-
- No automatic methods available for cancer analysis at this time.
+ if (this.clinicalAnalysis && this.settings) {
+ const probandId = this.clinicalAnalysis.proband?.id || "";
+ const type = this.clinicalAnalysis.type?.toUpperCase() || "";
+ const caseConfig = (this.settings.items || []).find(item => item.type === type);
+
+ (caseConfig?.methods || []).forEach(method => {
+ if (method.id === "exomiser") {
+ items.push({
+ id: "exomiser",
+ name: "Exomiser",
+ render: (clinicalAnalysis, active, opencgaSession) => {
+ return html`
+
+
+
+
-
- `;
- },
- });
- }
+ `;
+ },
+ });
+ }
+
+ if (method.id === "rd-tiering" || method.id === "rdtiering") {
+ items.push({
+ id: "rd-tiering",
+ name: "RD Tiering",
+ render: (clinicalAnalysis, active, opencgaSession) => {
+ const toolParams = {
+ clinicalAnalysis: clinicalAnalysis.id,
+ panels: clinicalAnalysis.panels?.map(panel => panel.id).join(","),
+ };
+ return html`
+
+
+
+
+
+ `;
+ },
+ });
+ }
+ });
}
return {
diff --git a/src/webcomponents/variant/interpretation/variant-interpreter.js b/src/webcomponents/variant/interpretation/variant-interpreter.js
index 6f3a2a8f49..a1acb9af85 100644
--- a/src/webcomponents/variant/interpretation/variant-interpreter.js
+++ b/src/webcomponents/variant/interpretation/variant-interpreter.js
@@ -30,6 +30,7 @@ import "../custom/steiner-report.js";
import "../../commons/opencga-active-filters.js";
import "../../download-button.js";
import "../../loading-spinner.js";
+import "../../clinical/clinical-analysis-review.js";
import NotificationUtils from "../../commons/utils/notification-utils.js";
class VariantInterpreter extends LitElement {
@@ -378,10 +379,9 @@ class VariantInterpreter extends LitElement {
-->
-
` : null}
diff --git a/src/webcomponents/variant/variant-browser-grid.js b/src/webcomponents/variant/variant-browser-grid.js
index 2275e2ad2c..973d8d20fe 100644
--- a/src/webcomponents/variant/variant-browser-grid.js
+++ b/src/webcomponents/variant/variant-browser-grid.js
@@ -132,7 +132,10 @@ export default class VariantBrowserGrid extends LitElement {
}
configObserver() {
- this._config = {...this.getDefaultConfig(), ...this.config};
+ this._config = {
+ ...this.getDefaultConfig(),
+ ...this.config,
+ };
this.gridCommons = new GridCommons(this.gridId, this, this._config);
// Config for the grid toolbar
@@ -551,7 +554,7 @@ export default class VariantBrowserGrid extends LitElement {
formatter: VariantInterpreterGridFormatter.sampleGenotypeFormatter,
align: "center",
nucleotideGenotype: true,
- visible: this.gridCommons.isColumnVisible(this.samples[i].id),
+ visible: this.gridCommons.isColumnVisible(this.samples[i].id, "samples"),
});
}
}
@@ -577,7 +580,7 @@ export default class VariantBrowserGrid extends LitElement {
formatter: this.cohortFormatter,
align: "center",
eligible: true,
- visible: this.gridCommons.isColumnVisible(study.id),
+ visible: this.gridCommons.isColumnVisible(study.id, "cohorts"),
});
}
}
@@ -617,7 +620,7 @@ export default class VariantBrowserGrid extends LitElement {
colspan: 1,
formatter: this.populationFrequenciesFormatter,
align: "center",
- visible: this.gridCommons.isColumnVisible(this.populationFrequencies.studies[j].id),
+ visible: this.gridCommons.isColumnVisible(this.populationFrequencies.studies[j].id, "popfreq"),
});
}
}
@@ -758,6 +761,7 @@ export default class VariantBrowserGrid extends LitElement {
},
// ...ExtensionsManager.getColumns("variant-browser-grid"),
{
+ id: "select",
title: "Select",
rowspan: 2,
colspan: 1,
@@ -766,7 +770,8 @@ export default class VariantBrowserGrid extends LitElement {
events: {
"click input": this.onCheck.bind(this)
},
- visible: this._config.showSelectCheckbox
+ visible: this._config.showSelectCheckbox,
