From e6ad086ed97790e1c5be84293aa87f5ab5447121 Mon Sep 17 00:00:00 2001 From: Josemi Date: Fri, 6 Sep 2024 16:41:38 +0200 Subject: [PATCH 01/51] wc: split variants track into small variants and structural variants #TASK-5769 --- .../variant-interpreter-browser-template.js | 13 ++++++++++++- 1 file changed, 12 insertions(+), 1 deletion(-) diff --git a/src/webcomponents/variant/interpretation/variant-interpreter-browser-template.js b/src/webcomponents/variant/interpretation/variant-interpreter-browser-template.js index 0573c70fa7..31711036c5 100644 --- a/src/webcomponents/variant/interpretation/variant-interpreter-browser-template.js +++ b/src/webcomponents/variant/interpretation/variant-interpreter-browser-template.js @@ -564,9 +564,20 @@ class VariantInterpreterBrowserTemplate extends LitElement { { type: "opencga-variant", config: { - title: "Variants", + title: "Variants (Small Variants)", query: { sample: this.clinicalAnalysis.proband.samples.map(s => s.id).join(","), + type: "SNV,INDEL", + }, + }, + }, + { + type: "opencga-variant", + config: { + title: "Variants (SV)", + query: { + sample: this.clinicalAnalysis.proband.samples.map(s => s.id).join(","), + type: "COPY_NUMBER,BREAKEND,INSERTION,DELETION,DUPLICATION", }, }, }, From a57a79bd5339293d3aa9467fe3144b5888bde091 Mon Sep 17 00:00:00 2001 From: Josemi Date: Fri, 6 Sep 2024 17:46:23 +0200 Subject: [PATCH 02/51] gb: Add check to prevent rendering variants twice #TASK-5769 --- src/genome-browser/renderers/variant-renderer.js | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/src/genome-browser/renderers/variant-renderer.js b/src/genome-browser/renderers/variant-renderer.js index 902ff98a72..e9b06d358e 100644 --- a/src/genome-browser/renderers/variant-renderer.js +++ b/src/genome-browser/renderers/variant-renderer.js @@ -61,6 +61,15 @@ export default class VariantRenderer extends Renderer { } (features || []).forEach((feature, featureIndex) => { + // Check if this variant has been previously rendered + if (options?.renderedFeatures && feature?.id) { + if (options.renderedFeatures.has(feature.id)) { + return; + } + // Prevent rendering this variant in next calls of this renderer + options.renderedFeatures.add(feature.id); + } + const group = SVG.addChild(options.svgCanvasFeatures, "g", { "data-cy": "gb-variant", "data-id": feature.id || "-", From 452af6bb1542547ebb2e42c37f0199b5c28ca2fa Mon Sep 17 00:00:00 2001 From: Josemi Date: Fri, 6 Sep 2024 17:53:51 +0200 Subject: [PATCH 03/51] gb: Fix hide/show content in feature track #TASK-5769 --- src/genome-browser/tracks/feature-track.js | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/src/genome-browser/tracks/feature-track.js b/src/genome-browser/tracks/feature-track.js index 22d5b4f211..faf9f19135 100644 --- a/src/genome-browser/tracks/feature-track.js +++ b/src/genome-browser/tracks/feature-track.js @@ -229,8 +229,8 @@ export default class FeatureTrack { hideContent() { this.contentVisible = false; - this.content.classList.add("hidden"); - this.resize.classList.add("hidden"); + this.content.classList.add("d-none"); + this.resize.classList.add("d-none"); this.titleToggleIcon.classList.remove("fa-minus"); this.titleToggleIcon.classList.add("fa-plus"); @@ -238,8 +238,8 @@ export default class FeatureTrack { showContent() { this.contentVisible = true; - this.content.classList.remove("hidden"); - this.resize.classList.remove("hidden"); + this.content.classList.remove("d-none"); + this.resize.classList.remove("d-none"); this.titleToggleIcon.classList.remove("fa-plus"); this.titleToggleIcon.classList.add("fa-minus"); From 29525079ff36882e98e601072f97700c8edc9f85 Mon Sep 17 00:00:00 2001 From: Josemi Date: Tue, 10 Sep 2024 13:35:24 +0200 Subject: [PATCH 04/51] wc: hide lollipos section in large variants track #TASK-5769 --- .../variant-interpreter-browser-template.js | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/src/webcomponents/variant/interpretation/variant-interpreter-browser-template.js