27517..b858b573 100644
--- a/wqflask/wqflask/marker_regression/gemma_mapping.py
+++ b/wqflask/wqflask/marker_regression/gemma_mapping.py
@@ -136,9 +136,7 @@ def gen_covariates_file(this_dataset, covariates, samples):
         #trait_samples = this_dataset.group.all_samples_ordered()
         this_dataset.group.get_samplelist()
         trait_samples = this_dataset.group.samplelist
-        logger.debug("SAMPLES:", trait_samples)
         trait_sample_data = trait_ob.data
-        logger.debug("SAMPLE DATA:", trait_sample_data)
         for index, sample in enumerate(trait_samples):
             if sample in samples:
                 if sample in trait_sample_data:
diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py
index 0711b852..c859fdaa 100644
--- a/wqflask/wqflask/marker_regression/run_mapping.py
+++ b/wqflask/wqflask/marker_regression/run_mapping.py
@@ -162,6 +162,7 @@ class RunMapping(object):
         self.perm_output = []
         self.bootstrap_results = []
         self.covariates = start_vars['covariates'] if "covariates" in start_vars else ""
+        self.categorical_vars = []
 
         #ZS: This is passed to GN1 code for single chr mapping
         self.selected_chr = -1
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index c77e247f..ed4ff0ad 100644
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -22,7 +22,7 @@ from base.trait import create_trait
 from base import data_set
 from db import webqtlDatabaseFunction
 from utility import webqtlUtil, Plot, Bunch, helper_functions
-from utility.authentication_tools import check_owner
+from utility.authentication_tools import check_owner_or_admin
 from utility.tools import locate_ignore_error
 from utility.redis_tools import get_redis_conn, get_resource_id
 Redis = get_redis_conn()
@@ -72,11 +72,11 @@ class ShowTrait(object):
                                            cellid=None)
             self.trait_vals = Redis.get(self.trait_id).split()
 
-        self.resource_id = check_owner(self.dataset, self.trait_id)
+        self.admin_status = check_owner_or_admin(self.dataset, self.trait_id)
 
         #ZS: Get verify/rna-seq link URLs
         try:
-            blatsequence = self.this_trait.sequence
+            blatsequence = self.this_trait.blatseq
             if not blatsequence:
                 #XZ, 06/03/2009: ProbeSet name is not unique among platforms. We should use ProbeSet Id instead.
                 query1 = """SELECT Probe.Sequence, Probe.Name
@@ -256,7 +256,7 @@ class ShowTrait(object):
         hddn['export_data'] = ""
         hddn['export_format'] = "excel"
         if len(self.scales_in_geno) < 2:
-            hddn['mapping_scale'] = self.scales_in_geno[self.scales_in_geno.keys()[0]][0]
+            hddn['mapping_scale'] = self.scales_in_geno[self.scales_in_geno.keys()[0]][0][0]
 
         # We'll need access to this_trait and hddn in the Jinja2 Template, so we put it inside self
         self.hddn = hddn
diff --git a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
index 01da3f74..db17af40 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
@@ -3,9 +3,9 @@
   var block_outliers, composite_mapping_fields, do_ajax_post, get_progress, mapping_method_fields, open_mapping_results, outlier_text, showalert, submit_special, toggle_enable_disable, update_time_remaining;
 
   submit_special = function(url) {
-    console.log("In submit_special");
     $("#trait_data_form").attr("action", url);
-    return $("#trait_data_form").submit();
+    $("#trait_data_form").submit();
+    return false;
   };
 
   update_time_remaining = function(percent_complete) {
diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html
index a2416ced..e851a81e 100755
--- a/wqflask/wqflask/templates/show_trait_mapping_tools.html
+++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html
@@ -140,6 +140,17 @@
                                 </select>
                             </div>
                         </div>
+                        {% else %}
+                        <div class="mapping_method_fields form-group">
+                            <label for="scale_select" style="text-align: right;" class="col-xs-3 control-label">Map Scale</label>
+                            <div style="margin-left:20px;" class="col-xs-2 controls">
+                                <select id="scale_reaper" class="form-control" style="width: 80px;">
+                                    {% for item in scales_in_geno[dataset.group.name + ".geno"] %}
+                                    <option value="{{ item[0] }}">{{ item[1] }}</option>
+                                    {% endfor %}
+                                </select>
+                            </div>
+                        </div>
                         {% endif %}
                         <div class="mapping_method_fields form-group">
                             <label style="text-align: right;" for="mapping_permutations" class="col-xs-3 control-label">Permutations</label>
-- 
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