--- before
+++ after
@@ -1,1649 +0,0 @@
-import { createHash } from "node:crypto";
-import { constants } from "node:fs";
-import { lstat, mkdir, open, realpath, stat } from "node:fs/promises";
-import path from "node:path";
-import { fileURLToPath } from "node:url";
-import { promisify } from "node:util";
-import { gunzip as gunzipCallback } from "node:zlib";
-
-import { ListRootsResultSchema } from "@modelcontextprotocol/sdk/types.js";
-import { z } from "zod";
-
-import { alignSequences, exportAlignedFasta } from "./msa/alignment-editing";
-import { parseMsa } from "./msa/parser";
-import {
-  sequencePublicExampleIdSchema,
-  sequenceViewerPublicExampleToolInputSchema,
-} from "./protocol";
-import { buildFastqExport } from "./sequence/exports";
-import { parseSequenceDocumentResult } from "./sequence/parser";
-import { reverseComplement, translateFrame } from "./sequence/translation";
-import type { RootsRequestExtra } from "./chat-file-resource";
-import { SEQUENCE_VIEWER_VERSION } from "./version";
-import {
-  isSequenceWorkspaceCollisionError,
-  publishSequenceWorkspacePair,
-} from "./workspace-atomic-publisher";
-
-const gunzip = promisify(gunzipCallback);
-
-const EXAMPLES_DIRECTORY_NAME = "codex-viewer-examples";
-const MAX_NETWORK_RESPONSE_BYTES = 16 * 1_024 * 1_024;
-const MAX_DECODED_RESPONSE_BYTES = 64 * 1_024 * 1_024;
-const MAX_PROVENANCE_BYTES = 64 * 1_024;
-const MAX_COLLISION_ATTEMPTS = 32;
-const REQUEST_TIMEOUT_MS = 30_000;
-const VALIDATOR_VERSION = 1;
-const ENA_SUBSET_RECORDS = 500;
-const NCBI_LAMBDA_CI_CODING_SHA256 =
-  "a51dec784e51f85a35d643a84820c89430b526cd9bf54a398b91c70045cc62e8";
-const NCBI_LAMBDA_CI_PROTEIN_SHA256 =
-  "ec5d954fd10be8c19c920e78badc5d9e9cc281f6801e2c5fde3803c9f133f580";
-const RFAM_RF00360_RELEASE_15_1_SEED_COUNT = 9;
-const UNIPROT_RAS_ALIGNMENT_BYTE_LENGTH = 786;
-const UNIPROT_RAS_ALIGNMENT_SHA256 =
-  "cb32dd89ca7855f7666fbdf3f2ff926f935b1dbc9e7f57573f884dda7e59c68f";
-const UNIPROT_RAS_RECORD_LENGTH = 189;
-const UNIPROT_RAS_ALIGNMENT_SCORES = Object.freeze({
-  gapPenalty: -2,
-  matchScore: 2,
-  mismatchScore: -1,
-});
-
-type PublicExampleIntegrityPins = {
-  ena: {
-    artifactByteLength: number;
-    artifactSha256: string;
-    compressedByteLength: number;
-    compressedMd5: string;
-    gcFraction: number;
-    q30Fraction: number;
-    readLengthMax: number;
-    readLengthMin: number;
-    sourceRecords: number;
-    totalBases: number;
-  };
-};
-
-const DEFAULT_PUBLIC_EXAMPLE_INTEGRITY_PINS: PublicExampleIntegrityPins = {
-  ena: {
-    artifactByteLength: 480_372,
-    artifactSha256:
-      "46bd72991d9c9c2bf64751e88e52548d852d5fa021da4815ee6f6517a51b18b9",
-    compressedByteLength: 127_526,
-    compressedMd5: "81735432a6f578b332aae58cdbd95231",
-    gcFraction: 67_930 / 235_490,
-    q30Fraction: 224_652 / 235_490,
-    readLengthMax: 471,
-    readLengthMin: 469,
-    sourceRecords: 967,
-    totalBases: 235_490,
-  },
-};
-
-const UNIPROT_RAS_ENTRIES = [
-  {
-    accession: "P01116",
-    caax: "CIIM",
-    entryName: "RASK_HUMAN",
-    gene: "KRAS",
-    proteinName: "GTPase KRas",
-    sequenceSha256:
-      "1d5a9ab11f64cb886d8ffa08a153c412b2d190fcf70e5690cd4b4c7efcdee53a",
-    sequenceVersion: 1,
-  },
-  {
-    accession: "P01111",
-    caax: "CVVM",
-    entryName: "RASN_HUMAN",
-    gene: "NRAS",
-    proteinName: "GTPase NRas",
-    sequenceSha256:
-      "89016168d82568aa2caa97166c99ff0b61c6fb19d5729272a7e3f03ab26ce518",
-    sequenceVersion: 1,
-  },
-  {
-    accession: "P01112",
-    caax: "CVLS",
-    entryName: "RASH_HUMAN",
-    gene: "HRAS",
-    proteinName: "GTPase HRas",
-    sequenceSha256:
-      "d9360238882c010c8474ef1eba1d2532cd96e706c7d7f689ea2014f37f8f886c",
-    sequenceVersion: 1,
-  },
-] as const;
-
-export const SEQUENCE_ACQUIRE_PUBLIC_EXAMPLE_TOOL_NAME =
-  "sequence.acquire_public_example";
-
-export { sequencePublicExampleIdSchema } from "./protocol";
-
-export const sequenceAcquirePublicExampleInputSchema =
-  sequenceViewerPublicExampleToolInputSchema.extend({
-    workspaceRoot:
-      sequenceViewerPublicExampleToolInputSchema.shape.workspaceRoot.refine(
-        (root) => root == null || path.isAbsolute(root),
-        "workspaceRoot must be an absolute local path.",
-      ),
-  });
-
-export type SequencePublicExampleId = z.infer<
-  typeof sequencePublicExampleIdSchema
->;
-
-export type SequenceAcquirePublicExampleInput = z.infer<
-  typeof sequenceAcquirePublicExampleInputSchema
->;
-
-type FetchLike = (
-  input: string | URL | Request,
-  init?: RequestInit,
-) => Promise<Response>;
-
-type FileSystemIdentity = {
-  device: bigint;
-  inode: bigint;
-};
-
-type HttpEvidence = {
-  byteLength: number;
-  contentType: string | null;
-  etag: string | null;
-  lastModified: string | null;
-  sha256: string;
-  url: string;
-};
-
-type ArtifactValidation = {
-  format: "aligned-fasta" | "fastq" | "genbank" | "stockholm";
-  recordCount?: number;
-  residueCount?: number;
-  rowCount?: number;
-  columnCount?: number;
-};
-
-type AcquiredBytes = {
-  artifactBytes: Buffer;
-  database: "ENA" | "NCBI Nuccore" | "Rfam" | "UniProtKB";
-  derivation?: Record<string, unknown>;
-  requestedIdentifier: string;
-  resolvedIdentifier: string;
-  sources: Array<HttpEvidence & Record<string, unknown>>;
-  subset: Record<string, unknown> | null;
-  termsUrl: string;
-  validation: ArtifactValidation;
-};
-
-export type SequencePublicExampleProvenanceSummary = {
-  artifactByteLength: number;
-  artifactRelativePath: string;
-  artifactSha256: string;
-  database: AcquiredBytes["database"];
-  derivation?: Record<string, unknown>;
-  exampleId: SequencePublicExampleId;
-  provenanceRelativePath: string;
-  requestedIdentifier: string;
-  resolvedIdentifier: string;
-  subset: Record<string, unknown> | null;
-};
-
-export type SequencePublicExampleAcquisition = {
-  absolutePath: string;
-  fileIdentity: SequencePublicExampleFileIdentity;
-  fileName: string;
-  provenance: SequencePublicExampleProvenanceSummary;
-};
-
-export type SequencePublicExampleFileIdentity = {
-  device: string;
-  inode: string;
-  modifiedAtNanoseconds: string;
-  size: string;
-};
-
-export type SequencePublicExampleAcquirer = {
-  acquire: (
-    input: SequenceAcquirePublicExampleInput,
-    extra: RootsRequestExtra,
-  ) => Promise<SequencePublicExampleAcquisition>;
-};
-
-export class PublicExampleAcquisitionError extends Error {
-  constructor(message: string) {
-    super(message);
-    this.name = "PublicExampleAcquisitionError";
-  }
-}
-
