wc: variant components refactoring

Author: imedina

src/core/webcomponents/alignment/gene-coverage-grid.js

@@ -16,7 +16,7 @@
 
 import {LitElement, html} from "/web_modules/lit-element.js";
 import UtilsNew from "../../utilsNew.js";
-import GridCommons from "../variant/grid-commons.js";
+import GridCommons from "../commons/grid-commons.js";
 import "../commons/opencb-grid-toolbar.js";
 import "../loading-spinner.js";
 // import DATA from "./data.js";

src/core/webcomponents/clinical/clinical-analysis-audit-browser.js

@@ -17,11 +17,11 @@
 import {LitElement, html} from "/web_modules/lit-element.js";
 import {classMap} from "/web_modules/lit-html/directives/class-map.js";
 import UtilsNew from "../../utilsNew.js";
-import "../tool-header.js";
+import "../commons/tool-header.js";
 import "../variant/interpretation/variant-interpreter-grid.js";
 import "../variant/interpretation/variant-interpreter-detail.js";
 import "../variant/opencga-variant-filter.js";
-import GridCommons from "../variant/grid-commons.js";
+import GridCommons from "../commons/grid-commons.js";
 
 class ClinicalAnalysisAuditBrowser extends LitElement {
 

src/core/webcomponents/clinical/clinical-analysis-interpretation-editor.js

@@ -17,7 +17,7 @@
 import {html, LitElement} from "/web_modules/lit-element.js";
 import {classMap} from "/web_modules/lit-html/directives/class-map.js";
 import UtilsNew from "../../utilsNew.js";
-import GridCommons from "../variant/grid-commons.js";
+import GridCommons from "../commons/grid-commons.js";
 import ClinicalAnalysisManager from "../clinical/clinical-analysis-manager.js";
 
 

src/core/webcomponents/clinical/opencga-clinical-analysis-grid.js

@@ -18,7 +18,7 @@ import {LitElement, html} from "/web_modules/lit-element.js";
 import {classMap} from "/web_modules/lit-html/directives/class-map.js";
 import OpencgaCatalogUtils from "../../clients/opencga/opencga-catalog-utils.js";
 import UtilsNew from "../../utilsNew.js";
-import GridCommons from "../variant/grid-commons.js";
+import GridCommons from "../commons/grid-commons.js";
 import CatalogGridFormatter from "../commons/catalog-grid-formatter.js";
 import "../commons/opencb-grid-toolbar.js";
 

src/core/webcomponents/clinical/opencga-clinical-portal.js

@@ -18,7 +18,7 @@ import {LitElement, html} from "/web_modules/lit-element.js";
 import OpencgaCatalogUtils from "../../clients/opencga/opencga-catalog-utils.js";
 import UtilsNew from "../../utilsNew.js";
 import PolymerUtils from "../PolymerUtils.js";
-import "../tool-header.js";
+import "../commons/tool-header.js";
 import "./opencga-clinical-review-cases.js";
 import "./opencga-clinical-analysis-writer.js";
 import "./../opencga/catalog/panel/opencga-panel-browser.js";

src/core/webcomponents/cohort/opencga-cohort-grid.js

@@ -16,7 +16,7 @@
 
 import {LitElement, html} from "/web_modules/lit-element.js";
 import UtilsNew from "../../utilsNew.js";
-import GridCommons from "../variant/grid-commons.js";
+import GridCommons from "../commons/grid-commons.js";
 import CatalogGridFormatter from "../commons/catalog-grid-formatter.js";
 import PolymerUtils from "../PolymerUtils.js";
 

src/core/webcomponents/variant/grid-commons.js src/core/webcomponents/commons/grid-commons.js

@@ -172,6 +172,8 @@ export default class GridCommons {
                 }
             }));
         }
+
+        // This init all grid tooltips
         UtilsNew.initTooltip(this.context);
     }
 

src/core/webcomponents/json-viewer.js src/core/webcomponents/commons/json-viewer.js

@@ -1,5 +1,5 @@
-/**
- * Copyright 2015-2019 OpenCB
+/*
+ * Copyright 2015-2016 OpenCB
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
@@ -15,8 +15,8 @@
  */
 
 import {LitElement, html} from "/web_modules/lit-element.js";
-import UtilsNew from "../utilsNew.js";
-import "./download-button.js";
+import UtilsNew from "../../utilsNew.js";
+import "../download-button.js";
 
 export default class JsonViewer extends LitElement {
 

src/core/webcomponents/commons/opencga-browser.js

@@ -22,7 +22,7 @@ import "./filters/select-field-filter.js";
 import "./opencb-facet-results.js";
 import "./facet-filter.js";
 import "../loading-spinner.js";
-import "../tool-header.js";
+import "./tool-header.js";
 import "../file/opencga-file-grid.js";
 import "../file/opencga-file-filter.js";
 import "../file/opencga-file-detail.js";

src/core/webcomponents/simple-chart.js src/core/webcomponents/commons/simple-chart.js

