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variant-interpreter-grid.js
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variant-interpreter-grid.js
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/*
* 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.
* You may obtain a copy of the License at
*
* 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.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
import {LitElement, html} from "lit";
import UtilsNew from "../../../core/utilsNew.js";
import ClinicalAnalysisManager from "../../clinical/clinical-analysis-manager.js";
import VariantInterpreterGridFormatter from "./variant-interpreter-grid-formatter.js";
import VariantGridFormatter from "../variant-grid-formatter.js";
import GridCommons from "../../commons/grid-commons.js";
import VariantUtils from "../variant-utils.js";
import "./variant-interpreter-grid-config.js";
import "../../clinical/interpretation/clinical-interpretation-variant-review.js";
import "../../clinical/interpretation/clinical-interpretation-variant-evidence-review.js";
import "../../commons/opencb-grid-toolbar.js";
import "../../loading-spinner.js";
import BioinfoUtils from "../../../core/bioinfo/bioinfo-utils.js";
import LitUtils from "../../commons/utils/lit-utils.js";
import NotificationUtils from "../../commons/utils/notification-utils.js";
export default class VariantInterpreterGrid extends LitElement {
constructor() {
super();
this._init();
}
createRenderRoot() {
return this;
}
static get properties() {
return {
opencgaSession: {
type: Object
},
clinicalAnalysis: {
type: Object
},
query: {
type: Object
},
clinicalVariants: {
type: Array
},
review: {
type: Boolean
},
config: {
type: Object
}
};
}
_init() {
this._prefix = UtilsNew.randomString(8);
this.gridId = this._prefix + "VariantBrowserGrid";
this.checkedVariants = new Map();
this.review = false;
// Set colors
this.consequenceTypeColors = VariantGridFormatter.assignColors(CONSEQUENCE_TYPES, PROTEIN_SUBSTITUTION_SCORE);
}
connectedCallback() {
super.connectedCallback();
// this._config = {...this.getDefaultConfig(), ...this.config, ...this.opencgaSession.user.configs?.IVA?.interpreterGrid};
// this.gridCommons = new GridCommons(this.gridId, this, this._config);
// this.clinicalAnalysisManager = new ClinicalAnalysisManager(this, this.clinicalAnalysis, this.opencgaSession);
}
firstUpdated(_changedProperties) {
this.table = $("#" + this.gridId);
this.downloadRefreshIcon = $("#" + this._prefix + "DownloadRefresh");
this.downloadIcon = $("#" + this._prefix + "DownloadIcon");
this._config = {
...this.getDefaultConfig(),
...this.config,
};
}
updated(changedProperties) {
if (changedProperties.has("opencgaSession")) {
this.opencgaSessionObserver();
}
if (changedProperties.has("clinicalAnalysis")) {
this.clinicalAnalysisObserver();
}
if (changedProperties.has("query")) {
this.renderVariants();
}
if (changedProperties.has("clinicalVariants")) {
this.renderVariants();
}
if (changedProperties.has("config")) {
this._config = {
...this.getDefaultConfig(),
...this.config,
};
this.gridCommons = new GridCommons(this.gridId, this, this._config);
// Config for the grid toolbar
// some columns have tooltips in title, we cannot used them for the dropdown
this.toolbarConfig = {
...this._config,
...this._config.toolbar, // it comes from external settings
resource: "CLINICAL_VARIANT",
// showExport: true,
columns: this._getDefaultColumns()[0].filter(col => col.rowspan === 2 && col.colspan === 1 && col.visible !== false),
gridColumns: this._getDefaultColumns() // original column structure
};
this.requestUpdate();
this.renderVariants();
}
}
opencgaSessionObserver() {
this._config = {
...this.getDefaultConfig(),
...this.config,
};
this.gridCommons = new GridCommons(this.gridId, this, this._config);
this.clinicalAnalysisManager = new ClinicalAnalysisManager(this, this.clinicalAnalysis, this.opencgaSession);
}
clinicalAnalysisObserver() {
// We need to load server config always.
