--- before
+++ after
@@ -1,1428 +0,0 @@
-import { createHash } from "node:crypto";
-import {
-  chmod,
-  mkdir,
-  mkdtemp,
-  readFile,
-  readdir,
-  realpath,
-  rename,
-  rm,
-  symlink,
-  writeFile,
-} from "node:fs/promises";
-import os from "node:os";
-import path from "node:path";
-import { pathToFileURL } from "node:url";
-import { gzipSync } from "node:zlib";
-
-import { afterEach, describe, expect, it, vi } from "vitest";
-
-import {
-  PublicExampleAcquisitionError,
-  SequencePublicExampleAcquisitionStore,
-  type SequencePublicExampleId,
-} from "./public-example-acquisition";
-import type { RootsRequestExtra } from "./chat-file-resource";
-import { calculatePDistance } from "./msa/guide-tree";
-import { parseMsa } from "./msa/parser";
-import { buildGuideTree } from "./msa/phylogenetic-tree";
-import { buildFastqExport } from "./sequence/exports";
-import { parseSequenceDocumentResult } from "./sequence/parser";
-
-const workspaces: string[] = [];
-
-const NCBI_LAMBDA_CI_GENOMIC_FORWARD =
-  "TCAGCCAAACGTCTCTTCAGGCCACTGACTAGCGATAACTTTCCCCACAACGGAACAACTCTCATTGCATGGGATCATTGGGTACTGTGGGTTTAGTGGTTGTAAAAACACCTGACCGCTATCCCTGATCAGTTTCTTGAAGGTAAACTCATCACCCCCAAGTCTGGCTATGCAGAAATCACCTGGCTCAACAGCCTGCTCAGGGTCAACGAGAATTAACATTCCGTCAGGAAAGCTTGGCTTGGAGCCTGTTGGTGCGGTCATGGAATTACCTTCAACCTCAAGCCAGAATGCAGAATCACTGGCTTTTTTGGTTGTGCTTACCCATCTCTCCGCATCACCTTTGGTAAAGGTTCTAAGCTCAGGTGAGAACATCCCTGCCTGAACATGAGAAAAAACAGGGTACTCATACTCACTTCTAAGTGACGGCTGCATACTAACCGCTTCATACATCTCGTAGATTTCTCTGGCGATTGAAGGGCTAAATTCTTCAACGCTAACTTTGAGAATTTTTGCAAGCAATGCGGCGTTATAAGCATTTAATGCATTGATGCCATTAAATAAAGCACCAACGCCTGACTGCCCCATCCCCATCTTGTCTGCGACAGATTCCTGGGATAAGCCAAGTTCATTTTTCTTTTTTTCATAAATTGCTTTAAGGCGACGTGCGTCCTCAAGCTGCTCTTGTGTTAATGGTTTCTTTTTTGTGCTCAT";
-const NCBI_LAMBDA_CI_PROTEIN =
-  "MSTKKKPLTQEQLEDARRLKAIYEKKKNELGLSQESVADKMGMGQSGVGALFNGINALNAYNAALLAKILKVSVEEFSPSIAREIYEMYEAVSMQPSLRSEYEYPVFSHVQAGMFSPELRTFTKGDAERWVSTTKKASDSAFWLEVEGNSMTAPTGSKPSFPDGMLILVDPEQAVEPGDFCIARLGGDEFTFKKLIRDSGQVFLQPLNPQYPMIPCNESCSVVGKVIASQWPEETFG";
-
-afterEach(async () => {
-  await Promise.all(
-    workspaces.splice(0).map((workspace) =>
-      rm(workspace, { force: true, recursive: true }),
-    ),
-  );
-});
-
-async function makeWorkspace(prefix = "sequence-public-example-") {
-  const workspace = await realpath(
-    await mkdtemp(path.join(os.tmpdir(), prefix)),
-  );
-  workspaces.push(workspace);
-  return workspace;
-}
-
-function rootsExtra(
-  roots: string[],
-  signal?: AbortSignal,
-): RootsRequestExtra {
-  return {
-    sendRequest: async () => ({
-      roots: roots.map((root) => ({ uri: pathToFileURL(root).href })),
-    }),
-    signal,
-  };
-}
-
-function createNcbiGenBank({
-  ciGenomicForward = NCBI_LAMBDA_CI_GENOMIC_FORWARD,
-  ciTranslation = NCBI_LAMBDA_CI_PROTEIN,
-  includeCi = true,
-  includeOperators = true,
-  length = 48_502,
-}: {
-  ciGenomicForward?: string;
-  ciTranslation?: string;
-  includeCi?: boolean;
-  includeOperators?: boolean;
-  length?: number;
-} = {}): string {
-  let sequence = "acgt".repeat(Math.ceil(length / 4)).slice(0, length);
-  if (length >= 37_940) {
-    sequence = `${sequence.slice(0, 37_226)}${ciGenomicForward.toLowerCase()}${sequence.slice(37_940)}`;
-  }
-  const features = [
-    `     source          1..${length}\n                     /organism="Escherichia phage Lambda"`,
-    ...(includeCi
-      ? [
-          `     gene            complement(37227..37940)\n                     /gene="cI"\n                     /locus_tag="lambdap88"`,
-          `     CDS             complement(37227..37940)\n                     /gene="cI"\n                     /locus_tag="lambdap88"\n                     /codon_start=1\n                     /transl_table=11\n                     /product="LexA family transcriptional regulator"\n                     /protein_id="NP_040628.1"\n                     /translation="${ciTranslation}"`,
-        ]
-      : []),
-    ...(includeOperators
-      ? [
-          `     regulatory      37951..37967\n                     /regulatory_class="other"\n                     /note="operator-r3"`,
-          `     regulatory      37974..37990\n                     /regulatory_class="other"\n                     /note="operator-r2"`,
-          `     regulatory      37998..38014\n                     /regulatory_class="other"\n                     /note="operator-r1"`,
-        ]
-      : []),
-  ].join("\n");
-  const origin = Array.from(
-    { length: Math.ceil(sequence.length / 60) },
-    (_, lineIndex) => {
-      const start = lineIndex * 60;
-      const residues = sequence
-        .slice(start, start + 60)
-        .match(/.{1,10}/gu)
-        ?.join(" ");
-      return `${String(start + 1).padStart(9)} ${residues}`;
-    },
-  ).join("\n");
-  return `LOCUS       NC_001416          ${length} bp    DNA     linear   PHG 01-JAN-2023
-DEFINITION  Enterobacteria phage lambda, complete genome.
-ACCESSION   NC_001416
-VERSION     NC_001416.1
-FEATURES             Location/Qualifiers
-${features}
-ORIGIN
-${origin}
-//
-`;
-}
-
-const NCBI_GENBANK = createNcbiGenBank();
-
-const RFAM_STOCKHOLM = `# STOCKHOLM 1.0
-#=GF ID snoZ107_R87
-#=GF AC RF00360
-#=GF BM cmbuild -F CM SEED
-#=GF SQ 9
-AJ298135.1/1-12 AC-GUACUGAUG
-AY013245.2/1-12 ACGGUACUGA-G
-AY013245.3/1-12 AC-GUACUGAUG
-AJ489952.1/1-12 ACGGUACUGA-G
-AJ307928.1/1-12 AC-GUACUGAUG
-AJ307662.1/1-12 ACGGUACUGA-G
-AC135465.1/1-12 AC-GUACUGAUG
-AJ489954.1/1-12 ACGGUACUGA-G
-AF318011.1/1-12 AC-GUACUGAUG
-#=GC SS_cons     <<<<....>>>>
-//
-`;
-
-const RFAM_DECOY_STOCKHOLM = `# STOCKHOLM 1.0
-#=GF ID decoy
-#=GF AC RF99999
-#=GF BM cmbuild -F CM SEED
-#=GF SQ 2
-DECOY.1/1-4 AC-G
-DECOY.2/1-4 ACG-
-//
-`;
-
-const UNIPROT_RAS_FASTA = {
-  P01111: `>sp|P01111|RASN_HUMAN GTPase NRas OS=Homo sapiens OX=9606 GN=NRAS PE=1 SV=1
-MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAG
-QEEYSAMRDQYMRTGEGFLCVFAINNSKSFADINLYREQIKRVKDSDDVPMVLVGNKCDL
-PTRTVDTKQAHELAKSYGIPFIETSAKTRQGVEDAFYTLVREIRQYRMKKLNSSDDGTQG
-CMGLPCVVM
-`,
-  P01112: `>sp|P01112|RASH_HUMAN GTPase HRas OS=Homo sapiens OX=9606 GN=HRAS PE=1 SV=1
-MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAG
-QEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHQYREQIKRVKDSDDVPMVLVGNKCDL
-AARTVESRQAQDLARSYGIPYIETSAKTRQGVEDAFYTLVREIRQHKLRKLNPPDESGPG
-CMSCKCVLS
-`,
-  P01116: `>sp|P01116|RASK_HUMAN GTPase KRas OS=Homo sapiens OX=9606 GN=KRAS PE=1 SV=1
-MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAG
-QEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKCDL
-PSRTVDTKQAQDLARSYGIPFIETSAKTRQRVEDAFYTLVREIRQYRLKKISKEEKTPGC
-VKIKKCIIM
-`,
-} as const;
-
-function createRfamSeedArchive(
-  rfamStockholm = RFAM_STOCKHOLM,
