Merge pull request #991 from opencb/TASK-6780

TASK-6780 - Port Patch 3.2.1 -> 4.0.0 XB 2.2.1 -> 3.0.0
opencb · Oct 14, 2024 · ae4f613 · ae4f613
2 parents 994564a + 7dd485e
commit ae4f613
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diff --git a/cypress/e2e/iva/variant-interpreter-grid-cancer-cnv.cy.js b/cypress/e2e/iva/variant-interpreter-grid-cancer-cnv.cy.js
@@ -168,11 +168,9 @@ context("Variant Interpreter Grid Cancer CNV", () => {
 
         it("should display Cohort Stats (Population Frequencies) tooltip", () => {
             cy.get("tbody tr:first > td")
-                .eq(10)
-                .within(() => {
-                    cy.get("a")
-                        .trigger("mouseover");
-                });
+                .eq(13)
+                .find("a")
+                .trigger("mouseover");
             cy.get(".qtip-content")
                 .should("be.visible");
         });

diff --git a/cypress/e2e/iva/variant-interpreter-grid-cancer.cy.js b/cypress/e2e/iva/variant-interpreter-grid-cancer.cy.js
@@ -208,23 +208,20 @@ context("Variant Interpreter Grid Cancer", () => {
             });
         });
 
-        it("should display cohort stats (population frequencies) tooltip", () => {
+        it("should display cohort stats tooltip", () => {
             cy.get("tbody tr:first > td")
-                .eq(10)
-                .within(() => {
-                    cy.get("a").trigger("mouseover");
-                });
+                .eq(13)
+                .find("a")
+                .trigger("mouseover");
             cy.get(".qtip-content")
                 .should("be.visible");
         });
 
-        it("should reference population frequencies tooltip", () => {
+        it("should display reference population frequencies tooltip", () => {
             cy.get("tbody tr:first > td")
-                .eq(11)
-                .within(() => {
-                    cy.get("a")
-                        .trigger("mouseover");
-                });
+                .eq(14)
+                .find("a")
+                .trigger("mouseover");
             cy.get(".qtip-content")
                 .should("be.visible");
         });

diff --git a/cypress/e2e/iva/variant-interpreter-grid-germline.cy.js b/cypress/e2e/iva/variant-interpreter-grid-germline.cy.js
@@ -168,51 +168,23 @@ context("Variant Interpreter Grid Germiline", () => {
             });
         });
 
-        it("should display cohort stats (Population Frequencies) tooltip", () => {
+        it("should display cohort stats tooltip", () => {
             cy.get("tbody tr:first > td")
-                .eq(9)
-                .within(() => {
-                    cy.get("a")
-                        .trigger("mouseover");
-                });
+                .eq(12)
+                .find("a")
+                .trigger("mouseover");
             cy.get(".qtip-content")
                 .should("be.visible");
         });
 
         it("should display reference population frequencies tooltip", () => {
             cy.get("tbody tr:first > td")
-                .eq(10)
-                .within(() => {
-                    cy.get("a")
-                        .trigger("mouseover");
-                });
-            cy.get(".qtip-content")
-                .should("be.visible");
-        });
-
-        it("should display ACMG Prediction (Classification) tooltip", () => {
-            cy.get("tbody tr:first > td")
-                .eq(16)
-                .within(() => {
-                    cy.get("a")
-                        .trigger("mouseover");
-                });
-            cy.get(".qtip-content")
-                .should("be.visible");
-        });
-
-        it("should display OMIM Prediction (Classification) tooltip", () => {
-            UtilsTest.changePage(browserInterpreterGrid,2);
-
-            cy.get("tbody tr:nth-child(6) > td:nth-child(15)")
-                .within(() => {
-                    cy.get("a")
-                        .trigger("mouseover");
-                });
+                .eq(13)
+                .find("a")
+                .trigger("mouseover");
             cy.get(".qtip-content")
                 .should("be.visible");
         });
-
     });
 
