Merge branch 'develop' into TASK-5963

opencb · Jul 10, 2024 · 9a5ce24 · 9a5ce24
2 parents 30aa080 + c188290
commit 9a5ce24
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Showing 18 changed files with 76 additions and 229 deletions.
diff --git a/cypress/e2e/iva/cohort-browser-grid.cy.js b/cypress/e2e/iva/cohort-browser-grid.cy.js
@@ -79,7 +79,7 @@ context("Cohort Browser Grid", () => {
             // eslint-disable-next-line cypress/unsafe-to-chain-command
             cy.get("@modal-create")
                 .find("h4.modal-title")
-                .should("contain.text", "Cohort create");
+                .should("contain.text", "Cohort Create");
         });
         // 3. Render button clear
         it("should render button clear", () => {

diff --git a/cypress/e2e/iva/disease-panel-browser-grid.cy.js b/cypress/e2e/iva/disease-panel-browser-grid.cy.js
@@ -78,7 +78,7 @@ context("Disease Panel Browser Grid", () => {
             // eslint-disable-next-line cypress/unsafe-to-chain-command
             cy.get("@modal-create")
                 .find("h4.modal-title")
-                .should("contain.text", "Disease panel create");
+                .should("contain.text", "Disease Panel Create");
         });
         // 3. Render button clear
         it("should render button clear", () => {
@@ -137,7 +137,7 @@ context("Disease Panel Browser Grid", () => {
             // eslint-disable-next-line cypress/unsafe-to-chain-command
             cy.get("@modal-update")
                 .find("h4.modal-title")
-                .should("contain.text", "Disease panel update");
+                .should("contain.text", "Disease Panel Update");
         });
         // 3. Render button clear
         it("should render button clear", () => {

diff --git a/cypress/e2e/iva/family-browser-grid.cy.js b/cypress/e2e/iva/family-browser-grid.cy.js
@@ -79,7 +79,7 @@ context("Family Browser Grid", () => {
             // eslint-disable-next-line cypress/unsafe-to-chain-command
             cy.get("@modal-create")
                 .find("h4.modal-title")
-                .should("contain.text", "Family create");
+                .should("contain.text", "Family Create");
         });
         // 3. Render button clear
         it("should render button clear", () => {
@@ -138,7 +138,7 @@ context("Family Browser Grid", () => {
             // eslint-disable-next-line cypress/unsafe-to-chain-command
             cy.get("@modal-update")
                 .find("h4.modal-title")
-                .should("contain.text", "Family update");
+                .should("contain.text", "Family Update");
         });
         // 3. Render button clear
         it("should render button clear", () => {

diff --git a/cypress/e2e/iva/individual-browser-grid.cy.js b/cypress/e2e/iva/individual-browser-grid.cy.js
@@ -79,7 +79,7 @@ context("Individual Browser Grid", () => {
             // eslint-disable-next-line cypress/unsafe-to-chain-command
             cy.get("@modal-create")
                 .find("h4.modal-title")
-                .should("contain.text", "Individual create");
+                .should("contain.text", "Individual Create");
         });
         // 3. Render button clear
         it("should render button clear", () => {
@@ -181,7 +181,7 @@ context("Individual Browser Grid", () => {
             // eslint-disable-next-line cypress/unsafe-to-chain-command
             cy.get("@modal-update")
                 .find("h4.modal-title")
-                .should("contain.text", "Individual update");
+                .should("contain.text", "Individual Update");
         });
         // 3. Render button clear
         it("should render button clear", () => {

