From 7a2a59f3d225f94bda5a9bc51a958d3203ea690c Mon Sep 17 00:00:00 2001
From: zsloan
Date: Wed, 18 Nov 2020 12:48:43 -0600
Subject: Fixed issue that was causing scatterplot cofactors to not work if the
 cofactors were genotypes (because it tried to get the "description_display"
 which doesn't exist for genotype traits)

---
 wqflask/base/trait.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

(limited to 'wqflask/base')

diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index cfc02f8b..7763dbe8 100644
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -265,11 +265,12 @@ def get_sample_data():
         trait_dict['species'] = trait_ob.dataset.group.species
         trait_dict['url'] = url_for(
             'show_trait_page', trait_id=trait, dataset=dataset)
-        trait_dict['description'] = trait_ob.description_display
         if trait_ob.dataset.type == "ProbeSet":
             trait_dict['symbol'] = trait_ob.symbol
             trait_dict['location'] = trait_ob.location_repr
+            trait_dict['description'] = trait_ob.description_display
         elif trait_ob.dataset.type == "Publish":
+            trait_dict['description'] = trait_ob.description_display
             if trait_ob.pubmed_id:
                 trait_dict['pubmed_link'] = trait_ob.pubmed_link
             trait_dict['pubmed_text'] = trait_ob.pubmed_text
-- 
cgit v1.2.3


From 6ed037083f0b2bac95021e5fb00c0c8877422a47 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Wed, 18 Nov 2020 14:06:27 -0600
Subject: Fixed issue where the cofactor trait descriptions didn't work
 correctly for genotype/snp cofactors (the code previously only accounted for
 probeset/phenotype cofactors,  so it was treating genotypes/snps like
 phenotype traits)

---
 wqflask/base/trait.py                              |  2 ++
 .../new/javascript/get_traits_from_collection.js   | 24 ++++++++++++++++------
 2 files changed, 20 insertions(+), 6 deletions(-)

(limited to 'wqflask/base')

diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index 7763dbe8..0f8f937c 100644
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -274,6 +274,8 @@ def get_sample_data():
             if trait_ob.pubmed_id:
                 trait_dict['pubmed_link'] = trait_ob.pubmed_link
             trait_dict['pubmed_text'] = trait_ob.pubmed_text
+        else:
+            trait_dict['location'] = trait_ob.location_repr
 
