From 43f084d8f40663ed39bceb6904413291907a53ab Mon Sep 17 00:00:00 2001 From: Josemi Date: Mon, 11 Mar 2024 12:41:42 +0100 Subject: [PATCH 01/16] gb: fix windowSize value used to request coverage data in opencga-alignment-track #TASK-5728 --- src/genome-browser/tracks/opencga-alignment-track.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/genome-browser/tracks/opencga-alignment-track.js b/src/genome-browser/tracks/opencga-alignment-track.js index 5db980ab24..48dfe89004 100644 --- a/src/genome-browser/tracks/opencga-alignment-track.js +++ b/src/genome-browser/tracks/opencga-alignment-track.js @@ -64,7 +64,7 @@ export default class OpenCGAAlignmentTrack extends FeatureTrack { const coverageRequest = this.config.opencgaClient.alignments().queryCoverage(this.alignmentInfo.id, { study: this.config.opencgaStudy, region: options.region.toString(), - windowSize: 1, + windowSize: Math.max(1, Math.round(10 / this.pixelBase)), offset: 0, }); From b182a21d0f56d1ef5a0fd6f58b0d02919740b38e Mon Sep 17 00:00:00 2001 From: Rodiel Martinez <10471758+Rodielm@users.noreply.github.com> Date: Fri, 22 Mar 2024 16:05:36 +0100 Subject: [PATCH 02/16] wc: use JSONEditor in 'json-viewer' #TASK-5744 --- src/webcomponents/commons/json-editor.js | 6 +- src/webcomponents/commons/json-viewer.js | 72 +++++++++++++++--------- 2 files changed, 48 insertions(+), 30 deletions(-) diff --git a/src/webcomponents/commons/json-editor.js b/src/webcomponents/commons/json-editor.js index adcbbcdc59..9b9854374c 100644 --- a/src/webcomponents/commons/json-editor.js +++ b/src/webcomponents/commons/json-editor.js @@ -126,16 +126,16 @@ export default class JsonEditor extends LitElement { return html` ${this._config.showDownloadButton ? html` -
+
+ .class="${"btn-sm"}">
` : null } -
+
`; } diff --git a/src/webcomponents/commons/json-viewer.js b/src/webcomponents/commons/json-viewer.js index 44b5d2be15..c8cab1bc70 100644 --- a/src/webcomponents/commons/json-viewer.js +++ b/src/webcomponents/commons/json-viewer.js @@ -15,6 +15,7 @@ */ import {LitElement, html} from "lit"; +import {JSONEditor} from "vanilla-jsoneditor"; import UtilsNew from "../../core/utils-new.js"; import "../download-button.js"; @@ -34,43 +35,54 @@ export default class JsonViewer extends LitElement { data: { type: Object }, - // title: { - // type: String - // }, - showDownloadButton: { - type: Boolean - }, active: { type: Boolean - } + }, + config: { + type: Object, + }, }; } _init() { this._prefix = UtilsNew.randomString(8); - - this.showDownloadButton = true; this.active = true; + this.jsonView = null; + this._config = this.getDefaultConfig(); } - connectedCallback() { - super.connectedCallback(); - - // this._config = {...this.getDefaultConfig(), ...this.config}; + update(changedProperties) { + if (changedProperties.has("config")) { + this._config = { + ...this.getDefaultConfig(), + ...this.config, + }; + } + super.update(changedProperties); } updated(changedProperties) { - if ((changedProperties.has("data") || changedProperties.has("active")) && this.active) { - if (this.data) { - // $(".json-renderer", this).jsonViewer(this.data); - $(`#${this._prefix}JsonView`, this).jsonViewer(this.data); + if ((changedProperties.has("data") || changedProperties.has("active") || changedProperties.has("config")) && this.active) { + if (!this.jsonView) { + this.initJsonView(); + } else { + this.jsonView.update({json: this.data}); } } - // super.update(changedProperties); } - getDefaultConfig() { - return {}; + initJsonView() { + this.jsonView = new JSONEditor({ + target: this.querySelector(`#${this._prefix}JsonView`), + props: { + content: { + json: this.data || {}, + }, + mode: this._config?.mode || "tree", + indentation: this._config?.indentation || 4, + readOnly: true, + } + }); } render() { @@ -79,20 +91,26 @@ export default class JsonViewer extends LitElement { } return html` - ${this.showDownloadButton ? html` -
