input-normalizer.test.ts•9.77 kB
#!/usr/bin/env node
/**
* UNIT TESTS for input normalizer
* Tests format normalization for various Ensembl input types including assembly-aware features
*/
import {
normalizeAssemblyName,
normalizeChromosomeName,
normalizeGenomicRegion,
normalizeCoordinateSystem,
normalizeCdnaCoordinates,
normalizeSpeciesName,
normalizeGeneIdentifier,
normalizeHgvsNotation,
normalizeScaffoldName,
normalizeEnsemblInputs,
} from "../src/utils/input-normalizer";
// Test framework
let totalTests = 0;
let passedTests = 0;
let failedTests = 0;
function test(name: string, expectedToPass = true) {
return {
async run(testFunction: () => Promise<void>) {
totalTests++;
console.log(`\n📍 ${name}`);
try {
await testFunction();
if (expectedToPass) {
passedTests++;
console.log(`✅ PASS`);
} else {
failedTests++;
console.log(`❌ FAIL - Expected this test to fail but it passed`);
}
} catch (error: unknown) {
if (!expectedToPass) {
passedTests++;
console.log(
`✅ PASS - Expected error: ${
error instanceof Error ? error.message : String(error)
}`
);
} else {
failedTests++;
console.log(
`❌ FAIL - Unexpected error: ${
error instanceof Error ? error.message : String(error)
}`
);
}
}
},
};
}
function assertEqual(actual: any, expected: any, message?: string): void {
if (actual !== expected) {
throw new Error(
`${
message || "Assertion failed"
}: expected '${expected}' but got '${actual}'`
);
}
}
async function runTests() {
console.log("🧪 Running Input Normalizer Tests...\n");
// ========== Assembly Name Tests ==========
await test("normalizeAssemblyName - GRCh38 variants").run(async () => {
assertEqual(normalizeAssemblyName("GRCh38"), "GRCh38");
assertEqual(normalizeAssemblyName("grch38"), "GRCh38");
assertEqual(normalizeAssemblyName("hg38"), "GRCh38");
assertEqual(normalizeAssemblyName("HG38"), "GRCh38");
});
await test("normalizeAssemblyName - GRCh37 variants").run(async () => {
assertEqual(normalizeAssemblyName("GRCh37"), "GRCh37");
assertEqual(normalizeAssemblyName("grch37"), "GRCh37");
assertEqual(normalizeAssemblyName("hg19"), "GRCh37");
assertEqual(normalizeAssemblyName("HG19"), "GRCh37");
});
// ========== Chromosome Name Tests ==========
await test("normalizeChromosomeName - chr prefixes").run(async () => {
assertEqual(normalizeChromosomeName("chr17"), "17");
assertEqual(normalizeChromosomeName("chromosome17"), "17");
assertEqual(normalizeChromosomeName("CHR17"), "17");
assertEqual(normalizeChromosomeName("17"), "17");
});
await test("normalizeChromosomeName - mitochondrial variations").run(
async () => {
assertEqual(normalizeChromosomeName("MT"), "MT");
assertEqual(normalizeChromosomeName("M"), "MT");
assertEqual(normalizeChromosomeName("chrM"), "MT");
assertEqual(normalizeChromosomeName("chrMT"), "MT");
assertEqual(normalizeChromosomeName("mitochondrial"), "MT");
assertEqual(normalizeChromosomeName("mito"), "MT");
}
);
await test("normalizeChromosomeName - sex chromosomes").run(async () => {
assertEqual(normalizeChromosomeName("X"), "X");
assertEqual(normalizeChromosomeName("chrX"), "X");
assertEqual(normalizeChromosomeName("Y"), "Y");
assertEqual(normalizeChromosomeName("chrY"), "Y");
});
await test("normalizeChromosomeName - pseudoautosomal regions").run(
async () => {
assertEqual(normalizeChromosomeName("PAR1"), "PAR1");
assertEqual(normalizeChromosomeName("PAR_1"), "PAR1");
assertEqual(normalizeChromosomeName("PAR#1"), "PAR1");
assertEqual(normalizeChromosomeName("PAR2"), "PAR2");
}
);
// ========== Genomic Region Tests ==========
await test("normalizeGenomicRegion - basic formats").run(async () => {
assertEqual(
normalizeGenomicRegion("chr17:43000000-44000000"),
"17:43000000-44000000"
);
assertEqual(
normalizeGenomicRegion("chromosome17:43000000-44000000"),
"17:43000000-44000000"
);
assertEqual(
normalizeGenomicRegion("17:43000000-44000000"),
"17:43000000-44000000"
);
});
await test("normalizeGenomicRegion - with spaces").run(async () => {
assertEqual(
normalizeGenomicRegion("17 : 43000000 - 44000000"),
"17:43000000-44000000"
);
assertEqual(
normalizeGenomicRegion("chr17 : 43000000 - 44000000"),
"17:43000000-44000000"
);
});
await test("normalizeGenomicRegion - with assembly context").run(async () => {
assertEqual(
normalizeGenomicRegion("chrMT:1000-2000", "GRCh38"),
"MT:1000-2000"
);