@@ -1,5 +1,5 @@
-/**
- * Copyright 2015-2019 OpenCB
+/*
+ * Copyright 2015-2016 OpenCB
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
@@ -15,7 +15,7 @@
  */
 
 import {LitElement, html} from "/web_modules/lit-element.js";
-import UtilsNew from "../utilsNew.js";
+import UtilsNew from "../../utilsNew.js";
 
 
 export default class SimpleChart extends LitElement {

src/core/webcomponents/tool-header.js src/core/webcomponents/commons/tool-header.js

@@ -1,5 +1,5 @@
-/**
- * Copyright 2015-2019 OpenCB
+/*
+ * Copyright 2015-2016 OpenCB
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
@@ -15,7 +15,7 @@
  */
 
 import {LitElement, html} from "/web_modules/lit-element.js";
-import UtilsNew from "../utilsNew.js";
+import UtilsNew from "../../utilsNew.js";
 
 export default class ToolHeader extends LitElement {
 

src/core/webcomponents/commons/view/data-form.js

@@ -16,8 +16,8 @@
 
 import {html, LitElement} from "/web_modules/lit-element.js";
 import UtilsNew from "../../../utilsNew.js";
-import "../../simple-chart.js";
-import "../../json-viewer.js";
+import "../simple-chart.js";
+import "../json-viewer.js";
 import "../../tree-viewer.js";
 import "../../download-button.js";
 import "../../commons/filters/text-field-filter.js";

src/core/webcomponents/commons/view/data-view.js

@@ -17,8 +17,8 @@
 import {html, LitElement} from "/web_modules/lit-element.js";
 // import {directive} from "/web_modules/lit-html.js";
 import UtilsNew from "../../../utilsNew.js";
-import "../../simple-chart.js";
-import "../../json-viewer.js";
+import "../simple-chart.js";
+import "../json-viewer.js";
 import "../../download-button.js";
 
 export default class DataView extends LitElement {

src/core/webcomponents/family/opencga-family-grid.js

@@ -16,7 +16,7 @@
 
 import {LitElement, html} from "/web_modules/lit-element.js";
 import UtilsNew from "../../utilsNew.js";
-import GridCommons from "../variant/grid-commons.js";
+import GridCommons from "../commons/grid-commons.js";
 import CatalogGridFormatter from "../commons/catalog-grid-formatter.js";
 import CatalogUtils from "../commons/catalog-utils.js";
 import "./opencga-family-filter.js";

src/core/webcomponents/file/opencga-file-grid.js

@@ -17,7 +17,7 @@
 import {LitElement, html} from "/web_modules/lit-element.js";
 import UtilsNew from "../../utilsNew.js";
 import {NotificationQueue} from "../Notification.js";
-import GridCommons from "../variant/grid-commons.js";
+import GridCommons from "../commons/grid-commons.js";
 import CatalogGridFormatter from "../commons/catalog-grid-formatter.js";
 import "../commons/opencb-grid-toolbar.js";
 import "../loading-spinner.js";

src/core/webcomponents/file/opencga-file-preview.js

@@ -15,7 +15,7 @@
  */
 
 import {LitElement, html} from "/web_modules/lit-element.js";
-import "../json-viewer.js";
+import "../commons/json-viewer.js";
 import UtilsNew from "../../utilsNew.js";
 
 

src/core/webcomponents/individual/opencga-individual-grid.js

@@ -17,7 +17,7 @@
 import {html, LitElement} from "/web_modules/lit-element.js";
 import UtilsNew from "../../utilsNew.js";
 import {NotificationQueue} from "../Notification.js";
-import GridCommons from "../variant/grid-commons.js";
+import GridCommons from "../commons/grid-commons.js";
 import CatalogGridFormatter from "../commons/catalog-grid-formatter.js";
 import CatalogUtils from "../commons/catalog-utils.js";
 import "../commons/opencb-grid-toolbar.js";

src/core/webcomponents/job/opencga-job-grid.js

@@ -16,7 +16,7 @@
 
 import {LitElement, html} from "/web_modules/lit-element.js";
 import UtilsNew from "../../utilsNew.js";
-import GridCommons from "../variant/grid-commons.js";
+import GridCommons from "../commons/grid-commons.js";
 import CatalogGridFormatter from "../commons/catalog-grid-formatter.js";
 import "../commons/opencb-grid-toolbar.js";
 import "../loading-spinner.js";

