From 9769245cf3595273055d686a689cdcecb4b3645a Mon Sep 17 00:00:00 2001
From: zsloan
Date: Thu, 7 Mar 2019 17:14:56 -0600
Subject: Changed the way covariates are displayed when selected for mapping

Made the outlier notification appear for all mapping methods

Removed some misleading text saying "Block samples" from the Transform and Filter Data section
---
 wqflask/base/trait.py                                   |  4 ++++
 .../new/javascript/get_covariates_from_collection.js    | 17 ++++++++++++++---
 .../static/new/javascript/show_trait_mapping_tools.js   |  2 +-
 .../templates/show_trait_transform_and_filter.html      |  1 -
 4 files changed, 19 insertions(+), 5 deletions(-)

diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index 9f76306f..79aa196f 100644
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -220,6 +220,7 @@ def jsonable(trait):
                         dataset=dataset.name,
                         dataset_name = dataset.shortname,
                         description=trait.description_display,
+                        abbreviation=trait.abbreviation,
                         authors=trait.authors,
                         pubmed_text=trait.pubmed_text,
                         pubmed_link=trait.pubmed_link,
@@ -232,6 +233,7 @@ def jsonable(trait):
                         dataset=dataset.name,
                         dataset_name = dataset.shortname,
                         description=trait.description_display,
+                        abbreviation=trait.abbreviation,
                         authors=trait.authors,
                         pubmed_text=trait.pubmed_text,
                         lrs_score=trait.LRS_score_repr,
@@ -397,6 +399,7 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
             #phenotype traits, then display the pre-publication description instead
             #of the post-publication description
             if trait.confidential:
+                trait.abbreviation = trait.pre_publication_abbreviation
                 trait.description_display = trait.pre_publication_description
 
                 #if not webqtlUtil.hasAccessToConfidentialPhenotypeTrait(
@@ -406,6 +409,7 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
                 #
                 #    description = self.pre_publication_description
             else:
+                trait.abbreviation = trait.post_publication_abbreviation
                 if description:
                     trait.description_display = description.strip()
                 else:
diff --git a/wqflask/wqflask/static/new/javascript/get_covariates_from_collection.js b/wqflask/wqflask/static/new/javascript/get_covariates_from_collection.js
index fc6e5a78..8cd6dac3 100644
--- a/wqflask/wqflask/static/new/javascript/get_covariates_from_collection.js
+++ b/wqflask/wqflask/static/new/javascript/get_covariates_from_collection.js
@@ -81,17 +81,22 @@ submit_click = function() {
   $('#collections_holder').find('input[type=checkbox]:checked').each(function() {
     var this_dataset, this_trait;
     this_trait = $(this).parents('tr').find('.trait').text();
+    this_trait_display = $(this).parents('tr').find('.trait').data("display_name");
     this_description = $(this).parents('tr').find('.description').text();
-    console.log("this_trait is:", this_trait);
+    console.log("this_trait is:", this_trait_display);
     this_dataset = $(this).parents('tr').find('.dataset').data("dataset");
     console.log("this_dataset is:", this_dataset);
     covariates_string += this_trait + ":" + this_dataset + ","
-    this_covariate_display_string = this_trait + ": " + this_description
+    //this_covariate_display_string = this_trait + ": " + this_description
+    this_covariate_display_string = this_trait_display
     if (this_covariate_display_string.length > 50) {
       this_covariate_display_string = this_covariate_display_string.substring(0, 45) + "..."
     }
     covariates_display_string += this_covariate_display_string + "\n"
   });
+  // Trim the last newline from display_string
+  covariates_display_string = covariates_display_string.replace(/\n$/, "")
+
   // Trim the last comma
   covariates_string = covariates_string.substring(0, covariates_string.length - 1)
   //covariates_display_string = covariates_display_string.substring(0, covariates_display_string.length - 2)
@@ -189,7 +194,13 @@ process_traits = function(trait_data, textStatus, jqXHR) {
     trait = trait_data[_i];
     the_html += "<tr class='trait_line'>";
     the_html += "<td class='select_trait'><input type='checkbox' name='selectCheck' class='checkbox edit_sample_checkbox'></td>";
-    the_html += "<td class='trait'>" + trait.name + "</td>";
+    if ("abbreviation" in trait) {
+        the_html += "<td class='trait' data-display_name='" + trait.name + " - " + trait.abbreviation + "'>" + trait.name + "</td>";
+    } else if ("symbol" in trait) {
+      the_html += "<td class='trait' data-display_name='" + trait.name + " - " + trait.symbol + "'>" + trait.name + "</td>";
+    } else {
+      the_html += "<td class='trait' data-display_name='" + trait.name + "'>" + trait.name + "</td>";
+    }
     the_html += "<td class='dataset' data-dataset='" + trait.dataset + "'>" + trait.dataset_name + "</td>";
     the_html += "<td class='description'>" + trait.description + "</td>";
   }
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 2ab87d03..28af232d 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
@@ -225,7 +225,7 @@
     };
   })(this));
 
-  $("#interval_mapping_compute").on("mouseover", (function(_this) {
+  $("#interval_mapping_compute, #gemma_compute, rqtl_geno_compute").on("mouseover", (function(_this) {
     return function() {
       if ($(".outlier").length && $(".outlier-alert").length < 1) {
         return showalert(outlier_text, "alert-success outlier-alert");
diff --git a/wqflask/wqflask/templates/show_trait_transform_and_filter.html b/wqflask/wqflask/templates/show_trait_transform_and_filter.html
index 6803da58..94b3fda3 100644
--- a/wqflask/wqflask/templates/show_trait_transform_and_filter.html
+++ b/wqflask/wqflask/templates/show_trait_transform_and_filter.html
@@ -1,6 +1,5 @@
 <div>
     <div class="form-horizontal">
-            <legend>Block samples</legend>
             <p>Edit or delete values in the Trait Data boxes, and use the
                 <strong>Reset</strong> option as
                 needed.
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