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TASK-4753 - Implement RD Tiering Disable/Enable option by configuration. Not currently working. #820

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merged 11 commits into from
Oct 2, 2023
Merged

TASK-4753 - Implement RD Tiering Disable/Enable option by configuration. Not currently working. #820

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faa5721
iva: add new configuration for interpretation methods #TASK-4753
jmjuanes Sep 26, 2023
017792c
wc: add a settings property to interpreter methods #TASK-4753
jmjuanes Sep 26, 2023
49a1ef6
wc: generate available methods from settings #TASK-4753
jmjuanes Sep 26, 2023
afce281
wc: display a warning message if no methods have been configured #TAS…
jmjuanes Sep 26, 2023
024f90d
wc: remove unused imports in variant-interpreter-methods #TASK-4753
jmjuanes Sep 26, 2023
7f308ea
iva: rename case option in methods configuration to items #TASK-4753
jmjuanes Sep 27, 2023
e983f90
wc: rename cases to items in methods tool settings #TASK-4753
jmjuanes Sep 27, 2023
31a0983
wc: removed unused config property in variant-interpreter-methods #TA…
jmjuanes Sep 27, 2023
c811008
wc: using visible key instead of hidden for displaying interpretation…
jmjuanes Sep 27, 2023
afc9c36
Merge branch 'release-2.8.x' into TASK-4753
jmjuanes Sep 28, 2023
5732164
Merge branch 'release-2.8.x' into TASK-4753
jmjuanes Sep 28, 2023
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20 changes: 19 additions & 1 deletion src/sites/iva/conf/browsers.settings.js
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Original file line number Diff line number Diff line change
Expand Up @@ -708,7 +708,25 @@ const INTERPRETER_SETTINGS = {
],
},
{
id: "methods"
id: "methods",
items: [
{
type: "SINGLE",
methods: [
{id: "exomiser"},
],
},
{
type: "FAMILY",
methods: [
{id: "exomiser"},
],
},
{
type: "CANCER",
methods: [],
},
],
},
{
id: "variant-browser",
Expand Down
170 changes: 72 additions & 98 deletions src/webcomponents/variant/interpretation/variant-interpreter-methods.js
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Original file line number Diff line number Diff line change
Expand Up @@ -15,11 +15,9 @@
*/

import {LitElement, html} from "lit";
import UtilsNew from "../../../core/utils-new.js";
import "../../commons/view/detail-tabs.js";
import "../../clinical/analysis/rd-tiering-analysis.js";
import "../../clinical/analysis/exomiser-analysis.js";
import "../../clinical/analysis/hrdetect-analysis.js";

class VariantInterpreterMethods extends LitElement {

Expand All @@ -44,46 +42,36 @@ class VariantInterpreterMethods extends LitElement {
clinicalAnalysisId: {
type: String
},
config: {
type: Object
}
settings: {
type: Object,
},
};
}

_init() {
this._prefix = UtilsNew.randomString(8);
this._config = this.getDefaultConfig();
}

connectedCallback() {
super.connectedCallback();
}

update(changedProperties) {
if (changedProperties.has("opencgaSession")) {
this.opencgaSessionObserver();
}
if (changedProperties.has("clinicalAnalysisId")) {
this.clinicalAnalysisIdObserver();
}
// if (changedProperties.has("clinicalAnalysis")) {
// this.clinicalAnalysisObserver();
// }
super.update(changedProperties);
}

opencgaSessionObserver() {
this._config = this.getDefaultConfig();
this.requestUpdate();
if (changedProperties.has("opencgaSession") || changedProperties.has("clinicalAnalysis") || changedProperties.has("settings")) {
this._config = this.getDefaultConfig();
}

super.update(changedProperties);
}

clinicalAnalysisIdObserver() {
if (this.opencgaSession?.opencgaClient && this.clinicalAnalysisId) {
this.opencgaSession.opencgaClient.clinical()
.info(this.clinicalAnalysisId, {study: this.opencgaSession.study.fqn})
.info(this.clinicalAnalysisId, {
study: this.opencgaSession.study.fqn,
})
.then(response => {
this.clinicalAnalysis = response.responses[0].results[0];
// this.requestUpdate();
})
.catch(response => {
console.error("An error occurred fetching clinicalAnalysis: ", response);
Expand All @@ -92,12 +80,23 @@ class VariantInterpreterMethods extends LitElement {
}

render() {
// Check Project exists
if (!this.opencgaSession.project) {
if (!this.opencgaSession?.project) {
return html`
<div>
<h3><i class="fas fa-lock"></i> No public projects available to browse. Please login to continue</h3>
</div>`;
</div>
`;
}