diff --git a/cypress/e2e/iva/sample-browser-grid.cy.js b/cypress/e2e/iva/sample-browser-grid.cy.js
@@ -79,7 +79,7 @@ context("Sample Browser Grid", () => {
             // eslint-disable-next-line cypress/unsafe-to-chain-command
             cy.get("@modal-create")
                 .find("h4.modal-title")
-                .should("contain.text", "Sample create");
+                .should("contain.text", "Sample Create");
         });
         // 3. Render button clear
         it("should render button clear", () => {
@@ -138,7 +138,7 @@ context("Sample Browser Grid", () => {
             // eslint-disable-next-line cypress/unsafe-to-chain-command
             cy.get("@modal-update")
                 .find("h4.modal-title")
-                .should("contain.text", "Sample update");
+                .should("contain.text", "Sample Update");
         });
         // 3. Render button clear
         it("should render button clear", () => {

diff --git a/src/core/clients/opencga/opencga-client.js b/src/core/clients/opencga/opencga-client.js
@@ -328,7 +328,6 @@ export class OpenCGAClient {
         if (this._config.cookies.active) {
             this.#setCookies();
         }
-        return Promise.resolve();
     }
 
     #setCookies(userId, token) {

diff --git a/src/sites/iva/iva-app.js b/src/sites/iva/iva-app.js
@@ -676,12 +676,22 @@ class IvaApp extends LitElement {
         this.opencgaClient.refresh();
     }
 
-    async logout() {
-        // this delete token in the client and removes the Cookies
-        await this.opencgaClient.logout();
+    logout() {
+        // 1. Check if logged user is a local user
+        // This is only needed if SSO mode is enabled. If not, logged user is always local
+        let isLocalUser = true;
+        if (this.opencgaClient?._config?.sso?.active && this.opencgaClient?._config?.token) {
+            // eslint-disable-next-line no-undef
+            const decoded = jwt_decode(this.opencgaClient._config.token);
+            isLocalUser = decoded?.authOrigin === "OPENCGA";
+        }
+
+        // 2. Delete token and remove cookies
+        this.opencgaClient.logout();
 
-        // Check if sso is active: we will redirect to 'meta/sso/logout' endpoint
-        if (this.opencgaClient?._config?.sso?.active) {
+        // 3. Check if sso is active and logged user is not local
+        // In this case, we will redirect to 'meta/sso/logout' endpoint
+        if (this.opencgaClient?._config?.sso?.active && !isLocalUser) {
             // eslint-disable-next-line no-undef
             Cookies.expire(this.opencgaClient._config.sso.cookie);
 

diff --git a/src/webcomponents/clinical/clinical-analysis-create.js b/src/webcomponents/clinical/clinical-analysis-create.js
@@ -458,9 +458,7 @@ export default class ClinicalAnalysisCreate extends LitElement {
                             display: {
                                 render: (panels, dataFormFilterChange) => {
                                     const handlePanelsFilterChange = e => {
-                                        // eslint-disable-next-line no-param-reassign
-                                        const panelList = e.detail.value
-                                            ?.split(",")
+                                        const panelList = (e.detail?.value?.split(",") || [])
                                             .filter(panelId => panelId)
                                             .map(panelId => ({id: panelId}));
                                         dataFormFilterChange(panelList);
@@ -496,8 +494,7 @@ export default class ClinicalAnalysisCreate extends LitElement {
                             display: {
                                 render: (flags, dataFormFilterChange) => {
                                     const handleFlagsFilterChange = e => {
-                                        const flagList = e.detail.value
-                                            ?.split(",")
+                                        const flagList = (e.detail?.value?.split(",") || [])
                                             .filter(flagId => flagId)
                                             .map(flagId => ({id: flagId}));
                                         dataFormFilterChange(flagList);
@@ -506,7 +503,7 @@ export default class ClinicalAnalysisCreate extends LitElement {
                                         <clinical-flag-filter
                                             .flag="${flags?.map(f => f.id).join(",")}"
                                             .flags="${this.opencgaSession.study.internal?.configuration?.clinical?.flags[this.clinicalAnalysis.type?.toUpperCase()]}"
-                                            .multiple=${true}
+                                            .multiple="${true}"
                                             @filterChange="${e => handleFlagsFilterChange(e, "flags.id")}">
                                         </clinical-flag-filter>
                                     `;
@@ -899,8 +896,7 @@ export default class ClinicalAnalysisCreate extends LitElement {
                             display: {
                                 render: (analysts, dataFormFilterChange) => {
                                     const handleAnalystsFilterChange = e => {
-                                        const analystList = e.detail.value
-                                            ?.split(",")
+                                        const analystList = (e.detail?.value?.split(",") || [])
                                             .filter(analystId => analystId)
                                             .map(analystId => ({id: analystId}));
                                         dataFormFilterChange(analystList);
@@ -909,7 +905,7 @@ export default class ClinicalAnalysisCreate extends LitElement {
                                         <clinical-analyst-filter
                                             .analyst="${analysts?.map(f => f.id).join(",")}"
                                             .analysts="${this._users}"
-                                            .multiple=${true}
+                                            .multiple="${true}"
                                             @filterChange="${e => handleAnalystsFilterChange(e, "analyst.id")}">
                                         </clinical-analyst-filter>
                                     `;