this._config = {
...this.getDefaultConfig(),
...this.config,
};
this.clinicalAnalysisManager = new ClinicalAnalysisManager(this, this.clinicalAnalysis, this.opencgaSession);
// Make sure somatic sample is the first one
if (this.clinicalAnalysis) {
if (!this.clinicalAnalysis.interpretation) {
this.clinicalAnalysis.interpretation = {};
}
this.checkedVariants = new Map();
if (this.clinicalAnalysis?.interpretation?.primaryFindings?.length > 0) {
for (const variant of this.clinicalAnalysis.interpretation.primaryFindings) {
this.checkedVariants.set(variant.id, variant);
}
} else {
this.checkedVariants.clear();
}
if (this.clinicalAnalysis.type.toUpperCase() === "CANCER") {
if (this.clinicalAnalysis.proband && this.clinicalAnalysis.proband.samples &&
this.clinicalAnalysis.proband.samples.length === 2 && this.clinicalAnalysis.proband.samples[1].somatic) {
this.clinicalAnalysis.proband.samples = this.clinicalAnalysis.proband.samples.reverse();
}
}
}
}
onColumnChange(e) {
this.gridCommons.onColumnChange(e);
}
renderVariants() {
if (this._config.renderLocal) {
// FIXME remove this ASAP
this.clinicalVariants = this.clinicalAnalysis.interpretation.primaryFindings;
}
if (this.clinicalVariants?.length > 0) {
this.renderLocalVariants();
} else {
this.renderRemoteVariants();
}
}
renderRemoteVariants() {
if (!this.clinicalAnalysis || !this.clinicalAnalysis.interpretation || !this._config) {
console.warn("clinicalAnalysis or interpretation do not exist");
return;
}
if (!this.query?.sample) {
console.warn("No sample found, query: ", this.query);
return;
}
if (this.opencgaSession && this.opencgaSession.project && this.opencgaSession.study) {
this.table = $("#" + this.gridId);
this.table.bootstrapTable("destroy");
this.table.bootstrapTable({
columns: this._getDefaultColumns(),
method: "get",
sidePagination: "server",
iconsPrefix: GridCommons.GRID_ICONS_PREFIX,
icons: GridCommons.GRID_ICONS,
// Set table properties, these are read from config property
uniqueId: "id",
silentSort: false,
pagination: this._config.pagination,
pageSize: this._config.pageSize,
pageList: this._config.pageList,
paginationVAlign: "both",
formatShowingRows: (pageFrom, pageTo, totalRows) => this.gridCommons.formatShowingRows(pageFrom, pageTo, totalRows, null, this.isApproximateCount),
showExport: this._config.showExport,
detailView: this._config.detailView,
detailFormatter: (value, row) => this.detailFormatter(value, row),
formatLoadingMessage: () => "<div><loading-spinner></loading-spinner></div>",
// this makes the opencga-interpreted-variant-grid properties available in the bootstrap-table formatters
variantGrid: this,
ajax: params => {
// Make a deep clone object to manipulate the query sent to OpenCGA
const internalQuery = JSON.parse(JSON.stringify(this.query));
// We need to make sure that the proband is the first sample when analysing Families
if (this.clinicalAnalysis.type.toUpperCase() === "FAMILY" && this.query?.sample) {
// Note:
// - sample=A;B;C
// - sample=A:0/1,1/1;B:1/1;C:1/1
// There is also another param called: 'includeSample'
const samples = internalQuery.sample.split(";");
const sortedSamples = [];
for (const sample of samples) {
const sampleFields = sample.split(":");
if (sampleFields && sampleFields[0] === this.clinicalAnalysis.proband.samples[0].id) {
sortedSamples.unshift(sample);
} else {
sortedSamples.push(sample);
}
}
// For all non proband samples
const newQuerySample = [sortedSamples[0]];
for (let i = 1; i < sortedSamples.length; i++) {
// Non proband samples must have a genotype filter BUT ir cannot have ALL the genotypes
if (sortedSamples[i].includes(":")) {
if (!sortedSamples[i].includes("0/0") || !sortedSamples[i].includes("0/1") || !sortedSamples[i].includes("1/1")) {
newQuerySample.push(sortedSamples[i]);
}
}
}
internalQuery.sample = newQuerySample.join(";");
const sortedSampleIds = [];
for (const member of this.clinicalAnalysis.family.members) {
if (member && member.id === this.clinicalAnalysis.proband.id) {
sortedSampleIds.unshift(member.samples[0].id);
} else {
if (member.samples?.[0]?.id) {
sortedSampleIds.push(member.samples[0].id);
}
}
}
internalQuery.includeSample = sortedSampleIds.join(",");
}
const tableOptions = $(this.table).bootstrapTable("getOptions");
this.filters = {
study: this.opencgaSession.study.fqn,
limit: params.data.limit || tableOptions.pageSize,
skip: params.data.offset || 0,
count: !tableOptions.pageNumber || tableOptions.pageNumber === 1,
includeSampleId: "true",
approximateCount: true,
approximateCountSamplingSize: 500,
...internalQuery,
unknownGenotype: "0/0"
};
this.opencgaSession.opencgaClient.clinical().queryVariant(this.filters)
.then(res => {
this.isApproximateCount = res.responses[0].attributes?.approximateCount ?? false;
params.success(res);
})
.catch(e => {
console.error(e);
params.error(e);
});
},
responseHandler: response => {
const result = this.gridCommons.responseHandler(response, $(this.table).bootstrapTable("getOptions"));
return result.response;
},
onClickRow: (row, selectedElement, field) => this.gridCommons.onClickRow(row.id, row, selectedElement),
onDblClickRow: (row, element, field) => {
// We detail view is active we expand the row automatically.
