Merge pull request #798 from opencb/TASK-4547

TASK-4547
opencb · Jul 25, 2023 · 7854469 · 7854469
2 parents eb0849d + bebc79d
commit 7854469
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Showing 14 changed files with 45 additions and 55 deletions.
diff --git a/src/sites/iva/iva-app.js b/src/sites/iva/iva-app.js
@@ -31,7 +31,6 @@ import UtilsNew from "../../core/utils-new.js";
 import NotificationUtils from "../../webcomponents/commons/utils/notification-utils.js";
 import NotificationManager from "../../core/notification-manager.js";
 
-import AnalysisRegistry from "../../webcomponents/variant/analysis/analysis-registry.js";
 import "../../webcomponents/clinical/clinical-analysis-browser.js";
 import "../../webcomponents/clinical/clinical-analysis-portal.js";
 import "../../webcomponents/variant/variant-browser.js";

diff --git a/src/webcomponents/job/job-view.js b/src/webcomponents/job/job-view.js
@@ -16,7 +16,6 @@
 
 import {LitElement, html} from "lit";
 import UtilsNew from "../../core/utils-new.js";
-import AnalysisRegistry from "../variant/analysis/analysis-registry.js";
 import LitUtils from "../commons/utils/lit-utils.js";
 import "../commons/forms/data-form.js";
 import "./job-detail-log.js";
@@ -345,6 +344,7 @@ export default class JobView extends LitElement {
                         },
                     ],
                 },
+                /*
                 {
                     title: "Results",
                     display: {
@@ -355,11 +355,12 @@ export default class JobView extends LitElement {
                             type: "custom",
                             display: {
                                 defaultLayout: "vertical",
-                                render: () => AnalysisRegistry.get(this.job.tool.id)?.result(this.job, this.opencgaSession)
+                                render: () => {}
                             },
                         },
                     ],
                 },
+                 */
                 {
                     title: "Job Dependencies",
                     display: {

diff --git a/...nts/variant/analysis/analysis-registry.js → .../analysis/deprecated/analysis-registry.js b/...nts/variant/analysis/analysis-registry.js → .../analysis/deprecated/analysis-registry.js
@@ -1,5 +1,5 @@
-import OpencgaKnockoutAnalysis from "./deprecated/opencga-knockout-analysis.js";
-import OpencgaRecessiveGeneAnalysis from "./deprecated/opencga-recessive-gene-analysis.js";
+import OpencgaKnockoutAnalysis from "./opencga-knockout-analysis.js";
+import OpencgaRecessiveGeneAnalysis from "./opencga-recessive-gene-analysis.js";
 
 export default class AnalysisRegistry {
 
@@ -17,18 +17,18 @@ export default class AnalysisRegistry {
     }
 
     static get(id) {
-        const ar = this.registry[id];
+        const AR = this.registry[id];
         // override the class default result config
-        if (ar) {
-            if (ar.result) {
-                ar.class.result = ar.result;
+        if (AR) {
+            if (AR.result) {
+                AR.class.result = AR.result;
             }
 
-            if (ar.config) {
-                ar.class.config = {...ar.class.config, ...ar.config};
+            if (AR.config) {
+                AR.class.config = {...AR.class.config, ...AR.config};
             }
             // return Reflect.constructor(ar.class, ar.config)
-            return new ar.class(ar.config);
+            return new AR.class(AR.config);
         } else {
             console.warn("Analysis Class not found:" + id);
         }

diff --git a/src/webcomponents/variant/analysis/deprecated/opencga-knockout-analysis-result.js b/src/webcomponents/variant/analysis/deprecated/opencga-knockout-analysis-result.js
@@ -19,11 +19,11 @@ import {classMap} from "lit/directives/class-map.js";
 import GridCommons from "../../../commons/grid-commons.js";
 import UtilsNew from "../../../../core/utils-new.js";
 import "../../../commons/analysis/opencga-analysis-tool.js";
-import AnalysisRegistry from "../analysis-registry.js";
+import AnalysisRegistry from "./analysis-registry.js";
 import "../../../commons/forms/select-field-filter.js";
-import "../opencga-knockout-analysis/knockout-gene-grid.js";
-import "../opencga-knockout-analysis/knockout-individual-view.js";
-import "../opencga-knockout-analysis/knockout-variant-view.js";
+import "./opencga-knockout-analysis/knockout-gene-grid.js";
+import "./opencga-knockout-analysis/knockout-individual-view.js";
+import "./opencga-knockout-analysis/knockout-variant-view.js";
 
 
 export default class OpencgaKnockoutAnalysisResult extends LitElement {
@@ -71,8 +71,6 @@ export default class OpencgaKnockoutAnalysisResult extends LitElement {
     }
 