src/core/webcomponents/opencga/opencga-gene-view.js

@@ -17,9 +17,9 @@
 import {LitElement, html} from "/web_modules/lit-element.js";
 import UtilsNew from "../../utilsNew.js";
 import PolymerUtils from "../PolymerUtils.js";
-import "../variant/opencga-variant-grid.js";
+import "../variant/variant-browser-grid.js";
 import "../variant/variant-protein-view.js";
-import "../variant/opencga-variant-detail-view.js";
+import "../variant/variant-browser-detail.js";
 
 
 export default class OpencgaGeneView extends LitElement {

src/core/webcomponents/opencga/opencga-protein-view.js

@@ -17,7 +17,7 @@
 import {LitElement, html} from "/web_modules/lit-element.js";
 import UtilsNew from "../../utilsNew.js";
 import PolymerUtils from "../PolymerUtils.js";
-import "./../variant/opencga-variant-grid.js";
+import "../variant/variant-browser-grid.js";
 
 
 export default class OpencgaProteinView extends LitElement {

src/core/webcomponents/opencga/opencga-transcript-view.js

@@ -17,7 +17,7 @@
 import {LitElement, html} from "/web_modules/lit-element.js";
 import UtilsNew from "../../utilsNew.js";
 import PolymerUtils from "../PolymerUtils.js";
-import "../variant/opencga-variant-grid.js";
+import "../variant/variant-browser-grid.js";
 import "../variant/variant-protein-view.js";
 
 

src/core/webcomponents/sample/opencga-sample-grid.js

@@ -16,7 +16,7 @@
 
 import {LitElement, html} from "/web_modules/lit-element.js";
 import UtilsNew from "../../utilsNew.js";
-import GridCommons from "../variant/grid-commons.js";
+import GridCommons from "../commons/grid-commons.js";
 import CatalogGridFormatter from "../commons/catalog-grid-formatter.js";
 import CatalogUtils from "../commons/catalog-utils.js";
 import "../commons/opencb-grid-toolbar.js";

src/core/webcomponents/sample/sample-qc-signature-view.js

@@ -18,7 +18,7 @@ import {LitElement, html} from "/web_modules/lit-element.js";
 import UtilsNew from "../../utilsNew.js";
 import "../commons/view/signature-view.js";
 import "../commons/view/data-form.js";
-import "../simple-chart.js";
+import "../commons/simple-chart.js";
 
 class SampleQcSignatureView extends LitElement {
 

src/core/webcomponents/sample/sample-variant-stats-view.js

@@ -17,7 +17,7 @@
 import {LitElement, html} from "/web_modules/lit-element.js";
 import UtilsNew from "../../utilsNew.js";
 import ClinicalAnalysisUtils from "../clinical/clinical-analysis-utils.js";
-import "../simple-chart.js";
+import "../commons/simple-chart.js";
 import "../commons/view/data-form.js";
 
 /**

src/core/webcomponents/user/opencga-projects.js

@@ -17,9 +17,9 @@
 import {LitElement, html} from "/web_modules/lit-element.js";
 import {RestResponse} from "../../clients/rest-response.js";
 import UtilsNew from "../../utilsNew.js";
-import "../tool-header.js";
+import "../commons/tool-header.js";
 import {CountUp} from "/node_modules/countup.js/dist/countUp.min.js";
-import "../simple-chart.js";
+import "../commons/simple-chart.js";
 
 export default class OpencgaProjects extends LitElement {
 

src/core/webcomponents/variant/analysis/opencga-knockout-analysis-result.js

@@ -16,7 +16,7 @@
 
 import {LitElement, html} from "/web_modules/lit-element.js";
 import {classMap} from "/web_modules/lit-html/directives/class-map.js";
-import GridCommons from "../grid-commons.js";
+import GridCommons from "../../commons/grid-commons.js";
 import UtilsNew from "./../../../utilsNew.js";
 import "../../commons/analysis/opencga-analysis-tool.js";
 import AnalysisRegistry from "./analysis-registry.js";

src/core/webcomponents/variant/analysis/opencga-knockout-analysis/knockout-gene-grid.js

@@ -18,7 +18,7 @@ import {LitElement, html} from "/web_modules/lit-element.js";
 import {classMap} from "/web_modules/lit-html/directives/class-map.js";
 import UtilsNew from "../../../../utilsNew.js";
 import AnalysisRegistry from "../analysis-registry.js";
-import GridCommons from "../../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 {

src/core/webcomponents/variant/analysis/opencga-knockout-analysis/knockout-individual-view.js

@@ -18,7 +18,7 @@ import {LitElement, html} from "/web_modules/lit-element.js";
 import UtilsNew from "../../../../utilsNew.js";
 import CatalogGridFormatter from "../../../commons/catalog-grid-formatter.js";
 import AnalysisRegistry from "../analysis-registry.js";
-import GridCommons from "../../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/opencga-family-view.js";

src/core/webcomponents/variant/analysis/opencga-knockout-analysis/knockout-variant-view.js