-export function throwIfPublicExampleAcquisitionAborted(
-  signal?: AbortSignal,
-): void {
-  if (!signal?.aborted) return;
-  throw new PublicExampleAcquisitionError(
-    "Public example acquisition was cancelled. No viewer was opened.",
-  );
-}
-
-type SequencePublicExampleAcquisitionLifecycleHooks = {
-  afterPublishedArtifactVerified?: () => Promise<void> | void;
-};
-
-export class SequencePublicExampleAcquisitionStore
-  implements SequencePublicExampleAcquirer
-{
-  readonly #lifecycleHooks: SequencePublicExampleAcquisitionLifecycleHooks;
-  readonly #fetch: FetchLike;
-  readonly #integrityPins: PublicExampleIntegrityPins;
-  readonly #now: () => Date;
-  readonly #requestTimeoutMs: number;
-
-  constructor({
-    lifecycleHooks = {},
-    fetchImpl = globalThis.fetch.bind(globalThis),
-    integrityPins = DEFAULT_PUBLIC_EXAMPLE_INTEGRITY_PINS,
-    now = () => new Date(),
-    requestTimeoutMs = REQUEST_TIMEOUT_MS,
-  }: {
-    lifecycleHooks?: SequencePublicExampleAcquisitionLifecycleHooks;
-    fetchImpl?: FetchLike;
-    /** Deterministic unit fixtures may supply equivalent pins; installed hosts use the catalog defaults. */
-    integrityPins?: PublicExampleIntegrityPins;
-    now?: () => Date;
-    requestTimeoutMs?: number;
-  } = {}) {
-    this.#lifecycleHooks = lifecycleHooks;
-    this.#fetch = fetchImpl;
-    this.#integrityPins = integrityPins;
-    this.#now = now;
-    this.#requestTimeoutMs = requestTimeoutMs;
-  }
-
-  async acquire(
-    input: SequenceAcquirePublicExampleInput,
-    extra: RootsRequestExtra,
-  ): Promise<SequencePublicExampleAcquisition> {
-    let parsedInput: SequenceAcquirePublicExampleInput;
-    let workspace: WorkspaceDestination;
-    try {
-      parsedInput = sequenceAcquirePublicExampleInputSchema.parse(input);
-      workspace = await resolveWorkspaceDestination(
-        parsedInput.workspaceRoot,
-        extra,
-      );
-    } catch (error) {
-      throw normalizeAcquisitionError(error, extra.signal);
-    }
-    const acquiredAt = this.#now().toISOString();
-    let acquired: AcquiredBytes;
-    try {
-      acquired = await this.#acquireBytes(parsedInput.exampleId, extra.signal);
-    } catch (error) {
-      throw normalizeAcquisitionError(error, extra.signal);
-    }
-    const artifactSha256 = sha256(acquired.artifactBytes);
-    try {
-      await assertUnchangedDirectory(workspace);
-      for (let attempt = 1; attempt <= MAX_COLLISION_ATTEMPTS; attempt += 1) {
-        await assertUnchangedDirectory(workspace);
-        const baseName = fileNameForExample(parsedInput.exampleId, attempt);
-        const artifactPath = path.join(workspace.examplesDirectory, baseName);
-        const provenancePath = `${artifactPath}.provenance.json`;
-        const artifactRelativePath = toWorkspaceRelativePath(
-          workspace.root,
-          artifactPath,
-        );
-        const provenanceRelativePath = toWorkspaceRelativePath(
-          workspace.root,
-          provenancePath,
-        );
-        const provenance = createProvenance({
-          acquired,
-          acquiredAt,
-          artifactRelativePath,
-          artifactSha256,
-          exampleId: parsedInput.exampleId,
-          provenanceRelativePath,
-        });
-        const provenanceText = `${JSON.stringify(provenance, null, 2)}\n`;
-        const provenanceBytes = Buffer.byteLength(provenanceText, "utf8");
-        if (provenanceBytes > MAX_PROVENANCE_BYTES) {
-          throw new PublicExampleAcquisitionError(
-            "The public-source provenance exceeded its safety budget. Retry after updating the plugin.",
-          );
-        }
-        try {
-          await publishSequenceWorkspacePair({
-            artifact: acquired.artifactBytes,
-            artifactPath,
-            hooks: {
-              beforeArtifactLink: () => assertUnchangedDirectory(workspace),
-              beforeCommit: async () => {
-                await assertUnchangedDirectory(workspace);
-                await verifyPublishedArtifact({
-                  artifactPath,
-                  expectedByteLength: acquired.artifactBytes.byteLength,
-                  expectedSha256: artifactSha256,
-                });
-                await this.#lifecycleHooks.afterPublishedArtifactVerified?.();
-                throwIfPublicExampleAcquisitionAborted(extra.signal);
-              },
-              beforeSidecarLink: () => assertUnchangedDirectory(workspace),
-            },
-            sidecar: provenanceText,
-            sidecarPath: provenancePath,
-            signal: extra.signal,
-          });
-        } catch (error) {
-          if (isSequenceWorkspaceCollisionError(error)) {
-            continue;
-          }
-          throw error;
-        }
-        const fileIdentity = await verifyPublishedArtifact({
-          artifactPath,
-          expectedByteLength: acquired.artifactBytes.byteLength,
-          expectedSha256: artifactSha256,
-        });
-        return {
-          absolutePath: artifactPath,
-          fileIdentity,
-          fileName: baseName,
-          provenance: {
-            artifactByteLength: acquired.artifactBytes.byteLength,
-            artifactRelativePath,
-            artifactSha256,
-            database: acquired.database,
-            ...(acquired.derivation == null
-              ? {}
-              : { derivation: acquired.derivation }),
-            exampleId: parsedInput.exampleId,
-            provenanceRelativePath,
-            requestedIdentifier: acquired.requestedIdentifier,
-            resolvedIdentifier: acquired.resolvedIdentifier,
-            subset: acquired.subset,
-          },
-        };
-      }
-      throw new PublicExampleAcquisitionError(
-        "The public example destination is full. Remove an old example version and retry.",
-      );
-    } catch (error) {
-      throw normalizeAcquisitionError(error, extra.signal);
-    }
-  }
-
-  async #acquireBytes(
-    exampleId: SequencePublicExampleId,
-    signal?: AbortSignal,
-  ): Promise<AcquiredBytes> {
-    switch (exampleId) {
-      case "ena-drr037765-first-500":
-        return this.#acquireEnaReads(signal);
-      case "ncbi-nc-001416-1":
-        return this.#acquireNcbiGenBank(signal);
-      case "rfam-rf00360-15-1":
-        return this.#acquireRfamAlignment(signal);
-      case "uniprot-human-ras-sv1":
-        return this.#acquireUniProtRas(signal);
-    }
-  }
-
-  async #acquireUniProtRas(signal?: AbortSignal): Promise<AcquiredBytes> {
-    const responses = await Promise.all(
-      UNIPROT_RAS_ENTRIES.map(async (entry) => {