     updated(changedProperties) {
-        if (changedProperties.has("opencgaSession")) {
-        }
         if (changedProperties.has("config")) {
             this._config = {...this.getDefaultConfig(), ...this.config};
             this.requestUpdate();
@@ -82,7 +80,7 @@ export default class OpencgaKnockoutAnalysisResult extends LitElement {
     _changeTab(e) {
         e.preventDefault();
         const tabId = e.currentTarget.dataset.id;
-        //the selectors are strictly defined to avoid conflics in tabs in children components
+        // the selectors are strictly defined to avoid conflics in tabs in children components
         $("#opencga-knockout-analysis-result > div > .content-pills", this).removeClass("active");
         $("#opencga-knockout-analysis-result > .content-tab-wrapper > .content-tab", this).hide();
         $("#" + this._prefix + tabId, this).show();
@@ -95,11 +93,11 @@ export default class OpencgaKnockoutAnalysisResult extends LitElement {
     }
 
     getDefaultConfig() {
-        return AnalysisRegistry.get("knockout").config;
+        // return AnalysisRegistry.get("knockout").config;
     }
 
     render() {
-        //wait for opencgaSession to be available because inner components use it
+        // wait for opencgaSession to be available because inner components use it
         return this.opencgaSession ? html`
             <div class="container" style="margin-top: 60px">
                 <div id="opencga-knockout-analysis-result">

diff --git a/...a-knockout-analysis/knockout-gene-grid.js → ...a-knockout-analysis/knockout-gene-grid.js b/...a-knockout-analysis/knockout-gene-grid.js → ...a-knockout-analysis/knockout-gene-grid.js
@@ -16,9 +16,9 @@
 
 import {LitElement, html} from "lit";
 import {classMap} from "lit/directives/class-map.js";
-import UtilsNew from "../../../../core/utils-new.js";
+import UtilsNew from "../../../../../core/utils-new.js";
 import AnalysisRegistry from "../analysis-registry.js";
-import GridCommons from "../../../commons/grid-commons.js";
+import GridCommons from "../../../../commons/grid-commons.js";
 import knockoutDataGene from "../test/knockout.20201103172343.kFIvpr.gene.js";
 
 export default class KnockoutGeneGrid extends LitElement {
@@ -99,7 +99,7 @@ export default class KnockoutGeneGrid extends LitElement {
         this.table = $("#" + this.gridId);
         this.table.bootstrapTable("destroy");
         this.table.bootstrapTable({
-            //data: this.tableData,
+            // data: this.tableData,
             columns: this._initTableColumns(),
             sidePagination: "local",
             iconsPrefix: GridCommons.GRID_ICONS_PREFIX,
@@ -115,7 +115,7 @@ export default class KnockoutGeneGrid extends LitElement {
             ajax: params => {
                 this.opencgaSession.opencgaClient.variants().queryKnockoutGene({job: this.jobId, study: this.opencgaSession.study.fqn})
                     .then(restResponse => {
-                        console.log("restResponse", restResponse)
+                        console.log("restResponse", restResponse);
                         this.tableData = restResponse.getResults();
                         params.success(this.tableData);
                     }).catch(e => {

diff --git a/...-analysis/knockout-individual-variants.js → ...-analysis/knockout-individual-variants.js b/...-analysis/knockout-individual-variants.js → ...-analysis/knockout-individual-variants.js
@@ -15,9 +15,9 @@
  */
 
 import {LitElement, html} from "lit";
-import UtilsNew from "../../../../core/utils-new.js";
-import GridCommons from "../../../commons/grid-commons.js";
-import "./../../../commons/view/detail-tabs.js";
+import UtilsNew from "../../../../../core/utils-new.js";
+import GridCommons from "../../../../commons/grid-commons.js";
+import "../../../../commons/view/detail-tabs.js";
 import knockoutDataIndividuals from "../test/knockout.20201103172343.kFIvpr.individuals.js";
 
 
@@ -55,9 +55,6 @@ export default class KnockoutIndividualVariants extends LitElement {
     }
 
     updated(changedProperties) {
-        if (changedProperties.has("opencgaSession")) {
-        }
-
         if (changedProperties.has("individual")) {
             this.prepareData();
             this.renderTable();

diff --git a/...kout-analysis/knockout-individual-view.js → ...kout-analysis/knockout-individual-view.js b/...kout-analysis/knockout-individual-view.js → ...kout-analysis/knockout-individual-view.js
@@ -15,13 +15,13 @@
  */
 
 import {LitElement, html} from "lit";
-import UtilsNew from "../../../../core/utils-new.js";
-import CatalogGridFormatter from "../../../commons/catalog-grid-formatter.js";
+import UtilsNew from "../../../../../core/utils-new.js";
+import CatalogGridFormatter from "../../../../commons/catalog-grid-formatter.js";
 import AnalysisRegistry from "../analysis-registry.js";
-import GridCommons from "../../../commons/grid-commons.js";
+import GridCommons from "../../../../commons/grid-commons.js";
 import knockoutDataIndividuals from "../test/knockout.20201103172343.kFIvpr.individuals.js";
 import "./knockout-individual-variants.js";
-import "../../../family/family-view.js";
+import "../../../../family/family-view.js";
 
 export default class KnockoutIndividualView extends LitElement {
 

diff --git a/...analysis/knockout-variant-allele-pairs.js → ...analysis/knockout-variant-allele-pairs.js b/...analysis/knockout-variant-allele-pairs.js → ...analysis/knockout-variant-allele-pairs.js
@@ -15,9 +15,9 @@
  */
 
 import {LitElement, html} from "lit";
-import UtilsNew from "../../../../core/utils-new.js";
-import GridCommons from "../../../commons/grid-commons.js";
-import "./../../../commons/view/detail-tabs.js";
+import UtilsNew from "../../../../../core/utils-new.js";
+import GridCommons from "../../../../commons/grid-commons.js";
+import "../../../../commons/view/detail-tabs.js";
 import knockoutDataIndividuals from "../test/knockout.20201103172343.kFIvpr.individuals.js";
 
