From 86a6e519697fbc2586da0de0953b4c8e78f2b34e Mon Sep 17 00:00:00 2001
From: Cesar Ferreyra-Mansilla <cesar_ferreyra-mansilla@hms.harvard.edu>
Date: Tue, 5 Mar 2024 14:51:32 -0500
Subject: [PATCH] feat: make CNV file optional (#132)

---
 docs/docs/loading-data/through-data-config.md | 2 +-
 src/data/samples.ts                           | 2 +-
 src/main-spec.ts                              | 4 ++--
 src/ui/sample-config-form.tsx                 | 5 ++---
 4 files changed, 6 insertions(+), 7 deletions(-)

diff --git a/docs/docs/loading-data/through-data-config.md b/docs/docs/loading-data/through-data-config.md
index d4a0eace..fbbe6a18 100644
--- a/docs/docs/loading-data/through-data-config.md
+++ b/docs/docs/loading-data/through-data-config.md
@@ -23,7 +23,7 @@ For each sample, you need to prepare the following information in a JSON object.
 | `cancer` | `string` | Required. Type of a cancer. |
 | `assembly` | `'hg38'` or `'hg19'` | Required. Assembly. |
 | `sv` | `string` | Required. An URL of the SV bedpe file (`.bedpe`). |
-| `cnv` | `string` | Required. An URL of the CNV text file (`.tsv`). |
+| `cnv` | `string` | Optional. An URL of the CNV text file (`.tsv`). |
 | `drivers` | `string` | Optional. An URL of a file that contains drivers (`.tsv` or `.json`). |
 | `vcf` | `string` | Optional. An URL of the point mutation file (`.vcf`). |
 | `vcfIndex` | `string` | Optional. An URL of the point mutation index file (`.tbi`). |
diff --git a/src/data/samples.ts b/src/data/samples.ts
index a152bf6a..c4bc19ea 100644
--- a/src/data/samples.ts
+++ b/src/data/samples.ts
@@ -20,7 +20,7 @@ export type SampleType = {
     cancer: string; // cancer type
     assembly: Assembly; // hg19 or 38
     sv: string; // URL of bedpe
-    cnv: string; // URL of txt
+    cnv?: string; // URL of txt
     drivers?: { [k: string]: string | number }[] | string;
     bam?: string;
     bai?: string;
diff --git a/src/main-spec.ts b/src/main-spec.ts
index e4c97a40..b4a52d5d 100644
--- a/src/main-spec.ts
+++ b/src/main-spec.ts
@@ -315,9 +315,9 @@ function getOverviewSpec(option: SpecOption): View[] {
                 },
                 tracks.driver(id, driversToTsvUrl(drivers), width, 40, 'top'),
                 tracks.boundary('driver', 'top'),
-                tracks.gain(id, cnv, width, 40, 'top', cnFields),
+                cnv ? [tracks.gain(id, cnv, width, 40, 'top', cnFields)] : [],
                 tracks.boundary('gain', 'top'),
-                tracks.loh(id, cnv, width, 40, 'top', cnFields),
+                cnv ? [tracks.loh(id, cnv, width, 40, 'top', cnFields)] : [],
                 tracks.boundary('loh', 'top'),
                 tracks.sv(id, sv, width, 80, 'top', selectedSvId)
             ]
diff --git a/src/ui/sample-config-form.tsx b/src/ui/sample-config-form.tsx
index 29b0211e..4fdf6d9b 100644
--- a/src/ui/sample-config-form.tsx
+++ b/src/ui/sample-config-form.tsx
@@ -24,8 +24,8 @@ const testOkay = {
     id: (_: SampleConfig) => _.id,
     cancer: (_: SampleConfig) => _.cancer,
     sv: (_: SampleConfig) => isValidUrl(_.sv),
-    cnv: (_: SampleConfig) => isValidUrl(_.cnv),
     // optional
+    cnv: (_: SampleConfig) => !_.cnv || isValidUrl(_.cnv),
     drivers: (_: SampleConfig) => !_.drivers || isValidUrl(_.drivers),
     vcf: (_: SampleConfig) => !_.vcf || isValidUrl(_.vcf),
     vcfIndex: (_: SampleConfig) => !_.vcfIndex || isValidUrl(_.vcfIndex),
@@ -155,14 +155,13 @@ export default function SampleConfigForm(props: { onAdd: (config: ValidSampleCon
                 />
 
                 <div className="menu-subtitle">
-                    CNV<sup>*</sup> <small>(.txt)</small>
+                    CNV <small>(.txt)</small>
                 </div>
                 {/* <span className="menu-subtitle-right">Required</span> */}
                 <input
                     type="text"
                     className={testOkay.cnv(sampleConfig) ? 'menu-text-input' : 'menu-text-input-invalid'}
                     placeholder="https://..."
-                    required
                     onChange={e => setSampleConfig({ ...sampleConfig, cnv: e.currentTarget.value })}
                     value={sampleConfig.cnv}
                 />