diff --git a/src/webcomponents/clinical/clinical-analysis-update.js b/src/webcomponents/clinical/clinical-analysis-update.js
@@ -323,18 +323,16 @@ export default class ClinicalAnalysisUpdate extends LitElement {
                                 render: (analysts, dataFormFilterChange, updateParams, clinicalAnalysis) => {
                                     const handleAnalystsFilterChange = e => {
                                         // We need to convert value from a string wth commas to an array of IDs
-                                        const analystList = e.detail.value
-                                            ?.split(",")
+                                        const analystList = (e.detail?.value?.split(",") || [])
                                             .filter(analystId => analystId)
                                             .map(analystId => ({id: analystId}));
                                         dataFormFilterChange(analystList);
                                     };
-
                                     return html `
                                         <clinical-analyst-filter
                                             .analyst="${analysts?.map(f => f.id).join(",")}"
                                             .analysts="${this._users}"
-                                            .multiple=${true}
+                                            .multiple="${true}"
                                             .classes="${updateParams?.analysts ? "selection-updated" : ""}"
                                             .disabled="${!!clinicalAnalysis?.locked}"
                                             @filterChange="${e => handleAnalystsFilterChange(e)}">
@@ -374,7 +372,7 @@ export default class ClinicalAnalysisUpdate extends LitElement {
                             display: {
                                 render: (panels, dataFormFilterChange, updateParams, clinicalAnalysis) => {
                                     const handlePanelsFilterChange = e => {
-                                        const panels = (e.detail.value?.split(",") || [])
+                                        const panels = (e.detail?.value?.split(",") || [])
                                             .filter(panelId => panelId)
                                             .map(panelId => ({id: panelId}));
                                         dataFormFilterChange(panels);
@@ -433,19 +431,16 @@ export default class ClinicalAnalysisUpdate extends LitElement {
                                 render: (flags, dataFormFilterChange, updateParams, clinicalAnalysis) => {
                                     const handleFlagsFilterChange = e => {
                                         // We need to convert value from a string wth commas to an array of IDs
-                                        // eslint-disable-next-line no-param-reassign
-                                        const flagList = e.detail.value
-                                            ?.split(",")
+                                        const flagList = (e.detail?.value?.split(",") || [])
                                             .filter(flagId => flagId)
                                             .map(flagId => ({id: flagId}));
                                         dataFormFilterChange(flagList);
                                     };
-
                                     return html `
                                         <clinical-flag-filter
                                             .flag="${flags?.map(f => f.id).join(",")}"
                                             .flags="${this.opencgaSession.study.internal?.configuration?.clinical?.flags[clinicalAnalysis?.type?.toUpperCase()]}"
-                                            .multiple=${true}
+                                            .multiple="${true}"
                                             .classes="${updateParams?.flags ? "selection-updated" : ""}"
                                             .disabled="${!!clinicalAnalysis?.locked}"
                                             @filterChange="${e => handleFlagsFilterChange(e)}">

