Merge branch 'release-3.2.x' into TASK-6783

src/core/clients/opencga/api/Job.js

@@ -13,11 +13,11 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  * WARNING: AUTOGENERATED CODE
- * 
+ *
  * This code was generated by a tool.
- * 
+ *
  * Manual changes to this file may cause unexpected behavior in your application.
- * Manual changes to this file will be overwritten if the code is regenerated. 
+ * Manual changes to this file will be overwritten if the code is regenerated.
  *
 **/
 
@@ -241,4 +241,4 @@ export default class Job extends OpenCGAParentClass {
         return this._get("jobs", job, "log", null, "tail", params);
     }
 
-}
+}

src/core/clients/opencga/api/Organization.js

@@ -13,11 +13,11 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  * WARNING: AUTOGENERATED CODE
- * 
+ *
  * This code was generated by a tool.
- * 
+ *
  * Manual changes to this file may cause unexpected behavior in your application.
- * Manual changes to this file will be overwritten if the code is regenerated. 
+ * Manual changes to this file will be overwritten if the code is regenerated.
  *
 **/
 
@@ -180,4 +180,4 @@ export default class Organization extends OpenCGAParentClass {
         return this._post("organizations", organization, null, null, "update", data, params);
     }
 
-}
+}

src/core/clients/opencga/api/Study.js

@@ -13,11 +13,11 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  * WARNING: AUTOGENERATED CODE
- * 
+ *
  * This code was generated by a tool.
- * 
+ *
  * Manual changes to this file may cause unexpected behavior in your application.
- * Manual changes to this file will be overwritten if the code is regenerated. 
+ * Manual changes to this file will be overwritten if the code is regenerated.
  *
 **/
 
@@ -342,4 +342,4 @@ export default class Study extends OpenCGAParentClass {
         return this._post("studies", study, "variableSets", variableSet, "variables/update", data, params);
     }
 
-}
+}

src/core/clients/opencga/opencga-catalog-utils.js

@@ -89,26 +89,34 @@ export default class OpencgaCatalogUtils {
         return false;
     }
 
-    // Check if the user has the right the permissions in the study.
-    static isAdmin(study, userLogged) {
-        if (!study || !userLogged) {
-            console.error(`No valid parameters, study: ${study}, user: ${userLogged}`);
+    // Check if the provided user is admin in the organization
+    static isOrganizationAdmin(organization, userId) {
+        if (!organization || !userId) {
             return false;
         }
-        // Check if user is the Study owner
-        const studyOwner = study.fqn.split("@")[0];
-        if (userLogged === studyOwner) {
+        // 1. Check if user is the organization admin
+        if (organization?.owner === userId) {
             return true;
         } else {
-            // Check if user is a Study admin, belongs to @admins group
-            const admins = study.groups.find(group => group.id === "@admins");
-            if (admins.userIds.includes(userLogged)) {
+            // Check if user is an admin of the organization
+            if (organization?.admins?.includes?.(userId)) {
                 return true;
             }
         }
+        // Other case, user is not admin of the organization
         return false;
     }
 
+    // Check if the user has the right the permissions in the study.
+    static isAdmin(study, userLogged) {
+        if (!study || !userLogged) {
+            console.error(`No valid parameters, study: ${study}, user: ${userLogged}`);
+            return false;
+        }
+        const admins = study.groups.find(group => group.id === "@admins");
+        return !!admins.userIds.includes(userLogged);
+    }
+
     // Check if the provided user is admin in the organization
     static isOrganizationAdmin(organization, userId) {
         if (!organization || !userId) {

src/core/clients/opencga/opencga-parent-class.js

@@ -33,11 +33,14 @@ export default class OpenCGAParentClass {
                 _options.token = sid;
             }
         }
-
+        // CAUTION Vero 2024-05-10: We believe this bit of code is useless. Temporarily commented out.
+        //  In users endpoint, we cannot find GET method where the path param {user/users} should be autocompleted.
+        //  When needed, they should be explicitly set.
         // If category == users and userId is not given, we try to set it
-        if (category1 === "users" && (ids1 === undefined || ids1 === null || ids1 === "")) {
-            ids1 = this._getUserId();
-        }
+        // if (category1 === "users" && (ids1 === undefined || ids1 === null || ids1 === "")) {
+        //     ids1 = this._getUserId();
+        // }
+
         let url = this._createRestUrl(host, version, category1, ids1, category2, ids2, action);
         // if (method === "GET") {
         url = this._addQueryParams(url, _params);

src/sites/iva/conf/config.js

@@ -25,8 +25,8 @@ const hosts = [
         url: "https://demo.app.zettagenomics.com/opencga"
     },
     {
-        id: "xeta-110e",
-        url: "https://test.app.zettagenomics.com/xeta-110e/opencga"
+        id: "reference",
+        url: "https://test.app.zettagenomics.com/reference/opencga"
     },
 ];
 
