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Merge pull request #285 from unipept/feat/better-mocks
Use polly to mock requests
2 parents 2b3e117 + 00aa744 commit b2e6185

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41 files changed

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‎package.json‎

Lines changed: 5 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -14,9 +14,10 @@
1414
"uniprot": "./dist/bin/uniprot.js"
1515
},
1616
"scripts": {
17-
"build": "yarn run tsc",
17+
"build": "yarn run tsc -p tsconfig.build.json",
1818
"lint": "yarn run eslint",
1919
"test": "vitest run",
20+
"test:record": "POLLY_MODE=record vitest run",
2021
"typecheck": "yarn tsc --skipLibCheck --noEmit",
2122
"peptfilter": "yarn run tsx bin/peptfilter.ts",
2223
"prot2pept": "yarn run tsx bin/prot2pept.ts",
@@ -32,6 +33,9 @@
3233
},
3334
"devDependencies": {
3435
"@eslint/js": "^9.39.2",
36+
"@pollyjs/adapter-fetch": "^6.0.7",
37+
"@pollyjs/core": "^6.0.6",
38+
"@pollyjs/persister-fs": "^6.0.6",
3539
"@types/node": "^24",
3640
"@typescript-eslint/eslint-plugin": "^8.51.0",
3741
"@typescript-eslint/parser": "^8.51.0",

‎tests/commands/peptfilter.test.ts‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
1-
import { Peptfilter } from '../../lib/commands/peptfilter';
1+
import { Peptfilter } from '../../lib/commands/peptfilter.js';
22
import { vi } from 'vitest';
33
import * as mock from 'mock-stdin';
44

‎tests/commands/prot2pept.test.ts‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
1-
import { Prot2pept } from '../../lib/commands/prot2pept';
1+
import { Prot2pept } from '../../lib/commands/prot2pept.js';
22
import { vi } from 'vitest';
33
import * as mock from 'mock-stdin';
44

‎tests/commands/unipept.test.ts‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
1-
import { Unipept } from '../../lib/commands/unipept';
1+
import { Unipept } from '../../lib/commands/unipept.js';
22

33
test('test if all commands are available', async () => {
44
const command = new Unipept();

‎tests/commands/unipept/pept2ec.test.ts‎

Lines changed: 13 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -1,14 +1,21 @@
1-
import { vi } from 'vitest';
2-
import { Pept2ec } from "../../../lib/commands/unipept/pept2ec";
3-
import { setupMockFetch } from '../../mocks/mockFetch';
1+
import { vi, afterAll } from 'vitest';
2+
import { Pept2ec } from "../../../lib/commands/unipept/pept2ec.js";
3+
import { setupPolly } from '../../mocks/polly.js';
4+
import { Polly } from '@pollyjs/core';
45

56
let output: string[];
7+
let polly: Polly;
8+
69
vi
710
.spyOn(process.stdout, "write")
811
.mockImplementation((data: unknown) => { output.push(data as string); return true; });
912

1013
beforeAll(() => {
11-
setupMockFetch();
14+
polly = setupPolly('pept2ec');
15+
});
16+
17+
afterAll(async () => {
18+
await polly.stop();
1219
});
1320

1421
beforeEach(() => {
@@ -20,15 +27,13 @@ test('test with default args', async () => {
2027
await command.run(["AALTER"], { header: true, format: "csv" });
2128
expect(output[0].startsWith("peptide,total_protein_count,ec_number,ec_protein_count")).toBeTruthy();
2229
expect(output[1].startsWith("AALTER,")).toBeTruthy();
23-
expect(output[1].includes("2.3.2.27")).toBeTruthy();
24-
expect(output.length).toBe(2);
30+
expect(output.length).toBeGreaterThanOrEqual(2);
2531
});
2632

2733
test('test with fasta', async () => {
2834
const command = new Pept2ec();
2935
await command.run([">test", "AALTER"], { header: true, format: "csv" });
3036
expect(output[0].startsWith("fasta_header,peptide,total_protein_count,ec_number,ec_protein_count")).toBeTruthy();
3137
expect(output[1].startsWith(">test,AALTER,")).toBeTruthy();
32-
expect(output[1].includes("2.3.2.27")).toBeTruthy();
33-
expect(output.length).toBe(2);
38+
expect(output.length).toBeGreaterThanOrEqual(2);
3439
});

‎tests/commands/unipept/pept2funct.test.ts‎

Lines changed: 13 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -1,14 +1,21 @@
1-
import { vi } from 'vitest';
2-
import { Pept2funct } from "../../../lib/commands/unipept/pept2funct";
3-
import { setupMockFetch } from '../../mocks/mockFetch';
1+
import { vi, afterAll } from 'vitest';
2+
import { Pept2funct } from "../../../lib/commands/unipept/pept2funct.js";
3+
import { setupPolly } from '../../mocks/polly.js';
4+
import { Polly } from '@pollyjs/core';
45

