-
Notifications
You must be signed in to change notification settings - Fork 29
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Merge pull request #1012 from opencb/TASK-7049
TASK-7049 - Liftover analysis
- Loading branch information
Showing
4 changed files
with
199 additions
and
1 deletion.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
180 changes: 180 additions & 0 deletions
180
src/webcomponents/variant/analysis/liftover-analysis.js
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,180 @@ | ||
| import {LitElement, html, render} from "lit"; | ||
| import UtilsNew from "../../../core/utils-new.js"; | ||
| import AnalysisUtils from "../../commons/analysis/analysis-utils"; | ||
| import "../../commons/forms/data-form.js"; | ||
| import "../../commons/filters/catalog-search-autocomplete.js"; | ||
|
|
||
| export default class LiftOverAnalysis extends LitElement { | ||
|
|
||
| constructor() { | ||
| super(); | ||
|
|
||
| this.#init(); | ||
| } | ||
|
|
||
| createRenderRoot() { | ||
| return this; | ||
| } | ||
|
|
||
| static get properties() { | ||
| return { | ||
| toolParams: { | ||
| type: Object, | ||
| }, | ||
| opencgaSession: { | ||
| type: Object, | ||
| }, | ||
| config: { | ||
| type: Object | ||
| }, | ||
| }; | ||
| } | ||
|
|
||
| #init() { | ||
| this.ANALYSIS_TOOL = "liftover"; | ||
| this.ANALYSIS_TITLE = "LiftOver Analysis"; | ||
| this.ANALYSIS_DESCRIPTION = "Liftover your VCF files from hg19 to hg38 (GRCH38 for Ensembl or HG38 for NCBI)."; | ||
|
|
||
| this.DEFAULT_TOOLPARAMS = { | ||
| targetAssembly: "GRCh38", | ||
| }; | ||
| // Make a deep copy to avoid modifying default object. | ||
| this._toolParams = { | ||
| ...UtilsNew.objectClone(this.DEFAULT_TOOLPARAMS) | ||
| }; | ||
|
|
||
| this._config = this.getDefaultConfig(); | ||
| } | ||
|
|
||
| update(changedProperties) { | ||
| if (changedProperties.has("toolParams")) { | ||
| this._toolParams = { | ||
| ...UtilsNew.objectClone(this.DEFAULT_TOOLPARAMS), | ||
| ...this.toolParams, | ||
| }; | ||
| } | ||
| if (changedProperties.has("config")) { | ||
| // Note: this.config is merged with the default config in the AnalysisUtils.getAnalysisConfiguration method. | ||
| this._config = this.getDefaultConfig(); | ||
| } | ||
| super.update(changedProperties); | ||
| } | ||
|
|
||
| check() { | ||
| return null; | ||
| } | ||
|
|
||
| onFieldChange() { | ||
| this._toolParams = {...this._toolParams}; | ||
| this.requestUpdate(); | ||
| } | ||
|
|
||
| onSubmit() { | ||
| const toolParams = { | ||
| files: this._toolParams.files.split(","), | ||
| targetAssembly: this._toolParams.targetAssembly, | ||
| outdir: this._toolParams.outdir || "", | ||
| }; | ||
| const params = { | ||
| study: this.opencgaSession.study.fqn, | ||
| ...AnalysisUtils.fillJobParams(this._toolParams, this.ANALYSIS_TOOL), | ||
| }; | ||
|
|
||
| AnalysisUtils.submit( | ||
| this.ANALYSIS_TITLE, | ||
| this.opencgaSession.opencgaClient.variants() | ||
| .runLiftover(toolParams, params), | ||
| this, | ||
| ); | ||
| } | ||
|
|
||
| onClear() { | ||
| this._toolParams = { | ||
| ...UtilsNew.objectClone(this.DEFAULT_TOOLPARAMS), | ||
| }; | ||
| this.requestUpdate(); | ||
| } | ||
|
|
||
| render() { | ||
| return html` | ||
| <data-form | ||
| .data="${this._toolParams}" | ||
| .config="${this._config}" | ||
| @fieldChange="${e => this.onFieldChange(e)}" | ||
| @clear="${this.onClear}" | ||
| @submit="${this.onSubmit}"> | ||
| </data-form> | ||
| `; | ||
| } | ||
|
|
||
| getDefaultConfig() { | ||
| const params = [ | ||
| { | ||
| title: "Input Parameters", | ||
| elements: [ | ||
| { | ||
| title: "VCF File", | ||
| required: true, | ||
| field: "files", | ||
| type: "custom", | ||
| display: { | ||
| render: (files, dataFormFilterChange) => { | ||
| return html ` | ||
| <catalog-search-autocomplete | ||
| .value="${files}" | ||
| .resource="${"FILE"}" | ||
| .query="${{format: "VCF"}}" | ||
| .opencgaSession="${this.opencgaSession}" | ||
| .config="${{multiple: true}}" | ||
| @filterChange="${e => dataFormFilterChange(e.detail.value)}"> | ||
| </catalog-search-autocomplete> | ||
| `; | ||
| } | ||
| } | ||
| }, | ||
| { | ||
| title: "Target Assembly", | ||
| field: "targetAssembly", | ||
| type: "select", | ||
| required: true, | ||
| allowedValues: ["GRCh38", "hg38"], | ||
| display: { | ||
| helpMessage: "Target assembly for lift over.", | ||
| }, | ||
| }, | ||
| { | ||
| title: "Output Directory", | ||
| field: "outdir", | ||
| type: "custom", | ||
| display: { | ||
| render: (outdir, dataFormFilterChange) => { | ||
| return html` | ||
| <catalog-search-autocomplete | ||
| .value="${outdir}" | ||
| .resource="${"DIRECTORY"}" | ||
| .opencgaSession="${this.opencgaSession}" | ||
| .config="${{multiple: false}}" | ||
| @filterChange="${e => dataFormFilterChange(e.detail.value)}"> | ||
| </catalog-search-autocomplete> | ||
| `; | ||
| }, | ||
| helpMessage: "Destination path where the lifted-over VCF files will be stored. If left empty, the VCF files will be stored in the job folder.", | ||
| }, | ||
| }, | ||
| ], | ||
| } | ||
| ]; | ||
|
|
||
| return AnalysisUtils.getAnalysisConfiguration( | ||
| this.ANALYSIS_TOOL, | ||
| this.ANALYSIS_TITLE, | ||
| this.ANALYSIS_DESCRIPTION, | ||
| params, | ||
| this.check(), | ||
| this.config, | ||
| ); | ||
| } | ||
|
|
||
| } | ||
|
|
||
| customElements.define("liftover-analysis", LiftOverAnalysis); |