+ excludeFromSettings: true, // If true, this column will not be visible in Settings column
},
{
id: "actions",
@@ -850,7 +855,8 @@ export default class VariantBrowserGrid extends LitElement {
"click a": (e, value, row) => this.onActionClick(e, value, row)
},
visible: this._config?.showActions,
- excludeFromExport: true // this is used in opencga-export
+ excludeFromSettings: true,
+ excludeFromExport: true, // this is used in opencga-export
},
],
[
@@ -862,7 +868,7 @@ export default class VariantBrowserGrid extends LitElement {
rowspan: 1,
formatter: this.siftPproteinScoreFormatter.bind(this),
halign: "center",
- visible: this.gridCommons.isColumnVisible("SIFT")
+ visible: this.gridCommons.isColumnVisible("SIFT", "deleteriousness")
},
{
id: "polyphen",
@@ -872,7 +878,7 @@ export default class VariantBrowserGrid extends LitElement {
rowspan: 1,
formatter: this.polyphenProteinScoreFormatter.bind(this),
halign: "center",
- visible: this.gridCommons.isColumnVisible("polyphen")
+ visible: this.gridCommons.isColumnVisible("polyphen", "deleteriousness")
},
{
id: "revel",
@@ -882,7 +888,7 @@ export default class VariantBrowserGrid extends LitElement {
rowspan: 1,
formatter: this.revelProteinScoreFormatter.bind(this),
halign: "center",
- visible: this.gridCommons.isColumnVisible("revel")
+ visible: this.gridCommons.isColumnVisible("revel", "deleteriousness")
},
{
id: "cadd",
@@ -893,10 +899,10 @@ export default class VariantBrowserGrid extends LitElement {
formatter: (value, row) => VariantGridFormatter.caddScaledFormatter(value, row),
align: "right",
halign: "center",
- visible: this.gridCommons.isColumnVisible("cadd")
+ visible: this.gridCommons.isColumnVisible("cadd", "deleteriousness")
},
{
- id: "splaiceai",
+ id: "spliceai",
title: "SpliceAI",
field: "spliceai",
colspan: 1,
@@ -904,7 +910,7 @@ export default class VariantBrowserGrid extends LitElement {
formatter: (value, row) => VariantGridFormatter.spliceAIFormatter(value, row),
align: "right",
halign: "center",
- visible: this.gridCommons.isColumnVisible("spliceai")
+ visible: this.gridCommons.isColumnVisible("spliceai", "deleteriousness")
},
{
id: "phylop",
@@ -915,7 +921,7 @@ export default class VariantBrowserGrid extends LitElement {
formatter: this.conservationFormatter,
align: "right",
halign: "center",
- visible: this.gridCommons.isColumnVisible("phylop")
+ visible: this.gridCommons.isColumnVisible("phylop", "conservation")
},
{
id: "phastCons",
@@ -926,7 +932,7 @@ export default class VariantBrowserGrid extends LitElement {
formatter: this.conservationFormatter,
align: "right",
halign: "center",
- visible: this.gridCommons.isColumnVisible("phastCons")
+ visible: this.gridCommons.isColumnVisible("phastCons", "conservation")
},
{
id: "gerp",
@@ -937,7 +943,7 @@ export default class VariantBrowserGrid extends LitElement {
formatter: this.conservationFormatter,
align: "right",
halign: "center",
- visible: this.gridCommons.isColumnVisible("gerp")
+ visible: this.gridCommons.isColumnVisible("gerp", "conservation")
// visible: this.opencgaSession.project.organism.assembly.toUpperCase() === "GRCH37"
},
...sampleColumns,
@@ -951,7 +957,7 @@ export default class VariantBrowserGrid extends LitElement {
rowspan: 1,
formatter: VariantGridFormatter.clinicalTraitAssociationFormatter,
align: "center",
- visible: this.gridCommons.isColumnVisible("clinvar")
+ visible: this.gridCommons.isColumnVisible("clinvar", "clinicalInfo")
},
{
id: "cosmic",
@@ -961,7 +967,7 @@ export default class VariantBrowserGrid extends LitElement {
rowspan: 1,
formatter: VariantGridFormatter.clinicalTraitAssociationFormatter,
align: "center",
- visible: this.gridCommons.isColumnVisible("cosmic")
+ visible: this.gridCommons.isColumnVisible("cosmic", "clinicalInfo")
},
]
];