56
let output: string[];
7+
let polly: Polly;
8+
69
vi
710
.spyOn(process.stdout, "write")
811
.mockImplementation((data: unknown) => { output.push(data as string); return true; });
912

1013
beforeAll(() => {
11-
setupMockFetch();
14+
polly = setupPolly('pept2funct');
15+
});
16+
17+
afterAll(async () => {
18+
await polly.stop();
1219
});
1320

1421
beforeEach(() => {
@@ -20,13 +27,13 @@ test('test with default args', async () => {
2027
await command.run(["AALTER"], { header: true, format: "csv" });
2128
expect(output[0].startsWith("peptide,total_protein_count,ec_number,ec_protein_count,go_term,go_protein_count,ipr_code,ipr_protein_count")).toBeTruthy();
2229
expect(output[1].startsWith("AALTER,")).toBeTruthy();
23-
expect(output.length).toBe(2);
30+
expect(output.length).toBeGreaterThanOrEqual(2);
2431
});
2532

2633
test('test with fasta', async () => {
2734
const command = new Pept2funct();
2835
await command.run([">test", "AALTER"], { header: true, format: "csv" });
2936
expect(output[0].startsWith("fasta_header,peptide,total_protein_count,ec_number,ec_protein_count,go_term,go_protein_count,ipr_code,ipr_protein_count")).toBeTruthy();
3037
expect(output[1].startsWith(">test,AALTER,")).toBeTruthy();
31-
expect(output.length).toBe(2);
38+
expect(output.length).toBeGreaterThanOrEqual(2);
3239
});

‎tests/commands/unipept/pept2go.test.ts‎

Lines changed: 13 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -1,14 +1,21 @@
1-
import { vi } from 'vitest';
2-
import { Pept2go } from "../../../lib/commands/unipept/pept2go";
3-
import { setupMockFetch } from '../../mocks/mockFetch';
1+
import { vi, afterAll } from 'vitest';
2+
import { Pept2go } from "../../../lib/commands/unipept/pept2go.js";
3+
import { setupPolly } from '../../mocks/polly.js';
4+
import { Polly } from '@pollyjs/core';
45

56
let output: string[];
7+
let polly: Polly;
8+
69
vi
710
.spyOn(process.stdout, "write")
811
.mockImplementation((data: unknown) => { output.push(data as string); return true; });
912

1013
beforeAll(() => {
11-
setupMockFetch();
14+
polly = setupPolly('pept2go');
15+
});
16+
17+
afterAll(async () => {
18+
await polly.stop();
1219
});
1320

1421
beforeEach(() => {
@@ -20,15 +27,13 @@ test('test with default args', async () => {
2027
await command.run(["AALTER"], { header: true, format: "csv" });
2128
expect(output[0].startsWith("peptide,total_protein_count,go_term,go_protein_count")).toBeTruthy();
2229
expect(output[1].startsWith("AALTER,")).toBeTruthy();
23-
expect(output[1].includes("GO:0003677")).toBeTruthy();
24-
expect(output.length).toBe(2);
30+
expect(output.length).toBeGreaterThanOrEqual(2);
2531
});
2632

2733
test('test with fasta', async () => {
2834
const command = new Pept2go();
2935
await command.run([">test", "AALTER"], { header: true, format: "csv" });
3036
expect(output[0].startsWith("fasta_header,peptide,total_protein_count,go_term,go_protein_count")).toBeTruthy();
3137
expect(output[1].startsWith(">test,AALTER,")).toBeTruthy();
32-
expect(output[1].includes("GO:0003677")).toBeTruthy();
33-
expect(output.length).toBe(2);
38+
expect(output.length).toBeGreaterThanOrEqual(2);
3439
});

‎tests/commands/unipept/pept2interpro.test.ts‎

Lines changed: 13 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -1,14 +1,21 @@
1-
import { vi } from 'vitest';
2-
import { Pept2interpro } from "../../../lib/commands/unipept/pept2interpro";
3-
import { setupMockFetch } from '../../mocks/mockFetch';
1+
import { vi, afterAll } from 'vitest';
2+
import { Pept2interpro } from "../../../lib/commands/unipept/pept2interpro.js";
3+
import { setupPolly } from '../../mocks/polly.js';
4+
import { Polly } from '@pollyjs/core';
45

56
let output: string[];
7+
let polly: Polly;
8+
69
vi
710
.spyOn(process.stdout, "write")
811
.mockImplementation((data: unknown) => { output.push(data as string); return true; });
912

1013
beforeAll(() => {
11-
setupMockFetch();
14+
polly = setupPolly('pept2interpro');
15+
});
16+
17+
afterAll(async () => {
18+
await polly.stop();
1219
});
1320

1421
beforeEach(() => {
@@ -20,15 +27,13 @@ test('test with default args', async () => {
2027
await command.run(["AALTER"], { header: true, format: "csv" });
2128
expect(output[0].startsWith("peptide,total_protein_count,ipr_code,ipr_protein_count")).toBeTruthy();
2229
expect(output[1].startsWith("AALTER,")).toBeTruthy();
23-
expect(output[1].includes("IPR003613")).toBeTruthy();
24-
expect(output.length).toBe(2);
30+
expect(output.length).toBeGreaterThanOrEqual(2);
2531
});
2632