         return json.dumps([trait_dict, {key: value.value for
                                         key, value in list(
diff --git a/wqflask/wqflask/static/new/javascript/get_traits_from_collection.js b/wqflask/wqflask/static/new/javascript/get_traits_from_collection.js
index a55ab356..626357d4 100644
--- a/wqflask/wqflask/static/new/javascript/get_traits_from_collection.js
+++ b/wqflask/wqflask/static/new/javascript/get_traits_from_collection.js
@@ -201,13 +201,17 @@ populate_cofactor_info = function(trait_info) {
     if (trait_info['type'] == "ProbeSet"){
       $('#cofactor1_trait_link').text(trait_info['species'] + " " + trait_info['group'] + " " + trait_info['tissue'] + " " + trait_info['db'] + ": " + trait_info['name'])
       $('#cofactor1_description').text("[" + trait_info['symbol'] + " on " + trait_info['location'] + " Mb]\n" + trait_info['description'])
-    } else {
+    } else if (trait_info['type'] == "Publish") {
       $('#cofactor1_trait_link').text(trait_info['species'] + " " + trait_info['group'] + " " + trait_info['db'] + ": " + trait_info['name'])
       if ('pubmed_link' in trait_info) {
         $('#cofactor1_description').html('<a href=\"' + trait_info['pubmed_link'] + '\">PubMed: ' + trait_info['pubmed_text'] + '</a><br>' + trait_info['description'])
       } else {
-        $('#cofactor1_description').html('PubMed: ' + trait_info['pubmed_text'] + '<br>' + trait_info['description'])
+        $('#cofactor1_trait_link').text(trait_info['species'] + " " + trait_info['group'] + " " + trait_info['db'] + ": " + trait_info['name'])
+        $('#cofactor1_description').text("[" + trait_info['name'] + " on " + trait_info['location'] + " Mb]\n" + trait_info['description'])
       }
+    } else {
+      $('#cofactor1_trait_link').text(trait_info['species'] + " " + trait_info['group'] + " " + trait_info['db'] + ": " + trait_info['name'])
+      $('#cofactor1_description').text("[" + trait_info['name'] + " on " + trait_info['location'] + " Mb]\n")
     }
     $('#select_cofactor1').text("Change Cofactor 1");
     $('#cofactor1_info_container').css("display", "inline");
@@ -217,13 +221,17 @@ populate_cofactor_info = function(trait_info) {
     if (trait_info['type'] == "ProbeSet"){
       $('#cofactor2_trait_link').text(trait_info['species'] + " " + trait_info['group'] + " " + trait_info['tissue'] + " " + trait_info['db'] + ": " + trait_info['name'])
       $('#cofactor2_description').text("[" + trait_info['symbol'] + " on " + trait_info['location'] + " Mb]\n" + trait_info['description'])
-    } else {
+    } else if (trait_info['type'] == "Publish") {
       $('#cofactor2_trait_link').text(trait_info['species'] + " " + trait_info['group'] + " " + trait_info['db'] + ": " + trait_info['name'])
       if ('pubmed_link' in trait_info) {
         $('#cofactor2_description').html('<a href=\"' + trait_info['pubmed_link'] + '\">PubMed: ' + trait_info['pubmed_text'] + '</a><br>' + trait_info['description'])
       } else {
-        $('#cofactor2_description').html('PubMed: ' + trait_info['pubmed_text'] + '<br>' + trait_info['description'])
+        $('#cofactor2_trait_link').text(trait_info['species'] + " " + trait_info['group'] + " " + trait_info['db'] + ": " + trait_info['name'])
+        $('#cofactor2_description').text("[" + trait_info['name'] + " on " + trait_info['location'] + " Mb]\n" + trait_info['description'])
       }
+    } else {
+      $('#cofactor2_trait_link').text(trait_info['species'] + " " + trait_info['group'] + " " + trait_info['db'] + ": " + trait_info['name'])
+      $('#cofactor2_description').text("[" + trait_info['name'] + " on " + trait_info['location'] + " Mb]\n")
     }
     $('#select_cofactor2').text("Change Cofactor 2");
     $('#cofactor2_info_container').css("display", "inline");
@@ -233,13 +241,17 @@ populate_cofactor_info = function(trait_info) {
     if (trait_info['type'] == "ProbeSet"){
       $('#cofactor3_trait_link').text(trait_info['species'] + " " + trait_info['group'] + " " + trait_info['tissue'] + " " + trait_info['db'] + ": " + trait_info['name'])
       $('#cofactor3_description').text("[" + trait_info['symbol'] + " on " + trait_info['location'] + " Mb]\n" + trait_info['description'])
-    } else {
+    } else if (trait_info['type'] == "Publish") {
       $('#cofactor3_trait_link').text(trait_info['species'] + " " + trait_info['group'] + " " + trait_info['db'] + ": " + trait_info['name'])
       if ('pubmed_link' in trait_info) {
         $('#cofactor3_description').html('<a href=\"' + trait_info['pubmed_link'] + '\">PubMed: ' + trait_info['pubmed_text'] + '</a><br>' + trait_info['description'])
       } else {
-        $('#cofactor3_description').html('PubMed: ' + trait_info['pubmed_text'] + '<br>' + trait_info['description'])
+        $('#cofactor3_trait_link').text(trait_info['species'] + " " + trait_info['group'] + " " + trait_info['db'] + ": " + trait_info['name'])
+        $('#cofactor3_description').text("[" + trait_info['name'] + " on " + trait_info['location'] + " Mb]\n" + trait_info['description'])
       }
+    } else {
+      $('#cofactor3_trait_link').text(trait_info['species'] + " " + trait_info['group'] + " " + trait_info['db'] + ": " + trait_info['name'])
+      $('#cofactor3_description').text("[" + trait_info['name'] + " on " + trait_info['location'] + " Mb]\n")
     }
     $('#select_cofactor3').text("Change Cofactor 3");
     $('#cofactor3_info_container').css("display", "inline");
-- 
cgit v1.2.3