-        const url = new URL(
-          `https://rest.uniprot.org/uniprotkb/${entry.accession}.fasta`,
-        );
-        const response = await this.#fetchBounded({
-          allowedHosts: new Set(["rest.uniprot.org"]),
-          maxBytes: 32 * 1_024,
-          signal,
-          url,
-        });
-        const text = decodeUtf8(
-          response.bytes,
-          `UniProtKB ${entry.accession} FASTA response`,
-        );
-        rejectHtmlPayload(text, `UniProtKB ${entry.accession} FASTA response`);
-        return {
-          entry,
-          evidence: response.evidence,
-          record: validateUniProtRasRecord(text, entry),
-        };
-      }),
-    );
-    signal?.throwIfAborted();
-    const alignment = alignSequences(
-      responses.map(({ entry, record }) => ({
-        description: `${entry.entryName} ${entry.proteinName}, UniProtKB reviewed sequence version ${entry.sequenceVersion}`,
-        id: entry.accession,
-        label: entry.accession,
-        metadata: {
-          entryName: entry.entryName,
-          gene: entry.gene,
-          sequenceSha256: entry.sequenceSha256,
-          sequenceVersion: String(entry.sequenceVersion),
-        },
-        sequence: record.sequence,
-        sourceId: entry.accession,
-      })),
-      UNIPROT_RAS_ALIGNMENT_SCORES,
-      "builtin-center-star",
-    );
-    if (
-      alignment.engine !== "builtin-center-star" ||
-      alignment.alignedLength !== 191 ||
-      alignment.rows.length !== UNIPROT_RAS_ENTRIES.length ||
-      alignment.rows.some(
-        (row, index) =>
-          row.label !== UNIPROT_RAS_ENTRIES[index]?.accession ||
-          row.alignedSequence.replaceAll("-", "").length !==
-            UNIPROT_RAS_RECORD_LENGTH ||
-          row.alignedSequence.length !== alignment.alignedLength,
-      )
-    ) {
-      throw new PublicExampleAcquisitionError(
-        "The bounded RAS center-star alignment did not match its deterministic contract.",
-      );
-    }
-    const artifactText = exportAlignedFasta(alignment.rows);
-    const artifactBytes = Buffer.from(artifactText, "utf8");
-    if (
-      artifactBytes.byteLength !== UNIPROT_RAS_ALIGNMENT_BYTE_LENGTH ||
-      sha256(artifactBytes) !== UNIPROT_RAS_ALIGNMENT_SHA256
-    ) {
-      throw new PublicExampleAcquisitionError(
-        "The bounded RAS center-star alignment artifact changed. Review the derivation before updating this starter.",
-      );
-    }
-    const parsed = parseMsa(artifactText, "human-RAS-UniProt-SV1.aln-fasta");
-    const expectedAccessions = UNIPROT_RAS_ENTRIES.map(
-      ({ accession }) => accession,
-    );
-    if (parsed.status !== "success") {
-      throw new PublicExampleAcquisitionError(
-        `The canonical UniProtKB RAS alignment failed production MSA validation: ${parsed.message}`,
-      );
-    }
-    if (
-      parsed.document.rows.length !== UNIPROT_RAS_ENTRIES.length ||
-      parsed.document.alignedLength !== alignment.alignedLength ||
-      parsed.document.rows.some(
-        (row, index) => row.label !== expectedAccessions[index],
-      )
-    ) {
-      throw new PublicExampleAcquisitionError(
-        "The canonical UniProtKB RAS alignment failed production MSA validation.",
-      );
-    }
-    const requestedIdentifier = UNIPROT_RAS_ENTRIES.map(
-      ({ accession }) => accession,
-    ).join(",");
-    const resolvedIdentifier = UNIPROT_RAS_ENTRIES.map(
-      ({ accession, sequenceVersion }) => `${accession}@SV${sequenceVersion}`,
-    ).join("+");
-    return {
-      artifactBytes,
-      database: "UniProtKB",
-      derivation: {
-        engine: alignment.engine,
-        inputOrder: expectedAccessions,
-        parameters: alignment.parameters,
-        warning: alignment.warning,
-      },
-      requestedIdentifier,
-      resolvedIdentifier,
-      sources: responses.map(({ entry, evidence }) => ({
-        ...evidence,
-        accession: entry.accession,
-        entryName: entry.entryName,
-        gene: entry.gene,
-        role: "reviewed-protein-sequence",
-        sequenceSha256: entry.sequenceSha256,
-        sequenceVersion: entry.sequenceVersion,
-      })),
-      subset: null,
-      termsUrl: "https://www.uniprot.org/help/license",
-      validation: {
-        columnCount: parsed.document.alignedLength,
-        format: "aligned-fasta",
-        rowCount: parsed.document.rows.length,
-      },
-    };
-  }
-
-  async #acquireNcbiGenBank(signal?: AbortSignal): Promise<AcquiredBytes> {
-    const requestedIdentifier = "NC_001416.1";
-    const url = new URL(
-      "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi",
-    );
-    url.search = new URLSearchParams({
-      db: "nuccore",
-      email: "support@openai.com",
-      id: requestedIdentifier,
-      retmode: "text",
-      rettype: "gbwithparts",
-      tool: "OpenAISequenceViewer",
-    }).toString();
-    const response = await this.#fetchBounded({
-      allowedHosts: new Set(["eutils.ncbi.nlm.nih.gov"]),
-      maxBytes: 2 * 1_024 * 1_024,
-      signal,
-      url,
-    });
-    const text = decodeUtf8(response.bytes, "NCBI GenBank response");
-    rejectHtmlPayload(text, "NCBI GenBank response");
-    if (
-      !/^LOCUS\s+/mu.test(text) ||
-      !/^ACCESSION\s+NC_001416(?:\s|$)/mu.test(text) ||
-      !/^VERSION\s+NC_001416\.1(?:\s|$)/mu.test(text) ||
-      !/^ORIGIN\s*$/mu.test(text) ||
-      !/\/\/\s*$/u.test(text)
-    ) {
-      throw new PublicExampleAcquisitionError(
-        "NCBI returned a record that did not match versioned accession NC_001416.1.",
-      );
-    }
-    const parsed = parseSequenceDocumentResult({
-      contents: text,
-      fileName: "NC_001416.1.gb",
-    });
-    if (
-      parsed.status !== "success" ||
-      parsed.document.format !== "genbank" ||
-      parsed.document.records.length !== 1
-    ) {
-      throw new PublicExampleAcquisitionError(
-        "NCBI returned malformed, incomplete, or ambiguous GenBank data for NC_001416.1.",
-      );
-    }
-    const [record] = parsed.document.records;
-    if (
-      record.sourceLabel !== "NC_001416" ||
-      record.length !== 48_502 ||
-      record.metadata.accession !== "NC_001416" ||
-      record.metadata.version !== "NC_001416.1" ||
-      !hasExactCiCds(record) ||
-      !hasExactLambdaOperator(record, "operator-r3", 37_951, 37_967) ||
-      !hasExactLambdaOperator(record, "operator-r2", 37_974, 37_990) ||
-      !hasExactLambdaOperator(record, "operator-r1", 37_998, 38_014)
-    ) {
-      throw new PublicExampleAcquisitionError(