+ ${this._config?.showDownloadButton ? html` +
+ .class="${"btn-sm"}">
- ` : null - } - -
+ ` : null} +
`; } + getDefaultConfig() { + return { + showDownloadButton: true, + indentation: 4, + mode: "tree", + }; + } + } customElements.define("json-viewer", JsonViewer); From 6f02e59c8cb28b3eb5f8cff6ba606ce6d5dce241 Mon Sep 17 00:00:00 2001 From: Josemi Date: Wed, 10 Apr 2024 14:01:31 +0200 Subject: [PATCH 03/16] wc: add params argument to sampleGenotypeFormatter #TASK-6003 --- .../variant-interpreter-grid-formatter.js | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/src/webcomponents/variant/interpretation/variant-interpreter-grid-formatter.js b/src/webcomponents/variant/interpretation/variant-interpreter-grid-formatter.js index 4294a83494..5b3bea024e 100644 --- a/src/webcomponents/variant/interpretation/variant-interpreter-grid-formatter.js +++ b/src/webcomponents/variant/interpretation/variant-interpreter-grid-formatter.js @@ -445,11 +445,11 @@ export default class VariantInterpreterGridFormatter { /* * SAMPLE GENOTYPE RENDERER */ - static sampleGenotypeFormatter(value, row, index) { + static sampleGenotypeFormatter(value, row, index, params) { let resultHtml = ""; if (row && row.studies?.length > 0 && row.studies[0].samples?.length > 0) { - const sampleId = this.field.sampleId; + const sampleId = params?.sampleId; let sampleEntries = [row.studies[0].samples.find(s => s.sampleId === sampleId)]; // If not sampleId is found and there is only one sample we take that one @@ -474,7 +474,7 @@ export default class VariantInterpreterGridFormatter { // Render genotypes let content = ""; - switch (this.field.config?.genotype?.type?.toUpperCase() || "VCF_CALL") { + switch (params?.config?.genotype?.type?.toUpperCase() || "VCF_CALL") { case "ALLELES": content = VariantInterpreterGridFormatter.alleleGenotypeRenderer(row, sampleEntry, "alleles"); break; @@ -482,7 +482,7 @@ export default class VariantInterpreterGridFormatter { content = VariantInterpreterGridFormatter.alleleGenotypeRenderer(row, sampleEntry, "call"); break; case "ZYGOSITY": - content = VariantInterpreterGridFormatter.zygosityGenotypeRenderer(row, sampleEntry, this.field.clinicalAnalysis); + content = VariantInterpreterGridFormatter.zygosityGenotypeRenderer(row, sampleEntry, params?.clinicalAnalysis); break; case "VAF": const vaf = VariantInterpreterGridFormatter._getVariantAlleleFraction(row, sampleEntry, file); @@ -508,7 +508,7 @@ export default class VariantInterpreterGridFormatter { content = VariantInterpreterGridFormatter.circleGenotypeRenderer(sampleEntry, file, 10); break; default: - console.error("No valid genotype render option:", this.field.config.genotype.type.toUpperCase()); + console.error("No valid genotype render option:", params?.config?.genotype?.type?.toUpperCase()); break; } From c8db6426db074e5b6ac2b2257c5c3acea60e9f13 Mon Sep 17 00:00:00 2001 From: Josemi Date: Wed, 10 Apr 2024 14:02:10 +0200 Subject: [PATCH 04/16] wc: fix usage of sampleGenotypeFormatter in variant-interpreter-grid #TASK-6003 --- .../variant-interpreter-grid.js | 34 ++++++++++--------- 1 file changed, 18 insertions(+), 16 deletions(-) diff --git a/src/webcomponents/variant/interpretation/variant-interpreter-grid.js b/src/webcomponents/variant/interpretation/variant-interpreter-grid.js index 85a6d897e3..0e7f1cd994 100644 --- a/src/webcomponents/variant/interpretation/variant-interpreter-grid.js +++ b/src/webcomponents/variant/interpretation/variant-interpreter-grid.js @@ -1069,17 +1069,18 @@ export default class VariantInterpreterGrid extends LitElement { title: `${samples[i].id}
