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TASK-7034 (v3.2.2) - Unable to display custom indexed fields in Variant Caller Sample Filter #990

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TASK-7034 (v3.2.2) - Unable to display custom indexed fields in Variant Caller Sample Filter #990

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d8285bc
Increment version to 2.12.8-dev
jmjuanes Oct 1, 2024
4894ac7
Display all configured filters in variant-file-format-filter
imedina Oct 1, 2024
dacc80c
Merge branch 'TASK-7034' into TASK-7034-3.2.2
jmjuanes Oct 2, 2024
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128 changes: 71 additions & 57 deletions src/webcomponents/commons/filters/variant-file-format-filter.js
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Original file line number Diff line number Diff line change
Expand Up @@ -22,7 +22,7 @@ export default class VariantFileFormatFilter extends LitElement {
constructor() {
super();

this._init();
this.#init();
}

createRenderRoot() {
Expand All @@ -40,10 +40,23 @@ export default class VariantFileFormatFilter extends LitElement {
};
}

_init() {
#init() {
this.sampleData = "";
this._sampleData = {};

this.fields = [
{
id: "DP", name: "Depth"
},
{
id: "AF", name: "AF"
},
{
id: "EXT_VAF", name: "VAF"
}
];
this.indexedFields = {};

this._config = this.getDefaultConfig();
}

Expand All @@ -58,33 +71,36 @@ export default class VariantFileFormatFilter extends LitElement {
}

opencgaSessionObserver() {
this.depthIndex = this.opencgaSession.study.internal.configuration.variantEngine.sampleIndex.fileIndexConfiguration.customFields
.find(field => field.key === "DP" && field.source === "SAMPLE");
this.afIndex = this.opencgaSession.study.internal.configuration.variantEngine.sampleIndex.fileIndexConfiguration.customFields
.find(field => field.key === "AF" && field.source === "SAMPLE");
this.extVafIndex = this.opencgaSession.study.internal.configuration.variantEngine.sampleIndex.fileIndexConfiguration.customFields
.find(field => field.key === "EXT_VAF" && field.source === "SAMPLE");
// Parse custom fields and add them to the fields array
for (const dataFilter of this.opencgaSession?.study?.internal?.configuration?.clinical?.interpretation?.variantCallers[0]?.dataFilters) {
if (dataFilter.source === "SAMPLE") {
const indexPosition = this.fields.findIndex(f => f.id === dataFilter.id);
if (indexPosition >= 0) {
this.fields[indexPosition] = {id: dataFilter.id, name: dataFilter.name};
} else {
this.fields.push({id: dataFilter.id, name: dataFilter.name});
}
}
}

// Search for the indexed fields
for (const field of this.fields) {
this.indexedFields[field.id] = this.opencgaSession.study.internal.configuration.variantEngine.sampleIndex.fileIndexConfiguration.customFields
.find(f => f.key === field.id && f.source === "SAMPLE");
}
this._config = this.getDefaultConfig();
}

sampleDataObserver() {
if (this.sampleData) {
const sampleDataFilters = this.sampleData.split(";");

const depth = sampleDataFilters.find(filter => filter.startsWith("DP"))?.replace("DP", "");
depth ? this._sampleData.DP = depth : delete this._sampleData.DP;
this.depthIndex = this.opencgaSession.study.internal.configuration.variantEngine.sampleIndex.fileIndexConfiguration.customFields
.find(field => field.key === "DP" && field.source === "SAMPLE");

const af = sampleDataFilters.find(filter => filter.startsWith("AF"))?.replace("AF", "");
af ? this._sampleData.AF = af : delete this._sampleData.AF;
this.afIndex = this.opencgaSession.study.internal.configuration.variantEngine.sampleIndex.fileIndexConfiguration.customFields
.find(field => field.key === "AF" && field.source === "SAMPLE");

const extVaf = sampleDataFilters.find(filter => filter.startsWith("EXT_VAF"))?.replace("EXT_VAF", "");
extVaf ? this._sampleData.EXT_VAF = extVaf : delete this._sampleData.EXT_VAF;
this.extVafIndex = this.opencgaSession.study.internal.configuration.variantEngine.sampleIndex.fileIndexConfiguration.customFields
.find(field => field.key === "EXT_VAF" && field.source === "SAMPLE");
for (const field of this.fields) {
const filter = sampleDataFilters.find(filter => filter.startsWith(field.id))?.replace(field.id, "");
filter ? this._sampleData[field.id] = filter : delete this._sampleData[field.id];
this.indexedFields[field.id] = this.opencgaSession.study.internal.configuration.variantEngine.sampleIndex.fileIndexConfiguration.customFields
.find(f => f.key === field.id && f.source === "SAMPLE");
}

this._config = this.getDefaultConfig();
} else {
Expand Down Expand Up @@ -116,6 +132,38 @@ export default class VariantFileFormatFilter extends LitElement {
}

getDefaultConfig() {
const elements = [];
for (const field of this.fields) {
// Check if the field is actually indexed, only indexed fields can be used for filtering
if (this.indexedFields[field.id]) {
if (this.indexedFields[field.id]?.type?.startsWith("RANGE_")) {
elements.push({
name: field.name,
field: field.id,
type: "input-number",
comparators: this.indexedFields[field.id]?.type === "RANGE_LT" ? "<,>=" : "<=,>",
allowedValues: this.indexedFields[field.id]?.thresholds,
display: {
defaultValue: "",
visible: () => this.indexedFields[field.id]?.thresholds?.length > 0,
}
});
} else {
// Categorical
elements.push({
name: field.name,
field: field.id,
type: "select",
allowedValues: this.indexedFields[field.id]?.values,
multiple: this.indexedFields[field.id]?.type === "CATEGORICAL_MULTI_VALUE",
display: {
defaultValue: "",
},
});
}
}
}

return {
title: "",
icon: "",
Expand All @@ -134,41 +182,7 @@ export default class VariantFileFormatFilter extends LitElement {
titleHeader: "h4",
titleStyle: "margin: 5px 0"
},
elements: [
{
name: "Depth",
field: "DP",
type: "input-number",
comparators: this.depthIndex?.type === "RANGE_LT" ? "<,>=" : "<=,>",
allowedValues: this.depthIndex?.thresholds,
display: {
defaultValue: "",
visible: () => this.depthIndex?.thresholds?.length > 0,
}
},
{
name: "AF",
field: "AF",
type: "input-number",
comparators: this.afIndex?.type === "RANGE_LT" ? "<,>=" : "<=,>",
allowedValues: this.afIndex?.thresholds,
display: {
defaultValue: "",
visible: () => this.afIndex?.thresholds?.length > 0,
}
},
{
name: "VAF",
field: "EXT_VAF",
type: "input-number",
comparators: this.extVafIndex?.type === "RANGE_LT" ? "<,>=" : "<=,>",
allowedValues: this.extVafIndex?.thresholds,
display: {
defaultValue: "",
visible: () => this.extVafIndex?.thresholds?.length > 0,
}
}
]
elements: elements
}
],
};
Expand Down
2 changes: 1 addition & 1 deletion src/webcomponents/variant/interpretation/variant-interpreter-browser-rd.js
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Original file line number Diff line number Diff line change
Expand Up @@ -255,7 +255,7 @@ class VariantInterpreterBrowserRd extends LitElement {
});

// Add 'file' filter if 'fileData' exists
if (this.files) {
if (this.files?.length > 1) {
const fileNames = this.files.map(f => f.name).join(",");
for (const filter of _activeFilterFilters) {
if (filter.query?.fileData && !filter.query?.file) {
Expand Down
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