-        "NCBI returned NC_001416.1 without the expected 48,502-base sequence, cI CDS, or lambda operator annotations.",
-      );
-    }
-    const locusDate = /^LOCUS\s+.*?\s(\d{2}-[A-Z]{3}-\d{4})\s*$/mu.exec(
-      text,
-    )?.[1];
-    return {
-      artifactBytes: response.bytes,
-      database: "NCBI Nuccore",
-      requestedIdentifier,
-      resolvedIdentifier: requestedIdentifier,
-      sources: [
-        {
-          ...response.evidence,
-          annotationDate: locusDate ?? null,
-          validatedCi: {
-            codingSequenceSha256: NCBI_LAMBDA_CI_CODING_SHA256,
-            geneticCodeId: 11,
-            proteinAccession: "NP_040628.1",
-            proteinLength: 237,
-            proteinSha256: NCBI_LAMBDA_CI_PROTEIN_SHA256,
-          },
-          sequenceVersion: requestedIdentifier,
-        },
-      ],
-      subset: null,
-      termsUrl: "https://www.ncbi.nlm.nih.gov/home/about/policies/",
-      validation: {
-        format: "genbank",
-        recordCount: parsed.document.records.length,
-        residueCount: record.sequence.length,
-      },
-    };
-  }
-
-  async #acquireRfamAlignment(signal?: AbortSignal): Promise<AcquiredBytes> {
-    const accession = "RF00360";
-    const release = "15.1";
-    const archiveUrl = new URL(
-      `https://ftp.ebi.ac.uk/pub/databases/Rfam/${release}/Rfam.seed.gz`,
-    );
-    const archive = await this.#fetchBounded({
-      allowedHosts: new Set(["ftp.ebi.ac.uk"]),
-      maxBytes: 8 * 1_024 * 1_024,
-      signal,
-      url: archiveUrl,
-    });
-    let decodedArchive: Buffer;
-    try {
-      signal?.throwIfAborted();
-      decodedArchive = await gunzip(archive.bytes, {
-        maxOutputLength: MAX_DECODED_RESPONSE_BYTES,
-      });
-      signal?.throwIfAborted();
-    } catch {
-      if (signal?.aborted) {
-        throw new PublicExampleAcquisitionError(
-          "Public example acquisition was cancelled. No viewer was opened.",
-        );
-      }
-      throw new PublicExampleAcquisitionError(
-        `The Rfam ${release} seed archive was truncated, malformed, or exceeded the decoded-size budget.`,
-      );
-    }
-    const alignmentBytes = extractRfamSeedAlignment(
-      decodedArchive,
-      accession,
-      release,
-    );
-    const text = decodeUtf8(alignmentBytes, "Rfam Stockholm response");
-    rejectHtmlPayload(text, "Rfam Stockholm response");
-    const seedCount = parseRfamSeedCount(text, accession, release);
-    if (
-      !/^# STOCKHOLM 1\.0\s*$/mu.test(text) ||
-      !new RegExp(`^#=GF\\s+AC\\s+${accession}\\s*$`, "mu").test(text) ||
-      !/^#=GF\s+BM\s+.*\bSEED\b.*$/mu.test(text) ||
-      !/\/\/\s*$/u.test(text)
-    ) {
-      throw new PublicExampleAcquisitionError(
-        `Rfam returned an alignment that did not identify ${accession}.`,
-      );
-    }
-    const parsed = parseMsa(text, `${accession}-rfam-${release}.sto`);
-    if (
-      parsed.status !== "success" ||
-      parsed.document.rows.length < 2 ||
-      parsed.document.rows.length !== seedCount ||
-      !parsed.document.rows.some(({ alignedSequence }) =>
-        /[-.]/u.test(alignedSequence),
-      )
-    ) {
-      throw new PublicExampleAcquisitionError(
-        `Rfam returned a malformed alignment or a row count that did not match the ${accession} seed metadata.`,
-      );
-    }
-    const requestedIdentifier = `${accession}@${release}:seed`;
-    const artifactBytes = alignmentBytes;
-    return {
-      artifactBytes,
-      database: "Rfam",
-      requestedIdentifier,
-      resolvedIdentifier: requestedIdentifier,
-      sources: [
-        {
-          ...archive.evidence,
-          archiveFormat: "gzip",
-          role: "release-seed-archive",
-          selectedAccession: accession,
-          selectedByteLength: artifactBytes.byteLength,
-          selectedSha256: sha256(artifactBytes),
-          upstreamCuration: { num_seed: seedCount },
-          upstreamRelease: {
-            archive: "Rfam.seed.gz",
-            number: release,
-          },
-        },
-      ],
-      subset: {
-        archiveRecordSelector: `exact #=GF AC ${accession}`,
-        archiveRelease: release,
-        selectedRecordCount: 1,
-        selectedSeedRows: seedCount,
-      },
-      termsUrl: "https://ftp.ebi.ac.uk/pub/databases/Rfam/15.1/COPYING",
-      validation: {
-        columnCount: parsed.document.alignedLength,
-        format: "stockholm",
-        rowCount: parsed.document.rows.length,
-      },
-    };
-  }
-
-  async #acquireEnaReads(signal?: AbortSignal): Promise<AcquiredBytes> {
-    const runAccession = "DRR037765";
-    const metadataUrl = new URL(
-      "https://www.ebi.ac.uk/ena/portal/api/filereport",
-    );
-    metadataUrl.search = new URLSearchParams({
-      accession: runAccession,
-      fields: "run_accession,fastq_ftp,fastq_md5,fastq_bytes",
-      result: "read_run",
-    }).toString();
-    const metadata = await this.#fetchBounded({
-      allowedHosts: new Set(["www.ebi.ac.uk"]),
-      maxBytes: 256 * 1_024,
-      signal,
-      url: metadataUrl,
-    });
-    const fastq = parseEnaFileReport(metadata.bytes, runAccession);
-    const pinned = this.#integrityPins.ena;
-    if (
-      fastq.byteLength !== pinned.compressedByteLength ||
-      fastq.md5 !== pinned.compressedMd5
-    ) {
-      throw new PublicExampleAcquisitionError(
-        "The pinned ENA source identity changed in the authoritative file report. Review the source before updating this starter.",
-      );
-    }
-    if (fastq.byteLength > MAX_NETWORK_RESPONSE_BYTES) {
-      throw new PublicExampleAcquisitionError(
-        "The pinned ENA read file now exceeds the starter download budget.",
-      );
-    }
-    const fastqUrl = enaFtpToHttps(fastq.ftpUrl);
-    const compressed = await this.#fetchBounded({
-      allowedHosts: new Set(["ftp.sra.ebi.ac.uk"]),
-      maxBytes: Math.min(
-        MAX_NETWORK_RESPONSE_BYTES,
-        Math.max(fastq.byteLength, 1),
-      ),
-      signal,
-      url: fastqUrl,
-    });
-    if (compressed.bytes.byteLength !== fastq.byteLength) {
-      throw new PublicExampleAcquisitionError(
-        "The ENA read file byte length did not match its authoritative file report.",
-      );
-    }
-    if (md5(compressed.bytes) !== fastq.md5) {
-      throw new PublicExampleAcquisitionError(
-        "The ENA read file checksum did not match its authoritative file report.",
-      );
-    }
-    let decoded: Buffer;
-    try {
-      signal?.throwIfAborted();
-      decoded = await gunzip(compressed.bytes, {
-        maxOutputLength: MAX_DECODED_RESPONSE_BYTES,