     context("Helpers", () => {

diff --git a/src/core/bioinfo/bioinfo-utils.js b/src/core/bioinfo/bioinfo-utils.js
@@ -262,7 +262,7 @@ export default class BioinfoUtils {
                 case "GO":
                     return this.getGeneOntologyLink(ontologyTermId);
                 case "OMIM":
-                    return this.getOmimLink(id);
+                    return this.getOmimOntologyLink(id);
                 case "ORPHA":
                     return this.getOrphanetLink(id);
                 case "MONDO":
@@ -293,16 +293,24 @@ export default class BioinfoUtils {
         return `https://hpo.jax.org/app/browse/term/${hpoTerm}`;
     }
 
+    // static getOmimLink(omimEntry) {
+    //     return `https://www.omim.org/entry/${omimEntry}`;
+    // }
+
     static getSequenceOntologyLink(soTerm) {
         return `http://www.sequenceontology.org/browser/current_svn/term/${soTerm}`;
     }
 
-    static getOmimLink(soTerm) {
-        return `https://omim.org/entry/${soTerm}"`;
+    static getOmimOntologyLink(soTerm) {
+        return `https://www.omim.org/entry/${soTerm}"`;
     }
 
     static getOrphanetLink(orphaId) {
         return `https://www.orpha.net/consor/cgi-bin/OC_Exp.php?lng=EN&Expert=${orphaId}`;
     }
 
+    static getPharmGKBLink(pharmGKBId) {
+        return `https://www.pharmgkb.org/chemical/${pharmGKBId}`;
+    }
+
 }
diff --git a/src/core/clients/opencga/api/Admin.js b/src/core/clients/opencga/api/Admin.js
@@ -1,9 +1,12 @@
 /**
- * Copyright 2015-2020 OpenCB
+ * Copyright 2015-2024 OpenCB
+ *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
  * You may obtain a copy of the License at
- * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
  * Unless required by applicable law or agreed to in writing, software
  * distributed under the License is distributed on an "AS IS" BASIS,
  * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
@@ -12,7 +15,6 @@
  * WARNING: AUTOGENERATED CODE
  * 
  * This code was generated by a tool.
- * Autogenerated on: 2024-03-06
  * 
  * 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. 
@@ -34,8 +36,8 @@ export default class Admin extends OpenCGAParentClass {
 
     /** Group by operation
     * @param {String} fields - Comma separated list of fields by which to group by.
-    * @param {"AUDIT ORGANIZATION USER PROJECT STUDY FILE SAMPLE JOB INDIVIDUAL COHORT DISEASE_PANEL FAMILY CLINICAL_ANALYSIS INTERPRETATION
-    *     VARIANT ALIGNMENT CLINICAL EXPRESSION RGA FUNCTIONAL"} entity - Entity to be grouped by.
+    * @param {"AUDIT NOTE ORGANIZATION USER PROJECT STUDY FILE SAMPLE JOB INDIVIDUAL COHORT DISEASE_PANEL FAMILY CLINICAL_ANALYSIS
+    *     INTERPRETATION VARIANT ALIGNMENT CLINICAL EXPRESSION RGA FUNCTIONAL"} entity - Entity to be grouped by.
     * @param {Object} [params] - The Object containing the following optional parameters:
     * @param {Boolean} [params.count] - Count the number of elements matching the group.
     * @param {Number} [params.limit = "50"] - Maximum number of documents (groups) to be returned. The default value is 50.
@@ -107,7 +109,6 @@ export default class Admin extends OpenCGAParentClass {
     *     value is false.
     * @param {String} [params.organization] - Organization id.
     * @param {String} [params.user] - User ID.
-    * @param {String} [params.account] - Account type [GUEST, FULL, ADMINISTRATOR].
     * @param {String} [params.authenticationId] - Authentication origin ID.
     * @returns {Promise} Promise object in the form of RestResponse instance.
     */