// FIXME: Note that we use a CSS class way of knowing if the row is expand or collapse, this is not ideal but works.
if (this._config.detailView) {
if (element[0].innerHTML.includes("fa-plus")) {
$("#" + this.gridId).bootstrapTable("expandRow", element[0].dataset.index);
} else {
$("#" + this.gridId).bootstrapTable("collapseRow", element[0].dataset.index);
}
}
},
onLoadSuccess: data => {
// We keep the table rows as global variable, needed to fetch the variant object when checked
this._rows = data.rows;
this.gridCommons.onLoadSuccess(data, 2);
// Add events for displaying genes list
const gridElement = document.querySelector(`#${this.gridId}`);
if (gridElement) {
Array.from(gridElement.querySelectorAll("div[data-role='genes-list']")).forEach(el => {
const genesList = el.querySelector("span[data-role='genes-list-extra']");
const genesShowLink = el.querySelector("a[data-role='genes-list-show']");
const genesHideLink = el.querySelector("a[data-role='genes-list-hide']");
// Click on show more genes link
genesShowLink.addEventListener("click", () => {
genesShowLink.style.display = "none";
genesHideLink.style.display = "block";
genesList.style.display = "inline-block";
});
// Click on show less genes link
genesHideLink.addEventListener("click", () => {
genesHideLink.style.display = "none";
genesShowLink.style.display = "block";
genesList.style.display = "none";
});
});
}
},
onLoadError: (e, restResponse) => this.gridCommons.onLoadError(e, restResponse),
onExpandRow: (index, row, $detail) => {
// Listen to Show/Hide link in the detail formatter consequence type table
// TODO remove this
document.getElementById(this._prefix + row.id + "ShowEvidence").addEventListener("click", VariantGridFormatter.toggleDetailClinicalEvidence.bind(this));
document.getElementById(this._prefix + row.id + "HideEvidence").addEventListener("click", VariantGridFormatter.toggleDetailClinicalEvidence.bind(this));
document.getElementById(this._prefix + row.id + "ShowCt").addEventListener("click", VariantGridFormatter.toggleDetailConsequenceType.bind(this));
document.getElementById(this._prefix + row.id + "HideCt").addEventListener("click", VariantGridFormatter.toggleDetailConsequenceType.bind(this));
// Enable or disable evidence select
Array.from(document.getElementsByClassName(`${this._prefix}EvidenceReviewCheckbox`)).forEach(element => {
if (row.id === element.dataset.variantId) {
// eslint-disable-next-line no-param-reassign
element.disabled = !this.checkedVariants.has(row.id) || this.clinicalAnalysis.locked;
element.addEventListener("change", e => this.onEvidenceCheck(e));
}
});
// Enable or disable evidence edit and register event listeners
Array.from(document.getElementsByClassName(this._prefix + "EvidenceReviewButton")).forEach(element => {
if (row.id === element.dataset.variantId) {
let isEvidenceSelected = false;
if (this.checkedVariants.has(row.id)) {
const evidenceIndex = parseInt(element.dataset.clinicalEvidenceIndex);
const evidence = this.checkedVariants.get(row.id).evidences[evidenceIndex];
isEvidenceSelected = evidence.review?.select || false;
}
// Prevent editing evidences of not selected variants
// eslint-disable-next-line no-param-reassign
element.disabled = !isEvidenceSelected || this.clinicalAnalysis.locked;
element.addEventListener("click", e => this.onVariantEvidenceReview(e));
}
});
UtilsNew.initTooltip(this);
},
rowStyle: (row, index) => this.gridCommons.rowHighlightStyle(row, index),
});
}
}
renderLocalVariants() {
this.table = $("#" + this.gridId);
this.table.bootstrapTable("destroy");
this.table.bootstrapTable({
data: this.clinicalVariants,
columns: this._getDefaultColumns(),
sidePagination: "local",
iconsPrefix: GridCommons.GRID_ICONS_PREFIX,
icons: GridCommons.GRID_ICONS,
// Set table properties, these are read from config property
uniqueId: "id",
pagination: this._config.pagination,
pageSize: this._config.pageSize,
pageList: this._config.pageList,
paginationVAlign: "both",
formatShowingRows: this.gridCommons.formatShowingRows,
showExport: this._config.showExport,
detailView: this._config.detailView,
detailFormatter: (value, row) => this.detailFormatter(value, row),
formatLoadingMessage: () => "<div><loading-spinner></loading-spinner></div>",
// this makes the opencga-interpreted-variant-grid properties available in the bootstrap-table formatters
variantGrid: this,
onClickRow: (row, selectedElement, field) => this.gridCommons.onClickRow(row.id, row, selectedElement),
onDblClickRow: (row, element, field) => {
// We detail view is active we expand the row automatically.