-      });
-      signal?.throwIfAborted();
-    } catch {
-      if (signal?.aborted) {
-        throw new PublicExampleAcquisitionError(
-          "Public example acquisition was cancelled. No viewer was opened.",
-        );
-      }
-      throw new PublicExampleAcquisitionError(
-        "The ENA read file was truncated, malformed, or exceeded the decoded-size budget.",
-      );
-    }
-    const text = decodeUtf8(decoded, "ENA FASTQ response");
-    rejectHtmlPayload(text, "ENA FASTQ response");
-    const parsedSource = parseSequenceDocumentResult({
-      contents: text,
-      fileName: `${runAccession}.fastq`,
-    });
-    if (
-      parsedSource.status !== "success" ||
-      parsedSource.document.format !== "fastq" ||
-      parsedSource.document.fastqSummary == null ||
-      parsedSource.document.fastqSummary.readCount < ENA_SUBSET_RECORDS ||
-      parsedSource.document.fastqSummary.readCount !== pinned.sourceRecords ||
-      parsedSource.document.records.length < ENA_SUBSET_RECORDS ||
-      parsedSource.document.records.some(
-        (record) =>
-          record.quality == null ||
-          !new RegExp(`^${runAccession}\\.\\d+$`, "u").test(record.sourceLabel),
-      )
-    ) {
-      throw new PublicExampleAcquisitionError(
-        `The pinned ENA run did not contain ${ENA_SUBSET_RECORDS} complete, identity-matched FASTQ reads.`,
-      );
-    }
-    const subsetText = `${parsedSource.document.records
-      .slice(0, ENA_SUBSET_RECORDS)
-      .map((record) => buildFastqExport(record))
-      .join("\n")}\n`;
-    const parsedSubset = parseSequenceDocumentResult({
-      contents: subsetText,
-      fileName: `${runAccession}-first-${ENA_SUBSET_RECORDS}.fastq`,
-    });
-    if (
-      parsedSubset.status !== "success" ||
-      parsedSubset.document.format !== "fastq" ||
-      parsedSubset.document.fastqSummary?.readCount !== ENA_SUBSET_RECORDS
-    ) {
-      throw new PublicExampleAcquisitionError(
-        "The deterministic ENA read subset failed FASTQ validation.",
-      );
-    }
-    const artifactBytes = Buffer.from(subsetText, "utf8");
-    const summary = parsedSubset.document.fastqSummary;
-    if (
-      artifactBytes.byteLength !== pinned.artifactByteLength ||
-      sha256(artifactBytes) !== pinned.artifactSha256 ||
-      summary.totalBases !== pinned.totalBases ||
-      summary.readLengthMin !== pinned.readLengthMin ||
-      summary.readLengthMax !== pinned.readLengthMax ||
-      summary.gcFraction !== pinned.gcFraction ||
-      summary.q30Fraction !== pinned.q30Fraction
-    ) {
-      throw new PublicExampleAcquisitionError(
-        "The deterministic ENA first-500 artifact or live QC baseline changed. Review the source before updating this starter.",
-      );
-    }
-    return {
-      artifactBytes,
-      database: "ENA",
-      requestedIdentifier: runAccession,
-      resolvedIdentifier: `${runAccession}/${fastq.fileName}@md5:${fastq.md5}`,
-      sources: [
-        {
-          ...metadata.evidence,
-          role: "file-report",
-          upstreamBytes: fastq.byteLength,
-          upstreamMd5: fastq.md5,
-        },
-        {
-          ...compressed.evidence,
-          role: "compressed-fastq",
-          upstreamBytes: fastq.byteLength,
-          upstreamMd5: fastq.md5,
-        },
-      ],
-      subset: {
-        emittedRecords: ENA_SUBSET_RECORDS,
-        rule: `first ${ENA_SUBSET_RECORDS} parsed records in source order after gzip decompression, canonical four-line FASTQ`,
-        sourceRecords: parsedSource.document.fastqSummary.readCount,
-      },
-      termsUrl: "https://www.ebi.ac.uk/ena/browser/about/policies",
-      validation: {
-        format: "fastq",
-        recordCount: parsedSubset.document.fastqSummary.readCount,
-        residueCount: parsedSubset.document.fastqSummary.totalBases,
-      },
-    };
-  }
-
-  async #fetchBounded({
-    allowedHosts,
-    maxBytes,
-    signal,
-    url,
-  }: {
-    allowedHosts: ReadonlySet<string>;
-    maxBytes: number;
-    signal?: AbortSignal;
-    url: URL;
-  }): Promise<{ bytes: Buffer; evidence: HttpEvidence }> {
-    const combined = createRequestSignal(signal, this.#requestTimeoutMs);
-    try {
-      let response: Response;
-      try {
-        response = await this.#fetch(url, {
-          headers: {
-            Accept:
-              "application/json, text/plain, application/octet-stream;q=0.9",
-            "User-Agent": `OpenAI-Sequence-Viewer/${SEQUENCE_VIEWER_VERSION}`,
-          },
-          redirect: "error",
-          signal: combined.signal,
-        });
-      } catch (error) {
-        if (combined.signal.aborted) {
-          throw new PublicExampleAcquisitionError(
-            signal?.aborted
-              ? "Public example acquisition was cancelled. No viewer was opened."
-              : "The authoritative database request timed out. Retry when the service is available.",
-          );
-        }
-        throw new PublicExampleAcquisitionError(
-          "The authoritative database could not be reached. Check network access and retry.",
-        );
-      }
-      const finalUrl = new URL(response.url || url.href);
-      if (
-        finalUrl.protocol !== "https:" ||
-        !allowedHosts.has(finalUrl.hostname.toLowerCase()) ||
-        finalUrl.username !== "" ||
-        finalUrl.password !== "" ||
-        finalUrl.hash !== ""
-      ) {
-        throw new PublicExampleAcquisitionError(
-          "The authoritative database redirected outside its approved HTTPS endpoint.",
-        );
-      }
-      if (!response.ok) {
-        const retryAfter = response.headers.get("retry-after");
-        const suffix = retryAfter == null ? "" : ` Retry after ${retryAfter}.`;
-        throw new PublicExampleAcquisitionError(
-          `The authoritative database returned HTTP ${response.status}.${suffix}`,
-        );
-      }
-      const declaredLength = parseContentLength(
-        response.headers.get("content-length"),
-      );
-      if (declaredLength != null && declaredLength > maxBytes) {
-        throw new PublicExampleAcquisitionError(
-          "The authoritative response exceeded the starter byte budget.",
-        );
-      }
-      let bytes: Buffer;
-      try {
-        bytes = await readBoundedBody(response, maxBytes, combined.signal);
-      } catch (error) {
-        if (combined.signal.aborted) {
-          throw new PublicExampleAcquisitionError(
-            signal?.aborted
-              ? "Public example acquisition was cancelled. No viewer was opened."