-): Buffer {
-  return gzipSync(
-    `${RFAM_DECOY_STOCKHOLM}${rfamStockholm}${RFAM_DECOY_STOCKHOLM}`,
-  );
-}
-
-function createFastq(recordCount = 501): string {
-  return Array.from({ length: recordCount }, (_, index) => {
-    const id = index + 1;
-    return `@DRR037765.${id}\nACGTACGT\n+\nIIIIIIII`;
-  }).join("\n") + "\n";
-}
-
-function createWrappedFastq(recordCount = 501): string {
-  return (
-    Array.from({ length: recordCount }, (_, index) => {
-      const id = index + 1;
-      return `@DRR037765.${id}\nACGT\nACGT\n+\nIIII\nIIII`;
-    }).join("\n") + "\n"
-  );
-}
-
-function createTestEnaIntegrityPins(enaFastq: string) {
-  const compressed = gzipSync(enaFastq);
-  const parsedSource = parseSequenceDocumentResult({
-    contents: enaFastq,
-    fileName: "DRR037765.fastq",
-  });
-  if (
-    parsedSource.status !== "success" ||
-    parsedSource.document.format !== "fastq" ||
-    parsedSource.document.fastqSummary == null ||
-    parsedSource.document.records.length < 500
-  ) {
-    return {
-      ena: {
-        artifactByteLength: 0,
-        artifactSha256: "0".repeat(64),
-        compressedByteLength: compressed.byteLength,
-        compressedMd5: createHash("md5").update(compressed).digest("hex"),
-        gcFraction: 0,
-        q30Fraction: 0,
-        readLengthMax: 0,
-        readLengthMin: 0,
-        sourceRecords: 0,
-        totalBases: 0,
-      },
-    };
-  }
-  const subsetText = `${parsedSource.document.records
-    .slice(0, 500)
-    .map((record) => buildFastqExport(record))
-    .join("\n")}\n`;
-  const parsedSubset = parseSequenceDocumentResult({
-    contents: subsetText,
-    fileName: "DRR037765-first-500.fastq",
-  });
-  if (
-    parsedSubset.status !== "success" ||
-    parsedSubset.document.fastqSummary == null
-  ) {
-    throw new Error("The deterministic test FASTQ subset did not parse.");
-  }
-  const artifact = Buffer.from(subsetText, "utf8");
-  const summary = parsedSubset.document.fastqSummary;
-  return {
-    ena: {
-      artifactByteLength: artifact.byteLength,
-      artifactSha256: createHash("sha256").update(artifact).digest("hex"),
-      compressedByteLength: compressed.byteLength,
-      compressedMd5: createHash("md5").update(compressed).digest("hex"),
-      gcFraction: summary.gcFraction,
-      q30Fraction: summary.q30Fraction,
-      readLengthMax: summary.readLengthMax,
-      readLengthMin: summary.readLengthMin,
-      sourceRecords: parsedSource.document.fastqSummary.readCount,
-      totalBases: summary.totalBases,
-    },
-  };
-}
-
-function mockOfficialFetch({
-  enaFastq = createFastq(),
-  enaMd5,
-  ncbi = NCBI_GENBANK,
-  rfamArchive,
-  rfamStockholm = RFAM_STOCKHOLM,
-  uniprot = {},
-}: {
-  enaFastq?: string;
-  enaMd5?: string;
-  ncbi?: string;
-  rfamArchive?: Buffer;
-  rfamStockholm?: string;
-  uniprot?: Partial<Record<keyof typeof UNIPROT_RAS_FASTA, string>>;
-} = {}) {
-  const compressed = gzipSync(enaFastq);
-  const selectedRfamArchive =
-    rfamArchive ?? createRfamSeedArchive(rfamStockholm);
-  const expectedMd5 =
-    enaMd5 ?? createHash("md5").update(compressed).digest("hex");
-  const fetchImpl = vi.fn(async (input: string | URL | Request) => {
-    const url = new URL(input instanceof Request ? input.url : input.toString());
-    if (url.hostname === "eutils.ncbi.nlm.nih.gov") {
-      return textResponse(ncbi);
-    }
-    if (url.hostname === "rest.uniprot.org") {
-      const accession = /^\/uniprotkb\/(P01111|P01112|P01116)\.fasta$/u.exec(
-        url.pathname,
-      )?.[1] as keyof typeof UNIPROT_RAS_FASTA | undefined;
-      if (accession == null) throw new Error(`Unexpected URL ${url.href}`);
-      return textResponse(uniprot[accession] ?? UNIPROT_RAS_FASTA[accession], {
-        "content-type": "text/plain;format=fasta",
-      });
-    }
-    if (
-      url.hostname === "ftp.ebi.ac.uk" &&
-      url.pathname === "/pub/databases/Rfam/15.1/Rfam.seed.gz"
-    ) {
-      return new Response(Uint8Array.from(selectedRfamArchive), {
-        headers: { "content-type": "application/x-gzip" },
-        status: 200,
-      });
-    }
-    if (url.hostname === "www.ebi.ac.uk") {
-      return textResponse(
-        `run_accession\tfastq_ftp\tfastq_md5\tfastq_bytes\nDRR037765\tftp.sra.ebi.ac.uk/vol1/fastq/DRR037/DRR037765/DRR037765.fastq.gz\t${expectedMd5}\t${compressed.byteLength}\n`,
-      );
-    }
-    if (url.hostname === "ftp.sra.ebi.ac.uk") {
-      return new Response(compressed, {
-        headers: { "content-type": "application/gzip" },
-        status: 200,
-      });
-    }
-    throw new Error(`Unexpected URL ${url.href}`);
-  });
-  return Object.assign(fetchImpl, {
-    integrityPins: createTestEnaIntegrityPins(enaFastq),
-  });
-}
-
-function textResponse(
-  body: string,
-  headers: Record<string, string> = { "content-type": "text/plain" },
-) {
-  return new Response(body, { headers, status: 200 });
-}
-
-async function acquire(
-  exampleId: SequencePublicExampleId,
-  fetchImpl = mockOfficialFetch(),
-) {
-  const workspace = await makeWorkspace();
-  const store = new SequencePublicExampleAcquisitionStore({
-    fetchImpl,
-    integrityPins: fetchImpl.integrityPins,
-    now: () => new Date("2026-07-01T12:00:00.000Z"),
-  });
-  const result = await store.acquire({ exampleId }, rootsExtra([workspace]));
-  return { result, workspace };
-}
-
-async function expectNoPublishedOrStagedOutput(workspace: string) {
-  await expect(
-    readdir(path.join(workspace, "codex-viewer-examples")),
-  ).resolves.toEqual([]);
-}
-
-describe("authoritative public example acquisition", () => {
-  it.each([
-    ["ncbi-nc-001416-1", "NCBI Nuccore", "NC_001416.1.gb"],
-    ["rfam-rf00360-15-1", "Rfam", "RF00360-rfam-15.1.sto"],
-    ["ena-drr037765-first-500", "ENA", "DRR037765-first-500.fastq"],
-    [
-      "uniprot-human-ras-sv1",
-      "UniProtKB",
-      "human-RAS-UniProt-SV1.aln-fasta",
-    ],
-  ] as const)(
-    "acquires, validates, hashes, and provenance-publishes %s",
-    async (exampleId, database, fileName) => {
-      const { result, workspace } = await acquire(exampleId);
-
-      expect(result.fileName).toBe(fileName);
-      expect(result.absolutePath).toBe(
-        path.join(workspace, "codex-viewer-examples", fileName),
-      );
-      expect(result.provenance).toEqual(
-        expect.objectContaining({
-          artifactByteLength: expect.any(Number),
-          artifactRelativePath: `codex-viewer-examples/${fileName}`,
-          artifactSha256: expect.stringMatching(/^[a-f0-9]{64}$/u),
-          database,
-          exampleId,
