feat: SJIP-1070 add sex and age at biospecimen collection years in sa…

…mple point
kids-first · Nov 5, 2024 · 45d232f · 45d232f
1 parent d95ea83
commit 45d232f
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Showing 4 changed files with 30 additions and 3 deletions.
diff --git a/src/app.test.ts b/src/app.test.ts
@@ -629,16 +629,26 @@ describe('Express app (without Arranger)', () => {
         it('should return 200 if Authorization header contains valid token and no error occurs', async () => {
             const sampleGeneExp: SampleGeneExpVolcano = {
                 data: [
-                    { sample_id: 'bs-aa000aaa', x: 1, y: 2.4399124042981217 },
+                    {
+                        sample_id: 'bs-aa000aaa',
+                        x: 1,
+                        y: 2.4399124042981217,
+                        age_at_biospecimen_collection_years: 1.6,
+                        sex: 'Female',
+                    },
                     {
                         sample_id: 'bs-bbbb11b1',
                         x: 0,
                         y: 0.90884870449667,
+                        age_at_biospecimen_collection_years: 2.7,
+                        sex: 'Male',
                     },
                     {
                         sample_id: 'bs-ccc22cc2',
                         x: 1,
                         y: 0.909129052666039,
+                        age_at_biospecimen_collection_years: 3.9,
+                        sex: 'Female',
                     },
                 ],
                 ensembl_gene_id: 'ENSG00000272368.2',

diff --git a/src/endpoints/transcriptomics/index.test.ts b/src/endpoints/transcriptomics/index.test.ts
@@ -269,6 +269,7 @@ describe('Transcriptomics', () => {
                                 x: 1,
                                 y: 2.4399124042981217,
                                 age_at_biospecimen_collection_years: 1.6,
+                                sex: 'Female',
                             },
                         },
                         {
@@ -281,6 +282,7 @@ describe('Transcriptomics', () => {
                                 x: 0,
                                 y: 0.90884870449667,
                                 age_at_biospecimen_collection_years: 2.7,
+                                sex: 'Male',
                             },
                         },
                         {
@@ -293,6 +295,7 @@ describe('Transcriptomics', () => {
                                 x: 1,
                                 y: 0.909129052666039,
                                 age_at_biospecimen_collection_years: 3.9,
+                                sex: 'Female',
                             },
                         },
                     ],
@@ -301,16 +304,26 @@ describe('Transcriptomics', () => {
 
             const expectedResponse: SampleGeneExpVolcano = {
                 data: [
-                    { sample_id: 'bs-aa000aaa', x: 1, y: 2.4399124042981217 },
+                    {
+                        sample_id: 'bs-aa000aaa',
+                        x: 1,
+                        y: 2.4399124042981217,
+                        age_at_biospecimen_collection_years: 1.6,
+                        sex: 'Female',
+                    },
                     {
                         sample_id: 'bs-bbbb11b1',
                         x: 0,
                         y: 0.90884870449667,
+                        age_at_biospecimen_collection_years: 2.7,
+                        sex: 'Male',
                     },
                     {
                         sample_id: 'bs-ccc22cc2',
                         x: 1,
                         y: 0.909129052666039,
+                        age_at_biospecimen_collection_years: 3.9,
+                        sex: 'Female',
                     },
                 ],
                 ensembl_gene_id: 'ENSG00000272368.2',

diff --git a/src/endpoints/transcriptomics/index.ts b/src/endpoints/transcriptomics/index.ts
@@ -80,7 +80,7 @@ export const fetchSampleGeneExp = async (ensembl_gene_id: string): Promise<Sampl
                     ensembl_gene_id,
                 },
             },
-            _source: ['sample_id', 'x', 'y', 'age_at_biospecimen_collection_years'],
+            _source: ['sample_id', 'x', 'y', 'age_at_biospecimen_collection_years', 'sex'],
         },
     });
 
@@ -100,6 +100,8 @@ export const fetchSampleGeneExp = async (ensembl_gene_id: string): Promise<Sampl
             sample_id: hit._source.sample_id,
             x: hit._source.x,
             y: hit._source.y,
+            sex: hit._source.sex,
+            age_at_biospecimen_collection_years: hit._source.age_at_biospecimen_collection_years,
         });
 
         // Add point to nT21 or nControl depending on x

diff --git a/src/endpoints/transcriptomics/types.ts b/src/endpoints/transcriptomics/types.ts
@@ -61,6 +61,8 @@ export type SampleGeneExpPoint = {
     sample_id: string;
     x: number;
     y: number;
+    age_at_biospecimen_collection_years: number;
+    sex: string;
 };
 
 export type SampleGeneExpVolcano = {