Merge pull request #824 from opencb/TASK-5120

TASK-5120 - Port Patch 1.6.5 -> 1.10.0
opencb · Oct 27, 2023 · 1b6a48a · 1b6a48a
2 parents 63c70a0 + 5444c20
commit 1b6a48a
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Showing 16 changed files with 161 additions and 1,454 deletions.
diff --git a/cypress/e2e/iva/variant-interpreter-grid-cancer-cnv.cy.js b/cypress/e2e/iva/variant-interpreter-grid-cancer-cnv.cy.js
@@ -168,7 +168,7 @@ context("Variant Interpreter Grid Cancer CNV", () => {
 
         it("should display Cohort Stats (Population Frequencies) tooltip", () => {
             cy.get("tbody tr:first > td")
-                .eq(8)
+                .eq(10)
                 .within(() => {
                     cy.get("a")
                         .trigger("mouseover");
@@ -177,7 +177,7 @@ context("Variant Interpreter Grid Cancer CNV", () => {
                 .should("be.visible");
         });
 
-        it("should display reference population frequencies tooltip", () => {
+        it.skip("should display reference population frequencies tooltip", () => {
             cy.get("tbody tr:first > td")
                 .eq(9)
                 .within(() => {

diff --git a/cypress/e2e/iva/variant-interpreter-grid-cancer.cy.js b/cypress/e2e/iva/variant-interpreter-grid-cancer.cy.js
@@ -210,7 +210,7 @@ context("Variant Interpreter Grid Cancer", () => {
 
         it("should display cohort stats (population frequencies) tooltip", () => {
             cy.get("tbody tr:first > td")
-                .eq(8)
+                .eq(10)
                 .within(() => {
                     cy.get("a").trigger("mouseover");
                 });
@@ -220,7 +220,7 @@ context("Variant Interpreter Grid Cancer", () => {
 
         it("should reference population frequencies tooltip", () => {
             cy.get("tbody tr:first > td")
-                .eq(9)
+                .eq(11)
                 .within(() => {
                     cy.get("a")
                         .trigger("mouseover");

diff --git a/cypress/e2e/iva/variant-interpreter-grid-germline.cy.js b/cypress/e2e/iva/variant-interpreter-grid-germline.cy.js
@@ -174,7 +174,7 @@ context("Variant Interpreter Grid Germiline", () => {
 
         it("should display cohort stats (Population Frequencies) tooltip", () => {
             cy.get("tbody tr:first > td")
-                .eq(8)
+                .eq(9)
                 .within(() => {
                     cy.get("a")
                         .trigger("mouseover");
@@ -185,7 +185,7 @@ context("Variant Interpreter Grid Germiline", () => {
 
         it("should display reference population frequencies tooltip", () => {
             cy.get("tbody tr:first > td")
-                .eq(9)
+                .eq(10)
                 .within(() => {
                     cy.get("a")
                         .trigger("mouseover");
@@ -196,7 +196,7 @@ context("Variant Interpreter Grid Germiline", () => {
 
         it("should display ACMG Prediction (Classification) tooltip", () => {
             cy.get("tbody tr:first > td")
-                .eq(14)
+                .eq(15)
                 .within(() => {
                     cy.get("a")
                         .trigger("mouseover");

diff --git a/src/sites/iva/conf/browsers.settings.js b/src/sites/iva/conf/browsers.settings.js
@@ -718,7 +718,25 @@ const INTERPRETER_SETTINGS = {
                 ],
             },
             {
-                id: "methods"
+                id: "methods",
+                items: [
+                    {
+                        type: "SINGLE",
+                        methods: [
+                            {id: "exomiser"},
+                        ],
+                    },
+                    {
+                        type: "FAMILY",
+                        methods: [
+                            {id: "exomiser"},
+                        ],
+                    },
+                    {
+                        type: "CANCER",
+                        methods: [],
+                    },
+                ],
             },
             {
                 id: "variant-browser",

diff --git a/src/webcomponents/commons/grid-commons.js b/src/webcomponents/commons/grid-commons.js
@@ -272,9 +272,9 @@ export default class GridCommons {
         }
     }
 
-    isColumnVisible(colName) {
+    isColumnVisible(colName, parentName) {
         if (this.config.columns?.length > 0) {
-            return this.config.columns.includes(colName);
+            return this.config.columns.includes(colName) || this.config.columns.includes(parentName);
         } else {
             // Columns are visible by default.
             return true;

diff --git a/src/webcomponents/deprecated/select-field-token.js b/src/webcomponents/deprecated/select-field-token.js
diff --git a/src/webcomponents/study/deprecated/variable-manager.js b/src/webcomponents/study/deprecated/variable-manager.js