@@ -762,9 +762,18 @@ const SUITE = {
                     <br>`
             },
             menu: [
+                {
+                    id: "organization-admin",
+                    name: "Organizations Admin",
+                    fa_icon: "fas fa-file-invoice",
+                    icon: "img/tools/icons/variant_browser.svg",
+                    description: "",
+                    visibility: "public",
+                    featured: true,
+                },
                 {
                     id: "study-admin",
-                    name: "Study admin",
+                    name: "Study Admin",
                     fa_icon: "fas fa-file-invoice",
                     icon: "img/tools/icons/variant_browser.svg",
                     description: "",
@@ -782,7 +791,7 @@ const SUITE = {
                 // },
                 {
                     id: "study-admin-iva",
-                    name: "IVA configuration",
+                    name: "IVA Configuration",
                     fa_icon: "fas fa-file-invoice",
                     icon: "img/tools/icons/variant_browser.svg",
                     description: "",
@@ -798,24 +807,33 @@ const SUITE = {
                 //     visibility: "public",
                 //     featured: false,
                 // },
+                // {
+                //     id: "study-variant-admin",
+                //     name: "Study Variant Admin",
+                //     fa_icon: "fas fa-file-invoice",
+                //     icon: "img/tools/icons/variant_browser.svg",
+                //     description: "",
+                //     visibility: "public",
+                //     featured: true,
+                // },
                 {
-                    id: "study-variant-admin",
-                    name: "Study Variant Admin",
-                    fa_icon: "fas fa-file-invoice",
-                    icon: "img/tools/icons/variant_browser.svg",
-                    description: "",
-                    visibility: "public",
-                    featured: true,
-                },
-                {
-                    id: "projects-admin",
-                    name: "Project Manager",
+                    id: "operations-admin",
+                    name: "Operations Admin",
                     fa_icon: "fas fa-file-invoice",
                     icon: "img/tools/icons/variant_browser.svg",
                     description: "",
                     visibility: "public",
                     featured: true,
                 },
+                // {
+                //     id: "projects-admin",
+                //     name: "Project Manager",
+                //     fa_icon: "fas fa-file-invoice",
+                //     icon: "img/tools/icons/variant_browser.svg",
+                //     description: "",
+                //     visibility: "public",
+                //     featured: true,
+                // },
             ],
             fileExplorer: {
                 visibility: "private"

src/sites/iva/iva-app.js

@@ -77,11 +77,13 @@ import "../../webcomponents/clinical/clinical-analysis-create.js";
 import "../../webcomponents/file/file-manager.js";
 import "../../webcomponents/job/job-monitor.js";
 import "../../webcomponents/loading-spinner.js";
+import "../../webcomponents/organization/admin/organization-admin.js";
 import "../../webcomponents/project/projects-admin.js";
 import "../../webcomponents/study/admin/study-admin.js";
 import "../../webcomponents/study/admin/study-admin-iva.js";
 import "../../webcomponents/study/admin/catalog-admin.js";
 import "../../webcomponents/study/admin/variant/study-variant-admin.js";
+import "../../webcomponents/study/admin/variant/operations-admin.js";
 import "../../webcomponents/user/user-profile.js";
 import "../../webcomponents/api/rest-api.js";
 import "../../webcomponents/note/note-browser.js";
@@ -224,13 +226,15 @@ class IvaApp extends LitElement {
             "diseasePanelUpdate",
             "clinicalAnalysis",
             // Admin
+            "organization-admin",
             "study-admin",
             "study-admin-iva",
             // "catalog-admin",
+            "operations-admin",
             "study-variant-admin",
             "opencga-admin",
             "variants-admin",
-            "projects-admin",
+            // "projects-admin",
             // REST-API
             "rest-api",
             // note
@@ -1135,6 +1139,10 @@ class IvaApp extends LitElement {
     // }
 
     onSessionUpdateRequest() {
+        NotificationUtils.dispatch(this, NotificationUtils.NOTIFY_SUCCESS, {
+            title: "Refresh Session: Session Update Request",
+            message: "Session updated correctly",
+        });
         this._createOpenCGASession();
     }
 
@@ -1979,13 +1987,15 @@ class IvaApp extends LitElement {
                     ` : nothing}
 
                     <!-- Admin -->
-                    ${this.config.enabledComponents["projects-admin"] ? html`
-                        <tool-header title="Projects Admin" icon="${"fas fa-rocket"}"></tool-header>
-                        <div id="projects-admin">
-                            <projects-admin
+                    ${this.config.enabledComponents["organization-admin"] ? html`
+                        <tool-header title="Organization Admin: ${this.opencgaSession?.user?.organization}" icon="${"fas fa-sitemap"}"></tool-header>
+                        <div id="organization-admin">
+                            <organization-admin
+                                .organization="${this.opencgaSession?.organization}"
                                 .opencgaSession="${this.opencgaSession}"
+                                @studyUpdateRequest="${this.onStudyUpdateRequest}"
                                 @sessionUpdateRequest="${this.onSessionUpdateRequest}">
-                            </projects-admin>
+                            </organization-admin>
                         </div>
                     ` : nothing}
 
@@ -1998,7 +2008,7 @@ class IvaApp extends LitElement {
                         </div>
                     ` : nothing}
 
