🔧 Upset: Add topN param and change sets naming for elems (#231)

kids-first · Jan 13, 2025 · 03b5133 · 03b5133
1 parent 0c6ed64
commit 03b5133
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Showing 3 changed files with 11 additions and 10 deletions.
diff --git a/src/app.ts b/src/app.ts
@@ -196,7 +196,7 @@ export default (keycloak: Keycloak, getProject: (projectId: string) => ArrangerP
 
     app.post('/upset', keycloak.protect(), async (req, res, next) => {
         try {
-            const data = await computeUpset(req.body.sqon);
+            const data = await computeUpset(req.body.sqon, req.body.topN);
             res.send(data);
         } catch (e) {
             next(e);

diff --git a/src/endpoints/upset.test.ts b/src/endpoints/upset.test.ts
@@ -263,13 +263,13 @@ describe('Upset', () => {
                 ],
                 op: 'and',
             };
-            const result = await computeUpset(sqon);
+            const result = await computeUpset(sqon, 5);
             expect(result).toEqual({
                 data: [
-                    { name: 'Abnormality of the eye (HP:0000478)', sets: ['pt-223twf8ytr', 'pt-2282xh6dem'] },
-                    { name: 'Seizure (HP:0001250)', sets: ['pt-223twf8ytr'] },
-                    { name: 'Ventricular septal defect (HP:0001629)', sets: ['pt-2282xh6dem'] },
-                    { name: 'Abnormality of the dentition (HP:0000164)', sets: ['pt-2282xh6dem'] },
+                    { name: 'Abnormality of the eye (HP:0000478)', elems: ['pt-223twf8ytr', 'pt-2282xh6dem'] },
+                    { name: 'Seizure (HP:0001250)', elems: ['pt-223twf8ytr'] },
+                    { name: 'Ventricular septal defect (HP:0001629)', elems: ['pt-2282xh6dem'] },
+                    { name: 'Abnormality of the dentition (HP:0000164)', elems: ['pt-2282xh6dem'] },
                 ],
                 participantsCount: 2,
             });

diff --git a/src/endpoints/upset.ts b/src/endpoints/upset.ts
@@ -5,7 +5,7 @@ import EsInstance from '../ElasticSearchClientInstance';
 
 export type UpsetData = {
     name: string;
-    sets: string[];
+    elems: string[];
 }[];
 
 export const countIt = (xs: string[]): Map<string, number> => {
@@ -48,9 +48,10 @@ const emptySQON = {
     content: [],
 };
 
-const TOP = 20;
+const DEFAULT_TOP = 10;
 export const computeUpset = async (
     sqon = emptySQON,
+    topMax = DEFAULT_TOP,
 ): Promise<{
     data: UpsetData;
     participantsCount: number;
@@ -108,13 +109,13 @@ export const computeUpset = async (
     const allQueryPhenotypes: string[] = ps.map(x => x.ph).flat();
 
     //countIt is sorted by descending counts
-    const top = topN(countIt(allQueryPhenotypes), TOP);
+    const top = topN(countIt(allQueryPhenotypes), topMax > 0 && topMax <= 25 ? topMax : DEFAULT_TOP);
 
     const data = top.map(x => {
         const pts = ps.reduce((ys, y) => (y.ph.includes(x) ? [...ys, y.patient] : ys), []);
         return {
             name: x,
-            sets: pts,
+            elems: pts,
         };
     });