// FIXME: Note that we use a CSS class way of knowing if the row is expand or collapse, this is not ideal but works.
if (this._config.detailView) {
if (element[0].innerHTML.includes("fa-plus")) {
$("#" + this.gridId).bootstrapTable("expandRow", element[0].dataset.index);
} else {
$("#" + this.gridId).bootstrapTable("collapseRow", element[0].dataset.index);
}
}
},
onExpandRow: (index, row, $detail) => {
// Listen to Show/Hide link in the detail formatter consequence type table
document.getElementById(this._prefix + row.id + "ShowEvidence").addEventListener("click", VariantGridFormatter.toggleDetailClinicalEvidence.bind(this));
document.getElementById(this._prefix + row.id + "HideEvidence").addEventListener("click", VariantGridFormatter.toggleDetailClinicalEvidence.bind(this));
document.getElementById(this._prefix + row.id + "ShowCt").addEventListener("click", VariantGridFormatter.toggleDetailConsequenceType.bind(this));
document.getElementById(this._prefix + row.id + "HideCt").addEventListener("click", VariantGridFormatter.toggleDetailConsequenceType.bind(this));
// Enable or disable evidence select
Array.from(document.getElementsByClassName(`${this._prefix}EvidenceReviewCheckbox`)).forEach(element => {
if (row.id === element.dataset.variantId) {
// eslint-disable-next-line no-param-reassign
element.disabled = !this.checkedVariants.has(row.id) || this.clinicalAnalysis.locked;
element.addEventListener("change", e => this.onEvidenceCheck(e));
}
});
// Enable or disable evidence edit and register event listeners
Array.from(document.getElementsByClassName(this._prefix + "EvidenceReviewButton")).forEach(element => {
if (row.id === element.dataset.variantId) {
let isEvidenceSelected = false;
if (this.checkedVariants.has(row.id)) {
const evidenceIndex = parseInt(element.dataset.clinicalEvidenceIndex);
const evidence = this.checkedVariants.get(row.id).evidences[evidenceIndex];
isEvidenceSelected = evidence.review?.select || false;
}
// Prevent editing evidences of not selected variants
// eslint-disable-next-line no-param-reassign
element.disabled = !isEvidenceSelected || this.clinicalAnalysis.locked;
element.addEventListener("click", e => this.onVariantEvidenceReview(e));
}
});
UtilsNew.initTooltip(this);
},
onPostBody: data => {
// We call onLoadSuccess to select first row, this is only needed when rendering from local
this.gridCommons.onLoadSuccess({rows: data, total: data.length}, 2);
},
onLoadSuccess: () => {
// Add events for displaying genes list
const gridElement = document.querySelector(`#${this.gridId}`);
if (gridElement) {
Array.from(gridElement.querySelectorAll("div[data-role='genes-list']")).forEach(el => {
const genesList = el.querySelector("span[data-role='genes-list-extra']");
const genesShowLink = el.querySelector("a[data-role='genes-list-show']");
const genesHideLink = el.querySelector("a[data-role='genes-list-hide']");
// Click on show more genes link
genesShowLink.addEventListener("click", () => {
genesShowLink.style.display = "none";
genesHideLink.style.display = "block";
genesList.style.display = "inline-block";
});
// Click on show less genes link
genesHideLink.addEventListener("click", () => {
genesHideLink.style.display = "none";
genesShowLink.style.display = "block";
genesList.style.display = "none";
});
});
}
},
rowStyle: (row, index) => this.gridCommons.rowHighlightStyle(row, index),
});
}
/*
* GRID FORMATTERS
*/
detailFormatter(value, row, a) {
let variant = row;
if (this.checkedVariants && this.checkedVariants.has(variant.id)) {