@@ -18,7 +18,7 @@ import {LitElement, html} from "/web_modules/lit-element.js";
 import UtilsNew from "../../../../utilsNew.js";
 import CatalogGridFormatter from "../../../commons/catalog-grid-formatter.js";
 import AnalysisRegistry from "../analysis-registry.js";
-import GridCommons from "../../grid-commons.js";
+import GridCommons from "../../../commons/grid-commons.js";
 import knockoutData from "../test/knockout.20201029141213.SChLEA.js";
 import "./knockout-individual-variants.js";
 import "../../../family/opencga-family-view.js";

src/core/webcomponents/variant/deprecated/interpretation-history.js

@@ -18,7 +18,7 @@ import {LitElement, html} from "/web_modules/lit-element.js";
 import ClinicalAnalysisUtils from "../../clinical/clinical-analysis-utils.js";
 import UtilsNew from "../../../utilsNew.js";
 import PolymerUtils from "../../PolymerUtils.js";
-import "../../tool-header.js";
+import "../../commons/tool-header.js";
 import "../interpretation/variant-interpreter-grid.js";
 import "../interpretation/variant-interpreter-detail.js";
 import "../opencga-variant-filter.js";
@@ -31,7 +31,7 @@ import "../../commons/filters/deprecated/ascat-caller-filter.js";
 import "../../commons/filters/deprecated/canvas-caller-filter.js";
 import "../../commons/filters/deprecated/brass-caller-filter.js";
 import "../../commons/filters/deprecated/manta-caller-filter.js";
-import GridCommons from "../grid-commons.js";
+import GridCommons from "../../commons/grid-commons.js";
 
 class InterpretationHistory extends LitElement {
 

src/core/webcomponents/variant/opencga-variant-detail.js src/core/webcomponents/variant/deprecated/opencga-variant-detail.js

@@ -15,13 +15,13 @@
  */
 
 import {LitElement, html} from "/web_modules/lit-element.js";
-import UtilsNew from "./../../utilsNew.js";
-import "./annotation/cellbase-variant-annotation-summary.js";
-import "./annotation/variant-consequence-type-view.js";
-import "./annotation/cellbase-population-frequency-grid.js";
-import "./annotation/variant-annotation-clinical-view.js";
-import "./opencga-variant-cohort-stats.js";
-import "./opencga-variant-samples.js";
+import UtilsNew from "../../../utilsNew.js";
+import "../annotation/cellbase-variant-annotation-summary.js";
+import "../annotation/variant-consequence-type-view.js";
+import "../annotation/cellbase-population-frequency-grid.js";
+import "../annotation/variant-annotation-clinical-view.js";
+import "../variant-cohort-stats.js";
+import "../opencga-variant-samples.js";
 
 /**
  * @deprecated

src/core/webcomponents/variant/interpretation/variant-interpreter-browser-cancer.js

@@ -23,7 +23,7 @@ import "./variant-interpreter-browser-toolbar.js";
 import "./variant-interpreter-grid.js";
 import "./variant-interpreter-detail.js";
 import "../opencga-variant-filter.js";
-import "../../tool-header.js";
+import "../../commons/tool-header.js";
 import "../../commons/opencga-active-filters.js";
 import "../../commons/filters/sample-genotype-filter.js";
 import "../../commons/filters/variant-caller-info-filter.js";

src/core/webcomponents/variant/interpretation/variant-interpreter-browser-rd.js

@@ -23,7 +23,7 @@ import "./variant-interpreter-browser-toolbar.js";
 import "./variant-interpreter-grid.js";
 import "./variant-interpreter-detail.js";
 import "../opencga-variant-filter.js";
-import "../../tool-header.js";
+import "../../commons/tool-header.js";
 import "../../commons/opencga-active-filters.js";
 
 

src/core/webcomponents/variant/interpretation/variant-interpreter-detail.js

@@ -244,10 +244,10 @@ export default class VariantInterpreterDetail extends LitElement {
                         <!-- Cohort Stats Tab -->
                         <div id="${this._prefix}cohortStats" role="tabpanel" class="tab-pane">
                             <div style="width: 90%;padding: 15px">
-                                <opencga-variant-cohort-stats .opencgaSession="${this.opencgaSession}"
-                                                              .variantId="${this.variant.id}"
-                                                              .active="${this.detailActiveTabs.cohortStats}">
-                                </opencga-variant-cohort-stats>
+                                <variant-cohort-stats .opencgaSession="${this.opencgaSession}"
+                                                      .variantId="${this.variant.id}"
+                                                      .active="${this.detailActiveTabs.cohortStats}">
+                                </variant-cohort-stats>
                             </div>
                         </div>