diff --git a/src/core/clients/opencga/api/Alignment.js b/src/core/clients/opencga/api/Alignment.js
@@ -1,9 +1,12 @@
 /**
- * Copyright 2015-2020 OpenCB
+ * Copyright 2015-2024 OpenCB
+ *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
  * You may obtain a copy of the License at
- * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
  * Unless required by applicable law or agreed to in writing, software
  * distributed under the License is distributed on an "AS IS" BASIS,
  * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
@@ -12,7 +15,6 @@
  * WARNING: AUTOGENERATED CODE
  * 
  * This code was generated by a tool.
- * Autogenerated on: 2024-03-06
  * 
  * 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. 
@@ -41,6 +43,10 @@ export default class Alignment extends OpenCGAParentClass {
     * @param {String} [params.jobDependsOn] - Comma separated list of existing job IDs the job will depend on.
     * @param {String} [params.jobDescription] - Job description.
     * @param {String} [params.jobTags] - Job tags.
+    * @param {String} [params.jobScheduledStartTime] - Time when the job is scheduled to start.
+    * @param {String} [params.jobPriority] - Priority of the job.
+    * @param {Boolean} [params.jobDryRun] - Flag indicating that the job will be executed in dry-run mode. In this mode, OpenCGA will
+    *     validate that all parameters and prerequisites are correctly set for successful execution, but the job will not actually run.
     * @returns {Promise} Promise object in the form of RestResponse instance.
     */
     runBwa(data, params) {
@@ -56,6 +62,10 @@ export default class Alignment extends OpenCGAParentClass {
     * @param {String} [params.jobDependsOn] - Comma separated list of existing job IDs the job will depend on.
     * @param {String} [params.jobDescription] - Job description.
     * @param {String} [params.jobTags] - Job tags.
+    * @param {String} [params.jobScheduledStartTime] - Time when the job is scheduled to start.
+    * @param {String} [params.jobPriority] - Priority of the job.
+    * @param {Boolean} [params.jobDryRun] - Flag indicating that the job will be executed in dry-run mode. In this mode, OpenCGA will
+    *     validate that all parameters and prerequisites are correctly set for successful execution, but the job will not actually run.
     * @returns {Promise} Promise object in the form of RestResponse instance.
     */
     runCoverageIndex(data, params) {
@@ -71,6 +81,10 @@ export default class Alignment extends OpenCGAParentClass {
     * @param {String} [params.jobDependsOn] - Comma separated list of existing job IDs the job will depend on.
     * @param {String} [params.jobDescription] - Job description.
     * @param {String} [params.jobTags] - Job tags.
+    * @param {String} [params.jobScheduledStartTime] - Time when the job is scheduled to start.
+    * @param {String} [params.jobPriority] - Priority of the job.
+    * @param {Boolean} [params.jobDryRun] - Flag indicating that the job will be executed in dry-run mode. In this mode, OpenCGA will
+    *     validate that all parameters and prerequisites are correctly set for successful execution, but the job will not actually run.
     * @returns {Promise} Promise object in the form of RestResponse instance.
     */
     coverageQcGeneCoverageStatsRun(data, params) {
@@ -136,6 +150,10 @@ export default class Alignment extends OpenCGAParentClass {
     * @param {String} [params.jobDependsOn] - Comma separated list of existing job IDs the job will depend on.
     * @param {String} [params.jobDescription] - Job description.
     * @param {String} [params.jobTags] - Job tags.
+    * @param {String} [params.jobScheduledStartTime] - Time when the job is scheduled to start.
+    * @param {String} [params.jobPriority] - Priority of the job.
+    * @param {Boolean} [params.jobDryRun] - Flag indicating that the job will be executed in dry-run mode. In this mode, OpenCGA will
+    *     validate that all parameters and prerequisites are correctly set for successful execution, but the job will not actually run.
     * @returns {Promise} Promise object in the form of RestResponse instance.
     */
     runDeeptools(data, params) {
@@ -151,6 +169,10 @@ export default class Alignment extends OpenCGAParentClass {