b/src/webcomponents/variant/interpretation/variant-interpreter-browser-template.js index 31711036c5..e6fb3c2029 100644 --- a/src/webcomponents/variant/interpretation/variant-interpreter-browser-template.js +++ b/src/webcomponents/variant/interpretation/variant-interpreter-browser-template.js @@ -564,21 +564,25 @@ class VariantInterpreterBrowserTemplate extends LitElement { { type: "opencga-variant", config: { - title: "Variants (Small Variants)", + title: "Small Variants (SNV & INDEL)", query: { sample: this.clinicalAnalysis.proband.samples.map(s => s.id).join(","), type: "SNV,INDEL", }, + headerHeight: 0, }, }, { type: "opencga-variant", config: { - title: "Variants (SV)", + title: "Large Variants (CNV & SV)", query: { sample: this.clinicalAnalysis.proband.samples.map(s => s.id).join(","), type: "COPY_NUMBER,BREAKEND,INSERTION,DELETION,DUPLICATION", }, + lollipopVisible: false, + highlightVisible: false, + headerHeight: 0, }, }, ...(this.clinicalAnalysis.proband?.samples || []).map(sample => ({ From abb9a91b32cd32a8eb40d873e86d4dc78cd88cff Mon Sep 17 00:00:00 2001 From: Josemi Date: Wed, 11 Sep 2024 12:19:52 +0200 Subject: [PATCH 05/51] wc: Unbind select2 events in select-field-filter #TASK-6543 --- src/webcomponents/commons/forms/select-field-filter.js | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/src/webcomponents/commons/forms/select-field-filter.js b/src/webcomponents/commons/forms/select-field-filter.js index 2d9683076d..1d344c32ba 100644 --- a/src/webcomponents/commons/forms/select-field-filter.js +++ b/src/webcomponents/commons/forms/select-field-filter.js @@ -108,6 +108,11 @@ export default class SelectFieldFilter extends LitElement { } this.select.empty(); + + // Force to unbind 'select2:select' and 'select2:unselect' listeners + this.select.off("select2:select"); + this.select.off("select2:unselect"); + const options = this.data.map(item => this.getOptions(item)); const selectConfig = { From f86bec5e6dc5e05013e175ec365ff645097840ef Mon Sep 17 00:00:00 2001 From: Josemi Date: Wed, 11 Sep 2024 12:39:46 +0200 Subject: [PATCH 06/51] wc: Fix displaying local variants in rearrangement grid #TASK-6849 --- .../interpretation/variant-interpreter-rearrangement-grid.js | 1 - 1 file changed, 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 5ae03b8963..cf524c59ba 100644 --- a/src/webcomponents/variant/interpretation/variant-interpreter-rearrangement-grid.js +++ b/src/webcomponents/variant/interpretation/variant-interpreter-rearrangement-grid.js @@ -376,7 +376,6 @@ export default class VariantInterpreterRearrangementGrid extends LitElement { this.table.bootstrapTable({ theadClasses: "table-light", buttonsClass: "light", - data: variants, columns: this._getDefaultColumns(), sidePagination: "server", // Josemi Note 2024-01-31: we have added the ajax function for local variants for getting genes info From 7632b48549d9b47c841d122130f89d03b6026bf7 Mon Sep 17 00:00:00 2001 From: Josemi Date: Wed, 11 Sep 2024 12:47:11 +0200 Subject: [PATCH 07/51] wc: Fix displaying actions column in rearrangement grid #TASK-6849 --- .../interpretation/variant-interpreter-rearrangement-grid.js | 3 ++- 1 file changed, 2 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 cf524c59ba..ee2c93783f 100644 --- a/src/webcomponents/variant/interpretation/variant-interpreter-rearrangement-grid.js +++ b/src/webcomponents/variant/interpretation/variant-interpreter-rearrangement-grid.js @@ -685,6 +685,7 @@ export default class VariantInterpreterRearrangementGrid extends LitElement { events: { "click a": this.onActionClick.bind(this) }, + visible: this._config?.showActions, excludeFromExport: true, excludeFromSettings: true, } @@ -1115,7 +1116,7 @@ export default class VariantInterpreterRearrangementGrid extends LitElement { showReview: true, showEditReview: true, showSelectCheckbox: false, - showActions: false, + showActions: true, multiSelection: false, nucleotideGenotype: true, hideVcfFileData: false, From e0df358fba135adc6bec4d9be652d4afcf4700c3 Mon Sep 17 