From e1f8f4a0ccbbd23237eca7a8bdef6f223e14d66e Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Tue, 16 Dec 2025 11:03:34 -0600
Subject: Provide UI for actions on existing phenotypes.

---
 .../templates/populations/sui-view-population.html | 144 +++++++++++++++++++++
 1 file changed, 144 insertions(+)

(limited to 'uploader')

diff --git a/uploader/templates/populations/sui-view-population.html b/uploader/templates/populations/sui-view-population.html
index 3bf8d0d..adb28db 100644
--- a/uploader/templates/populations/sui-view-population.html
+++ b/uploader/templates/populations/sui-view-population.html
@@ -105,7 +105,62 @@
           <!-- Provide other features for publications on loaded page. -->
         </div>
       </div>
+
+      <div class="row" style="margin-top: 1em;">
+        <h3> Phenotypes in  Population "{{population.FullName}} ({{population.Name}})"</h3>
+
+        <p>The table below lists the phenotypes that already exist for
+          population "<em>{{population.FullName}} ({{population.Name}})</em>" of
+          species "<em>{{species.FullName}} ({{species.Name}})</em>".</p>
+
+        <div class="row phenotypes-list-actions">
+          <div class="col">
+            <form id="frm-recompute-phenotype-means"
+                  method="POST"
+                  action="{{url_for(
+                          'species.populations.phenotypes.recompute_means',
+                          species_id=species['SpeciesId'],
+                          population_id=population['Id'],
+                          dataset_id=dataset['Id'])}}">
+              <input id="submit-frm-recompute-phenotype-means"
+                     class="btn btn-info"
+                     type="submit"
+                     title="Compute/Recompute the means for selected phenotypes (or all phenotypes if none selected)."
+                     value="(Rec/C)ompute means" />
+            </form>
+          </div>
+          <div class="col">
+            <form id="frm-rerun-qtlreaper"
+                  method="POST"
+                  action="{{url_for(
+                          'species.populations.phenotypes.rerun_qtlreaper',
+                          species_id=species['SpeciesId'],
+                          population_id=population['Id'],
+                          dataset_id=dataset['Id'])}}">
+              <input id="submit-frm-rerun-qtlreaper"
+                     class="btn btn-info"
+                     type="submit"
+                     title="Run/Rerun QTLReaper for selected phenotypes (or all phenotypes if none selected)."
+                     value="(rer/r)un QTLReaper" />
+            </form>
+          </div>
+        </div>
+
+        <table id="tbl-phenotypes-list" class="table compact stripe cell-border">
+          <thead>
+            <tr>
+              <th></th>
+              <th>Index</th>
+              <th>Record</th>
+              <th>Description</th>
+            </tr>
+          </thead>
+
+          <tbody></tbody>
+        </table>
+      </div>
     </div>
+
     <div class="tab-pane fade"
          id="genotypes-content"
          role="tabpanel"
@@ -136,3 +191,92 @@
 {%endblock%}
 
 
+
+
+{%block javascript%}
+<script type="text/javascript" src="/static/js/urls.js"></script>
+
+<script type="text/javascript">
+  $(function() {
+      /** JS to build list of phenotypes table. **/
+      var species_id = {{species.SpeciesId}};
+      var population_id = {{population.Id}};
+      var dataset_id = {{dataset.Id}};
+      var dataset_name = "{{dataset.Name}}";
+      var data = {{phenotypes | tojson}};
+
+      var dtPhenotypesList = buildDataTable(
+          "#tbl-phenotypes-list",
+          data,
+          [
+              {
+                  data: function(pheno) {
+                      return `<input type="checkbox" name="selected-phenotypes" `
+                          + `id="chk-selected-phenotypes-${pheno.InbredSetCode}_${pheno.xref_id}" `
+                          + `value="${pheno.InbredSetCode}_${pheno.xref_id}" `
+                          + `class="chk-row-select" />`
+                  }
+              },
+              {data: "sequence_number"},
+              {
+                  data: function(pheno, type, set, meta) {
+                      var spcs_id = {{species.SpeciesId}};
+                      var pop_id = {{population.Id}};
+                      var dtst_id = {{dataset.Id}};
+                      var url = buildURLFromCurrentURL(
+                          (`/species/${spcs_id}` +
+                          `/populations/${pop_id}` +
+                          `/phenotypes/datasets/${dtst_id}` +
+                           `/phenotype/${pheno.xref_id}`));
+                      return `<a href="${url.toString()}" target="_blank">` +
+                          `${pheno.InbredSetCode}_${pheno.xref_id}` +
+                          `</a>`;
+                  }
+              },
+              {
+                  data: function(pheno) {
+                      return (pheno.Post_publication_description ||
+                              pheno.Original_description ||
+                              pheno.Pre_publication_description);
+                  }
+              }
+          ],
+          {
+              select: "multi+shift",
+              layout: {
+                  top1Start: {
+                      pageLength: {
+                          text: "Show _MENU_ of _TOTAL_"
+                      }
+                  },
+                  topStart: "info",
+                  top1End: null
+              },
+              rowId: function(pheno) {
+                  return `${pheno.InbredSetCode}_${pheno.xref_id}`;
+              }
+          });
+
+
+      $("#submit-frm-rerun-qtlreaper").on(
+          "click",
+          function(event) {
+              // (Re)run the QTLReaper script for selected phenotypes.
+              event.preventDefault();
+              var form = $("#frm-rerun-qtlreaper");
+              form.find(".dynamically-added-element").remove();
+              dtPhenotypesList.rows({selected: true}).nodes().each((node, index) => {
+                  _cloned = $(node).find(".chk-row-select").clone();
+                  _cloned.removeAttr("id");
+                  _cloned.removeAttr("class");
+                  _cloned.attr("style", "display: none;");
+                  _cloned.attr("data-type", "dynamically-added-element");
+                  _cloned.attr("class", "dynamically-added-element checkbox");
+                  _cloned.prop("checked", true);
+                  form.append(_cloned);
+              });
+              form.submit();
+          });
+  });
+</script>
+{%endblock%}
-- 
cgit 1.4.1