Fixed issue where qnorm values were wrong

Fixed issue where traits couldn't be highlighted or added to a collection from global search results

Fixed issue where third party links threw an error for some traits on the trait page

Fixed issue where clicking a row's link unhighlighted it

5 files changed, 80 insertions, 5 deletions

diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index 5c349bf3..1dd80962 100644
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -278,7 +278,12 @@ class ShowTrait(object):
                             FROM GeneList
                             WHERE geneSymbol = '{}'""".format(self.this_trait.symbol)
 
-                    chr, transcript_start, transcript_end = g.db.execute(query).fetchall()[0] if len(g.db.execute(query).fetchall()) > 0 else None
+                    results = g.db.execute(query).fetchone()
+                    if results:
+                        chr, transcript_start, transcript_end = results
+                    else:
+                        chr = transcript_start = transcript_end = None
+
                     if chr and transcript_start and transcript_end and self.this_trait.refseq_transcriptid:
                         transcript_start = int(transcript_start*1000000)
                         transcript_end = int(transcript_end*1000000)
@@ -292,7 +297,7 @@ class ShowTrait(object):
                         WHERE geneSymbol = '{}'""".format(self.this_trait.symbol)
 
                 results = g.db.execute(query).fetchone()
-		if results:
+                if results:
                     kgId, chr, transcript_start, transcript_end = results
                 else:
                     kgId = chr = transcript_start = transcript_end = None
diff --git a/wqflask/wqflask/templates/gsearch_gene.html b/wqflask/wqflask/templates/gsearch_gene.html
index 9b584ea5..0ee98972 100644
--- a/wqflask/wqflask/templates/gsearch_gene.html
+++ b/wqflask/wqflask/templates/gsearch_gene.html
@@ -78,8 +78,43 @@
                 }
             });
 
+            function change_buttons() {
+                buttons = ["#add", "#remove"];
+                num_checked = $('.trait_checkbox:checked').length;
+                if (num_checked === 0) {
+                    for (_i = 0, _len = buttons.length; _i < _len; _i++) {
+                        button = buttons[_i];
+                        $(button).prop("disabled", true);
+                    }
+                } else {
+                    for (_j = 0, _len2 = buttons.length; _j < _len2; _j++) {
+                        button = buttons[_j];
+                        $(button).prop("disabled", false);
+                    }
+                }
+                         //});
+                if ($(this).is(":checked")) {
+                    if (!$(this).closest('tr').hasClass('selected')) {
+                        $(this).closest('tr').addClass('selected')
+                    }
+                }
+                else {
+                    if ($(this).closest('tr').hasClass('selected')) {
+                        $(this).closest('tr').removeClass('selected')
+                    }
+                }
+            }
+
             console.time("Creating table");
             $('#trait_table').DataTable( {
+                'drawCallback': function( settings ) {
+                     $('#trait_table tr').click(function(event) {
+                         if (event.target.type !== 'checkbox' && event.target.tagName.toLowerCase() !== 'a') {
+                             $(':checkbox', this).trigger('click');
+                         }
+                     });
+                     $('.trait_checkbox:checkbox').on("change", change_buttons);
+                },
                 'createdRow': function ( row, data, index ) {
                     $('td', row).eq(0).attr("style", "text-align: center; padding: 4px 10px 2px 10px;");
                     $('td', row).eq(1).attr("align", "right");
diff --git a/wqflask/wqflask/templates/gsearch_pheno.html b/wqflask/wqflask/templates/gsearch_pheno.html
index 609c1852..4e142846 100644
--- a/wqflask/wqflask/templates/gsearch_pheno.html
+++ b/wqflask/wqflask/templates/gsearch_pheno.html
@@ -78,8 +78,43 @@
                 }
             });
 
+            function change_buttons() {
+                buttons = ["#add", "#remove"];
+                num_checked = $('.trait_checkbox:checked').length;
+                if (num_checked === 0) {
+                    for (_i = 0, _len = buttons.length; _i < _len; _i++) {
+                        button = buttons[_i];
+                        $(button).prop("disabled", true);
+                    }
+                } else {
+                    for (_j = 0, _len2 = buttons.length; _j < _len2; _j++) {
+                        button = buttons[_j];
+                        $(button).prop("disabled", false);
+                    }
+                }
+                         //});
+                if ($(this).is(":checked")) {
+                    if (!$(this).closest('tr').hasClass('selected')) {
+                        $(this).closest('tr').addClass('selected')
+                    }
+                }
+                else {
+                    if ($(this).closest('tr').hasClass('selected')) {
+                        $(this).closest('tr').removeClass('selected')
+                    }
+                }
+            }
+
             console.time("Creating table");
             $('#trait_table').DataTable( {
+                'drawCallback': function( settings ) {
+                     $('#trait_table tr').click(function(event) {
+                         if (event.target.type !== 'checkbox' && event.target.tagName.toLowerCase() !== 'a') {
+                             $(':checkbox', this).trigger('click');
+                         }
+                     });
+                     $('.trait_checkbox:checkbox').on("change", change_buttons);
+                },
                 "createdRow": function ( row, data, index ) {
                     $('td', row).eq(0).attr("style", "text-align: center; padding: 4px 10px 2px 10px;");
                     $('td', row).eq(1).attr("align", "right");
diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html
index d1bfbd23..b1442b7f 100644
--- a/wqflask/wqflask/templates/search_result_page.html
+++ b/wqflask/wqflask/templates/search_result_page.html
@@ -205,7 +205,7 @@
             $('#trait_table').DataTable( {
                 'drawCallback': function( settings ) {
                      $('#trait_table tr').click(function(event) {
-                         if (event.target.type !== 'checkbox') {
+                         if (event.target.type !== 'checkbox' && event.target.tagName.toLowerCase() !== 'a') {
                              $(':checkbox', this).trigger('click');
                          }
                      });
@@ -398,7 +398,7 @@
                         postfixButtons: [ 'colvisRestore' ]
                     }
                 ],
-                'sDom': "Btir",
+                'sDom': "Bitir",
                 'autoWidth': false,
                 'deferRender': true,
                 'paging': false,
diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index d5473bca..ea7c5123 100644
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -296,7 +296,7 @@
                         if (data.value == null) {
                           return '<input type="text" data-value="x" data-qnorm="x" data-zscore="x" name="value:' + data.name + '" style="text-align: right;" class="trait_value_input edit_sample_value" value="x" size=6 maxlength=6>'
                         } else {
-                          return '<input type="text" data-value="' + data.value.toFixed(3) + '" data-qnorm="' + js_data['qnorm_values'][0][parseInt(data.this_id)] + '" data-zscore="' + js_data['zscore_values'][0][parseInt(data.this_id)] + '" name="value:' + data.name + '" style="text-align: right;" class="trait_value_input edit_sample_value" value="' + data.value.toFixed(3) + '" size=6 maxlength=6>'
+                          return '<input type="text" data-value="' + data.value.toFixed(3) + '" data-qnorm="' + js_data['qnorm_values'][0][parseInt(data.this_id) - 1] + '" data-zscore="' + js_data['zscore_values'][0][parseInt(data.this_id) - 1] + '" name="value:' + data.name + '" style="text-align: right;" class="trait_value_input edit_sample_value" value="' + data.value.toFixed(3) + '" size=6 maxlength=6>'
                         }
                       }
                     }{% if sample_groups[0].se_exists() %},