test: fix and reactivate nucleotide mutations tests

issue: #283
GenSpectrum · Jul 6, 2023 · ee40bae · ee40bae
1 parent 34b36f8
commit ee40bae
Show file tree

Hide file tree

Showing 3 changed files with 43 additions and 44 deletions.
diff --git a/lapis2/src/main/kotlin/org/genspectrum/lapis/response/SiloResponse.kt b/lapis2/src/main/kotlin/org/genspectrum/lapis/response/SiloResponse.kt
@@ -37,7 +37,7 @@ data class MutationData(
         example = "G29741T",
         description = "(nucleotide symbol in reference genome)(position in genome)" +
             "(mutation's target nucleotide symbol)",
-    ) val mutation: String,
+    ) val position: String,
     @Schema(
         example = "42",
         description = "Total number of sequences with this mutation matching the given sequence filter criteria",

diff --git a/siloLapisTests/test/aggregated.spec.ts b/siloLapisTests/test/aggregated.spec.ts
@@ -1,15 +1,15 @@
 import { expect } from 'chai';
 import { lapisClient } from './common';
 import fs from 'fs';
-import { AggregatedResponse, SequenceFiltersWithGroupByFields } from './lapisClient';
+import {AggregatedResponse, SequenceFiltersWithFields} from './lapisClient';
 
 const queriesPath = __dirname + '/aggregatedQueries';
 const aggregatedQueryFiles = fs.readdirSync(queriesPath);
 
 type TestCase = {
-  testCaseName: string;
-  lapisRequest: SequenceFiltersWithGroupByFields;
-  expected: AggregatedResponse[];
+    testCaseName: string;
+    lapisRequest: SequenceFiltersWithFields;
+    expected: AggregatedResponse[];
 };
 
 describe('The /aggregated endpoint', () => {
@@ -18,7 +18,7 @@ describe('The /aggregated endpoint', () => {
     .forEach((testCase: TestCase) =>
       it('should return data for the test case ' + testCase.testCaseName, async () => {
         const result = await lapisClient.postAggregated({
-          sequenceFiltersWithGroupByFields: testCase.lapisRequest,
+          sequenceFiltersWithFields: testCase.lapisRequest,
         });
 
         const resultWithoutUndefined = result.map((aggregatedResponse: AggregatedResponse) => {

diff --git a/siloLapisTests/test/nucleotideMutations.spec.ts b/siloLapisTests/test/nucleotideMutations.spec.ts
@@ -4,42 +4,41 @@ import fs from 'fs';
 import { SequenceFilters } from './lapisClient';
 
 describe('The /nucleotideMutationProportions endpoint', () => {
-  let mutationWithLessThan10PercentProportion = 'G29741T';
-  let mutationWithMoreThan50PercentProportion = 'G28880A';
-
-  // TODO: reenable this as soon as SILO supports nuc mutation queries again
-  // it('should return mutation proportions for Switzerland', async () => {
-  //   const result = await lapisClient.postNucleotideMutations({
-  //     sequenceFiltersWithMinProportion: { country: 'Switzerland' },
-  //   });
-  //
-  //   expect(result).to.have.length(362);
-  //
-  //   const rareMutationProportion = result.find(
-  //     mutationData => mutationData.mutation === mutationWithLessThan10PercentProportion
-  //   );
-  //   expect(rareMutationProportion?.count).to.equal(8);
-  //   expect(rareMutationProportion?.proportion).to.be.approximately(0.0816326, 0.0001);
-  //
-  //   const commonMutationProportion = result.find(
-  //     mutationProportion => mutationProportion.mutation === mutationWithMoreThan50PercentProportion
-  //   );
-  //   expect(commonMutationProportion?.count).to.equal(61);
-  //   expect(commonMutationProportion?.proportion).to.be.approximately(0.6288659793814433, 0.0001);
-  // });
-  //
-  // it('should return mutation proportions for Switzerland with minProportion 0.5', async () => {
-  //   const result = await lapisClient.postNucleotideMutations({
-  //     sequenceFiltersWithMinProportion: {
-  //       country: 'Switzerland',
-  //       minProportion: 0.5,
-  //     },
-  //   });
-  //
-  //   expect(result).to.have.length(108);
-  //
-  //   const mutationsAboveThreshold = result.map(mutationData => mutationData.mutation);
-  //   expect(mutationsAboveThreshold).to.contain(mutationWithMoreThan50PercentProportion);
-  //   expect(mutationsAboveThreshold).to.not.contain(mutationWithLessThan10PercentProportion);
-  // });
+  let mutationWithLessThan10PercentProportion = 'C19220T';
+  let mutationWithMoreThan50PercentProportion = 'G28280C';
+
+  it('should return mutation proportions for Switzerland', async () => {
+    const result = await lapisClient.postNucleotideMutations({
+      sequenceFiltersWithMinProportion: { country: 'Switzerland' },
+    });
+
+    expect(result).to.have.length(362);
+
+    const rareMutationProportion = result.find(
+      mutationData => mutationData.position === mutationWithLessThan10PercentProportion
+    );
+    expect(rareMutationProportion?.count).to.equal(8);
+    expect(rareMutationProportion?.proportion).to.be.approximately(0.0816, 0.0001);
+
+    const commonMutationProportion = result.find(
+      mutationProportion => mutationProportion.position === mutationWithMoreThan50PercentProportion
+    );
+    expect(commonMutationProportion?.count).to.equal(51);
+    expect(commonMutationProportion?.proportion).to.be.approximately(0.5204, 0.0001);
+  });
+
+  it('should return mutation proportions for Switzerland with minProportion 0.5', async () => {
+    const result = await lapisClient.postNucleotideMutations({
+      sequenceFiltersWithMinProportion: {
+        country: 'Switzerland',
+        minProportion: 0.5,
+      },
+    });
+
+    expect(result).to.have.length(108);
+
+    const mutationsAboveThreshold = result.map(mutationData => mutationData.position);
+    expect(mutationsAboveThreshold).to.contain(mutationWithMoreThan50PercentProportion);
+    expect(mutationsAboveThreshold).to.not.contain(mutationWithLessThan10PercentProportion);
+  });
 });