${sampleInfo[samples[i].id].role}, ${affected}`, - field: { - memberIdx: i, - memberName: samples[i].id, - sampleId: samples[i].id, - quality: this._config.quality, - clinicalAnalysis: this.clinicalAnalysis, - config: this._config - }, rowspan: 1, colspan: 1, - formatter: VariantInterpreterGridFormatter.sampleGenotypeFormatter, + formatter: (value, row, index) => { + return VariantInterpreterGridFormatter.sampleGenotypeFormatter(value, row, index, { + memberIdx: i, + memberName: samples[i].id, + sampleId: samples[i].id, + quality: this._config.quality, + clinicalAnalysis: this.clinicalAnalysis, + config: this._config + }); + }, align: "center", nucleotideGenotype: true, visible: this.gridCommons.isColumnVisible(samples[i].id, "sampleGenotypes"), @@ -1120,15 +1121,16 @@ export default class VariantInterpreterGrid extends LitElement {
${sample.id}
${sample?.somatic ? "somatic" : "germline"}
`, - field: { - sampleId: sample.id, - quality: this._config.quality, - config: this._config, - clinicalAnalysis: this.clinicalAnalysis - }, rowspan: 1, colspan: 1, - formatter: VariantInterpreterGridFormatter.sampleGenotypeFormatter, + formatter: (value, row, index) => { + return VariantInterpreterGridFormatter.sampleGenotypeFormatter(value, row, index, { + sampleId: sample.id, + quality: this._config.quality, + config: this._config, + clinicalAnalysis: this.clinicalAnalysis + }); + }, align: "center", nucleotideGenotype: true, visible: this.gridCommons.isColumnVisible(samples[i].id, "sampleGenotypes"), From 6fc4d3940d8f563a2d39b1a5a7682f5fd6a9a352 Mon Sep 17 00:00:00 2001 From: Josemi Date: Wed, 10 Apr 2024 14:03:36 +0200 Subject: [PATCH 05/16] wc: fix usage of sampleGenotypeFormatter in variant-browser-grid #TASK-6003 --- .../variant/variant-browser-grid.js | 17 ++++++++--------- 1 file changed, 8 insertions(+), 9 deletions(-) diff --git a/src/webcomponents/variant/variant-browser-grid.js b/src/webcomponents/variant/variant-browser-grid.js index 0dd40c9ef7..cb792b0e1c 100644 --- a/src/webcomponents/variant/variant-browser-grid.js +++ b/src/webcomponents/variant/variant-browser-grid.js @@ -562,18 +562,17 @@ export default class VariantBrowserGrid extends LitElement { sampleColumns.push({ id: this.samples[i].id, title: this.samples[i].id, - // field: "samples", - field: { - memberIdx: i, - memberName: this.samples[i].id, - sampleId: this.samples[i].id, - config: this._config - }, rowspan: 1, colspan: 1, - formatter: VariantInterpreterGridFormatter.sampleGenotypeFormatter, + formatter: (value, row, index) => { + return VariantInterpreterGridFormatter.sampleGenotypeFormatter(value, row, index, { + memberIdx: i, + memberName: this.samples[i].id, + sampleId: this.samples[i].id, + config: this._config + }); + }, align: "center", - // nucleotideGenotype: true, visible: this.gridCommons.isColumnVisible(this.samples[i].id, "samples"), }); } From 54cae174d031ce53d991cc6ff90096ea91bf014d Mon Sep 17 00:00:00 2001 From: Josemi Date: Wed, 10 Apr 2024 