// If no methods have been configured, we will display a warning message
if (!this._config || this._config.items.length === 0) {
return html`
<div class="col-md-6 col-md-offset-3" style="padding: 20px">
<div class="alert alert-warning" role="alert">
No automatic methods available at this time.
</div>
</div>
`;
}

return html`
Expand All @@ -112,79 +111,54 @@ class VariantInterpreterMethods extends LitElement {
getDefaultConfig() {
const items = [];

if (this.clinicalAnalysis) {
const probandId = this.clinicalAnalysis.proband.id;

if (this.clinicalAnalysis.type.toUpperCase() === "SINGLE") {
items.push({
id: "exomiser",
name: "Exomiser",
render: (clinicalAnalysis, active, opencgaSession) => {
return html`
<div class="col-md-6 col-md-offset-3">
<tool-header title="Exomiser - ${probandId}" class="bg-white"></tool-header>
<exomiser-analysis
.toolParams="${{clinicalAnalysis: clinicalAnalysis.id}}"
.opencgaSession="${opencgaSession}"
.title="${""}">
</exomiser-analysis>
</div>
`;
},
});
}

if (this.clinicalAnalysis.type.toUpperCase() === "FAMILY") {
items.push({
id: "exomiser",
name: "Exomiser",
active: true,
render: (clinicalAnalysis, active, opencgaSession) => {
return html`
<div class="col-md-6 col-md-offset-3">
<tool-header title="Exomiser - ${probandId}" class="bg-white"></tool-header>
<exomiser-analysis
.toolParams="${{clinicalAnalysis: clinicalAnalysis.id}}"
.opencgaSession="${opencgaSession}"
.title="${""}">
</exomiser-analysis>
</div>
`;
},
});
items.push({
id: "rd-tiering",
name: "RD Tiering",
render: (clinicalAnalysis, active, opencgaSession) => {
return html`
<div class="col-md-6 col-md-offset-3">
<tool-header title="RD Tiering - ${probandId}" class="bg-white"></tool-header>
<rd-tiering-analysis
.toolParams="${{clinicalAnalysis: clinicalAnalysis.id, panels: clinicalAnalysis.panels?.map(panel => panel.id).join(",")}}"
.opencgaSession="${opencgaSession}"
.title="${""}">
</rd-tiering-analysis>
</div>
`;
},
});
}

if (this.clinicalAnalysis.type.toUpperCase() === "CANCER") {
items.push({
id: "",
name: "Cancer Analysis",
render: (clinicalAnalysis, active, opencgaSession) => {
return html`
<div class="col-md-6 col-md-offset-3" style="padding: 20px">
<div class="alert alert-warning" role="alert">
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`
<div class="col-md-6 col-md-offset-3">
<tool-header title="Exomiser - ${probandId}" class="bg-white"></tool-header>
<exomiser-analysis
.toolParams="${{clinicalAnalysis: clinicalAnalysis.id}}"
.opencgaSession="${opencgaSession}"
.title="${""}">
</exomiser-analysis>
</div>
</div>
`;
},
});
}
`;
},
});
}

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`
<div class="col-md-6 col-md-offset-3">
<tool-header title="RD Tiering - ${probandId}" class="bg-white"></tool-header>
<rd-tiering-analysis
.toolParams="${toolParams}"
.opencgaSession="${opencgaSession}"
.title="${""}">
</rd-tiering-analysis>
</div>
`;
},
});
}
});
}

return {
Expand Down
5 changes: 2 additions & 3 deletions src/webcomponents/variant/interpretation/variant-interpreter.js
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Original file line number Diff line number Diff line change
Expand Up @@ -430,10 +430,9 @@ class VariantInterpreter extends LitElement {
-->
</div>
<div>
<!-- Controls aligned to the LEFT -->
<div class="row hi-icon-wrap wizard hi-icon-animation variant-interpreter-wizard">
${this._config?.tools?.map(item => html`
${!item.hidden ? html`
${(typeof item.visible === "undefined" || !!item.visible) ? html`
<a class="icon-wrapper variant-interpreter-step ${!this.clinicalAnalysis && item.id !== "select" || item.disabled ? "disabled" : ""} ${this.activeTab[item.id] ? "active" : ""}"
href="javascript: void 0" data-view="${item.id}"
@click="${this.onClickSection}">
Expand Down Expand Up @@ -480,7 +479,7 @@ class VariantInterpreter extends LitElement {
<variant-interpreter-methods
.opencgaSession="${this.opencgaSession}"
.clinicalAnalysis="${this.clinicalAnalysis}"
.config="${this._config}">
.settings="${this._config.tools.find(tool => tool.id === "methods")}">
</variant-interpreter-methods>
</div>
` : null}
Expand Down
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