00:00:00 2001 From: Josemi Date: Wed, 11 Sep 2024 14:13:29 +0200 Subject: [PATCH 08/51] gb: Allow to display lollipops for only some variant types #TASK-5769 --- src/genome-browser/renderers/variant-renderer.js | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/src/genome-browser/renderers/variant-renderer.js b/src/genome-browser/renderers/variant-renderer.js index e9b06d358e..fb8c3ad69a 100644 --- a/src/genome-browser/renderers/variant-renderer.js +++ b/src/genome-browser/renderers/variant-renderer.js @@ -49,7 +49,8 @@ export default class VariantRenderer extends Renderer { let topPosition = this.config.lollipopVisible ? this.config.lollipopHeight : this.config.headerHeight; if (this.config.lollipopVisible) { - lollipopPositions = LollipopLayout.fromFeaturesList(features || [], options.requestedRegion, lollipopRegionWidth, { + const featuresForLollipops = (features || []).filter(feature => this.config.lollipopVariantTypes.includes(feature.type)); + lollipopPositions = LollipopLayout.fromFeaturesList(featuresForLollipops, options.requestedRegion, lollipopRegionWidth, { minSeparation: this.config.lollipopMaxWidth, }); } @@ -95,8 +96,8 @@ export default class VariantRenderer extends Renderer { let variantElement = null; - // Check if lollipops are visible - if (this.config.lollipopVisible) { + // Check if lollipops are visible and the feature type is one of the allowed types for lollipops + if (this.config.lollipopVisible && this.config.lollipopVariantTypes?.includes?.(feature?.type)) { const lollipopX = lollipopStartX + lollipopPositions[featureIndex]; const lollipopWidth = Math.min(1, Math.max(0, this.getValueFromConfig("lollipopWidth", [feature]))); const lollipopPath = [ @@ -305,6 +306,7 @@ export default class VariantRenderer extends Renderer { lollipopMaxWidth: 15, lollipopShape: GenomeBrowserUtils.lollipopShapeFormatter, lollipopWidth: GenomeBrowserUtils.lollipopWidthFormatter, + lollipopVariantTypes: ["SNP", "INDEL", "BREAKEND"], // Lollipop focus lollipopFocusEnabled: true, lollipopFocusWidth: 2, From 36fd66c64d447d20cace451d1a6392c523cc6690 Mon Sep 17 00:00:00 2001 From: Josemi Date: Wed, 11 Sep 2024 14:22:59 +0200 Subject: [PATCH 09/51] gb: Fix bug getting lollipop position of the feature #TASK-5769 --- src/genome-browser/renderers/variant-renderer.js | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/src/genome-browser/renderers/variant-renderer.js b/src/genome-browser/renderers/variant-renderer.js index fb8c3ad69a..ea91dedc4b 100644 --- a/src/genome-browser/renderers/variant-renderer.js +++ b/src/genome-browser/renderers/variant-renderer.js @@ -46,6 +46,7 @@ export default class VariantRenderer extends Renderer { const lollipopStickHeight = this.config.lollipopHeight - this.config.lollipopFocusWidth - this.config.lollipopMaxWidth / 2; let lollipopStickStart = this.config.lollipopFocusWidth + this.config.lollipopMaxWidth / 2; let lollipopPositions = []; + let lollipopIndex = 0; let topPosition = this.config.lollipopVisible ? this.config.lollipopHeight : this.config.headerHeight; if (this.config.lollipopVisible) { @@ -53,6 +54,7 @@ export default class VariantRenderer extends Renderer { lollipopPositions = LollipopLayout.fromFeaturesList(featuresForLollipops, options.requestedRegion, lollipopRegionWidth, { minSeparation: this.config.lollipopMaxWidth, }); + console.log(lollipopPositions); } // Check if highlights are visible @@ -98,7 +100,7 @@ export default class VariantRenderer extends Renderer { // Check if lollipops are visible and the feature type is one of the allowed types for lollipops if (this.config.lollipopVisible && this.config.lollipopVariantTypes?.includes?.