Merging QA to master for April 2021 release (#347)

* undefined formatName bug fix (#317)

* undefined formatName bug fix

* remove unused prop

* restore prop checking: needs clean up in next release

* added Education to tools bar (#318)

* fixed the error message for variant search

* fixed the limit from 200 to 250 (#321)

* fixed the broken links in function summaries (#323)

* minor formatting change

* fixed the broken links in function summaries (#323)

* minor formatting change

* Allele project (#326)

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* adding allele name to the title

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* adding interaction section to Yeastmine for cellmap paper

* rebased with QA

* get rid of deepscan warning

* adding allele category (#327)

* fixed font issue

* suppressed the ref display associated with the affected gene

* fixing analyze buttons

* markupsafe update

* Allele project (#326)

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* adding allele name to the title

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* testing

* adding interaction section to Yeastmine for cellmap paper

* rebased with QA

* get rid of deepscan warning

* adding allele category (#327)

* fixed font issue

* suppressed the ref display associated with the affected gene

* fixing analyze buttons

* markupsafe update

* fixed font issue in interaction display

* separate interactions into positive & negative in the allele network diagram (#329)

* separate interactions into positive & negative

* separate genetic & physical interaction sections

* moved genetic interaction table above Physical Interactions

* fixed a typo

* adding alliance icons

* adding alliance icon links to LSP (#330)

* order icons by standard 'phylogenetic' order

* fixed 'i' text for allele network diagram and a highlight bug for interaction page (#331)

* minor fix

* fixed i note for network diagram

* fixed the download site url

* fixed download URL

* Fixes to attach allele papers to proper data points (#333)

* fixed to attach the papers with allele name/type/description properly

* fixed to attach the papers with allele name/type/description properly

* fixed to attach the papers with allele name/type/description properly

* adding primary/additional/reviews papers

* adding primary/additional/reviews papers

* adding primary/additional/reviews papers

* fixed to get correct paper count

* adding missed allele name

* testing

* fixed to display multiple affected genes

* fixed display_name to display_text

* rebasing it to master

* changed it back

* adding sgdid to complex page

* adding sgdid to complex page

* fix link for genome-wide analysis papers (#335)

* fixed PTM bug

* fixed default dataset for protein

* fixed to not display Definition for go term if there is no def

* fixed broken seq display

* new code/files for homology tab (#341)

* adding code for homology tab

* adding code for homology tab

* making species names italicized

* fixing yeastmine link

* adding homology tab for narrow window

* making padding smaller for tabs

* redirect the ref index to LSP

* adjust tab padding

* adjust tab padding

* adjust tab padding

* testing

* adding link to fungal homolog gene ID

* expand the 'resistent to chemicals' display

* adding code for complementation data display (#345)

* adding/fixing code for functional complementation data display

* fixing bugs

* fixing bugs

* fixing bugs

* adding Gene column

* adding gene column

* adding gene column

* testing

* testing

* testing

* testing

* updated the dataset update date

* data update date

Co-authored-by: Felix Gondwe <[email protected]>
Co-authored-by: Kalpana Karra <[email protected]>

src/sgd/frontend/yeastgenome/static/js/reference.js

@@ -78,6 +78,18 @@ $(document).ready(function() {
         hide_section("disease");
     }
 
+    if(reference['counts']['complement'] > 0) {
+        $.getJSON('/backend/reference/' + reference['sgdid'] + '/functional_complement_details', function(data) {
+            var complement_table = create_complement_table(data);
+            create_download_button("complement_table_download", complement_table, reference['display_name'] + "_complements");
+            create_analyze_button("complement_table_analyze", complement_table, reference['display_name'] + " functional complementation genes", true);
+        });
+    }
+    else {
+        hide_section("complement");
+    }
+
+
     if(reference['counts']["regulation"] > 0) {
         $.getJSON('/backend/reference/' + reference['sgdid'] + '/regulation_details', function(data) {
             var regulation_table = create_regulation_table(data);
@@ -101,6 +113,30 @@ $(document).ready(function() {
 
 });
 
+function create_complement_table(data) {
+        var datatable = [];
+        var complements = {};
+        for (var i=0; i < data.length; i++) {
+        datatable.push(complement_data_to_table(data[i], i));
+                complements[data[i]["id"]] = true;
+        }
+
+        set_up_header('complement_table', datatable.length, 'entry', 'entries', Object.keys(complements).length, 'complement', 'complements');
+
+        var options = {};
+        options["bPaginate"] = true;
+        options["aaSorting"] = [[4, "asc"]];
+
+        options["aoColumns"] = [{"bSearchable":false, "bVisible":false}, {"bSearchable":false, "bVisible":false}, null, null, null, null, null, {"sWidth": "250px"}, null, {"bSearchable":false, "bVisible":false}];
+
+
+        options["oLanguage"] = {"sEmptyTable": "No complement data for this paper"};
+        options["aaData"] = datatable;
+
+        return create_table("complement_table", options);
+
+}
+
 function create_literature_list(list_id, data, topic) {
     var primary_list = $("#" + list_id + "_list");
     var see_more_list = document.createElement('span');