variant = this.checkedVariants.get(variant.id);
}
let result = "<div class='row' style='padding-bottom: 20px'>";
let detailHtml = "";
if (row?.annotation) {
detailHtml += "<div style='padding: 10px 0px 5px 25px'><h4>Clinical Evidences</h4></div>";
detailHtml += "<div style='padding: 5px 40px'>";
detailHtml += VariantInterpreterGridFormatter.reportedEventDetailFormatter(value, variant, this, this.query, this.review, this._config);
detailHtml += "</div>";
detailHtml += "<div style='padding: 25px 0px 5px 25px'><h4>Consequence Types</h4></div>";
detailHtml += "<div style='padding: 5px 40px'>";
detailHtml += VariantGridFormatter.consequenceTypeDetailFormatter(value, row, this, this.query, this._config, this.opencgaSession.project.organism.assembly);
detailHtml += "</div>";
detailHtml += "<div style='padding: 20px 0px 5px 25px'><h4>Clinical Phenotypes</h4></div>";
detailHtml += "<div style='padding: 5px 40px'>";
detailHtml += VariantGridFormatter.clinicalTableDetail(value, row);
detailHtml += "</div>";
}
result += detailHtml + "</div>";
return result;
}
vcfDataFormatter(value, row) {
if (row.studies?.length > 0) {
let source = "FILE";
if (this.field.variantCaller?.dataFilters) {
const dataFilter = this.field.variantCaller.dataFilters.find(filter => filter.id === this.field.key);
source = dataFilter?.source || "FILE";
} else {
// TODO Search in file.attributes to guess eh source
}
if (source === "FILE") {
for (const file of row.studies[0].files) {
if (file.data[this.field.key]) {
return file.data[this.field.key];
}
}
} else {
const sampleIndex = row.studies[0].samples.findIndex(sample => sample.sampleId === this.field.sampleId);
const index = row.studies[0].sampleDataKeys.findIndex(key => key === this.field.key);
// debugger;
if (index >= 0) {
return row.studies[0].samples[sampleIndex].data[index];
}
}
} else {
console.error("This should never happen: row.studies[] is not valid");
}
return "-";
}
_getDefaultColumns() {
// This code creates dynamically the columns for the VCF INFO and FORMAT column data.
// Multiple file callers are supported.
let vcfDataColumns = [];
const vcfDataColumnNames = [];
const variantTypes = new Set(this._config.variantTypes || []);
const fileCallers = (this.clinicalAnalysis.files || [])
.filter(file => file.format === "VCF" && file.software?.name)
.map(file => file.software.name.toUpperCase());
if (this.opencgaSession?.study?.internal?.configuration?.clinical?.interpretation?.variantCallers?.length > 0) {
// FIXME remove specific code for ASCAT!
const variantCallers = this.opencgaSession.study.internal.configuration.clinical.interpretation.variantCallers
.filter(vc => vc.somatic === this._config.somatic)
.filter(vc => vc.types.some(type => variantTypes.has(type)));
if (variantCallers?.length > 0) {
for (const variantCaller of variantCallers) {
if (fileCallers.includes(variantCaller.id.toUpperCase())) {
// INFO column
if (!vcfDataColumnNames.includes(variantCaller.id)) {
vcfDataColumnNames.push(variantCaller.id);
}
if (variantCaller.columns?.length > 0) {
for (const column of variantCaller.columns) {
vcfDataColumns.push({
id: column.replace("EXT_", ""),
title: column.replace("EXT_", ""),
field: {
key: column,
sampleId: this.clinicalAnalysis?.proband?.samples?.[0]?.id,
variantCaller: variantCaller
},
rowspan: 1,
colspan: 1,
formatter: this.vcfDataFormatter,
halign: "center"
});
}
}
}
}
}
}
// IMPORTANT: empty columns are not supported in boostrap-table,
// we need to create an empty not visible column when no VCF file data is configured.