(feature?.type)) { - const lollipopX = lollipopStartX + lollipopPositions[featureIndex]; + const lollipopX = lollipopStartX + lollipopPositions[lollipopIndex]; const lollipopWidth = Math.min(1, Math.max(0, this.getValueFromConfig("lollipopWidth", [feature]))); const lollipopPath = [ `M ${lollipopX},${lollipopStickStart}`, @@ -140,6 +142,8 @@ export default class VariantRenderer extends Renderer { variantElement.setAttribute("stroke-width", 0); }); } + // increment lollipop index + lollipopIndex = lollipopIndex + 1; } else { variantElement = SVG.addChild(group, "rect", { "data-cy": "gb-variant-lollipop-shape", From 61e38e67fc432bf9b8bac38d95d3fc7221aacd4a Mon Sep 17 00:00:00 2001 From: Josemi Date: Wed, 11 Sep 2024 14:23:31 +0200 Subject: [PATCH 10/51] gb: Fix typo in allowed variant types for lollipops #TASK-5769 --- src/genome-browser/renderers/variant-renderer.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/genome-browser/renderers/variant-renderer.js b/src/genome-browser/renderers/variant-renderer.js index ea91dedc4b..63d312068d 100644 --- a/src/genome-browser/renderers/variant-renderer.js +++ b/src/genome-browser/renderers/variant-renderer.js @@ -310,7 +310,7 @@ export default class VariantRenderer extends Renderer { lollipopMaxWidth: 15, lollipopShape: GenomeBrowserUtils.lollipopShapeFormatter, lollipopWidth: GenomeBrowserUtils.lollipopWidthFormatter, - lollipopVariantTypes: ["SNP", "INDEL", "BREAKEND"], + lollipopVariantTypes: ["SNV", "INDEL", "BREAKEND"], // Lollipop focus lollipopFocusEnabled: true, lollipopFocusWidth: 2, From 2816761dde45b515c01f0391093871a2cc2461c3 Mon Sep 17 00:00:00 2001 From: Josemi Date: Wed, 11 Sep 2024 16:55:29 +0200 Subject: [PATCH 11/51] wc: Add new track for displaying rearrangements in GB #TASK-5769 --- .../variant-interpreter-browser-template.js | 15 +++++++++++++-- 1 file changed, 13 insertions(+), 2 deletions(-) diff --git a/src/webcomponents/variant/interpretation/variant-interpreter-browser-template.js b/src/webcomponents/variant/interpretation/variant-interpreter-browser-template.js index e6fb3c2029..75370f83e5 100644 --- a/src/webcomponents/variant/interpretation/variant-interpreter-browser-template.js +++ b/src/webcomponents/variant/interpretation/variant-interpreter-browser-template.js @@ -575,16 +575,27 @@ class VariantInterpreterBrowserTemplate extends LitElement { { type: "opencga-variant", config: { - title: "Large Variants (CNV & SV)", + title: "Large Variants (CNV)", query: { sample: this.clinicalAnalysis.proband.samples.map(s => s.id).join(","), - type: "COPY_NUMBER,BREAKEND,INSERTION,DELETION,DUPLICATION", + type: "COPY_NUMBER,INSERTION,DELETION,DUPLICATION", }, lollipopVisible: false, highlightVisible: false, headerHeight: 0, }, }, + { + type: "opencga-variant", + config: { + title: "Large Variants (SV)", + query: { + sample: this.clinicalAnalysis.proband.samples.map(s => s.id).join(","), + type: "BREAKEND", + }, + headerHeight: 0, + }, + }, ...(this.clinicalAnalysis.proband?.samples || []).map(sample => ({ type: "opencga-alignment", config: { From 84477408de36aaa2686c424bd27b63a7f50af9cd Mon Sep 17 00:00:00 2001 From: Josemi Date: Wed, 11 Sep 2024 16:55:34 +0200 Subject: [PATCH 12/51] gb: Fix bug with displaced lollipops in variant track #TASK-5769 --- src/genome-browser/renderers/variant-renderer.js | 14 +++++++++++--- 1 file changed, 11 insertions(+), 3 deletions(-) diff --git a/src/genome-browser/renderers/variant-renderer.js b/src/genome-browser/renderers/variant-renderer.js index 63d312068d..febe48a579 100644 --- a/src/genome-browser/renderers/variant-renderer.js +++ b/src/genome-browser/renderers/variant-renderer.js @@ -49,12 +49,20 @@ export default class VariantRenderer extends Renderer { let lollipopIndex = 0; let topPosition = this.config.lollipopVisible ? this.config.lollipopHeight : this.config.headerHeight; + // We have to filter features and consider only the ones that are in the current region + // this is important because when we request for breakends to OpenCGA it returns both variants of the breakend + const region = options.requestedRegion; + const featuresToDisplay = (features || []).filter(feature => { + return feature.chromosome === region.chromosome && feature.start <= region.end && region.start <= feature.end; + }); + if (this.config.lollipopVisible) { - const