-          provenanceRelativePath: `codex-viewer-examples/${fileName}.provenance.json`,
-        }),
-      );
-      const artifact = await readFile(result.absolutePath);
-      expect(createHash("sha256").update(artifact).digest("hex")).toBe(
-        result.provenance.artifactSha256,
-      );
-      const receipt = JSON.parse(
-        await readFile(`${result.absolutePath}.provenance.json`, "utf8"),
-      );
-      expect(receipt).toEqual(
-        expect.objectContaining({
-          acquisition: expect.objectContaining({
-            route: "official-database-endpoint",
-            sources: expect.any(Array),
-          }),
-          artifact: expect.objectContaining({
-            relativePath: result.provenance.artifactRelativePath,
-            sha256: result.provenance.artifactSha256,
-          }),
-          database,
-          exampleId,
-          retrievedAt: "2026-07-01T12:00:00.000Z",
-          schemaVersion: 1,
-          validatorVersion: 1,
-        }),
-      );
-      const entries = await readdir(path.dirname(result.absolutePath));
-      expect(entries.every((entry) => !entry.startsWith(".sequence-viewer-acquire-"))).toBe(true);
-    },
-  );
-
-  it.each([
-    "ncbi-nc-001416-1",
-    "rfam-rf00360-15-1",
-    "ena-drr037765-first-500",
-    "uniprot-human-ras-sv1",
-  ] as const)(
-    "rejects spoofed foreign-task metadata for %s before fetching or writing",
-    async (exampleId) => {
-      const activeWorkspace = await makeWorkspace("sequence-active-task-");
-      const foreignWorkspace = await makeWorkspace("sequence-foreign-task-");
-      const untrustedSessionDirectory = await makeWorkspace(
-        "sequence-untrusted-sessions-",
-      );
-      const activeThreadId = "019ef63e-4f6d-7573-b174-33fbf80cc79f";
-      const foreignThreadId = "019ef63e-4f6d-7573-b174-33fbf80cc790";
-      const activeSessionPath = path.join(
-        untrustedSessionDirectory,
-        `rollout-active-${activeThreadId}.jsonl`,
-      );
-      const foreignSessionPath = path.join(
-        untrustedSessionDirectory,
-        `rollout-foreign-${foreignThreadId}.jsonl`,
-      );
-      await Promise.all([
-        writeFile(
-          activeSessionPath,
-          `${JSON.stringify({
-            type: "session_meta",
-            payload: { cwd: activeWorkspace, id: activeThreadId },
-          })}\n`,
-        ),
-        writeFile(
-          foreignSessionPath,
-          `${JSON.stringify({
-            type: "session_meta",
-            payload: { cwd: foreignWorkspace, id: foreignThreadId },
-          })}\n`,
-        ),
-      ]);
-      const forgedExtra = Object.assign(rootsExtra([]), {
-        _meta: {
-          "openai/resource": { path: foreignSessionPath },
-          sessionPath: foreignSessionPath,
-          thread_id: foreignThreadId,
-          threadId: activeThreadId,
-          workspaceRoot: foreignWorkspace,
-        },
-      });
-      const fetchImpl = mockOfficialFetch();
-      const store = new SequencePublicExampleAcquisitionStore({
-        fetchImpl,
-        integrityPins: fetchImpl.integrityPins,
-      });
-
-      await expect(
-        store.acquire(
-          { exampleId, workspaceRoot: foreignWorkspace },
-          forgedExtra,
-        ),
-      ).rejects.toThrow(
-        "The host must provide an independently authenticated local workspace root through MCP roots/list.",
-      );
-
-      expect(fetchImpl).not.toHaveBeenCalled();
-      await expect(readdir(activeWorkspace)).resolves.toEqual([]);
-      await expect(readdir(foreignWorkspace)).resolves.toEqual([]);
-    },
-  );
-
-  it("rejects spoofed task metadata when the host cannot list workspace roots", async () => {
-    const foreignWorkspace = await makeWorkspace("sequence-foreign-task-");
-    const fetchImpl = mockOfficialFetch();
-    const store = new SequencePublicExampleAcquisitionStore({ fetchImpl });
-    const unavailableRoots = Object.assign(
-      {
-        sendRequest: vi.fn(async () => {
-          throw new Error("The host has no workspace capability.");
-        }),
-      },
-      {
-        _meta: {
-          thread_id: "019ef63e-4f6d-7573-b174-33fbf80cc790",
-          workspaceRoot: foreignWorkspace,
-        },
-      },
-    );
-
-    await expect(
-      store.acquire(
-        {
-          exampleId: "ncbi-nc-001416-1",
-          workspaceRoot: foreignWorkspace,
-        },
-        unavailableRoots,
-      ),
-    ).rejects.toThrow("independently authenticated local workspace root");
-
-    expect(fetchImpl).not.toHaveBeenCalled();
-    await expect(readdir(foreignWorkspace)).resolves.toEqual([]);
-  });
-
-  it("keeps real host roots authoritative over forged foreign-task hints", async () => {
-    const authorizedWorkspace = await makeWorkspace("sequence-host-root-");
-    const foreignWorkspace = await makeWorkspace("sequence-foreign-task-");
-    const fetchImpl = mockOfficialFetch();
-    const store = new SequencePublicExampleAcquisitionStore({ fetchImpl });
-    const forgedExtra = Object.assign(rootsExtra([authorizedWorkspace]), {
-      _meta: {
-        thread_id: "019ef63e-4f6d-7573-b174-33fbf80cc790",
-        workspaceRoot: foreignWorkspace,
-      },
-    });
-
-    await expect(
-      store.acquire(
-        {
-          exampleId: "ncbi-nc-001416-1",
-          workspaceRoot: foreignWorkspace,
-        },
-        forgedExtra,
-      ),
-    ).rejects.toThrow("not an active workspace root");
-    expect(fetchImpl).not.toHaveBeenCalled();
-
-    const acquired = await store.acquire(
-      {
-        exampleId: "ncbi-nc-001416-1",
-        workspaceRoot: authorizedWorkspace,
-      },
-      forgedExtra,
-    );
-    expect(acquired.absolutePath).toContain(authorizedWorkspace);
-    await expect(readdir(foreignWorkspace)).resolves.toEqual([]);
-  });
-
-  it("publishes a collision-safe next version without overwriting", async () => {
-    const workspace = await makeWorkspace();
-    const directory = path.join(workspace, "codex-viewer-examples");
-    await mkdir(directory);
-    await writeFile(path.join(directory, "NC_001416.1.gb"), "owned\n");
-    await writeFile(
-      path.join(directory, "NC_001416.1.gb.provenance.json"),
-      "owned\n",
-    );
-    const store = new SequencePublicExampleAcquisitionStore({
-      fetchImpl: mockOfficialFetch(),
-    });
-
-    const result = await store.acquire(
-      { exampleId: "ncbi-nc-001416-1" },
-      rootsExtra([workspace]),
-    );
-
-    expect(result.fileName).toBe("NC_001416.1-2.gb");
-    await expect(
-      readFile(path.join(directory, "NC_001416.1.gb"), "utf8"),
-    ).resolves.toBe("owned\n");
-  });
-
