Merge pull request #901 from opencb/TASK-6003

TASK-6003 - New selected variants or new changes to primary findings cannot be saved with a specific sample variant browser configuration
opencb · Apr 16, 2024 · 8ce5d35 · 8ce5d35
2 parents d51f579 + 7c969fb
commit 8ce5d35
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Showing 3 changed files with 30 additions and 35 deletions.
diff --git a/src/webcomponents/variant/interpretation/variant-interpreter-grid-formatter.js b/src/webcomponents/variant/interpretation/variant-interpreter-grid-formatter.js
@@ -445,11 +445,11 @@ export default class VariantInterpreterGridFormatter {
     /*
      *  SAMPLE GENOTYPE RENDERER
      */
-    static sampleGenotypeFormatter(value, row, index) {
+    static sampleGenotypeFormatter(value, row, index, params) {
         let resultHtml = "";
 
         if (row && row.studies?.length > 0 && row.studies[0].samples?.length > 0) {
-            const sampleId = this.field.sampleId;
+            const sampleId = params?.sampleId;
             let sampleEntries = [row.studies[0].samples.find(s => s.sampleId === sampleId)];
 
             // If not sampleId is found and there is only one sample we take that one
@@ -474,15 +474,15 @@ export default class VariantInterpreterGridFormatter {
 
                 // Render genotypes
                 let content = "";
-                switch (this.field.config?.genotype?.type?.toUpperCase() || "VCF_CALL") {
+                switch (params?.config?.genotype?.type?.toUpperCase() || "VCF_CALL") {
                     case "ALLELES":
                         content = VariantInterpreterGridFormatter.alleleGenotypeRenderer(row, sampleEntry, "alleles");
                         break;
                     case "VCF_CALL":
                         content = VariantInterpreterGridFormatter.alleleGenotypeRenderer(row, sampleEntry, "call");
                         break;
                     case "ZYGOSITY":
-                        content = VariantInterpreterGridFormatter.zygosityGenotypeRenderer(row, sampleEntry, this.field.clinicalAnalysis);
+                        content = VariantInterpreterGridFormatter.zygosityGenotypeRenderer(row, sampleEntry, params?.clinicalAnalysis);
                         break;
                     case "VAF":
                         const vaf = VariantInterpreterGridFormatter._getVariantAlleleFraction(row, sampleEntry, file);
@@ -508,15 +508,17 @@ export default class VariantInterpreterGridFormatter {
                         content = VariantInterpreterGridFormatter.circleGenotypeRenderer(sampleEntry, file, 10);
                         break;
                     default:
-                        console.error("No valid genotype render option:", this.field.config.genotype.type.toUpperCase());
+                        console.error("No valid genotype render option:", params?.config?.genotype?.type?.toUpperCase());
                         break;
                 }
 
                 // Get tooltip text
                 const tooltipText = VariantInterpreterGridFormatter._getSampleGenotypeTooltipText(row, sampleEntry, file);
-                resultHtml += `<a class="zygositySampleTooltip" tooltip-title="Variant Call Information" tooltip-text='${tooltipText}'>
-                                ${content}
-                              </a><br>`;
+                resultHtml += `
+                    <a class="zygositySampleTooltip" tooltip-title="Variant Call Information" tooltip-text='${tooltipText}'>
+                        ${content}
+                    </a><br>
+                `;
             }
         }
 

diff --git a/src/webcomponents/variant/interpretation/variant-interpreter-grid.js b/src/webcomponents/variant/interpretation/variant-interpreter-grid.js
@@ -1070,19 +1070,16 @@ export default class VariantInterpreterGrid extends LitElement {
                         title: `<span style="color: ${color}">${samples[i].id}</span>
                                 <br>
                                 <span style="font-style: italic">${sampleInfo[samples[i].id].role}, ${affected}</span>`,
-                        field: {
-                            memberIdx: i,
-                            memberName: samples[i].id,
-                            sampleId: samples[i].id,
-                            quality: this._config.quality,
-                            clinicalAnalysis: this.clinicalAnalysis,
-                            config: this._config
-                        },
                         rowspan: 1,
                         colspan: 1,
-                        formatter: VariantInterpreterGridFormatter.sampleGenotypeFormatter,
+                        formatter: (value, row, index) => {
+                            return VariantInterpreterGridFormatter.sampleGenotypeFormatter(value, row, index, {
+                                sampleId: samples[i].id,
+                                clinicalAnalysis: this.clinicalAnalysis,
+                                config: this._config
+                            });
+                        },
                         align: "center",
-                        nucleotideGenotype: true,
                         excludeFromSettings: true,
                         visible: !this._config.hideSampleGenotypes,
                     });
@@ -1122,17 +1119,16 @@ export default class VariantInterpreterGrid extends LitElement {
                             <div style="word-break:break-all;max-width:192px;white-space:break-spaces;">${sample.id}</div>
                             <div style="color:${color};font-style:italic;">${sample?.somatic ? "somatic" : "germline"}</div>
                         `,
-                        field: {
-                            sampleId: sample.id,
-                            quality: this._config.quality,
-                            config: this._config,
-                            clinicalAnalysis: this.clinicalAnalysis
-                        },
                         rowspan: 1,
                         colspan: 1,
-                        formatter: VariantInterpreterGridFormatter.sampleGenotypeFormatter,
+                        formatter: (value, row, index) => {
+                            return VariantInterpreterGridFormatter.sampleGenotypeFormatter(value, row, index, {
+                                sampleId: sample.id,
+                                config: this._config,
+                                clinicalAnalysis: this.clinicalAnalysis
+                            });
+                        },
                         align: "center",
-                        nucleotideGenotype: true,
                         excludeFromSettings: true,
                         visible: !this._config.hideSampleGenotypes,
                     });

diff --git a/src/webcomponents/variant/variant-browser-grid.js b/src/webcomponents/variant/variant-browser-grid.js
@@ -562,18 +562,15 @@ export default class VariantBrowserGrid extends LitElement {
                 sampleColumns.push({
                     id: this.samples[i].id,
                     title: this.samples[i].id,
-                    // field: "samples",
-                    field: {
-                        memberIdx: i,
-                        memberName: this.samples[i].id,
-                        sampleId: this.samples[i].id,
-                        config: this._config
-                    },
                     rowspan: 1,
                     colspan: 1,
-                    formatter: VariantInterpreterGridFormatter.sampleGenotypeFormatter,
+                    formatter: (value, row, index) => {
+                        return VariantInterpreterGridFormatter.sampleGenotypeFormatter(value, row, index, {
+                            sampleId: this.samples[i].id,
+                            config: this._config
+                        });
+                    },
                     align: "center",
-                    // nucleotideGenotype: true,
                     visible: this.gridCommons.isColumnVisible(this.samples[i].id, "samples"),
                 });
             }