featuresForLollipops = (features || []).filter(feature => this.config.lollipopVariantTypes.includes(feature.type)); + const featuresForLollipops = featuresToDisplay.filter(feature => { + return this.config.lollipopVariantTypes.includes(feature.type); + }); lollipopPositions = LollipopLayout.fromFeaturesList(featuresForLollipops, options.requestedRegion, lollipopRegionWidth, { minSeparation: this.config.lollipopMaxWidth, }); - console.log(lollipopPositions); } // Check if highlights are visible @@ -63,7 +71,7 @@ export default class VariantRenderer extends Renderer { lollipopStickStart = lollipopStickStart + this.config.highlightHeight; } - (features || []).forEach((feature, featureIndex) => { + featuresToDisplay.forEach((feature, featureIndex) => { // Check if this variant has been previously rendered if (options?.renderedFeatures && feature?.id) { if (options.renderedFeatures.has(feature.id)) { From ffed4a1f5fba015d25794c2df37d4f3b1f59bafc Mon Sep 17 00:00:00 2001 From: Josemi Date: Wed, 11 Sep 2024 18:09:43 +0200 Subject: [PATCH 13/51] wc: Remove debugger line in clinical-analysis-grid #TASK-6702 --- src/webcomponents/clinical/clinical-analysis-grid.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/webcomponents/clinical/clinical-analysis-grid.js b/src/webcomponents/clinical/clinical-analysis-grid.js index bd670c9114..a996ee6112 100644 --- a/src/webcomponents/clinical/clinical-analysis-grid.js +++ b/src/webcomponents/clinical/clinical-analysis-grid.js @@ -372,7 +372,7 @@ export default class ClinicalAnalysisGrid extends LitElement { // const btnClassName = "d-inline-flex align-items-center btn btn-light dropdown-toggle"; const btnClassName = "d-flex justify-content-between align-items-center btn btn-light dropdown-toggle w-100"; // const btnStyle = "display:inline-flex;align-items:center;"; -debugger + return `
${this.variantsReview ? html` ` : null}
- +
@@ -1082,8 +1083,8 @@ export default class VariantInterpreterRearrangementGrid extends LitElement {
-

Settings

- +

Settings

+
@@ -1096,7 +1097,7 @@ export default class VariantInterpreterRearrangementGrid extends LitElement {
- +
From 6bb78d3b3b3541a445f57a4b47d37b1be5ee7a32 Mon Sep 17 00:00:00 2001 From: Josemi Date: Fri, 13 Sep 2024 13:42:14 +0200 Subject: [PATCH 19/51] wc: Add missing close button in variant evidence review modal #TASK-6850 --- .../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 ad88e5c294..85745ac3a8 100644 --- a/src/webcomponents/variant/interpretation/variant-interpreter-grid.js +++ b/src/webcomponents/variant/interpretation/variant-interpreter-grid.js @@ -1598,6 +1598,7 @@ export default class VariantInterpreterGrid extends LitElement {

Review Variant Evidence

+
${this.evidenceReview ? html` Date: Fri, 13 Sep 2024 13:45:43 +0200 Subject: [PATCH 20/51] wc: Remove unused config modal in rearrangement grid #TASK-6850 --- .../variant-interpreter-rearrangement-grid.js | 32 ------------------- 1 file changed, 32 deletions(-) diff --git a/src/webcomponents/variant/interpretation/variant-interpreter-rearrangement-grid.js b/src/webcomponents/variant/interpretation/variant-interpreter-rearrangement-grid.js index 4294b33904..80d89cada8 100644 --- a/src/webcomponents/variant/interpretation/variant-interpreter-rearrangement-grid.js +++ b/src/webcomponents/variant/interpretation/variant-interpreter-rearrangement-grid.js @@ -979,12 +979,6 @@ export default class VariantInterpreterRearrangementGrid extends LitElement { } } - onConfigClick(e) { - // eslint-disable-next-line no-undef - const configModal = new bootstrap.Modal("#" + this._prefix + "ConfigModal"); - configModal.show(); - } - onVariantChange(e) { this.variantsReview[0] = e.detail.value; } @@ -1077,32 +1071,6 @@ export default class VariantInterpreterRearrangementGrid extends LitElement {