diff --git a/src/webcomponents/clinical/interpretation/clinical-interpretation-create.js b/src/webcomponents/clinical/interpretation/clinical-interpretation-create.js
@@ -225,8 +225,7 @@ export default class ClinicalInterpretationCreate extends LitElement {
                                     const panelLock = !!this.clinicalAnalysis?.panelLock;
                                     const panelList = panelLock ? this.clinicalAnalysis.panels : this.opencgaSession.study?.panels;
                                     const handlePanelsFilterChange = e => {
-                                        const panelList = e.detail.value
-                                            ?.split(",")
+                                        const panelList = (e.detail?.value?.split(",") || [])
                                             .filter(panelId => panelId)
                                             .map(panelId => ({id: panelId}));
                                         dataFormFilterChange(panelList);
@@ -284,7 +283,7 @@ export default class ClinicalInterpretationCreate extends LitElement {
                                                 <div class="text-muted">Tags: ${(comment.tags || []).join(" ") || "-"}</div>
                                             </div>
                                         </div>
-                                `;
+                                    `;
                                 }
                             },
                             elements: [

diff --git a/src/webcomponents/clinical/interpretation/clinical-interpretation-update.js b/src/webcomponents/clinical/interpretation/clinical-interpretation-update.js
@@ -191,8 +191,7 @@ export default class ClinicalInterpretationUpdate extends LitElement {
                                     const panelLock = !!this.clinicalAnalysis?.panelLock;
                                     const panelList = panelLock ? this.clinicalAnalysis?.panels : this.opencgaSession.study?.panels;
                                     const handlePanelsFilterChange = e => {
-                                        const panelList = e.detail.value
-                                            ?.split(",")
+                                        const panelList = (e.detail?.value?.split(",") || [])
                                             .filter(panelId => panelId)
                                             .map(panelId => ({id: panelId}));
                                         dataFormFilterChange(panelList);

diff --git a/src/webcomponents/cohort/cohort-update.js b/src/webcomponents/cohort/cohort-update.js
@@ -114,17 +114,13 @@ export default class CohortUpdate extends LitElement {
                                     const sampleIds = Array.isArray(samples) ?
                                         samples?.map(sample => sample.id).join(",") :
                                         samples;
-
                                     const handleSamplesFilterChange = e => {
                                         // We need to convert value from a string wth commas to an array of IDs
-                                        // eslint-disable-next-line no-param-reassign
-                                        const sampleList = e.detail.value
-                                            ?.split(",")
+                                        const sampleList = (e.detail?.value?.split(",") || [])
                                             .filter(sampleId => sampleId)
                                             .map(sampleId => ({id: sampleId}));
                                         dataFormFilterChange(sampleList);
                                     };
-
                                     return html `
                                         <catalog-search-autocomplete
                                             .value="${sampleIds}"

diff --git a/src/webcomponents/commons/forms/data-form.js b/src/webcomponents/commons/forms/data-form.js
@@ -954,26 +954,20 @@ export default class DataForm extends LitElement {
     _createToggleSwitchElement(element) {
         const value = this.getValue(element.field);
         const disabled = this._getBooleanValue(element.display?.disabled, false, element);
-        const activeClassName = element.display?.activeClassName ?? element.display?.activeClass ?? "";
-        const inactiveClassName = element.display?.inactiveClassName ?? element.display?.inactiveClass ?? "";
-
         const content = html`
             <div class="">
                 <toggle-switch
                     .disabled="${disabled}"
                     .value="${value}"
                     .onText="${element.display?.onText}"
                     .offText="${element.display?.offText}"
-                    .activeClass="${activeClassName}"
-                    .inactiveClass="${inactiveClassName}"
                     .classes="${this._isUpdated(element) ? "updated" : ""}"
                     @filterChange="${e => this.onFilterChange(element, e.detail.value)}">
                 </toggle-switch>
             </div>
         `;
 
         return this._createElementTemplate(element, value, content);
-
     }
 
     _createToggleButtonsElement(element) {