diff --git a/src/sites/iva/conf/config.js b/src/sites/iva/conf/config.js index 6c8636bd0e..969767902c 100644 --- a/src/sites/iva/conf/config.js +++ b/src/sites/iva/conf/config.js @@ -26,16 +26,16 @@ const hosts = [ url: "https://ws.opencb.org/opencga-test" }, { - id: "testteam", - url: "https://test.app.zettagenomics.com/testteam/opencga" + id: "reference", + url: "https://test.app.zettagenomics.com/reference/opencga" }, ]; const opencga = { - host: hosts[1].url, + host: hosts[2].url, version: "v2", cookie: { - prefix: "iva-" + hosts[1].id + prefix: "iva-" + hosts[2].id }, sso: { active: false, diff --git a/src/webcomponents/commons/opencb-grid-toolbar.js b/src/webcomponents/commons/opencb-grid-toolbar.js index f756a12934..e77f0fe705 100644 --- a/src/webcomponents/commons/opencb-grid-toolbar.js +++ b/src/webcomponents/commons/opencb-grid-toolbar.js @@ -192,15 +192,14 @@ export default class OpencbGridToolbar extends LitElement { + ${(this._config?.create && (this._settings.showCreate || this._settings.showNew) + && OpencgaCatalogUtils.checkPermissions(this.opencgaSession?.study, this.opencgaSession?.user?.id, `WRITE_${this._config.resource}`)) ? + ModalUtils.create(this, `${this._prefix}CreateModal`, this._config.create) : + nothing} + ${this._settings?.showExport && this._config?.export ? ModalUtils.create(this, `${this._prefix}ExportModal`, this._config.export) : nothing} ${this._settings?.showSettings && this._config?.settings ? ModalUtils.create(this, `${this._prefix}SettingModal`, this._config.settings) : nothing} - - ${(this._config?.create && - (this._settings.showCreate || this._settings.showNew) && - OpencgaCatalogUtils.checkPermissions(this.opencgaSession?.study, this.opencgaSession?.user?.id, `WRITE_${this._config.resource}`)) ? - ModalUtils.create(this, `${this._prefix}CreateModal`, this._config.create) : - nothing} `; } @@ -208,10 +207,10 @@ export default class OpencbGridToolbar extends LitElement { return { // label: "records", showCreate: true, - showDownload: true, + showExport: true, showSettings: true, - download: ["Tab", "JSON"], - buttons: ["columns", "download"], + // download: ["Tab", "JSON"], + // buttons: ["columns", "download"], }; } diff --git a/src/webcomponents/variant/annotation/cellbase-variant-annotation-summary.js b/src/webcomponents/variant/annotation/cellbase-variant-annotation-summary.js index 4f8c909e23..bc1926b036 100644 --- a/src/webcomponents/variant/annotation/cellbase-variant-annotation-summary.js +++ b/src/webcomponents/variant/annotation/cellbase-variant-annotation-summary.js @@ -191,10 +191,10 @@ export default class CellbaseVariantAnnotationSummary extends LitElement { } render() { - const variantRegion = this.variantAnnotation.chromosome + ":" + this.variantAnnotation.start + "-" + this.variantAnnotation.start; if (this.variantAnnotation === undefined || this.variantAnnotation === "" || this.proteinSubScore === undefined) { return; } + const variantRegion = this.variantAnnotation.chromosome + ":" + this.variantAnnotation.start + "-" + this.variantAnnotation.start; const variantId = this.variantAnnotation.id ? this.variantAnnotation.id : `${this.variantAnnotation.chromosome}:${this.variantAnnotation.start}:${this.variantAnnotation.reference}:${this.variantAnnotation.alternate}`; diff --git a/src/webcomponents/variant/interpretation/variant-interpreter-browser-cancer.js b/src/webcomponents/variant/interpretation/variant-interpreter-browser-cancer.js index 4b0503dbab..79943d3568 100644 --- a/src/webcomponents/variant/interpretation/variant-interpreter-browser-cancer.js +++ b/src/webcomponents/variant/interpretation/variant-interpreter-browser-cancer.js @@ -530,17 +530,17 @@ class VariantInterpreterBrowserCancer extends LitElement { ], result: { grid: { - pagination: true, - pageSize: 10, - pageList: [5, 10, 25], - showExport: false, - detailView: true, - showReview: false, - showActions: true, + // pagination: true, + // pageSize: 10, + // pageList: [5, 10, 25], + // showExport: false, + // detailView: true, + // showReview: false, + // showActions: true, showSelectCheckbox: true, - multiSelection: false, - nucleotideGenotype: true, - alleleStringLengthMax: 10, + // multiSelection: false, + // nucleotideGenotype: true, + // alleleStringLengthMax: 10, genotype: { type: "VAF" diff --git a/src/webcomponents/variant/interpretation/variant-interpreter-browser-cnv.js b/src/webcomponents/variant/interpretation/variant-interpreter-browser-cnv.js index