- - `; } From 4ebf9e525d8258bc03b98619c17d5db72a9d07b1 Mon Sep 17 00:00:00 2001 From: Josemi Date: Fri, 13 Sep 2024 13:46:28 +0200 Subject: [PATCH 21/51] wc: Remove unused columns in rearrangement grid #TASK-6850 --- .../variant-interpreter-rearrangement-grid.js | 19 ------------------- 1 file changed, 19 deletions(-) diff --git a/src/webcomponents/variant/interpretation/variant-interpreter-rearrangement-grid.js b/src/webcomponents/variant/interpretation/variant-interpreter-rearrangement-grid.js index 80d89cada8..06ab60dfd9 100644 --- a/src/webcomponents/variant/interpretation/variant-interpreter-rearrangement-grid.js +++ b/src/webcomponents/variant/interpretation/variant-interpreter-rearrangement-grid.js @@ -717,25 +717,6 @@ export default class VariantInterpreterRearrangementGrid extends LitElement { }, ...vcfDataColumns.vcf1, ...vcfDataColumns.vcf2, - { - id: "cohorts", - title: "Cohorts", - field: "cohort", - colspan: 1, - rowspan: 1, - formatter: VariantInterpreterGridFormatter.studyCohortsFormatter.bind(this), - visible: (this.clinicalAnalysis.type.toUpperCase() === "SINGLE" || this.clinicalAnalysis.type.toUpperCase() === "FAMILY") && this.gridCommons.isColumnVisible("cohorts",) - }, - { - id: "prediction", - title: `${this.clinicalAnalysis.type !== "CANCER" ? "ACMG
Prediction" : "Prediction"}`, - field: "prediction", - rowspan: 1, - colspan: 1, - formatter: VariantInterpreterGridFormatter.predictionFormatter, - halign: "center", - visible: (this.clinicalAnalysis.type.toUpperCase() === "SINGLE" || this.clinicalAnalysis.type.toUpperCase() === "FAMILY") && this.gridCommons.isColumnVisible("prediction"), - }, { title: "Select", rowspan: 1, From 72530ad8d5463bc78272d00f0c433736daf61928 Mon Sep 17 00:00:00 2001 From: Josemi Date: Fri, 13 Sep 2024 13:47:23 +0200 Subject: [PATCH 22/51] wc: Clean and remove unused code in rearrangement grid #TASK-6850 --- .../variant-interpreter-rearrangement-grid.js | 28 ++----------------- 1 file changed, 2 insertions(+), 26 deletions(-) diff --git a/src/webcomponents/variant/interpretation/variant-interpreter-rearrangement-grid.js b/src/webcomponents/variant/interpretation/variant-interpreter-rearrangement-grid.js index 06ab60dfd9..3b9523c9bd 100644 --- a/src/webcomponents/variant/interpretation/variant-interpreter-rearrangement-grid.js +++ b/src/webcomponents/variant/interpretation/variant-interpreter-rearrangement-grid.js @@ -430,7 +430,7 @@ export default class VariantInterpreterRearrangementGrid extends LitElement { /* * GRID FORMATTERS */ - detailFormatter(value, row, a) { + detailFormatter(value, row) { let result = "
"; let detailHtml = ""; if (row && row.annotation) { @@ -489,29 +489,6 @@ export default class VariantInterpreterRearrangementGrid extends LitElement { return "-"; } - // DEPRECATED - pathogeniticyFormatter(value, row, index) { - // TODO we must call to PathDB to get the frequency of each variant, next code is just an example - return ` -
-
-
- -
- -
${Number(Math.random()).toFixed(2)}
-
-
- -
${Number(Math.random()).toFixed(2)}
-
- -
- -
- `; - } - _getDefaultColumns() { // This code creates dynamically the columns for the VCF INFO and FORMAT column data. // Multiple file callers are supported. @@ -991,10 +968,9 @@ export default class VariantInterpreterRearrangementGrid extends LitElement { this.requestUpdate(); } - onCancelVariant(e) { + onCancelVariant() { this.variantsReview = null; this.requestUpdate(); - // this._variantChanged = null; } render() { From 8554e1d4a04466e7d0d7dee300cb23213d6eeb75 Mon Sep 17 00:00:00 2001 From: Josemi Date: Fri, 13 Sep 2024 13:48:34 +0200 Subject: [PATCH 23/51] wc: Fix disabling edit action in interpreter grid #TASK-6850 --- .../variant/interpretation/variant-interpreter-grid.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/webcomponents/variant/interpretation/variant-interpreter-grid.js b/src/webcomponents/variant/interpretation/variant-interpreter-grid.js index 85745ac3a8..1dbb6587aa 100644 --- a/src/webcomponents/variant/interpretation/variant-interpreter-grid.js +++ b/src/webcomponents/variant/interpretation/variant-interpreter-grid.js @@ -805,7 +805,7 @@ export default class VariantInterpreterGrid extends LitElement {