if (!vcfDataColumns || vcfDataColumns.length === 0) {
vcfDataColumns = [
{
visible: false
}
];
}
// Prepare Grid columns
this._columns = [
[
{
id: "id",
title: "Variant",
field: "id",
rowspan: 2,
colspan: 1,
formatter: (value, row, index) => VariantGridFormatter.variantFormatter(value, row, index, this.opencgaSession.project.organism.assembly, this._config),
halign: "center",
// sortable: true
},
{
id: "type",
title: "Type",
field: "type",
rowspan: 2,
colspan: 1,
formatter: VariantGridFormatter.typeFormatter.bind(this),
halign: "center",
visible: !this._config.hideType,
},
{
id: "gene",
title: "Gene",
field: "gene",
rowspan: 2,
colspan: 1,
formatter: (value, row, index) => VariantGridFormatter.geneFormatter(row, index, this.query, this.opencgaSession, this._config),
halign: "center"
},
{
id: "hgvs",
title: "HGVS",
rowspan: 2,
colspan: 1,
formatter: (value, row) => VariantGridFormatter.hgvsFormatter(row, this._config),
halign: "center",
visible: !!this._config.showHgvs,
},
{
id: "consequenceType",
title: "Gene Annotation",
field: "consequenceType",
rowspan: 2,
colspan: 1,
formatter: (value, row, index) => VariantGridFormatter.consequenceTypeFormatter(value, row, this?.query?.ct, this._config),
halign: "center"
},
{
id: "evidences",
title: "Role in Cancer",
field: "evidences",
rowspan: 2,
colspan: 1,
formatter: VariantInterpreterGridFormatter.roleInCancerFormatter.bind(this),
halign: "center",
visible: this.clinicalAnalysis.type.toUpperCase() === "CANCER"
},
{
id: "VCF_Data",
title: "VCF File Data: " + vcfDataColumnNames.join(", "),
rowspan: 1,
colspan: vcfDataColumns?.length,
halign: "center",
visible: vcfDataColumns?.length > 1
},
{
id: "frequencies",
title: `Variant Allele Frequency
<a class="pop-preq-info-icon"
tooltip-title="Population Frequencies"
tooltip-text="${VariantGridFormatter.populationFrequenciesInfoTooltipContent(POPULATION_FREQUENCIES)}"
tooltip-position-at="left bottom" tooltip-position-my="right top">
<i class="fa fa-info-circle" aria-hidden="true"></i>
</a>`,
field: "frequencies",
rowspan: 1,
colspan: 2,
align: "center",
},
{
id: "clinicalInfo",
title: `Clinical Info <a id="phenotypesInfoIcon" tooltip-title="Phenotypes" tooltip-text="
<div>
<span style='font-weight: bold'>ClinVar</span> is a freely accessible, public archive of reports of the relationships among human variations
and phenotypes, with supporting evidence.
</div>
<div style='padding-top: 10px'>
<span style='font-weight: bold'>COSMIC</span> is the world's largest and most comprehensive resource for exploring the impact of somatic mutations in human cancer.
</div>"
tooltip-position-at="left bottom" tooltip-position-my="right top"><i class="fa fa-info-circle" aria-hidden="true"></i></a>`,
rowspan: 1,
colspan: 2,
align: "center"
},
{
id: "interpretation",
title: `Interpretation
<a class='interpretation-info-icon'
tooltip-title='Interpretation'
tooltip-text="<span style='font-weight: bold'>Prediction</span> column shows the Clinical Significance prediction and Tier following the ACMG guide recommendations"
tooltip-position-at="left bottom"
tooltip-position-my="right top">
<i class='fa fa-info-circle' aria-hidden='true'></i>
</a>`,
field: "interpretation",
rowspan: 1,
colspan: 3,
halign: "center"
},
{
id: "actions",
title: "Actions",
rowspan: 2,
colspan: 1,
formatter: (value, row) => {
let copiesHtml = "";
if (this._config.copies) {
for (const copy of this._config.copies) {
copiesHtml = `
<li>
<a href="javascript: void 0" class="btn force-text-left" data-action="${copy.id}">
<i class="fas fa-copy icon-padding" aria-hidden="true" alt="${copy.description}"></i> ${copy.name}
</a>
</li>
`;
}
}
const reviewId = `${this._prefix}${row.id}VariantReviewActionButton`;
const reviewDisabled = !this.checkedVariants.has(row.id) || this.clinicalAnalysis.locked ? "disabled" : "";
return `
<div class="dropdown">
<button class="btn btn-default btn-sm dropdown-toggle one-line" type="button" data-toggle="dropdown">Actions
<span class="caret"></span>
</button>
<ul class="dropdown-menu dropdown-menu-right">
<li>
<a id="${reviewId}" href="javascript: void 0" class="btn force-text-left reviewButton" data-action="edit" ${reviewDisabled}>
<i class="fas fa-edit icon-padding reviewButton" aria-hidden="true"></i> Edit ...