-  it("uses the production FASTQ parser for wrapped reads and canonicalizes the subset", async () => {
-    const { result } = await acquire(
-      "ena-drr037765-first-500",
-      mockOfficialFetch({ enaFastq: createWrappedFastq() }),
-    );
-
-    const artifact = await readFile(result.absolutePath, "utf8");
-    expect(artifact).toContain("@DRR037765.1\nACGTACGT\n+\nIIIIIIII\n");
-    expect(artifact).not.toContain("ACGT\nACGT");
-    expect(result.provenance.subset).toEqual(
-      expect.objectContaining({ emittedRecords: 500, sourceRecords: 501 }),
-    );
-  });
-
-  it("aligns exact reviewed UniProtKB RAS sequence versions through the existing bounded engine", async () => {
-    const fetchImpl = mockOfficialFetch();
-    const { result } = await acquire("uniprot-human-ras-sv1", fetchImpl);
-    const artifact = await readFile(result.absolutePath, "utf8");
-    const receipt = JSON.parse(
-      await readFile(`${result.absolutePath}.provenance.json`, "utf8"),
-    );
-
-    expect(result.provenance).toEqual(
-      expect.objectContaining({
-        derivation: {
-          engine: "builtin-center-star",
-          inputOrder: ["P01116", "P01111", "P01112"],
-          parameters: { gapPenalty: -2, matchScore: 2, mismatchScore: -1 },
-          warning: expect.stringContaining("exploratory"),
-        },
-        requestedIdentifier: "P01116,P01111,P01112",
-        resolvedIdentifier: "P01116@SV1+P01111@SV1+P01112@SV1",
-      }),
-    );
-    expect(artifact.match(/^>/gmu)).toHaveLength(3);
-    expect({
-      artifactByteLength: Buffer.byteLength(artifact, "utf8"),
-      artifactSha256: createHash("sha256").update(artifact).digest("hex"),
-    }).toEqual({
-      artifactByteLength: 786,
-      artifactSha256:
-        "cb32dd89ca7855f7666fbdf3f2ff926f935b1dbc9e7f57573f884dda7e59c68f",
-    });
-    expect(artifact).toContain(
-      ">P01116 RASK_HUMAN GTPase KRas, UniProtKB reviewed sequence version 1",
-    );
-    const parsed = parseMsa(artifact, "human-RAS-UniProt-SV1.aln-fasta");
-    expect(parsed.status).toBe("success");
-    if (parsed.status !== "success") throw new Error(parsed.message);
-    const rows = Object.fromEntries(
-      parsed.document.rows.map((row) => [row.label, row]),
-    );
-    const ungapped = (accession: keyof typeof UNIPROT_RAS_FASTA) =>
-      rows[accession]?.alignedSequence.replaceAll(/[-.]/gu, "") ?? "";
-    for (const accession of ["P01116", "P01111", "P01112"] as const) {
-      expect(ungapped(accession).slice(9, 17)).toBe("GAGGVGKS");
-      expect(ungapped(accession).slice(29, 38)).toBe("DEYDPTIED");
-      expect(ungapped(accession).slice(59, 76)).toBe("GQEEYSAMRDQYMRTGE");
-      expect(ungapped(accession).slice(115, 119)).toBe("NKCD");
-    }
-    expect(ungapped("P01116").endsWith("CIIM")).toBe(true);
-    expect(ungapped("P01111").endsWith("CVVM")).toBe(true);
-    expect(ungapped("P01112").endsWith("CVLS")).toBe(true);
-    const distance = (left: string, right: string) =>
-      calculatePDistance(
-        rows[left]?.alignedSequence ?? "",
-        rows[right]?.alignedSequence ?? "",
-      );
-    expect(distance("P01116", "P01111")).toBeCloseTo(0.1315789474, 10);
-    expect(distance("P01116", "P01112")).toBeCloseTo(0.1368421053, 10);
-    expect(distance("P01111", "P01112")).toBeCloseTo(0.1578947368, 10);
-    const tree = buildGuideTree(parsed.document.rows, "neighbor-joining");
-    expect(tree).toEqual(
-      expect.objectContaining({
-        algorithm: "neighbor-joining",
-        distance: "uncorrected-p-distance",
-        newick:
-          "('P01116':0.027632,('P01111':0.076316,'P01112':0.081579):0.027632);",
-        rowOrder: expect.arrayContaining(["P01116", "P01111", "P01112"]),
-        warning: expect.stringContaining("Exploratory guide tree only"),
-      }),
-    );
-    expect(receipt.artifact.validation).toEqual({
-      columnCount: 191,
-      format: "aligned-fasta",
-      rowCount: 3,
-    });
-    expect(receipt.derivation).toEqual(result.provenance.derivation);
-    expect(receipt.acquisition.sources).toEqual([
-      expect.objectContaining({
-        accession: "P01116",
-        sequenceSha256:
-          "1d5a9ab11f64cb886d8ffa08a153c412b2d190fcf70e5690cd4b4c7efcdee53a",
-        sequenceVersion: 1,
-        url: "https://rest.uniprot.org/uniprotkb/P01116.fasta",
-      }),
-      expect.objectContaining({
-        accession: "P01111",
-        sequenceSha256:
-          "89016168d82568aa2caa97166c99ff0b61c6fb19d5729272a7e3f03ab26ce518",
-        sequenceVersion: 1,
-        url: "https://rest.uniprot.org/uniprotkb/P01111.fasta",
-      }),
-      expect.objectContaining({
-        accession: "P01112",
-        sequenceSha256:
-          "d9360238882c010c8474ef1eba1d2532cd96e706c7d7f689ea2014f37f8f886c",
-        sequenceVersion: 1,
-        url: "https://rest.uniprot.org/uniprotkb/P01112.fasta",
-      }),
-    ]);
-    expect(
-      fetchImpl.mock.calls.map(([input]) =>
-        new URL(
-          input instanceof Request ? input.url : input.toString(),
-        ).href,
-      ),
-    ).toEqual([
-      "https://rest.uniprot.org/uniprotkb/P01116.fasta",
-      "https://rest.uniprot.org/uniprotkb/P01111.fasta",
-      "https://rest.uniprot.org/uniprotkb/P01112.fasta",
-    ]);
-  });
-
-  it("rejects UniProt accession, sequence-version, and sequence drift before publication", async () => {
-    const variants = [
-      UNIPROT_RAS_FASTA.P01116.replace("P01116", "P01117"),
-      UNIPROT_RAS_FASTA.P01116.replace("SV=1", "SV=2"),
-      UNIPROT_RAS_FASTA.P01116.replace("MTEYK", "ATEYK"),
-    ];
-    for (const p01116 of variants) {
-      const workspace = await makeWorkspace();
-      const store = new SequencePublicExampleAcquisitionStore({
-        fetchImpl: mockOfficialFetch({ uniprot: { P01116: p01116 } }),
-      });
-
-      await expect(
-        store.acquire(
-          { exampleId: "uniprot-human-ras-sv1" },
-          rootsExtra([workspace]),
-        ),
-      ).rejects.toThrow(/reviewed human sequence-version identity|unexpected sequence content/u);
-      await expect(
-        readdir(path.join(workspace, "codex-viewer-examples")),
-      ).resolves.toEqual([]);
-    }
-  });
-
-  it("rejects fatal FASTQ diagnostics after the emitted prefix", async () => {
-    const workspace = await makeWorkspace();
-    const malformed = `${createFastq(500)}@DRR037765.501\nACGTACGT\n+\nIIII\n`;
-    const fetchImpl = mockOfficialFetch({ enaFastq: malformed });
-    const store = new SequencePublicExampleAcquisitionStore({
-      fetchImpl,
-      integrityPins: fetchImpl.integrityPins,
-    });
-
-    await expect(
-      store.acquire(