-              : "The authoritative database response timed out. Retry when the service is available.",
-          );
-        }
-        if (error instanceof PublicExampleAcquisitionError) throw error;
-        throw new PublicExampleAcquisitionError(
-          "The authoritative database response was interrupted. Retry when the service is available.",
-        );
-      }
-      if (bytes.byteLength === 0) {
-        throw new PublicExampleAcquisitionError(
-          "The authoritative database returned an empty response.",
-        );
-      }
-      return {
-        bytes,
-        evidence: {
-          byteLength: bytes.byteLength,
-          contentType: response.headers.get("content-type"),
-          etag: response.headers.get("etag"),
-          lastModified: response.headers.get("last-modified"),
-          sha256: sha256(bytes),
-          url: finalUrl.href,
-        },
-      };
-    } finally {
-      combined.dispose();
-    }
-  }
-}
-
-type WorkspaceDestination = {
-  directoryIdentity: FileSystemIdentity;
-  examplesDirectory: string;
-  root: string;
-  rootIdentity: FileSystemIdentity;
-};
-
-function hasExactCiCds(record: {
-  sequence: string;
-  features: Array<{
-    end: number;
-    geneticCodeId?: number;
-    qualifiers: Record<string, string | string[]>;
-    sourceLocation?: string;
-    start: number;
-    strand: string;
-    translation?: string;
-    translationTrackReliable?: boolean;
-    type: string;
-  }>;
-}): boolean {
-  const feature = record.features.find(
-    (feature) =>
-      feature.type === "CDS" &&
-      feature.start === 37_227 &&
-      feature.end === 37_940 &&
-      feature.strand === "-" &&
-      feature.sourceLocation === "complement(37227..37940)" &&
-      feature.geneticCodeId === 11 &&
-      feature.translationTrackReliable === true &&
-      hasQualifier(feature.qualifiers, "gene", "cI") &&
-      hasQualifier(feature.qualifiers, "protein_id", "NP_040628.1") &&
-      hasQualifier(
-        feature.qualifiers,
-        "product",
-        "LexA family transcriptional regulator",
-      ),
-  );
-  if (feature == null) return false;
-  const codingSequence = reverseComplement(
-    record.sequence.slice(feature.start - 1, feature.end),
-  );
-  const translationWithStop = translateFrame(codingSequence, 0, 11);
-  if (!translationWithStop.endsWith("*")) return false;
-  const translatedProtein = translationWithStop.slice(0, -1);
-  return (
-    sha256(Buffer.from(codingSequence, "ascii")) ===
-      NCBI_LAMBDA_CI_CODING_SHA256 &&
-    translatedProtein.length === 237 &&
-    sha256(Buffer.from(translatedProtein, "ascii")) ===
-      NCBI_LAMBDA_CI_PROTEIN_SHA256 &&
-    feature.translation === translatedProtein
-  );
-}
-
-function hasExactLambdaOperator(
-  record: {
-    features: Array<{
-      end: number;
-      qualifiers: Record<string, string | string[]>;
-      start: number;
-      type: string;
-    }>;
-  },
-  note: string,
-  start: number,
-  end: number,
-): boolean {
-  return record.features.some(
-    (feature) =>
-      feature.type === "regulatory" &&
-      feature.start === start &&
-      feature.end === end &&
-      hasQualifier(feature.qualifiers, "regulatory_class", "other") &&
-      hasQualifier(feature.qualifiers, "note", note),
-  );
-}
-
-function hasQualifier(
-  qualifiers: Record<string, string | string[]>,
-  name: string,
-  expected: string,
-): boolean {
-  const value = qualifiers[name];
-  return Array.isArray(value) ? value.includes(expected) : value === expected;
-}
-
-function validateUniProtRasRecord(
-  text: string,
-  entry: (typeof UNIPROT_RAS_ENTRIES)[number],
-) {
-  const header = text.split(/\r?\n/u, 1)[0] ?? "";
-  if (
-    !header.startsWith(`>sp|${entry.accession}|${entry.entryName} `) ||
-    !hasFastaHeaderField(header, "OS", "Homo sapiens") ||
-    !hasFastaHeaderField(header, "OX", "9606") ||
-    !hasFastaHeaderField(header, "GN", entry.gene) ||
-    !hasFastaHeaderField(header, "PE", "1") ||
-    !hasFastaHeaderField(header, "SV", String(entry.sequenceVersion))
-  ) {
-    throw new PublicExampleAcquisitionError(
-      `UniProtKB returned ${entry.accession} without the expected reviewed human sequence-version identity.`,
-    );
-  }
-  const parsed = parseSequenceDocumentResult({
-    contents: text,
-    fileName: `${entry.accession}.fasta`,
-  });
-  if (
-    parsed.status !== "success" ||
-    parsed.document.format !== "fasta" ||
-    parsed.document.records.length !== 1
-  ) {
-    throw new PublicExampleAcquisitionError(
-      `UniProtKB returned malformed or ambiguous FASTA data for ${entry.accession}.`,
-    );
-  }
-  const [record] = parsed.document.records;
-  if (
-    record.sourceLabel !== `sp|${entry.accession}|${entry.entryName}` ||
-    record.length !== UNIPROT_RAS_RECORD_LENGTH ||
-    record.molecule !== "protein" ||
-    sha256(Buffer.from(record.sequence, "ascii")) !== entry.sequenceSha256 ||
-    record.sequence.slice(9, 17) !== "GAGGVGKS" ||
-    record.sequence.slice(29, 38) !== "DEYDPTIED" ||
-    record.sequence.slice(59, 76) !== "GQEEYSAMRDQYMRTGE" ||
-    record.sequence.slice(115, 119) !== "NKCD" ||
-    !record.sequence.endsWith(entry.caax)
-  ) {
-    throw new PublicExampleAcquisitionError(
-      `UniProtKB returned ${entry.accession} with unexpected sequence content or RAS motif identity.`,
-    );
-  }
-  return record;
-}
-
-function hasFastaHeaderField(
-  header: string,
-  name: string,
-  expected: string,
-): boolean {
-  return new RegExp(
-    `(?:^|\\s)${name}=${escapeRegExp(expected)}(?=\\s[A-Z]{2}=|$)`,
-    "u",
-  ).test(header);
-}
-
-function escapeRegExp(value: string): string {
-  return value.replace(/[.*+?^${}()|[\]\\]/gu, "\\$&");
-}
-
-async function verifyPublishedArtifact({
-  artifactPath,
-  expectedByteLength,
-  expectedSha256,
-}: {
-  artifactPath: string;
-  expectedByteLength: number;
-  expectedSha256: string;
-}): Promise<SequencePublicExampleFileIdentity> {
-  const handle = await open(
-    artifactPath,
-    constants.O_RDONLY | constants.O_NOFOLLOW,
-  );
-  try {
-    const before = await handle.stat({ bigint: true });
-    if (!before.isFile() || before.size !== BigInt(expectedByteLength)) {
-      throw new PublicExampleAcquisitionError(
-        "The published public example did not retain its validated file identity.",
-      );
-    }
-    const bytes = await handle.readFile();
-    const after = await handle.stat({ bigint: true });
-    const current = await lstat(artifactPath, { bigint: true });
-    if (
-      !current.isFile() ||
-      sha256(bytes) !== expectedSha256 ||
-      !sameFileStat(before, after) ||
-      !sameFileStat(after, current)
-    ) {
-      throw new PublicExampleAcquisitionError(
-        "The published public example changed before it could be opened.",
-      );
-    }
-    return {
-      device: after.dev.toString(),
-      inode: after.ino.toString(),
-      modifiedAtNanoseconds: after.mtimeNs.toString(),
-      size: after.size.toString(),
-    };
-  } finally {
-    await handle.close();
-  }
-}
-
-function sameFileStat(
-  left: { dev: bigint; ino: bigint; mtimeNs: bigint; size: bigint },
-  right: { dev: bigint; ino: bigint; mtimeNs: bigint; size: bigint },
-): boolean {
-  return (
-    left.dev === right.dev &&
-    left.ino === right.ino &&
-    left.mtimeNs === right.mtimeNs &&
-    left.size === right.size
-  );
-}
-
-async function resolveWorkspaceDestination(
-  requestedRoot: string | undefined,
-  extra: RootsRequestExtra,
-): Promise<WorkspaceDestination> {
-  let rootsResult: { roots: Array<{ uri: string }> };
-  try {
