Merge pull request #979 from opencb/TASK-6838

TASK-6838 - Simplify HRDetect Interface for non-advanced users
opencb · Sep 25, 2024 · 8d848fd · 8d848fd
2 parents b45bf93 + 83f0c76
commit 8d848fd
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Showing 3 changed files with 19 additions and 86 deletions.
diff --git a/src/webcomponents/clinical/analysis/hrdetect-analysis.js b/src/webcomponents/clinical/analysis/hrdetect-analysis.js
@@ -115,10 +115,6 @@ export default class HRDetectAnalysis extends LitElement {
                 sampleId: this.toolParams.query?.sample,
                 snvFittingId: this.toolParams.snvFittingId,
                 svFittingId: this.toolParams.svFittingId,
-                snv3CustomName: this.toolParams.snv3CustomName || "",
-                snv8CustomName: this.toolParams.snv8CustomName || "",
-                sv3CustomName: this.toolParams.sv3CustomName || "",
-                sv8CustomName: this.toolParams.sv8CustomName || "",
                 bootstrap: !!this.toolParams.bootstrap,
             };
 
@@ -290,48 +286,8 @@ export default class HRDetectAnalysis extends LitElement {
                 ],
             },
             {
-                title: "Advanced Parameters",
+                title: "HRDetect Parameters",
                 elements: [
-                    {
-                        title: "SNV3 Custom Name",
-                        field: "snv3CustomName",
-                        type: "input-text",
-                        display: {
-                            help: {
-                                text: "Custom signature name that will be considered as SNV3 input for HRDetect.",
-                            },
-                        },
-                    },
-                    {
-                        title: "SNV8 Custom Name",
-                        field: "snv8CustomName",
-                        type: "input-text",
-                        display: {
-                            help: {
-                                text: "Custom signature name that will be considered as SNV8 input for HRDetect.",
-                            },
-                        },
-                    },
-                    {
-                        title: "SV3 Custom Name",
-                        field: "sv3CustomName",
-                        type: "input-text",
-                        display: {
-                            help: {
-                                text: "Custom signature name that will be considered as SV3 input for HRDetect.",
-                            },
-                        },
-                    },
-                    {
-                        title: "SV8 Custom Name",
-                        field: "sv8CustomName",
-                        type: "input-text",
-                        display: {
-                            help: {
-                                text: "Custom signature name that will be considered as SV8 input for HRDetect.",
-                            },
-                        },
-                    },
                     {
                         title: "Bootstrap",
                         field: "bootstrap",

diff --git a/src/webcomponents/clinical/analysis/hrdetect-view.js b/src/webcomponents/clinical/analysis/hrdetect-view.js
@@ -169,20 +169,35 @@ class HRDetectView extends LitElement {
                             },
                         },
                         {
-                            name: "Scores",
+                            name: "Probability",
+                            field: "scores",
+                            display: {
+                                format: scores => {
+                                    return scores.find(row => row.key?.toLowerCase?.() === "probability")?.value?.toFixed?.(2) || "-";
+                                },
+                            },
+                        },
+                        {
+                            name: "Contributions",
                             field: "scores",
                             type: "table",
                             display: {
-                                // style: "width:auto",
                                 showHeader: false,
+                                filter: data => (data || []).filter(row => {
+                                    return !["intercept", "probability"].includes(row?.key?.toLowerCase?.());
+                                }),
+                                transform: data => data.toSorted((a, b) => b.value - a.value),
                                 columns: [
                                     {
                                         title: "key",
                                         field: "key"
                                     },
                                     {
                                         title: "value",
-                                        field: "value"
+                                        field: "value",
+                                        display: {
+                                            format: value => value.toFixed(2),
+                                        },
                                     },
                                 ],
                             },

diff --git a/src/webcomponents/clinical/analysis/mutational-signature-analysis.js b/src/webcomponents/clinical/analysis/mutational-signature-analysis.js
@@ -163,8 +163,6 @@ export default class MutationalSignatureAnalysis extends LitElement {
                 fitNBoot: this.toolParams.fitNBoot,
                 fitThresholdPerc: this.toolParams.fitThresholdPerc,
                 fitThresholdPval: this.toolParams.fitThresholdPval,
-                fitSignaturesFile: this.toolParams.fitSignaturesFile,
-                fitRareSignaturesFile: this.toolParams.fitRareSignaturesFile,
             };
 
             // Check if we have provided an existing signature list
@@ -411,42 +409,6 @@ export default class MutationalSignatureAnalysis extends LitElement {
                         field: "fitNBoot",
                         type: "input-text",
                     },
-                    {
-                        title: "Fit Signatures File",
-                        field: "fitSignaturesFile",
-                        type: "custom",
-                        display: {
-                            render: (fitSignaturesFile, dataFormFilterChange) => html`
-                                <catalog-search-autocomplete
-                                    .value="${fitSignaturesFile}"
-                                    .resource="${"FILE"}"
-                                    .opencgaSession="${this.opencgaSession}"
-                                    .config="${{multiple: false}}"
-                                    .searchField="${"id"}"
-                                    .query="${fileQuery}"
-                                    @filterChange="${e => dataFormFilterChange(e.detail.value)}">
-                                </catalog-search-autocomplete>
-                            `,
-                        },
-                    },
-                    {
-                        title: "Fit Rare Signatures File",
-                        field: "fitRareSignaturesFile",
-                        type: "custom",
-                        display: {
-                            render: (fitRareSignaturesFile, dataFormFilterChange) => html`
-                                <catalog-search-autocomplete
-                                    .value="${fitRareSignaturesFile}"
-                                    .resource="${"FILE"}"
-                                    .opencgaSession="${this.opencgaSession}"
-                                    .config="${{multiple: false}}"
-                                    .searchField="${"id"}"
-                                    .query="${fileQuery}"
-                                    @filterChange="${e => dataFormFilterChange(e.detail.value)}">
-                                </catalog-search-autocomplete>
-                            `,
-                        },
-                    },
                 ]
             }
         ];