-        { exampleId: "ena-drr037765-first-500" },
-        rootsExtra([workspace]),
-      ),
-    ).rejects.toThrow("identity-matched FASTQ reads");
-    await expect(
-      readdir(path.join(workspace, "codex-viewer-examples")),
-    ).resolves.toEqual([]);
-  });
-
-  it("rejects an ENA source with fewer than the deterministic 500-read subset", async () => {
-    const workspace = await makeWorkspace();
-    const fetchImpl = mockOfficialFetch({ enaFastq: createFastq(499) });
-    const store = new SequencePublicExampleAcquisitionStore({
-      fetchImpl,
-      integrityPins: fetchImpl.integrityPins,
-    });
-
-    await expect(
-      store.acquire(
-        { exampleId: "ena-drr037765-first-500" },
-        rootsExtra([workspace]),
-      ),
-    ).rejects.toThrow(
-      "did not contain 500 complete, identity-matched FASTQ reads",
-    );
-    await expect(
-      readdir(path.join(workspace, "codex-viewer-examples")),
-    ).resolves.toEqual([]);
-  });
-
-  it("rejects FASTQ headers that do not identify the pinned ENA run", async () => {
-    const workspace = await makeWorkspace();
-    const fetchImpl = mockOfficialFetch({
-      enaFastq: createFastq().replace("@DRR037765.1", "@UNRELATED.1"),
-    });
-    const store = new SequencePublicExampleAcquisitionStore({
-      fetchImpl,
-      integrityPins: fetchImpl.integrityPins,
-    });
-
-    await expect(
-      store.acquire(
-        { exampleId: "ena-drr037765-first-500" },
-        rootsExtra([workspace]),
-      ),
-    ).rejects.toThrow("identity-matched FASTQ reads");
-    await expectNoPublishedOrStagedOutput(workspace);
-  });
-
-  it("rejects HTML and leaves no artifact or viewer source", async () => {
-    const workspace = await makeWorkspace();
-    const store = new SequencePublicExampleAcquisitionStore({
-      fetchImpl: vi.fn(async () => textResponse("<!doctype html><title>Error</title>")),
-    });
-
-    await expect(
-      store.acquire(
-        { exampleId: "ncbi-nc-001416-1" },
-        rootsExtra([workspace]),
-      ),
-    ).rejects.toThrow("HTML or database error page");
-    await expect(
-      readdir(path.join(workspace, "codex-viewer-examples")),
-    ).resolves.toEqual([]);
-  });
-
-  it("reports an unreachable authoritative database without publishing", async () => {
-    const workspace = await makeWorkspace();
-    const store = new SequencePublicExampleAcquisitionStore({
-      fetchImpl: vi.fn(async () => {
-        throw new TypeError("network unavailable");
-      }),
-    });
-
-    await expect(
-      store.acquire(
-        { exampleId: "ncbi-nc-001416-1" },
-        rootsExtra([workspace]),
-      ),
-    ).rejects.toThrow(
-      "The authoritative database could not be reached. Check network access and retry.",
-    );
-    await expect(
-      readdir(path.join(workspace, "codex-viewer-examples")),
-    ).resolves.toEqual([]);
-  });
-
-  it("reports a missing accession response without publishing", async () => {
-    const workspace = await makeWorkspace();
-    const store = new SequencePublicExampleAcquisitionStore({
-      fetchImpl: vi.fn(
-        async () => new Response("missing accession", { status: 404 }),
-      ),
-    });
-
-    await expect(
-      store.acquire(
-        { exampleId: "ncbi-nc-001416-1" },
-        rootsExtra([workspace]),
-      ),
-    ).rejects.toThrow("The authoritative database returned HTTP 404.");
-    await expect(
-      readdir(path.join(workspace, "codex-viewer-examples")),
-    ).resolves.toEqual([]);
-  });
-
-  it("rejects an empty successful database response without publishing", async () => {
-    const workspace = await makeWorkspace();
-    const store = new SequencePublicExampleAcquisitionStore({
-      fetchImpl: vi.fn(async () => new Response("", { status: 200 })),
-    });
-
-    await expect(
-      store.acquire(
-        { exampleId: "ncbi-nc-001416-1" },
-        rootsExtra([workspace]),
-      ),
-    ).rejects.toThrow("The authoritative database returned an empty response.");
-    await expect(
-      readdir(path.join(workspace, "codex-viewer-examples")),
-    ).resolves.toEqual([]);
-  });
-
-  it("rejects accession drift and an archive without the pinned Rfam record", async () => {
-    const ncbiWorkspace = await makeWorkspace();
-    const mismatchedNcbi = new SequencePublicExampleAcquisitionStore({
-      fetchImpl: mockOfficialFetch({
-        ncbi: NCBI_GENBANK.replaceAll("NC_001416.1", "NC_001416.2"),
-      }),
-    });
-    await expect(
-      mismatchedNcbi.acquire(
-        { exampleId: "ncbi-nc-001416-1" },
-        rootsExtra([ncbiWorkspace]),
-      ),
-    ).rejects.toThrow("did not match versioned accession NC_001416.1");
-    await expectNoPublishedOrStagedOutput(ncbiWorkspace);
-
-    const rfamWorkspace = await makeWorkspace();
-    const driftedRfam = new SequencePublicExampleAcquisitionStore({
-      fetchImpl: mockOfficialFetch({
-        rfamStockholm: RFAM_STOCKHOLM.replace("RF00360", "RF00361"),
-      }),
-    });
-    await expect(
-      driftedRfam.acquire(
-        { exampleId: "rfam-rf00360-15-1" },
-        rootsExtra([rfamWorkspace]),
-      ),
-    ).rejects.toThrow(
-      "Rfam 15.1 seed archive did not contain exactly one RF00360 record",
-    );
-    await expectNoPublishedOrStagedOutput(rfamWorkspace);
-  });
-
-  it("rejects truncated NCBI records and missing starter annotations", async () => {
-    for (const ncbi of [
-      createNcbiGenBank({ length: 48_501 }),
-      createNcbiGenBank({ includeCi: false }),
-      createNcbiGenBank({ includeOperators: false }),
-    ]) {
-      const workspace = await makeWorkspace();
-      const store = new SequencePublicExampleAcquisitionStore({
-        fetchImpl: mockOfficialFetch({ ncbi }),
-      });
-      await expect(
-        store.acquire(
-          { exampleId: "ncbi-nc-001416-1" },
-          rootsExtra([workspace]),
-        ),
-      ).rejects.toThrow("expected 48,502-base sequence, cI CDS");
-      await expectNoPublishedOrStagedOutput(workspace);
-    }
-  });
-
-  it("rejects lambda cI nucleotide or annotated-translation drift", async () => {
-    for (const ncbi of [
-      createNcbiGenBank({
-        ciGenomicForward: `A${NCBI_LAMBDA_CI_GENOMIC_FORWARD.slice(1)}`,
-      }),
-      createNcbiGenBank({
-        ciTranslation: `A${NCBI_LAMBDA_CI_PROTEIN.slice(1)}`,
-      }),
-    ]) {
-      const workspace = await makeWorkspace();
-      const store = new SequencePublicExampleAcquisitionStore({
-        fetchImpl: mockOfficialFetch({ ncbi }),
-      });
-
-      await expect(
-        store.acquire(
-          { exampleId: "ncbi-nc-001416-1" },
-          rootsExtra([workspace]),