14:04:11 +0200 Subject: [PATCH 06/16] wc: removed unused fields provided to sampleGenotypeFormatter in variant-browser-grid #TAKS-6003 --- src/webcomponents/variant/variant-browser-grid.js | 2 -- 1 file changed, 2 deletions(-) diff --git a/src/webcomponents/variant/variant-browser-grid.js b/src/webcomponents/variant/variant-browser-grid.js index cb792b0e1c..d82da129fa 100644 --- a/src/webcomponents/variant/variant-browser-grid.js +++ b/src/webcomponents/variant/variant-browser-grid.js @@ -566,8 +566,6 @@ export default class VariantBrowserGrid extends LitElement { colspan: 1, formatter: (value, row, index) => { return VariantInterpreterGridFormatter.sampleGenotypeFormatter(value, row, index, { - memberIdx: i, - memberName: this.samples[i].id, sampleId: this.samples[i].id, config: this._config }); From a02053aed27fd24bcc1daaaf0c1c09be2684653c Mon Sep 17 00:00:00 2001 From: Josemi Date: Wed, 10 Apr 2024 14:06:16 +0200 Subject: [PATCH 07/16] wc: removed unused fields provided as params to sampleGenotypeFormatter in variant-interpreter-grid #TASK-6003 --- .../variant/interpretation/variant-interpreter-grid.js | 6 ------ 1 file changed, 6 deletions(-) diff --git a/src/webcomponents/variant/interpretation/variant-interpreter-grid.js b/src/webcomponents/variant/interpretation/variant-interpreter-grid.js index 0e7f1cd994..de23fe3234 100644 --- a/src/webcomponents/variant/interpretation/variant-interpreter-grid.js +++ b/src/webcomponents/variant/interpretation/variant-interpreter-grid.js @@ -1073,16 +1073,12 @@ export default class VariantInterpreterGrid extends LitElement { colspan: 1, formatter: (value, row, index) => { return VariantInterpreterGridFormatter.sampleGenotypeFormatter(value, row, index, { - memberIdx: i, - memberName: samples[i].id, sampleId: samples[i].id, - quality: this._config.quality, clinicalAnalysis: this.clinicalAnalysis, config: this._config }); }, align: "center", - nucleotideGenotype: true, visible: this.gridCommons.isColumnVisible(samples[i].id, "sampleGenotypes"), }); } @@ -1126,13 +1122,11 @@ export default class VariantInterpreterGrid extends LitElement { formatter: (value, row, index) => { return VariantInterpreterGridFormatter.sampleGenotypeFormatter(value, row, index, { sampleId: sample.id, - quality: this._config.quality, config: this._config, clinicalAnalysis: this.clinicalAnalysis }); }, align: "center", - nucleotideGenotype: true, visible: this.gridCommons.isColumnVisible(samples[i].id, "sampleGenotypes"), }); } From 6b4ec0bb684062daa17185d99c2a88dfb706ce14 Mon Sep 17 00:00:00 2001 From: Josemi Date: Wed, 10 Apr 2024 14:07:05 +0200 Subject: [PATCH 08/16] wc: minor style fix in sampleGenotypeFormatter #TASK-6003 --- .../interpretation/variant-interpreter-grid-formatter.js | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/src/webcomponents/variant/interpretation/variant-interpreter-grid-formatter.js b/src/webcomponents/variant/interpretation/variant-interpreter-grid-formatter.js index 5b3bea024e..fbcd742470 100644 --- a/src/webcomponents/variant/interpretation/variant-interpreter-grid-formatter.js +++ b/src/webcomponents/variant/interpretation/variant-interpreter-grid-formatter.js @@ -514,9 +514,11 @@ export default class VariantInterpreterGridFormatter { // Get tooltip text const tooltipText = VariantInterpreterGridFormatter._getSampleGenotypeTooltipText(row, sampleEntry, file); - resultHtml += ` - ${content} -
`; + resultHtml += ` + + ${content} +