-                    ${this.config.enabledComponents["opencga-admin"] ? html`
+                    ${this.config.enabledComponents["projects-admin"] ? html`
                         <tool-header title="Study Dashboard" icon="${"fas fa-rocket"}"></tool-header>
                         <div id="projects-admin">
                             <projects-admin
@@ -2011,7 +2021,6 @@ class IvaApp extends LitElement {
                     ${this.config.enabledComponents["study-admin"] ? html`
                         <div class="content" id="study-admin">
                             <study-admin
-                                .study="${this.opencgaSession.study}"
                                 .opencgaSession="${this.opencgaSession}"
                                 @studyUpdateRequest="${this.onStudyUpdateRequest}">
                             </study-admin>
@@ -2023,20 +2032,22 @@ class IvaApp extends LitElement {
                     ${this.config.enabledComponents["study-admin-iva"] ? html`
                         <div class="content row">
                             <study-admin-iva
+                                .organizationId="${this.opencgaSession?.user?.organization}"
                                 .opencgaSession="${this.opencgaSession}"
                                 .settings="${this.settings}"
                                 @studyUpdateRequest="${this.onStudyUpdateRequest}">
                             </study-admin-iva>
                         </div>
                     ` : nothing}
 
-                    ${this.config.enabledComponents["study-variant-admin"] ? html`
+                    ${this.config.enabledComponents["operations-admin"] ? html`
                         <div class="content row">
-                            <study-variant-admin
+                            <operations-admin
+                                .organizationId="${this.opencgaSession?.user?.organization}"
                                 .study="${this.opencgaSession.study}"
                                 .opencgaSession="${this.opencgaSession}"
                                 @studyUpdateRequest="${this.onStudyUpdateRequest}">
-                            </study-variant-admin>
+                            </operations-admin>
                         </div>
                     ` : nothing}
 

src/webcomponents/api/opencga-rest-input.js

@@ -408,7 +408,8 @@ export default class OpencgaRestInput extends LitElement {
 
     #postEndpoint(url, isForm) {
         // Add Study
-        url += "study=" + encodeURIComponent(this.opencgaSession.study.fqn);
+        // Fixme: not all endpoints require study. E.g. POST /users/password/
+        url += "study=" + encodeURIComponent(this.opencgaSession?.study?.fqn);
 
         // Replace PATH params
         this.endpoint.parameters

src/webcomponents/cohort/cohort-grid.js

@@ -346,6 +346,7 @@ export default class CohortGrid extends LitElement {
                 id: "actions",
                 title: "Actions",
                 field: "actions",
+                align: "center",
                 formatter: () => `
                     <div class="d-inline-block dropdown">
                         <button class="btn btn-light btn-sm dropdown-toggle" type="button" data-bs-toggle="dropdown">
@@ -367,7 +368,6 @@ export default class CohortGrid extends LitElement {
                         </ul>
                     </div>
                 `,
-                align: "center",
                 events: {
                     "click a": this.onActionClick.bind(this),
                 },

src/webcomponents/commons/catalog-grid-formatter.js

@@ -19,6 +19,16 @@ import BioinfoUtils from "../../core/bioinfo/bioinfo-utils.js";
 
 export default class CatalogGridFormatter {
 
+    static userStatusFormatter(status, config) {
+        const _config = config || [];
+        const currentStatus = status.id || status.name || "UNDEFINED"; // Get current status
+        const displayCurrentStatus = _config.find(status => status.id === currentStatus);
+        return `
+            <span class="badge" style="background-color: ${displayCurrentStatus.displayColor}">
+                <strong>${displayCurrentStatus.displayLabel}</strong>
+            </span>
+        `;
+    }
     static sexFormatter(value, row) {
         let sexHtml = `${UtilsNew.isEmpty(row?.sex) ? "Not specified" : row.sex.id || row.sex}`;
         if (row?.karyotypicSex && row.karyotypicSex !== "UNKNOWN") {

src/webcomponents/commons/filters/catalog-search-autocomplete.js

@@ -82,7 +82,7 @@ export default class CatalogSearchAutocomplete extends LitElement {
                 searchField: "id",
                 placeholder: "project...",
                 // client: this.opencgaSession.opencgaClient.projects(),
-                fetch: filters => this.opencgaSession.opencgaClient.projects().search(filters),
+                fetch: ({study, ...params}) => this.opencgaSession.opencgaClient.projects().search(params),
                 fields: item => ({
                     "name": item.id,
                 }),
@@ -94,7 +94,7 @@ export default class CatalogSearchAutocomplete extends LitElement {
                 searchField: "id",
                 placeholder: "study...",
                 // client: this.opencgaSession.opencgaClient.studies(),
-                fetch: filters => this.opencgaSession.opencgaClient.studies().search(filters),
+                fetch: ({study, ...params}) => this.opencgaSession.opencgaClient.studies().search(params),
                 fields: item => ({
                     "name": item.id,
                 }),
@@ -286,6 +286,7 @@ export default class CatalogSearchAutocomplete extends LitElement {
                     ...this.query || this.RESOURCES[this.resource].query,
                     ...attr,
                 };
+
                 this.RESOURCES[this.resource].fetch(filters)
                     .then(response => success(response))
                     .catch(error => failure(error));