Merge branch 'release-3.x.x' into TASK-6866

opencb · Oct 14, 2024 · 24d048b · 24d048b
2 parents 23a7626 + a1438e3
commit 24d048b
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Showing 10 changed files with 371 additions and 319 deletions.
diff --git a/src/sites/iva/iva-app.js b/src/sites/iva/iva-app.js
@@ -82,7 +82,6 @@ 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";
@@ -231,7 +230,6 @@ class IvaApp extends LitElement {
             "study-admin-iva",
             // "catalog-admin",
             "operations-admin",
-            "study-variant-admin",
             "opencga-admin",
             "variants-admin",
             // "projects-admin",

diff --git a/src/webcomponents/commons/analysis/analysis-utils.js b/src/webcomponents/commons/analysis/analysis-utils.js
@@ -3,6 +3,7 @@ import NotificationUtils from "../utils/notification-utils";
 import UtilsNew from "../../../core/utils-new";
 import "../filters/feature-filter.js";
 import "../filters/disease-panel-filter.js";
+import LitUtils from "../utils/lit-utils";
 
 export default class AnalysisUtils {
 
@@ -14,15 +15,18 @@ export default class AnalysisUtils {
     // }
 
     static submit(id, promise, context) {
-        promise
+        return promise
             .then(response => {
                 console.log(response);
                 NotificationUtils.dispatch(context, NotificationUtils.NOTIFY_SUCCESS, {
                     title: `${id} launched`,
                     message: `${id} has been launched successfully`,
                 });
                 // Call to analysis onClear() method
-                context.onClear();
+                if (typeof context.onClear === "function") {
+                    context.onClear();
+                }
+                return response;
             })
             .catch(response => {
                 console.log(response);
@@ -114,13 +118,14 @@ export default class AnalysisUtils {
     static getAnalysisConfiguration(id, title, description, paramSections, check, config = {}) {
         return {
             id: id,
-            icon: config.icon,
+            icon: config.icon || "",
             title: config.title || title,
             description: config.description || description,
             display: {
                 // defaultLayout: "vertical"
-                ...config.display
+                ...config?.display
             },
+            buttons: config?.buttons || {},
             sections: [
                 {
                     display: {},
@@ -139,6 +144,9 @@ export default class AnalysisUtils {
                 ...paramSections,
                 {
                     title: "Job Info",
+                    display: {
+                        visible: config.isJob !== undefined ? config.isJob : true,
+                    },
                     elements: [
                         {
                             title: "Job ID",

diff --git a/src/webcomponents/commons/filters/catalog-search-autocomplete.js b/src/webcomponents/commons/filters/catalog-search-autocomplete.js
@@ -80,7 +80,7 @@ export default class CatalogSearchAutocomplete extends LitElement {
         this.RESOURCES = {
             "PROJECT": {
                 searchField: "id",
-                placeholder: "project...",
+                placeholder: "Project...",
                 // client: this.opencgaSession.opencgaClient.projects(),
                 fetch: ({study, ...params}) => this.opencgaSession.opencgaClient.projects().search(params),
                 fields: item => ({
@@ -91,16 +91,15 @@ export default class CatalogSearchAutocomplete extends LitElement {
                 }
             },
             "STUDY": {
-                searchField: "id",
-                placeholder: "study...",
+                searchField: "fqn",
+                placeholder: "Study...",
                 // client: this.opencgaSession.opencgaClient.studies(),
-                fetch: ({study, ...params}) => this.opencgaSession.opencgaClient.studies().search(params),
+                fetch: ({study, ...params}) => this.opencgaSession.opencgaClient.studies().search(this.opencgaSession.project.id, params),
                 fields: item => ({
                     "name": item.id,
                 }),
                 query: {
-                    project: this.opencgaSession.project.id,
-                    include: "id,name"
+                    include: "id,name,fqn"
                 }
             },
             "SAMPLE": {

diff --git a/src/webcomponents/commons/view/detail-tabs.js b/src/webcomponents/commons/view/detail-tabs.js
@@ -129,7 +129,7 @@ export default class DetailTabs extends LitElement {
     }
 
     renderTitle() {
-        const title = typeof this._config.title === "function" ? this._config.title(this.data) : this._config.title + " " + (this.data?.id || "");
+        const title = typeof this._config.title === "function" ? this._config.title(this.data) : this._config.title + " " + UtilsNew.substring(this.data?.id || "", this._config.display?.idMaxLength);
         return html`
             <div class="mt-3 ${this._config?.display?.titleClass || ""}" style="${this._config?.display?.titleStyle || ""}">
                 <h3>${title}</h3>
@@ -241,6 +241,9 @@ export default class DetailTabs extends LitElement {
 
                 contentClass: "p-3",
                 contentStyle: "",
+
+                // maximum length of the displayed id in the title
+                idMaxLength: 100,
             },
             items: [],
             // Example:

diff --git a/src/webcomponents/study/admin/study-admin.js b/src/webcomponents/study/admin/study-admin.js
@@ -22,7 +22,7 @@ import "./study-admin-permissions.js";
 import "./study-admin-variable.js";
 import "./study-admin-audit.js";
 import "./study-admin-configuration.js";
-import "../../variant/operation/clinical-analysis-configuration-operation.js";
+import "../../variant/operation/clinical-analysis-configuration-update.js";
 import "../../variant/operation/variant-secondary-sample-index-configure-operation.js";
 import "../../commons/layouts/custom-vertical-navbar.js";
 
@@ -228,10 +228,10 @@ export default class StudyAdmin extends LitElement {
                             visibility: "private",
                             render: (opencgaSession, study) => {
                                 return html `
-                                    <clinical-analysis-configuration-operation
+                                    <clinical-analysis-configuration-update
                                             .toolParams="${{study: study.id}}"
                                             .opencgaSession="${opencgaSession}">
-                                    </clinical-analysis-configuration-operation>
+                                    </clinical-analysis-configuration-update>
                                 `;
                             }
                         },

diff --git a/src/webcomponents/study/admin/variant/study-variant-admin.js b/src/webcomponents/study/admin/variant/study-variant-admin.js
@@ -22,7 +22,7 @@ import "../study-admin-family.js";
 import "../study-admin-cohort.js";
 import "../study-admin-configuration.js";
 import "../../../variant/operation/variant-annotation-index-operation.js";
-import "../../../variant/operation/clinical-analysis-configuration-operation.js";
+import "../../../variant/operation/clinical-analysis-configuration-update.js";
 import "../../../variant/operation/variant-index-operation.js";
 import "../../../variant/operation/variant-stats-index-operation.js";
 import "../../../variant/operation/variant-secondary-annotation-index-operation.js";

diff --git a/src/webcomponents/variant/operation/clinical-analysis-configuration-operation.js b/src/webcomponents/variant/operation/clinical-analysis-configuration-operation.js