</a>
</li>
<li role="separator" class="divider"></li>
<li class="dropdown-header">Genome Browser</li>
<li>
<a target="_blank" class="btn force-text-left"
href="${BioinfoUtils.getVariantLink(row.id, row.chromosome + ":" + row.start + "-" + row.end, "ensembl_genome_browser")}">
<i class="fas fa-external-link-alt icon-padding" aria-hidden="true"></i> Ensembl Genome Browser
</a>
</li>
<li>
<a target="_blank" class="btn force-text-left"
href="${BioinfoUtils.getVariantLink(row.id, row.chromosome + ":" + row.start + "-" + row.end, "ucsc_genome_browser")}">
<i class="fas fa-external-link-alt icon-padding" aria-hidden="true"></i> UCSC Genome Browser
</a>
</li>
<li role="separator" class="divider"></li>
<li class="dropdown-header">Fetch Variant</li>
<li>
<a href="javascript: void 0" class="btn force-text-left" data-action="copy-json">
<i class="fas fa-copy icon-padding" aria-hidden="true"></i> Copy JSON
</a>
</li>
<li>
<a href="javascript: void 0" class="btn force-text-left" data-action="download">
<i class="fas fa-download icon-padding" aria-hidden="true"></i> Download JSON
</a>
</li>
${copiesHtml ? `
<li role="separator" class="divider"></li>
<li class="dropdown-header">Custom Copy</li>
${copiesHtml}
` : ""}
</ul>
</div>`;
},
align: "center",
events: {
"click a": (e, value, row) => this.onActionClick(e, value, row)
},
excludeFromExport: true // this is used in opencga-export
// visible: this._config.showActions && !this._config?.columns?.hidden?.includes("actions")
},
],
[
...vcfDataColumns,
{
id: "cohort",
title: "Cohorts",
field: "cohort",
colspan: 1,
rowspan: 1,
formatter: VariantInterpreterGridFormatter.studyCohortsFormatter.bind(this),
visible: this.clinicalAnalysis.type.toUpperCase() === "SINGLE" || this.clinicalAnalysis.type.toUpperCase() === "FAMILY"
},
{
id: "populationFrequencies",
title: "Population Frequencies",
field: "populationFrequencies",
colspan: 1,
rowspan: 1,
formatter: VariantInterpreterGridFormatter.clinicalPopulationFrequenciesFormatter.bind(this),
visible: !this._config.hidePopulationFrequencies,
},
{
id: "clinvar",
title: "ClinVar",
field: "clinvar",
colspan: 1,
rowspan: 1,
formatter: VariantGridFormatter.clinicalPhenotypeFormatter,
align: "center",
visible: !this._config.hideClinicalInfo,
},
{
id: "cosmic",
title: "Cosmic",
field: "cosmic",
colspan: 1,
rowspan: 1,
formatter: VariantGridFormatter.clinicalPhenotypeFormatter,
align: "center",
visible: !this._config.hideClinicalInfo,
},
// Interpretation Column
{
id: "prediction",
title: `${this.clinicalAnalysis.type !== "CANCER" ? "ACMG <br> Prediction" : "Prediction"}`,
field: "prediction",
rowspan: 1,
colspan: 1,
formatter: (value, row) => {
const checkedVariant = this.checkedVariants?.has(row.id) ? this.checkedVariants.get(row.id) : row;
return VariantInterpreterGridFormatter.predictionFormatter(value, checkedVariant);
},
align: "center",
visible: this.clinicalAnalysis.type.toUpperCase() === "SINGLE" || this.clinicalAnalysis.type.toUpperCase() === "FAMILY"
},
{
id: "Select",
title: "Select",
rowspan: 1,
colspan: 1,
formatter: (value, row) => {
const checked = this.checkedVariants?.has(row.id) ? "checked" : "";
const disabled = this.clinicalAnalysis.locked ? "disabled" : "";
return `<input class="check check-variant" type="checkbox" data-variant-id="${row.id}" ${checked} ${disabled}>`;
},
align: "center",
events: {
"click input": e => this.onVariantCheck(e)
},
visible: this._config.showSelectCheckbox,
excludeFromExport: true // this is used in opencga-export
},
{
id: "review",
title: "Review",
rowspan: 1,
colspan: 1,
formatter: (value, row) => {
const disabled = !this.checkedVariants?.has(row.id) || this.clinicalAnalysis.locked ? "disabled" : "";
return `
<button id="${this._prefix}${row.id}VariantReviewButton" class="btn btn-link" data-variant-id="${row.id}" ${disabled}>
<i class="fa fa-edit icon-padding" aria-hidden="true"></i> Edit ...