-    rootsResult = await extra.sendRequest(
-      { method: "roots/list" },
-      ListRootsResultSchema,
-    );
-  } catch {
-    throw new PublicExampleAcquisitionError(
-      "The installed host did not expose an active workspace root. Open a workspace and retry. The host must provide an independently authenticated local workspace root through MCP roots/list.",
-    );
-  }
-  const roots = Array.from(
-    new Set(
-      (
-        await Promise.all(
-          rootsResult.roots.map(async ({ uri }) => {
-            if (!uri.startsWith("file://")) {
-              return null;
-            }
-            try {
-              return await realpath(fileURLToPath(uri));
-            } catch {
-              return null;
-            }
-          }),
-        )
-      ).filter((root): root is string => root != null),
-    ),
-  );
-  if (roots.length === 0) {
-    throw new PublicExampleAcquisitionError(
-      "The installed host did not expose a readable local workspace root. Open a local workspace and retry. The host must provide an independently authenticated local workspace root through MCP roots/list.",
-    );
-  }
-  let root: string;
-  if (requestedRoot == null) {
-    if (roots.length !== 1) {
-      throw new PublicExampleAcquisitionError(
-        "Multiple workspace roots are active. Retry with the exact intended workspace root.",
-      );
-    }
-    root = roots[0];
-  } else {
-    let canonicalRequestedRoot: string;
-    try {
-      canonicalRequestedRoot = await realpath(requestedRoot);
-    } catch {
-      throw new PublicExampleAcquisitionError(
-        "The requested workspace root is unavailable.",
-      );
-    }
-    if (!roots.includes(canonicalRequestedRoot)) {
-      throw new PublicExampleAcquisitionError(
-        "The requested destination is not an active workspace root.",
-      );
-    }
-    root = canonicalRequestedRoot;
-  }
-  const rootIdentity = await readDirectoryIdentity(root);
-  const requestedDirectory = path.join(root, EXAMPLES_DIRECTORY_NAME);
-  await mkdir(requestedDirectory, { mode: 0o700, recursive: true });
-  const examplesDirectory = await realpath(requestedDirectory);
-  if (
-    examplesDirectory !== requestedDirectory ||
-    !isPathWithin(root, examplesDirectory)
-  ) {
-    throw new PublicExampleAcquisitionError(
-      "The public example directory is not a safe workspace directory.",
-    );
-  }
-  const directoryIdentity = await readDirectoryIdentity(examplesDirectory);
-  return { directoryIdentity, examplesDirectory, root, rootIdentity };
-}
-
-async function assertUnchangedDirectory(
-  workspace: WorkspaceDestination,
-): Promise<void> {
-  const [rootIdentity, directoryIdentity, canonicalDirectory] =
-    await Promise.all([
-      readDirectoryIdentity(workspace.root),
-      readDirectoryIdentity(workspace.examplesDirectory),
-      realpath(workspace.examplesDirectory),
-    ]);
-  if (
-    canonicalDirectory !== workspace.examplesDirectory ||
-    !sameIdentity(rootIdentity, workspace.rootIdentity) ||
-    !sameIdentity(directoryIdentity, workspace.directoryIdentity)
-  ) {
-    throw new PublicExampleAcquisitionError(
-      "The workspace destination changed during acquisition. No viewer was opened.",
-    );
-  }
-}
-
-async function readDirectoryIdentity(
-  directoryPath: string,
-): Promise<FileSystemIdentity> {
-  const directoryStat = await stat(directoryPath, { bigint: true });
-  if (!directoryStat.isDirectory()) {
-    throw new PublicExampleAcquisitionError(
-      "The public example destination is not a directory.",
-    );
-  }
-  return { device: directoryStat.dev, inode: directoryStat.ino };
-}
-
-function sameIdentity(
-  left: FileSystemIdentity,
-  right: FileSystemIdentity,
-): boolean {
-  return left.device === right.device && left.inode === right.inode;
-}
-
-function createProvenance({
-  acquired,
-  acquiredAt,
-  artifactRelativePath,
-  artifactSha256,
-  exampleId,
-  provenanceRelativePath,
-}: {
-  acquired: AcquiredBytes;
-  acquiredAt: string;
-  artifactRelativePath: string;
-  artifactSha256: string;
-  exampleId: SequencePublicExampleId;
-  provenanceRelativePath: string;
-}): Record<string, unknown> {
-  return {
-    acquisition: {
-      route: "official-database-endpoint",
-      sources: acquired.sources,
-    },
-    artifact: {
-      byteLength: acquired.artifactBytes.byteLength,
-      format: acquired.validation.format,
-      relativePath: artifactRelativePath,
-      sha256: artifactSha256,
-      validation: acquired.validation,
-    },
-    database: acquired.database,
-    derivation: acquired.derivation ?? null,
-    exampleId,
-    pluginVersion: SEQUENCE_VIEWER_VERSION,
-    provenanceRelativePath,
-    requestedIdentifier: acquired.requestedIdentifier,
-    resolvedIdentifier: acquired.resolvedIdentifier,
-    retrievedAt: acquiredAt,
-    schemaVersion: 1,
-    subset: acquired.subset,
-    termsUrl: acquired.termsUrl,
-    validatorVersion: VALIDATOR_VERSION,
-  };
-}
-
-function fileNameForExample(
-  exampleId: SequencePublicExampleId,
-  attempt: number,
-): string {
-  const [stem, extension] = (() => {
-    switch (exampleId) {
-      case "ena-drr037765-first-500":
-        return ["DRR037765-first-500", ".fastq"];
-      case "ncbi-nc-001416-1":
-        return ["NC_001416.1", ".gb"];
-      case "rfam-rf00360-15-1":
-        return ["RF00360-rfam-15.1", ".sto"];
-      case "uniprot-human-ras-sv1":
-        return ["human-RAS-UniProt-SV1", ".aln-fasta"];
-    }
-  })();
-  return `${stem}${attempt === 1 ? "" : `-${attempt}`}${extension}`;
-}
-
-function toWorkspaceRelativePath(root: string, filePath: string): string {
-  if (!isPathWithin(root, filePath)) {
-    throw new PublicExampleAcquisitionError(
-      "The public example destination left the active workspace.",
-    );
-  }
-  return path.relative(root, filePath).split(path.sep).join("/");
-}
-
-function isPathWithin(root: string, candidate: string): boolean {
-  const relativePath = path.relative(root, candidate);
-  return (
-    relativePath === "" ||
-    (!path.isAbsolute(relativePath) &&
-      relativePath !== ".." &&
-      !relativePath.startsWith(`..${path.sep}`))
-  );
-}
-
-function extractRfamSeedAlignment(
-  archiveBytes: Buffer,
-  accession: string,
-  release: string,
-): Buffer {
-  const recordStartMarker = Buffer.from("# STOCKHOLM 1.0", "ascii");
-  const recordTerminatorMarker = Buffer.from("\n//", "ascii");
-  const accessionMarker = Buffer.from(accession, "ascii");
-  const accessionPattern = new RegExp(`^#=GF\\s+AC\\s+${accession}\\s*$`, "mu");
-  const matches: Buffer[] = [];
-  let cursor = 0;
-  while (cursor < archiveBytes.length) {
-    const recordStart = archiveBytes.indexOf(recordStartMarker, cursor);
-    if (recordStart === -1) {
-      break;
-    }
-    const terminatorStart = archiveBytes.indexOf(
-      recordTerminatorMarker,
-      recordStart,
-    );
-    if (terminatorStart === -1) {
-      throw new PublicExampleAcquisitionError(
-        `The Rfam ${release} seed archive contained a truncated Stockholm record.`,
-      );
-    }
-    let recordEnd = terminatorStart + recordTerminatorMarker.length;
-    if (archiveBytes[recordEnd] === 13) {
-      recordEnd += 1;
-    }
-    if (archiveBytes[recordEnd] === 10) {
-      recordEnd += 1;
-    }
-    const record = archiveBytes.subarray(recordStart, recordEnd);
-    if (record.indexOf(accessionMarker) !== -1) {
-      const text = decodeUtf8(record, "Rfam Stockholm record");
-      if (accessionPattern.test(text)) {
-        matches.push(Buffer.from(record));
-      }
-    }
-    cursor = recordEnd;
-  }
-  if (matches.length !== 1) {