 
@@ -54,9 +54,6 @@ export default class KnockoutVariantAllelePairs extends LitElement {
     }
 
     updated(changedProperties) {
-        if (changedProperties.has("opencgaSession")) {
-        }
-
         if (changedProperties.has("variantId")) {
             this.prepareData();
             this.renderTable();

diff --git a/...t-analysis/knockout-variant-individual.js → ...t-analysis/knockout-variant-individual.js b/...t-analysis/knockout-variant-individual.js → ...t-analysis/knockout-variant-individual.js
@@ -15,9 +15,9 @@
  */
 
 import {LitElement, html} from "lit";
-import UtilsNew from "../../../../core/utils-new.js";
-import GridCommons from "../../../commons/grid-commons.js";
-import "./../../../commons/view/detail-tabs.js";
+import UtilsNew from "../../../../../core/utils-new.js";
+import GridCommons from "../../../../commons/grid-commons.js";
+import "../../../../commons/view/detail-tabs.js";
 import knockoutDataIndividuals from "../test/knockout.20201103172343.kFIvpr.individuals.js";
 
 
@@ -54,8 +54,6 @@ export default class KnockoutVariantIndividual extends LitElement {
     }
 
     updated(changedProperties) {
-        if (changedProperties.has("opencgaSession")) {
-        }
 
         if (changedProperties.has("variant")) {
             this.prepareData();
@@ -86,7 +84,7 @@ export default class KnockoutVariantIndividual extends LitElement {
             uniqueId: "id",
             pagination: true,
             paginationVAlign: "both",
-            //formatShowingRows: this.gridCommons.formatShowingRows,
+            // formatShowingRows: this.gridCommons.formatShowingRows,
             gridContext: this,
             formatLoadingMessage: () => "<div><loading-spinner></loading-spinner></div>",
             onClickRow: (row, selectedElement, field) => {

diff --git a/...nockout-analysis/knockout-variant-view.js → ...nockout-analysis/knockout-variant-view.js b/...nockout-analysis/knockout-variant-view.js → ...nockout-analysis/knockout-variant-view.js
@@ -15,17 +15,17 @@
  */
 
 import {LitElement, html} from "lit";
-import UtilsNew from "../../../../core/utils-new.js";
-import CatalogGridFormatter from "../../../commons/catalog-grid-formatter.js";
+import UtilsNew from "../../../../../core/utils-new.js";
+import CatalogGridFormatter from "../../../../commons/catalog-grid-formatter.js";
 import AnalysisRegistry from "../analysis-registry.js";
-import GridCommons from "../../../commons/grid-commons.js";
+import GridCommons from "../../../../commons/grid-commons.js";
 import knockoutData from "../test/knockout.20201029141213.SChLEA.js";
 import "./knockout-individual-variants.js";
 import "./knockout-variant-allele-pairs.js";
 import "./knockout-variant-individual.js";
-import "../../../family/family-view.js";
-import "../../annotation/cellbase-population-frequency-grid.js";
-import "../../annotation/variant-annotation-clinical-view.js";
+import "../../../../family/family-view.js";
+import "../../../annotation/cellbase-population-frequency-grid.js";
+import "../../../annotation/variant-annotation-clinical-view.js";
 
 
 export default class KnockoutVariantView extends LitElement {

diff --git a/...is/test/knockout.20201029141213.SChLEA.js → ...ed/test/knockout.20201029141213.SChLEA.js b/...is/test/knockout.20201029141213.SChLEA.js → ...ed/test/knockout.20201029141213.SChLEA.js
@@ -375,4 +375,4 @@ export default [
             }
         ]
     }
-]
+];
diff --git a/...st/knockout.20201103172343.kFIvpr.gene.js → ...st/knockout.20201103172343.kFIvpr.gene.js b/...st/knockout.20201103172343.kFIvpr.gene.js → ...st/knockout.20201103172343.kFIvpr.gene.js
diff --git a/...kout.20201103172343.kFIvpr.individuals.js → ...kout.20201103172343.kFIvpr.individuals.js b/...kout.20201103172343.kFIvpr.individuals.js → ...kout.20201103172343.kFIvpr.individuals.js
@@ -240,4 +240,4 @@ export default [
             }
         ]
     }
-]
+];
diff --git a/...est/opencga-knockout-analysis-result.html → ...est/opencga-knockout-analysis-result.html b/...est/opencga-knockout-analysis-result.html → ...est/opencga-knockout-analysis-result.html
-Original file line number
+Diff line change
@@ Expand Up / @@ -375,4 +375,4 @@ export default [ @@
                 }
             ]
         }
-    ]
+    ];