import { describe, it, expect } from "vitest";
import { processResponse } from "../../src/utils/response-processor.js";
describe("processResponse", () => {
it("returns wrapped raw response when fullResponse is true", () => {
const data = { foo: "bar" };
const result = processResponse("ensembl_lookup", data, { fullResponse: true }) as any;
expect(result.raw_response).toBe(true);
expect(result.data).toBe(data);
expect(result.note).toContain("ONLY the JSON");
});
it("passes through error responses", () => {
const data = { error: "not found", success: false };
expect(processResponse("ensembl_lookup", data)).toBe(data);
});
describe("sequence truncation", () => {
it("truncates long string sequences", () => {
const longSeq = "A".repeat(20000);
const result = processResponse("ensembl_sequence", longSeq) as string;
expect(result).toContain("[truncated");
expect(result.length).toBeLessThan(longSeq.length);
});
it("truncates object with long seq property", () => {
const data = { id: "ENST00000288602", seq: "A".repeat(20000) };
const result = processResponse("ensembl_sequence", data) as any;
expect(result.seq).toContain("[truncated");
expect(result._original_length).toBe(20000);
});
it("leaves short sequences unchanged", () => {
const data = { id: "ENST00000288602", seq: "ATCG" };
const result = processResponse("ensembl_sequence", data) as any;
expect(result.seq).toBe("ATCG");
});
});
describe("feature overlap", () => {
it("truncates large arrays with field selection", () => {
const data = Array.from({ length: 100 }, (_, i) => ({
id: `feat_${i}`,
feature_type: "gene",
seq_region_name: "17",
start: i * 1000,
end: i * 1000 + 999,
strand: 1,
biotype: "protein_coding",
external_name: `Gene${i}`,
extra_field: "should_be_removed",
}));
const result = processResponse("ensembl_feature_overlap", data) as any;
expect(result.metadata.total_results).toBe(100);
expect(result.metadata.returned).toBe(50);
expect(result.metadata.truncated).toBe(true);
expect(result.summary).toContain("100");
// field selection applied
expect(result.data[0]).not.toHaveProperty("extra_field");
expect(result.data[0]).toHaveProperty("id");
});
it("returns data unchanged when under limit", () => {
const data = [{ id: "feat_1", feature_type: "gene" }];
expect(processResponse("ensembl_feature_overlap", data)).toBe(data);
});
});
describe("meta species", () => {
it("truncates large species list", () => {
const data = Array.from({ length: 100 }, (_, i) => ({
name: `species_${i}`,
common_name: `Species ${i}`,
assembly: "GRCh38",
taxonomy_id: 9606 + i,
display_name: `Species ${i}`,
}));
const result = processResponse("ensembl_meta", data) as any;
expect(result.metadata.total_results).toBe(100);
expect(result.metadata.returned).toBe(50);
expect(result.metadata.truncated).toBe(true);
});
});
describe("compara gene tree", () => {
it("flattens gene tree structure", () => {
const data = {
tree: {
children: [
{
taxonomy: { scientific_name: "Homo sapiens" },
gene: { external_name: "TP53" },
id: "ENSG00000141510",
sequence: { id: "ENSP00000269305" },
},
{
taxonomy: { scientific_name: "Mus musculus" },
gene: { external_name: "Trp53" },
id: "ENSMUSG00000059552",
sequence: { id: "ENSMUSP00000071902" },
},
],
},
};
const result = processResponse("ensembl_compara", data) as any;
expect(result.metadata.total_results).toBe(2);
expect(result.data).toHaveLength(2);
expect(result.data[0].species).toBe("Homo sapiens");
expect(result.data[0].gene_symbol).toBe("TP53");
});
});
describe("compara homology", () => {
it("extracts homologies from nested structure", () => {
const data = {
data: [
{
homologies: Array.from({ length: 150 }, (_, i) => ({