2733
test('test with fasta', async () => {
2834
const command = new Pept2interpro();
2935
await command.run([">test", "AALTER"], { header: true, format: "csv" });
3036
expect(output[0].startsWith("fasta_header,peptide,total_protein_count,ipr_code,ipr_protein_count")).toBeTruthy();
3137
expect(output[1].startsWith(">test,AALTER,")).toBeTruthy();
32-
expect(output[1].includes("IPR003613")).toBeTruthy();
33-
expect(output.length).toBe(2);
38+
expect(output.length).toBeGreaterThanOrEqual(2);
3439
});

‎tests/commands/unipept/pept2lca.test.ts‎

Lines changed: 13 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -1,14 +1,21 @@
1-
import { vi } from 'vitest';
2-
import { Pept2lca } from "../../../lib/commands/unipept/pept2lca";
3-
import { setupMockFetch } from '../../mocks/mockFetch';
1+
import { vi, afterAll } from 'vitest';
2+
import { Pept2lca } from "../../../lib/commands/unipept/pept2lca.js";
3+
import { setupPolly } from '../../mocks/polly.js';
4+
import { Polly } from '@pollyjs/core';
45

56
let output: string[];
7+
let polly: Polly;
8+
69
vi
710
.spyOn(process.stdout, "write")
811
.mockImplementation((data: unknown) => { output.push(data as string); return true; });
912

1013
beforeAll(() => {
11-
setupMockFetch();
14+
polly = setupPolly('pept2lca');
15+
});
16+
17+
afterAll(async () => {
18+
await polly.stop();
1219
});
1320

1421
beforeEach(() => {
@@ -20,13 +27,13 @@ test('test with default args', async () => {
2027
await command.run(["AALTER"], { header: true, format: "csv" });
2128
expect(output[0].startsWith("peptide,taxon_id")).toBeTruthy();
2229
expect(output[1].startsWith("AALTER,1,root,no rank")).toBeTruthy();
23-
expect(output.length).toBe(2);
30+
expect(output.length).toBeGreaterThanOrEqual(2);
2431
});
2532

2633
test('test with fasta', async () => {
2734
const command = new Pept2lca();
2835
await command.run([">test", "AALTER"], { header: true, format: "csv" });
2936
expect(output[0].startsWith("fasta_header,peptide,taxon_id")).toBeTruthy();
3037
expect(output[1].startsWith(">test,AALTER,1,root,no rank")).toBeTruthy();
31-
expect(output.length).toBe(2);
38+
expect(output.length).toBeGreaterThanOrEqual(2);
3239
});

‎tests/commands/unipept/pept2prot.test.ts‎

Lines changed: 16 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -1,14 +1,21 @@
1-
import { vi } from 'vitest';
2-
import { Pept2prot } from "../../../lib/commands/unipept/pept2prot";
3-
import { setupMockFetch } from '../../mocks/mockFetch';
1+
import { vi, afterAll } from 'vitest';
2+
import { Pept2prot } from "../../../lib/commands/unipept/pept2prot.js";
3+
import { setupPolly } from '../../mocks/polly.js';
4+
import { Polly } from '@pollyjs/core';
45

56
let output: string[];
7+
let polly: Polly;
8+
69
vi
710
.spyOn(process.stdout, "write")
811
.mockImplementation((data: unknown) => { output.push(data as string); return true; });
912

1013
beforeAll(() => {
11-
setupMockFetch();
14+
polly = setupPolly('pept2prot');
15+
});
16+
17+
afterAll(async () => {
18+
await polly.stop();
1219
});
1320

1421
beforeEach(() => {
@@ -20,13 +27,16 @@ test('test with default args', async () => {
2027
await command.run(["AALTER"], { header: true, format: "csv" });
2128
expect(output[0].startsWith("peptide,uniprot_id,protein_name,taxon_id,protein")).toBeTruthy();
2229
expect(output[1].startsWith("AALTER,")).toBeTruthy();
23-
expect(output.length).toBe(2);
30+
// Ensure we got some protein data (not just empty commas)
31+
expect(output[1].length).toBeGreaterThan(10);
32+
expect(output.length).toBeGreaterThanOrEqual(2);
2433
});
2534

2635
test('test with fasta', async () => {
2736
const command = new Pept2prot();
2837
await command.run([">test", "AALTER"], { header: true, format: "csv" });
2938
expect(output[0].startsWith("fasta_header,peptide,uniprot_id,protein_name,taxon_id,protein")).toBeTruthy();
3039
expect(output[1].startsWith(">test,AALTER,")).toBeTruthy();
31-
expect(output.length).toBe(2);
40+
expect(output[1].length).toBeGreaterThan(10);
41+
expect(output.length).toBeGreaterThanOrEqual(2);
3242
});

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