</button>
${this.checkedVariants?.has(row.id) ? `
<div class="help-block" style="margin: 5px 0">${this.checkedVariants.get(row.id).status}</div>
` : ""
}
`;
},
align: "center",
events: {
"click button": e => this.onVariantReview(e)
},
visible: this.review,
excludeFromExport: true // this is used in opencga-export
},
]
];
// update columns dynamically
this._columns = this._updateTableColumns(this._columns);
this._columns = UtilsNew.mergeTable(this._columns, this._config.columns || this._config.hiddenColumns, !!this._config.hiddenColumns);
return this._columns;
}
_updateTableColumns(_columns) {
let samples = [];
if (!_columns) {
return;
}
if (this.clinicalAnalysis && (this.clinicalAnalysis.type.toUpperCase() === "SINGLE" || this.clinicalAnalysis.type.toUpperCase() === "FAMILY")) {
// Add Samples
// const samples = [];
const sampleInfo = {};
if (this.clinicalAnalysis.family && this.clinicalAnalysis.family.members) {
for (const member of this.clinicalAnalysis.family.members) {
if (member.samples && member.samples.length > 0) {
// Proband must be the first column
if (member.id === this.clinicalAnalysis.proband.id) {
samples.unshift(member.samples[0]);
} else {
samples.push(member.samples[0]);
}
sampleInfo[member.samples[0].id] = {
proband: member.id === this.clinicalAnalysis.proband.id,
affected: member.disorders && member.disorders.length > 0 && member.disorders[0].id === this.clinicalAnalysis.disorder.id,
role: this.clinicalAnalysis.family?.roles[this.clinicalAnalysis.proband.id][member.id]?.toLowerCase(),
sex: member.sex
};
}
}
} else {
if (this.clinicalAnalysis.proband && this.clinicalAnalysis.proband.samples) {
samples.push(this.clinicalAnalysis.proband.samples[0]);
sampleInfo[this.clinicalAnalysis.proband.samples[0].id] = {
proband: true,
affected: this.clinicalAnalysis.proband.disorders && this.clinicalAnalysis.proband.disorders.length > 0,
role: "proband",
sex: this.clinicalAnalysis.proband.sex
};
}
}
if (samples.length > 0) {
_columns[0].splice(5, 0, {
id: "zygosity",
title: "Sample Genotypes",
field: "zygosity",
rowspan: 1,
colspan: samples.length,
align: "center"
});
for (let i = 0; i < samples.length; i++) {
let color = "black";
if (sampleInfo[samples[i].id].proband) {
color = "darkred";
if (UtilsNew.isEmpty(sampleInfo[samples[i].id].role)) {
sampleInfo[samples[i].id].role = "proband";
}
}
let affected = "<span>UnAff.</span>";
if (sampleInfo[samples[i].id].affected) {
affected = "<span style='color: red'>Aff.</span>";
}
_columns[1].splice(i, 0, {
id: samples[i].id,
title: `<span style="color: ${color}">${samples[i].id}</span>
<br>
<span style="font-style: italic">${sampleInfo[samples[i].id].role}, ${affected}</span>`,
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,
align: "center",
nucleotideGenotype: true
});
}
}
}
if (this.clinicalAnalysis && this.clinicalAnalysis.type.toUpperCase() === "CANCER") {
// Add sample columns
// let samples = null;
if (this.clinicalAnalysis.proband && this.clinicalAnalysis.proband.samples) {
// We only render somatic sample
if (this.query && this.query.sample) {
const _sampleGenotypes = this.query.sample.split(";");
for (const sampleGenotype of _sampleGenotypes) {
const sampleId = sampleGenotype.split(":")[0];
samples.push(this.clinicalAnalysis.proband.samples.find(s => s.id === sampleId));
}