type: "ortholog",
target: { id: `ENSG${i}`, species: `species_${i}` },
})),
},
],
};
const result = processResponse("ensembl_compara", data) as any;
expect(result.metadata.total_results).toBe(150);
expect(result.metadata.returned).toBe(100);
expect(result.metadata.truncated).toBe(true);
});
});
describe("variation VEP", () => {
it("processes VEP consequences", () => {
const data = [
{
id: "rs699",
most_severe_consequence: "missense_variant",
transcript_consequences: [
{
gene_symbol: "AGT",
gene_id: "ENSG00000135744",
transcript_id: "ENST00000366667",
consequence_terms: ["missense_variant"],
impact: "MODERATE",
biotype: "protein_coding",
amino_acids: "M/T",
codons: "aTg/aCg",
extra_field: "removed",
},
],
extra: "removed",
},
];
const result = processResponse("ensembl_variation", data) as any;
expect(result.data).toHaveLength(1);
expect(result.data[0].id).toBe("rs699");
expect(result.data[0].most_severe_consequence).toBe("missense_variant");
expect(result.data[0].transcript_consequences[0].gene_symbol).toBe("AGT");
expect(result.data[0].transcript_consequences[0]).not.toHaveProperty("extra_field");
});
});
it("passes through unknown tool data unchanged", () => {
const data = { anything: "goes" };
expect(processResponse("unknown_tool", data)).toBe(data);
});
describe("pagination", () => {
const makeItems = (n: number) =>
Array.from({ length: n }, (_, i) => ({
id: `feat_${i}`,
feature_type: "gene",
seq_region_name: "17",
start: i * 1000,
end: i * 1000 + 999,
strand: 1,
biotype: "protein_coding",
external_name: `Gene${i}`,
}));
it("page 1 returns first N items with correct metadata", () => {
const data = makeItems(100);
const result = processResponse("ensembl_feature_overlap", data, {
page: 1,
pageSize: 25,
}) as any;
expect(result.metadata.total_results).toBe(100);
expect(result.metadata.returned).toBe(25);
expect(result.metadata.page).toBe(1);
expect(result.metadata.page_size).toBe(25);
expect(result.metadata.total_pages).toBe(4);
expect(result.metadata.has_next).toBe(true);
expect(result.data[0].id).toBe("feat_0");
expect(result.data[24].id).toBe("feat_24");
});
it("page 2 returns correct offset slice", () => {
const data = makeItems(100);
const result = processResponse("ensembl_feature_overlap", data, {
page: 2,
pageSize: 25,
}) as any;
expect(result.metadata.page).toBe(2);
expect(result.metadata.returned).toBe(25);
expect(result.data[0].id).toBe("feat_25");
expect(result.data[24].id).toBe("feat_49");
});
it("last page has has_next: false", () => {
const data = makeItems(100);
const result = processResponse("ensembl_feature_overlap", data, {
page: 4,
pageSize: 25,
}) as any;
expect(result.metadata.page).toBe(4);
expect(result.metadata.has_next).toBe(false);
expect(result.metadata.total_pages).toBe(4);
expect(result.data[0].id).toBe("feat_75");
});
it("out-of-range page returns empty data with correct metadata", () => {
const data = makeItems(100);
const result = processResponse("ensembl_feature_overlap", data, {
page: 10,
pageSize: 25,
}) as any;
expect(result.metadata.total_results).toBe(100);
expect(result.metadata.returned).toBe(0);
expect(result.metadata.total_pages).toBe(4);
expect(result.metadata.has_next).toBe(false);
expect(result.data).toEqual([]);
});
it("field filtering works with pagination", () => {
const data = Array.from({ length: 100 }, (_, i) => ({
id: `feat_${i}`,
feature_type: "gene",
seq_region_name: "17",
start: i * 1000,
end: i * 1000 + 999,
strand: 1,
biotype: "protein_coding",
external_name: `Gene${i}`,
extra_field: "should_be_removed",
}));
const result = processResponse("ensembl_feature_overlap", data, {