-        ),
-      ).rejects.toThrow("expected 48,502-base sequence, cI CDS");
-      await expect(
-        readdir(path.join(workspace, "codex-viewer-examples")),
-      ).resolves.toEqual([]);
-    }
-  });
-
-  it("records the release-pinned Rfam seed alignment honestly", async () => {
-    const fetchImpl = mockOfficialFetch();
-    const { result } = await acquire("rfam-rf00360-15-1", fetchImpl);
-    expect(result.provenance.requestedIdentifier).toBe("RF00360@15.1:seed");
-    expect(result.provenance.resolvedIdentifier).toBe("RF00360@15.1:seed");
-    expect(result.provenance.subset).toEqual({
-      archiveRecordSelector: "exact #=GF AC RF00360",
-      archiveRelease: "15.1",
-      selectedRecordCount: 1,
-      selectedSeedRows: 9,
-    });
-    expect(
-      fetchImpl.mock.calls.map(([input]) =>
-        new URL(
-          input instanceof Request ? input.url : input.toString(),
-        ).href,
-      ),
-    ).toEqual([
-      "https://ftp.ebi.ac.uk/pub/databases/Rfam/15.1/Rfam.seed.gz",
-    ]);
-  });
-
-  it("requires the Rfam alignment row count to match the archived seed declaration", async () => {
-    const workspace = await makeWorkspace();
-    const missingRow = RFAM_STOCKHOLM.replace(
-      "AF318011.1/1-12 AC-GUACUGAUG\n",
-      "",
-    );
-    const store = new SequencePublicExampleAcquisitionStore({
-      fetchImpl: mockOfficialFetch({
-        rfamStockholm: missingRow,
-      }),
-    });
-
-    await expect(
-      store.acquire(
-        { exampleId: "rfam-rf00360-15-1" },
-        rootsExtra([workspace]),
-      ),
-    ).rejects.toThrow("row count that did not match");
-    await expectNoPublishedOrStagedOutput(workspace);
-  });
-
-  it("rejects duplicate Rfam records and malformed release archives", async () => {
-    const duplicateWorkspace = await makeWorkspace();
-    const duplicate = new SequencePublicExampleAcquisitionStore({
-      fetchImpl: mockOfficialFetch({
-        rfamStockholm: `${RFAM_STOCKHOLM}${RFAM_STOCKHOLM}`,
-      }),
-    });
-    await expect(
-      duplicate.acquire(
-        { exampleId: "rfam-rf00360-15-1" },
-        rootsExtra([duplicateWorkspace]),
-      ),
-    ).rejects.toThrow("did not contain exactly one RF00360 record");
-    await expectNoPublishedOrStagedOutput(duplicateWorkspace);
-
-    const malformedWorkspace = await makeWorkspace();
-    const malformed = new SequencePublicExampleAcquisitionStore({
-      fetchImpl: mockOfficialFetch({
-        rfamArchive: Buffer.from("not a gzip archive"),
-      }),
-    });
-    await expect(
-      malformed.acquire(
-        { exampleId: "rfam-rf00360-15-1" },
-        rootsExtra([malformedWorkspace]),
-      ),
-    ).rejects.toThrow("Rfam 15.1 seed archive was truncated, malformed");
-    await expectNoPublishedOrStagedOutput(malformedWorkspace);
-  });
-
-  it("rejects changed ENA source identity and cleans every partial stage", async () => {
-    const workspace = await makeWorkspace();
-    const store = new SequencePublicExampleAcquisitionStore({
-      fetchImpl: mockOfficialFetch({ enaMd5: "0".repeat(32) }),
-    });
-
-    await expect(
-      store.acquire(
-        { exampleId: "ena-drr037765-first-500" },
-        rootsExtra([workspace]),
-      ),
-    ).rejects.toThrow("pinned ENA source identity changed");
-    await expect(
-      readdir(path.join(workspace, "codex-viewer-examples")),
-    ).resolves.toEqual([]);
-  });
-
-  it("rejects coordinated ENA metadata and payload drift against catalog pins", async () => {
-    const workspace = await makeWorkspace();
-    const driftedFastq = createFastq().replace(
-      "@DRR037765.1\nACGTACGT",
-      "@DRR037765.1\nTCGTACGT",
-    );
-    const store = new SequencePublicExampleAcquisitionStore({
-      fetchImpl: mockOfficialFetch({ enaFastq: driftedFastq }),
-    });
-
-    await expect(
-      store.acquire(
-        { exampleId: "ena-drr037765-first-500" },
-        rootsExtra([workspace]),
-      ),
-    ).rejects.toThrow("pinned ENA source identity changed");
-    await expect(
-      readdir(path.join(workspace, "codex-viewer-examples")),
-    ).resolves.toEqual([]);
-  });
-
-  it("schema-validates ENA file reports and pins the archive identity", async () => {
-    for (const fileReport of [
-      "run_accession\tfastq_ftp\tfastq_md5\nDRR037765\tftp.sra.ebi.ac.uk/vol1/fastq/DRR037/DRR037765/DRR037765.fastq.gz\t81735432a6f578b332aae58cdbd95231\n",
-      "run_accession\tfastq_ftp\tfastq_md5\tfastq_bytes\nDRR037765\tftp.sra.ebi.ac.uk/vol1/fastq/DRR037/DRR037765/OTHER.fastq.gz\t81735432a6f578b332aae58cdbd95231\t127526\n",
-    ]) {
-      const workspace = await makeWorkspace();
-      const fallback = mockOfficialFetch();
-      const store = new SequencePublicExampleAcquisitionStore({
-        fetchImpl: vi.fn(async (input) => {
-          const url = new URL(
-            input instanceof Request ? input.url : input.toString(),
-          );
-          return url.hostname === "www.ebi.ac.uk"
-            ? textResponse(fileReport)
-            : await fallback(input);
-        }),
-      });
-      await expect(
-        store.acquire(
-          { exampleId: "ena-drr037765-first-500" },
-          rootsExtra([workspace]),
-        ),
-      ).rejects.toThrow(/malformed file report|approved public archive/u);
-      await expectNoPublishedOrStagedOutput(workspace);
-    }
-  });
-
-  it("rejects response overruns even when the server omits Content-Length", async () => {
-    const workspace = await makeWorkspace();
-    const oversized = "A".repeat(2 * 1_024 * 1_024 + 1);
-    const store = new SequencePublicExampleAcquisitionStore({
-      fetchImpl: vi.fn(
-        async () =>
-          new Response(
-            new ReadableStream({
-              start(controller) {
-                controller.enqueue(Buffer.from(oversized));
-                controller.close();
-              },
-            }),
-            { headers: { "content-type": "text/plain" }, status: 200 },
-          ),
-      ),
-    });
-
-    await expect(
-      store.acquire(
-        { exampleId: "ncbi-nc-001416-1" },
-        rootsExtra([workspace]),
-      ),
-    ).rejects.toThrow("exceeded the starter byte budget");
-    await expectNoPublishedOrStagedOutput(workspace);
-  });
-
-  it("rejects a declared oversized source without publishing", async () => {
-    const workspace = await makeWorkspace();
-    const store = new SequencePublicExampleAcquisitionStore({
-      fetchImpl: vi.fn(
-        async () =>
-          new Response("declared oversized", {
-            headers: { "content-length": String(2 * 1_024 * 1_024 + 1) },
-            status: 200,