d541f7c37e..f092630f9c 100644 --- a/src/webcomponents/variant/interpretation/variant-interpreter-browser-cnv.js +++ b/src/webcomponents/variant/interpretation/variant-interpreter-browser-cnv.js @@ -413,17 +413,17 @@ class VariantInterpreterBrowserCNV extends LitElement { ], result: { grid: { - pagination: true, - pageSize: 10, - pageList: [5, 10, 25], - showExport: false, - detailView: true, - showReview: false, - showActions: true, + // pagination: true, + // pageSize: 10, + // pageList: [5, 10, 25], + // showExport: false, + // detailView: true, + // showReview: false, + // showActions: true, showSelectCheckbox: true, - multiSelection: false, - nucleotideGenotype: true, - alleleStringLengthMax: 10, + // multiSelection: false, + // nucleotideGenotype: true, + // alleleStringLengthMax: 10, hideType: true, hidePopulationFrequencies: true, diff --git a/src/webcomponents/variant/interpretation/variant-interpreter-browser-rd.js b/src/webcomponents/variant/interpretation/variant-interpreter-browser-rd.js index 27ce208b1f..1bae76ad40 100644 --- a/src/webcomponents/variant/interpretation/variant-interpreter-browser-rd.js +++ b/src/webcomponents/variant/interpretation/variant-interpreter-browser-rd.js @@ -545,17 +545,17 @@ class VariantInterpreterBrowserRd extends LitElement { ], result: { grid: { - pagination: true, - pageSize: 10, - pageList: [5, 10, 25], - showExport: false, - detailView: true, - showReview: true, - showActions: true, + // pagination: true, + // pageSize: 10, + // pageList: [5, 10, 25], + // showExport: false, + // detailView: true, + // showReview: true, + // showActions: true, showSelectCheckbox: true, - multiSelection: false, - nucleotideGenotype: true, - alleleStringLengthMax: 10, + // multiSelection: false, + // nucleotideGenotype: true, + // alleleStringLengthMax: 10, header: { horizontalAlign: "center", diff --git a/src/webcomponents/variant/interpretation/variant-interpreter-browser-rearrangement.js b/src/webcomponents/variant/interpretation/variant-interpreter-browser-rearrangement.js index cb88ff7c2d..c4d43f56f3 100644 --- a/src/webcomponents/variant/interpretation/variant-interpreter-browser-rearrangement.js +++ b/src/webcomponents/variant/interpretation/variant-interpreter-browser-rearrangement.js @@ -418,16 +418,16 @@ class VariantInterpreterBrowserRearrangement extends LitElement { ], result: { grid: { - pagination: true, - pageSize: 10, - pageList: [5, 10, 25], - showExport: true, - detailView: true, - showReview: false, - showActions: true, + // pagination: true, + // pageSize: 10, + // pageList: [5, 10, 25], + // showExport: true, + // detailView: true, + // showReview: false, + // showActions: true, showSelectCheckbox: true, - multiSelection: false, - nucleotideGenotype: true, + // multiSelection: false, + // nucleotideGenotype: true, alleleStringLengthMax: 25, header: { horizontalAlign: "center", diff --git a/src/webcomponents/variant/interpretation/variant-interpreter-grid.js b/src/webcomponents/variant/interpretation/variant-interpreter-grid.js index 39a7e100ab..986d9b5324 100644 --- a/src/webcomponents/variant/interpretation/variant-interpreter-grid.js +++ b/src/webcomponents/variant/interpretation/variant-interpreter-grid.js @@ -164,12 +164,12 @@ export default class VariantInterpreterGrid extends LitElement { this.gridCommons = new GridCommons(this.gridId, this, this._config); this.toolbarSetting = { + showCreate: false, showExport: true, + showSettings: true, exportTabs: ["download", "export", "link", "code"], // this is customisable in external settings in `table.toolbar` - // ...this._config, // it comes from external settings showColumns: false, - showSettings: true, ...this._config, // columns: defaultColumns[0].filter(col => col.rowspan === 2 && col.colspan === 1 && col.visible !== false), // gridColumns: defaultColumns, // original column structure @@ -178,6 +178,7 @@ export default class VariantInterpreterGrid extends LitElement { this.toolbarConfig = { toolId: this.toolId, resource: "CLINICAL_VARIANT", + disableCreate: true, showInterpreterConfig: true, columns: this._getDefaultColumns() }; @@ -472,7 +473,7 @@ export default class VariantInterpreterGrid extends LitElement { formatShowingRows: this.gridCommons.formatShowingRows, showExport: this._config.showExport, detailView: this._config.detailView, - detailFormatter: (value, row) => this.detailFormatter(value, row), + detailFormatter: this._config.detailFormatter, formatLoadingMessage: () => "