Merge pull request #983 from opencb/TASK-6700

TASK-6700 - Update the Steiner tool to include COSMIC count
opencb · Sep 24, 2024 · 0d42375 · 0d42375
2 parents a0346ae + 55da40a
commit 0d42375
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Showing 2 changed files with 35 additions and 2 deletions.
diff --git a/cypress/e2e/iva/variant-browser-grid.cy.js b/cypress/e2e/iva/variant-browser-grid.cy.js
@@ -271,6 +271,38 @@ context("Variant Browser Grid", () => {
         });
     });
 
+    context("clinical info", () => {
+        context("cosmic column", () => {
+            const columnIndex = 18;
+            it("should display an 'x' icon if no cosmic information is available", () => {
+                cy.get("@variantBrowser")
+                    .find(`tbody > tr[data-uniqueid="14:91649938:A:G"] > td`)
+                    .eq(columnIndex)
+                    .find("i")
+                    .should("have.class", "fa-times");
+            });
+
+            it("should display the number of entries and total trait associations", () => {
+                cy.get("@variantBrowser")
+                    .find("tbody tr:first > td")
+                    .eq(columnIndex)
+                    .should("contain.text", "1 entry (1)");
+            });
+
+            it("should display a tooltip with a link to cosmic", () => {
+                cy.get("@variantBrowser")
+                    .find("tbody tr:first > td")
+                    .eq(columnIndex)
+                    .find("a")
+                    .trigger("mouseover");
+
+                cy.get(`div[class="qtip-content"]`)
+                    .find(`a[href^="https://cancer.sanger.ac.uk/cosmic/search?q="]`)
+                    .should("exist");
+            });
+        });
+    });
+
     context("actions", () => {
         const variant = "14:91649858:C:T";
         beforeEach(() => {

diff --git a/src/webcomponents/variant/variant-grid-formatter.js b/src/webcomponents/variant/variant-grid-formatter.js
@@ -1192,8 +1192,9 @@ export default class VariantGridFormatter {
 
                     return `
                         <a class="cosmic-tooltip" tooltip-title='Links' tooltip-text='${tooltipText}' tooltip-position-at="left bottom" tooltip-position-my="right top">
-                            <span style="color: green">${cosmicMap.size} ${cosmicMap.size > 1 ? "studies" : "study" }</span>
-                        </a>`;
+                            <span style="color: green">${cosmicMap.size} ${cosmicMap.size > 1 ? "entries" : "entry"} (${traits.length})</span>
+                        </a>
+                    `;
                 case "HGMD":
                     // Prepare the tooltip links
                     const hgmdMap = new Map();