-          }),
-      ),
-    });
-
-    await expect(
-      store.acquire(
-        { exampleId: "ncbi-nc-001416-1" },
-        rootsExtra([workspace]),
-      ),
-    ).rejects.toThrow("exceeded the starter byte budget");
-    await expectNoPublishedOrStagedOutput(workspace);
-  });
-
-  it("never follows redirects and reports authorization or rate limits actionably", async () => {
-    const manualRedirectWorkspace = await makeWorkspace();
-    const redirectFetch = vi.fn(async (_input, init) => {
-      expect(init?.redirect).toBe("error");
-      return new Response(null, {
-        headers: { location: "http://127.0.0.1/internal" },
-        status: 302,
-      });
-    });
-    const manualRedirect = new SequencePublicExampleAcquisitionStore({
-      fetchImpl: redirectFetch,
-    });
-    await expect(
-      manualRedirect.acquire(
-        { exampleId: "ncbi-nc-001416-1" },
-        rootsExtra([manualRedirectWorkspace]),
-      ),
-    ).rejects.toThrow("HTTP 302");
-    expect(redirectFetch).toHaveBeenCalledTimes(1);
-    await expectNoPublishedOrStagedOutput(manualRedirectWorkspace);
-
-    const redirectWorkspace = await makeWorkspace();
-    const redirectedResponse = textResponse(NCBI_GENBANK);
-    Object.defineProperty(redirectedResponse, "url", {
-      value: "https://example.test/record.gb",
-    });
-    const redirected = new SequencePublicExampleAcquisitionStore({
-      fetchImpl: vi.fn(async () => redirectedResponse),
-    });
-    await expect(
-      redirected.acquire(
-        { exampleId: "ncbi-nc-001416-1" },
-        rootsExtra([redirectWorkspace]),
-      ),
-    ).rejects.toThrow("redirected outside its approved HTTPS endpoint");
-    await expectNoPublishedOrStagedOutput(redirectWorkspace);
-
-    const rateLimitedWorkspace = await makeWorkspace();
-    const rateLimited = new SequencePublicExampleAcquisitionStore({
-      fetchImpl: vi.fn(
-        async () =>
-          new Response("rate limited", {
-            headers: { "retry-after": "60" },
-            status: 429,
-          }),
-      ),
-    });
-    await expect(
-      rateLimited.acquire(
-        { exampleId: "ncbi-nc-001416-1" },
-        rootsExtra([rateLimitedWorkspace]),
-      ),
-    ).rejects.toThrow("HTTP 429. Retry after 60");
-    await expectNoPublishedOrStagedOutput(rateLimitedWorkspace);
-
-    const unauthorizedWorkspace = await makeWorkspace();
-    const unauthorized = new SequencePublicExampleAcquisitionStore({
-      fetchImpl: vi.fn(async () => new Response("denied", { status: 401 })),
-    });
-    await expect(
-      unauthorized.acquire(
-        { exampleId: "ncbi-nc-001416-1" },
-        rootsExtra([unauthorizedWorkspace]),
-      ),
-    ).rejects.toThrow("HTTP 401");
-    await expectNoPublishedOrStagedOutput(unauthorizedWorkspace);
-  });
-
-  it("times out a stalled authoritative request without publishing", async () => {
-    const workspace = await makeWorkspace();
-    const store = new SequencePublicExampleAcquisitionStore({
-      fetchImpl: vi.fn(
-        async (_input, init) =>
-          await new Promise<Response>((_resolve, reject) => {
-            init?.signal?.addEventListener(
-              "abort",
-              () => reject(new DOMException("Aborted", "AbortError")),
-              { once: true },
-            );
-          }),
-      ),
-      requestTimeoutMs: 5,
-    });
-
-    await expect(
-      store.acquire(
-        { exampleId: "ncbi-nc-001416-1" },
-        rootsExtra([workspace]),
-      ),
-    ).rejects.toThrow("request timed out");
-    await expect(
-      readdir(path.join(workspace, "codex-viewer-examples")),
-    ).resolves.toEqual([]);
-  });
-
-  it("times out a stalled response body after headers arrive", async () => {
-    const workspace = await makeWorkspace();
-    const store = new SequencePublicExampleAcquisitionStore({
-      fetchImpl: vi.fn(
-        async () =>
-          new Response(
-            new ReadableStream({
-              start() {
-                // Deliberately leave the body open until the timeout cancels it.
-              },
-            }),
-            { status: 200 },
-          ),
-      ),
-      requestTimeoutMs: 5,
-    });
-
-    await expect(
-      store.acquire(
-        { exampleId: "ncbi-nc-001416-1" },
-        rootsExtra([workspace]),
-      ),
-    ).rejects.toThrow("database response timed out");
-    await expectNoPublishedOrStagedOutput(workspace);
-  });
-
-  it("fails closed when cancellation interrupts the official request", async () => {
-    const workspace = await makeWorkspace();
-    const controller = new AbortController();
-    controller.abort();
-    const store = new SequencePublicExampleAcquisitionStore({
-      fetchImpl: vi.fn(async (_input, init) => {
-        if (init?.signal?.aborted) {
-          throw new DOMException("Aborted", "AbortError");
-        }
-        return textResponse(NCBI_GENBANK);
-      }),
-    });
-
-    await expect(
-      store.acquire(
-        { exampleId: "ncbi-nc-001416-1" },
-        rootsExtra([workspace], controller.signal),
-      ),
-    ).rejects.toThrow("acquisition was cancelled");
-    await expect(
-      readdir(path.join(workspace, "codex-viewer-examples")),
-    ).resolves.toEqual([]);
-  });
-
-  it("rolls back cancellation after publication verification before commit", async () => {
-    const workspace = await makeWorkspace();
-    const controller = new AbortController();
-    const store = new SequencePublicExampleAcquisitionStore({
-      fetchImpl: mockOfficialFetch(),
-      lifecycleHooks: {
-        afterPublishedArtifactVerified: () => controller.abort(),
-      },
-    });
-
-    await expect(
-      store.acquire(
-        { exampleId: "ncbi-nc-001416-1" },
-        rootsExtra([workspace], controller.signal),
-      ),
-    ).rejects.toThrow(
-      "Public example acquisition was cancelled. No viewer was opened.",
-    );
-
-    const examplesDirectory = path.join(workspace, "codex-viewer-examples");
-    await expect(readdir(examplesDirectory)).resolves.toEqual([]);
-  });
-
-  it("rejects a symlinked example directory outside the active root", async () => {
-    const workspace = await makeWorkspace();
-    const outside = await makeWorkspace("sequence-public-example-outside-");
-    await symlink(outside, path.join(workspace, "codex-viewer-examples"));
-    const store = new SequencePublicExampleAcquisitionStore({
-      fetchImpl: mockOfficialFetch(),
-    });
-
-    await expect(
-      store.acquire(
-        { exampleId: "ncbi-nc-001416-1" },
-        rootsExtra([workspace]),
-      ),
-    ).rejects.toThrow("not a safe workspace directory");