     * @param {String} [params.jobDependsOn] - Comma separated list of existing job IDs the job will depend on.
     * @param {String} [params.jobDescription] - Job description.
     * @param {String} [params.jobTags] - Job tags.
+    * @param {String} [params.jobScheduledStartTime] - Time when the job is scheduled to start.
+    * @param {String} [params.jobPriority] - Priority of the job.
+    * @param {Boolean} [params.jobDryRun] - Flag indicating that the job will be executed in dry-run mode. In this mode, OpenCGA will
+    *     validate that all parameters and prerequisites are correctly set for successful execution, but the job will not actually run.
     * @returns {Promise} Promise object in the form of RestResponse instance.
     */
     runFastqc(data, params) {
@@ -166,6 +188,10 @@ export default class Alignment extends OpenCGAParentClass {
     * @param {String} [params.jobDependsOn] - Comma separated list of existing job IDs the job will depend on.
     * @param {String} [params.jobDescription] - Job description.
     * @param {String} [params.jobTags] - Job tags.
+    * @param {String} [params.jobScheduledStartTime] - Time when the job is scheduled to start.
+    * @param {String} [params.jobPriority] - Priority of the job.
+    * @param {Boolean} [params.jobDryRun] - Flag indicating that the job will be executed in dry-run mode. In this mode, OpenCGA will
+    *     validate that all parameters and prerequisites are correctly set for successful execution, but the job will not actually run.
     * @returns {Promise} Promise object in the form of RestResponse instance.
     */
     runIndex(data, params) {
@@ -182,6 +208,10 @@ export default class Alignment extends OpenCGAParentClass {
     * @param {String} [params.jobDependsOn] - Comma separated list of existing job IDs the job will depend on.
     * @param {String} [params.jobDescription] - Job description.
     * @param {String} [params.jobTags] - Job tags.
+    * @param {String} [params.jobScheduledStartTime] - Time when the job is scheduled to start.
+    * @param {String} [params.jobPriority] - Priority of the job.
+    * @param {Boolean} [params.jobDryRun] - Flag indicating that the job will be executed in dry-run mode. In this mode, OpenCGA will
+    *     validate that all parameters and prerequisites are correctly set for successful execution, but the job will not actually run.
     * @returns {Promise} Promise object in the form of RestResponse instance.
     */
     runPicard(data, params) {
@@ -198,6 +228,10 @@ export default class Alignment extends OpenCGAParentClass {
     * @param {String} [params.jobDependsOn] - Comma separated list of existing job IDs the job will depend on.
     * @param {String} [params.jobDescription] - Job description.
     * @param {String} [params.jobTags] - Job tags.
+    * @param {String} [params.jobScheduledStartTime] - Time when the job is scheduled to start.
+    * @param {String} [params.jobPriority] - Priority of the job.
+    * @param {Boolean} [params.jobDryRun] - Flag indicating that the job will be executed in dry-run mode. In this mode, OpenCGA will
+    *     validate that all parameters and prerequisites are correctly set for successful execution, but the job will not actually run.
     * @returns {Promise} Promise object in the form of RestResponse instance.
     */
     runQc(data, params) {
@@ -244,6 +278,10 @@ export default class Alignment extends OpenCGAParentClass {
     * @param {String} [params.jobDependsOn] - Comma separated list of existing job IDs the job will depend on.
     * @param {String} [params.jobDescription] - Job description.
     * @param {String} [params.jobTags] - Job tags.
+    * @param {String} [params.jobScheduledStartTime] - Time when the job is scheduled to start.
+    * @param {String} [params.jobPriority] - Priority of the job.
+    * @param {Boolean} [params.jobDryRun] - Flag indicating that the job will be executed in dry-run mode. In this mode, OpenCGA will
+    *     validate that all parameters and prerequisites are correctly set for successful execution, but the job will not actually run.
     * @returns {Promise} Promise object in the form of RestResponse instance.
     */
     runSamtools(data, params) {