+ `; } } From 397320d5523f371c64e94cbbdbb902bffcccfa3f Mon Sep 17 00:00:00 2001 From: Josemi Date: Wed, 10 Apr 2024 17:54:41 +0200 Subject: [PATCH 09/16] wc: exclude sample genotypes columns from settings in variant-interpreter-grid #TASK-6014 --- .../variant/interpretation/variant-interpreter-grid.js | 2 ++ 1 file changed, 2 insertions(+) diff --git a/src/webcomponents/variant/interpretation/variant-interpreter-grid.js b/src/webcomponents/variant/interpretation/variant-interpreter-grid.js index 85a6d897e3..7e2ad5f0d8 100644 --- a/src/webcomponents/variant/interpretation/variant-interpreter-grid.js +++ b/src/webcomponents/variant/interpretation/variant-interpreter-grid.js @@ -1082,6 +1082,7 @@ export default class VariantInterpreterGrid extends LitElement { formatter: VariantInterpreterGridFormatter.sampleGenotypeFormatter, align: "center", nucleotideGenotype: true, + excludeFromSettings: true, visible: this.gridCommons.isColumnVisible(samples[i].id, "sampleGenotypes"), }); } @@ -1131,6 +1132,7 @@ export default class VariantInterpreterGrid extends LitElement { formatter: VariantInterpreterGridFormatter.sampleGenotypeFormatter, align: "center", nucleotideGenotype: true, + excludeFromSettings: true, visible: this.gridCommons.isColumnVisible(samples[i].id, "sampleGenotypes"), }); } From d9081de2cd2a9e1de2472b49b53b53a5a2ba3ce0 Mon Sep 17 00:00:00 2001 From: Josemi Date: Wed, 10 Apr 2024 17:55:52 +0200 Subject: [PATCH 10/16] wc: exclude from settings vcf file data columns in variant-interpreter-grid #TASK-6014 --- .../variant/interpretation/variant-interpreter-grid.js | 1 + 1 file changed, 1 insertion(+) diff --git a/src/webcomponents/variant/interpretation/variant-interpreter-grid.js b/src/webcomponents/variant/interpretation/variant-interpreter-grid.js index 7e2ad5f0d8..d109bd6d77 100644 --- a/src/webcomponents/variant/interpretation/variant-interpreter-grid.js +++ b/src/webcomponents/variant/interpretation/variant-interpreter-grid.js @@ -562,6 +562,7 @@ export default class VariantInterpreterGrid extends LitElement { colspan: 1, formatter: this.vcfDataFormatter, halign: this.displayConfigDefault.header.horizontalAlign, + excludeFromSettings: true, visible: this.gridCommons.isColumnVisible(columnId, "VCF_Data"), }); } From 35039e412e723d34e62687dd16e178c8e3c61b69 Mon Sep 17 00:00:00 2001 From: Josemi Date: Wed, 10 Apr 2024 17:56:51 +0200 Subject: [PATCH 11/16] wc: exclude from settings vcf file data columns in variant-interpreter-rearrangement-grid #TASK-6014 --- .../interpretation/variant-interpreter-rearrangement-grid.js | 1 + 1 file changed, 1 insertion(+) diff --git a/src/webcomponents/variant/interpretation/variant-interpreter-rearrangement-grid.js b/src/webcomponents/variant/interpretation/variant-interpreter-rearrangement-grid.js index 57e54d65a4..fcd3670d56 100644 --- a/src/webcomponents/variant/interpretation/variant-interpreter-rearrangement-grid.js +++ b/src/webcomponents/variant/interpretation/variant-interpreter-rearrangement-grid.js @@ -544,6 +544,7 @@ export default class VariantInterpreterRearrangementGrid extends LitElement { colspan: 1, formatter: (value, row) => this.vcfDataFormatter(value, row[index], field), halign: "center", + excludeFromSettings: true, visible: this.gridCommons.isColumnVisible(id), }); }); From 6272cdeee598b7f147760aa91ba3d1fec28ea985 Mon Sep 17 00:00:00 2001 From: Josemi Date: Wed, 10 Apr 2024 18:01:16 +0200 Subject: [PATCH 12/16] wc: using configuration variable to control when sample genotypes columns are visible in variant-interpreter-grid #TASK-6014 --- .../variant/interpretation/variant-interpreter-grid.js | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/src/webcomponents/variant/interpretation/variant-interpreter-grid.js b/src/webcomponents/variant/interpretation/variant-interpreter-grid.js index d109bd6d77..82848269ba 100644 --- a/src/webcomponents/variant/interpretation/variant-interpreter-grid.js +++ b/src/webcomponents/variant/interpretation/variant-interpreter-grid.js @@ -1084,7 +1084,8 @@ export default class VariantInterpreterGrid extends LitElement { align: "center", nucleotideGenotype: true, excludeFromSettings: true, - visible: this.gridCommons.isColumnVisible(samples[i].id, "sampleGenotypes"), + // visible: this.gridCommons.isColumnVisible(samples[i].id, "sampleGenotypes"), + visible: !this._config.hideSampleGenotypes, }); } } @@ -1134,7 +1135,8 @@ export default class VariantInterpreterGrid extends LitElement { align: "center", nucleotideGenotype: true, excludeFromSettings: true, - visible: this.gridCommons.isColumnVisible(samples[i].id, "sampleGenotypes"), + // visible: this.gridCommons.isColumnVisible(samples[i].id, "sampleGenotypes"), + visible: !this._config.hideSampleGenotypes, }); } } @@ -1552,6 +1554,7 @@ export default class VariantInterpreterGrid extends LitElement { hidePopulationFrequencies: false, hideClinicalInfo: false, hideDeleteriousness: false, + hideSampleGenotypes: false, quality: { qual: 30, From ddf246990bb47bfe10de06826e3aaf1aa3694107 Mon Sep 17 00:00:00 2001 From: Josemi Date: Wed, 10 Apr 2024 18:06:00 +0200 Subject: [PATCH 13/16] wc: using configuration variable to control when vcf file data columns are visible in variant-interpreter-grid #TASK-6014 --- .../variant/interpretation/variant-interpreter-grid.js | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/src/webcomponents/variant/interpretation/variant-interpreter-grid.js b/src/webcomponents/variant/interpretation/variant-interpreter-grid.js index 82848269ba..1fd66ddf26 100644 --- a/src/webcomponents/variant/interpretation/variant-interpreter-grid.js +++ b/src/webcomponents/variant/interpretation/variant-interpreter-grid.js @@ -563,7 +563,8 @@ export default class VariantInterpreterGrid extends LitElement { formatter: this.vcfDataFormatter, halign: this.displayConfigDefault.header.horizontalAlign, excludeFromSettings: true, - visible: this.gridCommons.isColumnVisible(columnId, "VCF_Data"), + // visible: this.gridCommons.isColumnVisible(columnId, "VCF_Data"), + visible: !this._config.hideVcfFileData, }); } } @@ -1555,6 +1556,7 @@ export default class VariantInterpreterGrid extends LitElement { hideClinicalInfo: false, hideDeleteriousness: false, hideSampleGenotypes: false, + hideVcfFileData: false, quality: { qual: 30, From 72ba0f1213e77757d038cd34dfac3b522dc078f0 Mon Sep 17 00:00:00 2001 From: Josemi Date: Wed, 10 Apr 2024 18:06:42 +0200 Subject: [PATCH 14/16] wc: using configuration variable to control when vcf file data columns are visible in variant-interpreter-rearrangement-grid #TASK-6014 --- .../interpretation/variant-interpreter-rearrangement-grid.js | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/src/webcomponents/variant/interpretation/variant-interpreter-rearrangement-grid.js b/src/webcomponents/variant/interpretation/variant-interpreter-rearrangement-grid.js index fcd3670d56..fb7146f57a 100644 --- a/src/webcomponents/variant/interpretation/variant-interpreter-rearrangement-grid.js +++ b/src/webcomponents/variant/interpretation/variant-interpreter-rearrangement-grid.js @@ -545,7 +545,8 @@ export default class VariantInterpreterRearrangementGrid extends LitElement { formatter: (value, row) => this.vcfDataFormatter(value, row[index], field), halign: "center", excludeFromSettings: true, - visible: this.gridCommons.isColumnVisible(id), + // visible: this.gridCommons.isColumnVisible(id), + visible: !this._config.hideVcfFileData, }); }); }); @@ -1108,6 +1109,8 @@ export default class VariantInterpreterRearrangementGrid extends LitElement { alleleStringLengthMax: 50, + hideVcfFileData: false, + // genotype: { // type: "VCF_CALL" // }, From 12b088fadf4faec4818103a4c1eb1537a2544635 Mon Sep 17 00:00:00 2001 From: Josemi Date: Wed, 10 Apr 2024 18:11:48 +0200 Subject: [PATCH 15/16] wc: remove commented code in variant-interpreter-rearrangement-grid #TASK-6014 --- .../interpretation/variant-interpreter-rearrangement-grid.js | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/src/webcomponents/variant/interpretation/variant-interpreter-rearrangement-grid.js b/src/webcomponents/variant/interpretation/variant-interpreter-rearrangement-grid.js index fb7146f57a..24f7274091 100644 --- a/src/webcomponents/variant/interpretation/variant-interpreter-rearrangement-grid.js +++ b/src/webcomponents/variant/interpretation/variant-interpreter-rearrangement-grid.js @@ -545,7 +545,6 @@ export default class VariantInterpreterRearrangementGrid extends LitElement { formatter: (value, row) => this.vcfDataFormatter(value, row[index], field), halign: "center", excludeFromSettings: true, - // visible: this.gridCommons.isColumnVisible(id), visible: !this._config.hideVcfFileData, }); }); @@ -1106,11 +1105,10 @@ export default class VariantInterpreterRearrangementGrid extends LitElement { showActions: false, multiSelection: false, nucleotideGenotype: true, + hideVcfFileData: false, alleleStringLengthMax: 50, - hideVcfFileData: false, - // genotype: { // type: "VCF_CALL" // }, From 9e466b5ab818c542e45ada99666bd2f783cf794a Mon Sep 17 00:00:00 2001 From: Josemi Date: Wed, 10 Apr 2024 18:12:02 +0200 Subject: [PATCH 16/16] wc: remove commented code in variant-interpreter-grid #TASK-6014 --- .../variant/interpretation/variant-interpreter-grid.js | 3 --- 1 file changed, 3 deletions(-) diff --git a/src/webcomponents/variant/interpretation/variant-interpreter-grid.js b/src/webcomponents/variant/interpretation/variant-interpreter-grid.js index 1fd66ddf26..2fb3f7b1d5 100644 --- a/src/webcomponents/variant/interpretation/variant-interpreter-grid.js +++ b/src/webcomponents/variant/interpretation/variant-interpreter-grid.js @@ -563,7 +563,6 @@ export default class VariantInterpreterGrid extends LitElement { formatter: this.vcfDataFormatter, halign: this.displayConfigDefault.header.horizontalAlign, excludeFromSettings: true, - // visible: this.gridCommons.isColumnVisible(columnId, "VCF_Data"), visible: !this._config.hideVcfFileData, }); } @@ -1085,7 +1084,6 @@ export default class VariantInterpreterGrid extends LitElement { align: "center", nucleotideGenotype: true, excludeFromSettings: true, - // visible: this.gridCommons.isColumnVisible(samples[i].id, "sampleGenotypes"), visible: !this._config.hideSampleGenotypes, }); } @@ -1136,7 +1134,6 @@ export default class VariantInterpreterGrid extends LitElement { align: "center", nucleotideGenotype: true, excludeFromSettings: true, - // visible: this.gridCommons.isColumnVisible(samples[i].id, "sampleGenotypes"), visible: !this._config.hideSampleGenotypes, }); }