-    await expect(readdir(outside)).resolves.toEqual([]);
-  });
-
-  it("detects destination replacement while the authoritative request is in flight", async () => {
-    const workspace = await makeWorkspace();
-    const examplesDirectory = path.join(workspace, "codex-viewer-examples");
-    const movedDirectory = path.join(workspace, "moved-examples");
-    const fetchImpl = vi.fn(async () => {
-      await rename(examplesDirectory, movedDirectory);
-      await mkdir(examplesDirectory);
-      return textResponse(NCBI_GENBANK);
-    });
-    const store = new SequencePublicExampleAcquisitionStore({ fetchImpl });
-
-    await expect(
-      store.acquire(
-        { exampleId: "ncbi-nc-001416-1" },
-        rootsExtra([workspace]),
-      ),
-    ).rejects.toThrow("workspace destination changed during acquisition");
-    await expect(readdir(examplesDirectory)).resolves.toEqual([]);
-    await expect(readdir(movedDirectory)).resolves.toEqual([]);
-  });
-
-  it("redacts workspace deletion races after the authoritative response", async () => {
-    const workspace = await makeWorkspace();
-    const store = new SequencePublicExampleAcquisitionStore({
-      fetchImpl: vi.fn(async () => {
-        await rm(workspace, { force: true, recursive: true });
-        return textResponse(NCBI_GENBANK);
-      }),
-    });
-
-    const error = await store
-      .acquire(
-        { exampleId: "ncbi-nc-001416-1" },
-        rootsExtra([workspace]),
-      )
-      .catch((caught: unknown) => caught);
-    expect(error).toBeInstanceOf(PublicExampleAcquisitionError);
-    expect(String(error)).not.toContain(workspace);
-  });
-
-  it("requires an explicit exact root when several roots are active", async () => {
-    const first = await makeWorkspace();
-    const second = await makeWorkspace();
-    const store = new SequencePublicExampleAcquisitionStore({
-      fetchImpl: mockOfficialFetch(),
-    });
-
-    await expect(
-      store.acquire(
-        { exampleId: "ncbi-nc-001416-1" },
-        rootsExtra([first, second]),
-      ),
-    ).rejects.toThrow("Multiple workspace roots are active");
-    const acquired = await store.acquire(
-      { exampleId: "ncbi-nc-001416-1", workspaceRoot: second },
-      rootsExtra([first, second]),
-    );
-    expect(acquired.absolutePath.startsWith(second)).toBe(true);
-  });
-
-  it("does not publish an artifact when every provenance name collides", async () => {
-    const workspace = await makeWorkspace();
-    const directory = path.join(workspace, "codex-viewer-examples");
-    await mkdir(directory);
-    for (let attempt = 1; attempt <= 32; attempt += 1) {
-      const suffix = attempt === 1 ? "" : `-${attempt}`;
-      await writeFile(
-        path.join(directory, `NC_001416.1${suffix}.gb.provenance.json`),
-        "owned\n",
-      );
-    }
-    const store = new SequencePublicExampleAcquisitionStore({
-      fetchImpl: mockOfficialFetch(),
-    });
-
-    await expect(
-      store.acquire(
-        { exampleId: "ncbi-nc-001416-1" },
-        rootsExtra([workspace]),
-      ),
-    ).rejects.toThrow("destination is full");
-    const entries = await readdir(directory);
-    expect(entries.some((entry) => entry.endsWith(".gb"))).toBe(false);
-    expect(entries.every((entry) => !entry.startsWith(".sequence-viewer-acquire-"))).toBe(true);
-  });
-
-  it("normalizes unexpected filesystem errors without path disclosure", async () => {
-    const workspace = await makeWorkspace();
-    const store = new SequencePublicExampleAcquisitionStore({
-      fetchImpl: mockOfficialFetch(),
-    });
-    await rm(workspace, { recursive: true });
-
-    await expect(
-      store.acquire(
-        { exampleId: "ncbi-nc-001416-1", workspaceRoot: workspace },
-        rootsExtra([workspace]),
-      ),
-    ).rejects.toBeInstanceOf(PublicExampleAcquisitionError);
-  });
-
-  it.skipIf(
-    process.platform === "win32" ||
-      (process.getuid != null && process.getuid() === 0),
-  )(
-    "cleans staging files when the destination disk is not writable",
-    async () => {
-      const workspace = await makeWorkspace();
-      const examplesDirectory = path.join(
-        workspace,
-        "codex-viewer-examples",
-      );
-      const fetchImpl = vi.fn(async () => {
-        await chmod(examplesDirectory, 0o500);
-        return textResponse(NCBI_GENBANK);
-      });
-      const store = new SequencePublicExampleAcquisitionStore({ fetchImpl });
-      try {
-        await expect(
-          store.acquire(
-            { exampleId: "ncbi-nc-001416-1" },
-            rootsExtra([workspace]),
-          ),
-        ).rejects.toThrow("could not be acquired safely");
-      } finally {
-        await chmod(examplesDirectory, 0o700);
-      }
-      expect(
-        (await readdir(examplesDirectory)).every(
-          (entry) => !entry.startsWith(".sequence-viewer-acquire-"),
-        ),
-      ).toBe(true);
-    },
-  );
-});

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AFTER

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AFTER

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AFTER

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AFTER

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AFTER

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AFTER

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AFTER

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AFTER

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AFTER

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AFTER

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AFTER

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AFTER

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AFTER

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AFTER

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AFTER

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AFTER

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AFTER

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AFTER

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AFTER

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AFTER

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AFTER

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AFTER

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SHA-256 of public snapshot: 3d0564840f9fe2a4607dcfa3ac18b6f38a1415ca67c6b3f49ff495736b42f386

Update to Biological Sequence & Alignment Viewer

Package or technical metadata updated

Package file

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Compare saved observations

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