Merged taxonomy_tree branch into bwm

DNA-BarKeeper · Jul 16, 2021 · 296368c · 296368c
2 parents c349dd0 + be3c547
commit 296368c
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Showing 140 changed files with 2,789 additions and 2,568 deletions.
diff --git a/app/assets/javascripts/application.js b/app/assets/javascripts/application.js
@@ -37,5 +37,31 @@
 //= require bootstrap-multiselect
 //= require_tree .
 
+
 // Make datatables warning more meaningful
 $.fn.dataTable.ext.errMode = () => alert('An error occurred while loading the data table. Please contact an admin if the error persists.');
+
+// Function to replace html relevant characters to prevent XSS attacks
+function htmlSafe(str) {
+    return String(str).replace(/&/g, '&amp;').replace(/</g, '&lt;').replace(/>/g, '&gt;').replace(/"/g, '&quot;');
+}
+
+function enableButton(button, message = null) {
+    button.removeAttr('disabled');
+    if (message) {
+        button.attr('title', message);
+    }
+    else {
+        button.removeAttr('title');
+    }
+}
+
+function disableButton(button, message) {
+    button.attr('disabled', 'disabled');
+    button.attr('title', message);
+}
+
+// Delete previous diagram
+function deleteVisualization(id) {
+    d3.select(id).selectAll("svg").remove();
+}
diff --git a/app/assets/javascripts/contig_searches.js b/app/assets/javascripts/contig_searches.js
@@ -74,17 +74,8 @@ jQuery(function() {
         minLength: 2
     });
 
-    $('#contig_search_species').autocomplete({
-        source: $('#contig_search_species').data('autocomplete-source'),
-        minLength: 2
-    });
-
-    $('#contig_search_family').autocomplete({
-        source: $('#contig_search_family').data('autocomplete-source')
-    });
-
-    $('#contig_search_order').autocomplete({
-        source: $('#contig_search_order').data('autocomplete-source')
+    $('#contig_search_taxon').autocomplete({
+        source: $('#contig_search_taxon').data('autocomplete-source')
     });
 
     $('#contig_search_verified_by').autocomplete({

diff --git a/app/assets/javascripts/gens.js.coffee b/app/assets/javascripts/gens.js.coffee
diff --git a/app/assets/javascripts/individual_searches.js b/app/assets/javascripts/individual_searches.js
@@ -53,16 +53,8 @@ jQuery(function() {
         source: $('#individual_search_herbarium').data('autocomplete-source')
     });
 
-    $('#individual_search_species').autocomplete({
-        source: $('#individual_search_species').data('autocomplete-source'),
+    $('#individual_search_taxon').autocomplete({
+        source: $('#individual_search_taxon').data('autocomplete-source'),
         minLength: 2
     });
-
-    $('#individual_search_family').autocomplete({
-        source: $('#individual_search_family').data('autocomplete-source')
-    });
-
-    $('#individual_search_order').autocomplete({
-        source: $('#individual_search_order').data('autocomplete-source')
-    });
 });
diff --git a/app/assets/javascripts/individuals.js b/app/assets/javascripts/individuals.js
@@ -37,8 +37,8 @@ jQuery(function() {
         no_results_text: 'No results matched'
     });
 
-    $('#individual_species_name').autocomplete({
-        source: $('#individual_species_name').data('autocomplete-source')
+    $('#individual_taxon_name').autocomplete({
+        source: $('#individual_taxon_name').data('autocomplete-source')
     });
 
     $('#individual_collected').datepicker({

diff --git a/app/assets/javascripts/marker_sequence_searches.js b/app/assets/javascripts/marker_sequence_searches.js
@@ -74,23 +74,11 @@ jQuery(function() {
         minLength: 2
     });
 
-    $('#marker_sequence_search_species').autocomplete({
-        source: $('#marker_sequence_search_species').data('autocomplete-source'),
+    $('#marker_sequence_search_taxon').autocomplete({
+        source: $('#marker_sequence_search_taxon').data('autocomplete-source'),
         minLength: 2
     });
 
-    $('#marker_sequence_search_family').autocomplete({
-        source: $('#marker_sequence_search_family').data('autocomplete-source')
-    });
-
-    $('#marker_sequence_search_order').autocomplete({
-        source: $('#marker_sequence_search_order').data('autocomplete-source')
-    })
-
-    $('#marker_sequence_search_higher_order_taxon').autocomplete({
-        source: $('#marker_sequence_search_higher_order_taxon').data('autocomplete-source')
-    });
-
     $('#marker_sequence_search_verified_by').autocomplete({
         source: $('#marker_sequence_search_verified_by').data('autocomplete-source')
     });

diff --git a/app/assets/javascripts/ngs_runs.js b/app/assets/javascripts/ngs_runs.js
@@ -71,4 +71,8 @@ jQuery(function() {
             tag_primer_map.val("");
         }
     });
+
+    $('#ngs_run_taxon_name').autocomplete({
+        source: $('#ngs_run_taxon_name').data('autocomplete-source')
+    });
 });
diff --git a/app/assets/javascripts/overview_diagram.js b/app/assets/javascripts/overview_diagram.js