assertEqual(
normalizeGenomicRegion("chrX:1000000-2000000", "GRCh37"),
"X:1000000-2000000"
);
});
// ========== Coordinate System Tests ==========
await test("normalizeCoordinateSystem - zero to one based").run(async () => {
const result = normalizeCoordinateSystem(99, 200, "zero-based");
assertEqual(result.start, 100);
assertEqual(result.end, 200);
});
await test("normalizeCoordinateSystem - one based unchanged").run(
async () => {
const result = normalizeCoordinateSystem(100, 200, "one-based");
assertEqual(result.start, 100);
assertEqual(result.end, 200);
}
);
// ========== cDNA Coordinates Tests ==========
await test("normalizeCdnaCoordinates - various formats").run(async () => {
assertEqual(normalizeCdnaCoordinates("100..200"), "100-200");
assertEqual(normalizeCdnaCoordinates("c.100..200"), "100-200");
assertEqual(normalizeCdnaCoordinates("100 to 200"), "100-200");
assertEqual(normalizeCdnaCoordinates("100→200"), "100-200");
});
// ========== Species Name Tests ==========
await test("normalizeSpeciesName - common mappings").run(async () => {
assertEqual(normalizeSpeciesName("human"), "homo_sapiens");
assertEqual(normalizeSpeciesName("mouse"), "mus_musculus");
assertEqual(normalizeSpeciesName("fruit fly"), "drosophila_melanogaster");
assertEqual(normalizeSpeciesName("worm"), "caenorhabditis_elegans");
});
await test("normalizeSpeciesName - assembly context defaults").run(
async () => {
assertEqual(normalizeSpeciesName("", "GRCh38"), "homo_sapiens");
assertEqual(normalizeSpeciesName("", "hg19"), "homo_sapiens");
}
);
// ========== Gene Identifier Tests ==========
await test("normalizeGeneIdentifier - preserve case sensitivity").run(
async () => {
assertEqual(normalizeGeneIdentifier("TP53"), "TP53");
assertEqual(normalizeGeneIdentifier("BRCA1"), "BRCA1");
assertEqual(normalizeGeneIdentifier(" EGFR "), "EGFR");
}
);
await test("normalizeGeneIdentifier - variant IDs unchanged").run(
async () => {
assertEqual(normalizeGeneIdentifier("rs699"), "rs699");
assertEqual(normalizeGeneIdentifier("COSM476"), "COSM476");
assertEqual(
normalizeGeneIdentifier("ENSP00000288602"),
"ENSP00000288602"
);
}
);
// ========== HGVS Notation Tests ==========
await test("normalizeHgvsNotation - basic formatting").run(async () => {
assertEqual(
normalizeHgvsNotation("NM_000546.6 : c.215C>G"),
"NM_000546.6:c.215C>G"
);
assertEqual(
normalizeHgvsNotation("NM_000546.6 > c.215C>G"),
"NM_000546.6>c.215C>G"
);
});
await test("normalizeHgvsNotation - assembly-specific references").run(
async () => {
assertEqual(
normalizeHgvsNotation("NM_000546:c.215C>G", "GRCh38"),
"NM_000546.6:c.215C>G"
);
assertEqual(
normalizeHgvsNotation("NM_000546.6:c.215C>G", "GRCh37"),
"NM_000546.5:c.215C>G"
);
}
);
// ========== Scaffold Name Tests ==========
await test("normalizeScaffoldName - patch naming").run(async () => {
assertEqual(
normalizeScaffoldName("CHR_HSCHR1_1_CTG1", "GRCh38"),
"chr1_patch_1_CTG1"
);
assertEqual(
normalizeScaffoldName("ALT_REF_LOCI_1_scaffold", "GRCh38"),
"ALT_REF_LOCI_1:scaffold"
);
});
// ========== Integration Tests ==========
await test("normalizeEnsemblInputs - full integration").run(async () => {
const input = {
assembly: "hg38",
species: "human",
region: "chr17:43,000,000-44,000,000",
gene_id: " TP53 ",
hgvs: "NM_000546 : c.215C>G",
};
const result = normalizeEnsemblInputs(input);
assertEqual(result.assembly, "GRCh38");
assertEqual(result.species, "homo_sapiens");
assertEqual(result.region, "17:43000000-44000000");
assertEqual(result.gene_id, "TP53");
assertEqual(result.hgvs, "NM_000546.6:c.215C>G");
});
await test("normalizeEnsemblInputs - coordinate system conversion").run(
async () => {
const input = {
start: 99,
end: 200,
coordinate_system: "zero-based",
};
const result = normalizeEnsemblInputs(input);
assertEqual(result.start, 100);
assertEqual(result.end, 200);
assertEqual(result.coordinate_system, undefined); // Should be removed
}
);
// ========== Summary ==========
console.log(`\n📊 Test Results:`);
console.log(`✅ Passed: ${passedTests}`);
console.log(`❌ Failed: ${failedTests}`);
console.log(`📋 Total: ${totalTests}`);
if (failedTests === 0) {
console.log(`\n🎉 All tests passed!`);
process.exit(0);
} else {
console.log(`\n💥 ${failedTests} test(s) failed`);
process.exit(1);
}
}
runTests().catch(console.error);