page: 1,
pageSize: 10,
}) as any;
expect(result.data).toHaveLength(10);
expect(result.data[0]).not.toHaveProperty("extra_field");
expect(result.data[0]).toHaveProperty("id");
});
it("no page/pageSize is backward-compatible", () => {
const data = makeItems(30);
// Under default limit of 50, returns raw data
const result = processResponse("ensembl_feature_overlap", data);
expect(result).toBe(data);
});
it("total_pages edge case: 0 items", () => {
const data: unknown[] = [];
const result = processResponse("ensembl_feature_overlap", data, {
page: 1,
pageSize: 25,
}) as any;
expect(result.metadata.total_results).toBe(0);
expect(result.metadata.total_pages).toBe(0);
expect(result.metadata.has_next).toBe(false);
expect(result.data).toEqual([]);
});
it("total_pages edge case: 1 item", () => {
const data = makeItems(1);
const result = processResponse("ensembl_feature_overlap", data, {
page: 1,
pageSize: 25,
}) as any;
expect(result.metadata.total_results).toBe(1);
expect(result.metadata.returned).toBe(1);
expect(result.metadata.total_pages).toBe(1);
expect(result.metadata.has_next).toBe(false);
});
it("total_pages edge case: exact multiple", () => {
const data = makeItems(50);
const result = processResponse("ensembl_feature_overlap", data, {
page: 1,
pageSize: 25,
}) as any;
expect(result.metadata.total_pages).toBe(2);
expect(result.metadata.has_next).toBe(true);
});
it("page_size supersedes max_results", () => {
const data = makeItems(100);
const result = processResponse("ensembl_feature_overlap", data, {
maxResults: 10,
page: 1,
pageSize: 30,
}) as any;
expect(result.metadata.returned).toBe(30);
expect(result.metadata.page_size).toBe(30);
expect(result.metadata.total_pages).toBe(4);
});
it("works with ensembl_variation", () => {
const data = Array.from({ length: 80 }, (_, i) => ({
id: `var_${i}`,
type: "variant",
}));
const result = processResponse("ensembl_variation", data, {
page: 2,
pageSize: 20,
}) as any;
expect(result.metadata.page).toBe(2);
expect(result.metadata.total_results).toBe(80);
expect(result.metadata.returned).toBe(20);
expect(result.data[0].id).toBe("var_20");
});
it("works with ensembl_meta", () => {
const data = Array.from({ length: 60 }, (_, i) => ({
name: `species_${i}`,
common_name: `Species ${i}`,
}));
const result = processResponse("ensembl_meta", data, {
page: 3,
pageSize: 20,
}) as any;
expect(result.metadata.page).toBe(3);
expect(result.metadata.total_pages).toBe(3);
expect(result.metadata.has_next).toBe(false);
});
it("works with ensembl_regulatory", () => {
const data = Array.from({ length: 75 }, (_, i) => ({
id: `reg_${i}`,
feature_type: "RegulatoryFeature",
}));
const result = processResponse("ensembl_regulatory", data, {
page: 1,
pageSize: 25,
}) as any;
expect(result.metadata.page).toBe(1);
expect(result.metadata.total_results).toBe(75);
expect(result.metadata.total_pages).toBe(3);
});
it("works with ensembl_compara homology", () => {
const data = {
data: [
{
homologies: Array.from({ length: 150 }, (_, i) => ({
type: "ortholog",
target: { id: `ENSG${i}`, species: `species_${i}` },
})),
},
],
};
const result = processResponse("ensembl_compara", data, {
page: 2,
pageSize: 50,
}) as any;
expect(result.metadata.page).toBe(2);
expect(result.metadata.total_results).toBe(150);
expect(result.metadata.returned).toBe(50);
expect(result.metadata.has_next).toBe(true);
});
it("summary message includes page info when paginated", () => {
const data = makeItems(100);
const result = processResponse("ensembl_feature_overlap", data, {
page: 2,
pageSize: 25,
}) as any;
expect(result.summary).toContain("page 2 of 4");
});
});
});