-    throw new PublicExampleAcquisitionError(
-      `The Rfam ${release} seed archive did not contain exactly one ${accession} record.`,
-    );
-  }
-  return matches[0];
-}
-
-function parseRfamSeedCount(
-  text: string,
-  accession: string,
-  release: string,
-): number {
-  const matches = [...text.matchAll(/^#=GF\s+SQ\s+(\d+)\s*$/gmu)];
-  const seedCount = Number(matches[0]?.[1]);
-  if (
-    matches.length !== 1 ||
-    seedCount !== RFAM_RF00360_RELEASE_15_1_SEED_COUNT
-  ) {
-    throw new PublicExampleAcquisitionError(
-      `The Rfam ${accession} release ${release} seed count did not match the pinned archive contract.`,
-    );
-  }
-  return seedCount;
-}
-
-function parseEnaFileReport(
-  bytes: Uint8Array,
-  runAccession: string,
-): {
-  byteLength: number;
-  fileName: string;
-  ftpUrl: string;
-  md5: string;
-} {
-  const text = decodeUtf8(bytes, "ENA file report");
-  rejectHtmlPayload(text, "ENA file report");
-  const lines = text.trim().split(/\r?\n/u);
-  if (lines.length !== 2) {
-    throw new PublicExampleAcquisitionError(
-      "ENA returned an ambiguous or empty file report for the pinned run.",
-    );
-  }
-  const headers = lines[0].split("\t");
-  const values = lines[1].split("\t");
-  const requiredHeaders = [
-    "run_accession",
-    "fastq_ftp",
-    "fastq_md5",
-    "fastq_bytes",
-  ];
-  if (
-    headers.length !== requiredHeaders.length ||
-    values.length !== requiredHeaders.length ||
-    new Set(headers).size !== requiredHeaders.length ||
-    requiredHeaders.some((header) => !headers.includes(header))
-  ) {
-    throw new PublicExampleAcquisitionError(
-      "ENA returned a malformed file report without the required pinned-run fields.",
-    );
-  }
-  const row = Object.fromEntries(
-    headers.map((header, index) => [header, values[index] ?? ""]),
-  ) as Record<(typeof requiredHeaders)[number], string>;
-  if (
-    row.run_accession !== runAccession ||
-    row.fastq_ftp.includes(";") ||
-    row.fastq_md5.includes(";") ||
-    row.fastq_bytes.includes(";") ||
-    !/^[a-f0-9]{32}$/u.test(row.fastq_md5)
-  ) {
-    throw new PublicExampleAcquisitionError(
-      "ENA file metadata did not uniquely match the pinned run and FASTQ file.",
-    );
-  }
-  const byteLength = Number(row.fastq_bytes);
-  if (!Number.isSafeInteger(byteLength) || byteLength <= 0) {
-    throw new PublicExampleAcquisitionError(
-      "ENA returned an invalid authoritative FASTQ byte length.",
-    );
-  }
-  let ftpUrl: URL;
-  try {
-    ftpUrl = new URL(
-      row.fastq_ftp.startsWith("ftp://")
-        ? row.fastq_ftp
-        : `ftp://${row.fastq_ftp}`,
-    );
-  } catch {
-    throw new PublicExampleAcquisitionError(
-      "ENA returned an invalid authoritative FASTQ location.",
-    );
-  }
-  if (
-    ftpUrl.protocol !== "ftp:" ||
-    ftpUrl.hostname !== "ftp.sra.ebi.ac.uk" ||
-    ftpUrl.username !== "" ||
-    ftpUrl.password !== "" ||
-    ftpUrl.hash !== "" ||
-    ftpUrl.search !== "" ||
-    ftpUrl.pathname !== "/vol1/fastq/DRR037/DRR037765/DRR037765.fastq.gz"
-  ) {
-    throw new PublicExampleAcquisitionError(
-      "ENA returned a FASTQ location outside its approved public archive.",
-    );
-  }
-  return {
-    byteLength,
-    fileName: path.posix.basename(ftpUrl.pathname),
-    ftpUrl: ftpUrl.href,
-    md5: row.fastq_md5,
-  };
-}
-
-function enaFtpToHttps(value: string): URL {
-  const ftpUrl = new URL(value);
-  return new URL(`https://ftp.sra.ebi.ac.uk${ftpUrl.pathname}${ftpUrl.search}`);
-}
-
-function rejectHtmlPayload(text: string, label: string): void {
-  const prefix = text.trimStart().slice(0, 256).toLowerCase();
-  if (
-    prefix.startsWith("<!doctype html") ||
-    prefix.startsWith("<html") ||
-    prefix.includes("<title>error")
-  ) {
-    throw new PublicExampleAcquisitionError(
-      `${label} contained an HTML or database error page.`,
-    );
-  }
-}
-
-function decodeUtf8(bytes: Uint8Array, label: string): string {
-  try {
-    return new TextDecoder("utf-8", { fatal: true }).decode(bytes);
-  } catch {
-    throw new PublicExampleAcquisitionError(`${label} was not valid UTF-8.`);
-  }
-}
-
-async function readBoundedBody(
-  response: Response,
-  maxBytes: number,
-  signal: AbortSignal,
-): Promise<Buffer> {
-  if (response.body == null) {
-    throw new PublicExampleAcquisitionError(
-      "The authoritative database returned no response body.",
-    );
-  }
-  const reader = response.body.getReader();
-  const chunks: Uint8Array[] = [];
-  let byteLength = 0;
-  const abortRead = () => void reader.cancel().catch(() => undefined);
-  signal.addEventListener("abort", abortRead, { once: true });
-  try {
-    while (true) {
-      if (signal.aborted) {
-        throw new PublicExampleAcquisitionError(
-          "Public example acquisition was cancelled. No viewer was opened.",
-        );
-      }
-      const { done, value } = await reader.read();
-      if (done) {
-        break;
-      }
-      byteLength += value.byteLength;
-      if (byteLength > maxBytes) {
-        throw new PublicExampleAcquisitionError(
-          "The authoritative response exceeded the starter byte budget.",
-        );
-      }
-      chunks.push(value);
-    }
-    if (signal.aborted) {
-      throw new PublicExampleAcquisitionError(
-        "Public example acquisition was cancelled. No viewer was opened.",
-      );
-    }
-    return Buffer.concat(chunks, byteLength);
-  } finally {
-    signal.removeEventListener("abort", abortRead);
-    await reader.cancel().catch(() => undefined);
-  }
-}
-
-function createRequestSignal(
-  externalSignal: AbortSignal | undefined,
-  timeoutMs: number,
-): { dispose: () => void; signal: AbortSignal } {
-  const controller = new AbortController();
-  const timeout = setTimeout(() => controller.abort(), timeoutMs);
-  const onAbort = () => controller.abort();
-  externalSignal?.addEventListener("abort", onAbort, { once: true });
-  if (externalSignal?.aborted) {
-    controller.abort();
-  }
-  return {
-    dispose: () => {
-      clearTimeout(timeout);
-      externalSignal?.removeEventListener("abort", onAbort);
-    },
-    signal: controller.signal,
-  };
-}
-
-function parseContentLength(value: string | null): number | null {
-  if (value == null) {
-    return null;
-  }
-  const parsed = Number(value);
-  return Number.isSafeInteger(parsed) && parsed >= 0 ? parsed : null;
-}
-
-function sha256(bytes: Uint8Array): string {
-  return createHash("sha256").update(bytes).digest("hex");
-}
-
-function md5(bytes: Uint8Array): string {
-  return createHash("md5").update(bytes).digest("hex");
-}
-
-function normalizeAcquisitionError(
-  error: unknown,
-  signal?: AbortSignal,
-): PublicExampleAcquisitionError {
-  if (error instanceof PublicExampleAcquisitionError) {
-    return error;
-  }
-  if (signal?.aborted) {
-    return new PublicExampleAcquisitionError(
-      "Public example acquisition was cancelled. No viewer was opened.",
-    );
-  }
-  if (error instanceof z.ZodError) {
-    return new PublicExampleAcquisitionError(
-      "The public example request did not match the versioned starter catalog.",
-    );
-  }
-  return new PublicExampleAcquisitionError(
-    "The public example could not be acquired safely. No viewer was opened; check workspace capacity and retry.",
-  );
-}

Full technical diff · 395 changed fields

changed `/files/.codex-plugin~1plugin.json/sha256`

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"5b10b3961e87259ffc258d7e43c8de81b441fc7c1fc548c3acf7f9443fe669b2"

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"458a047b8d1b108a9131d381d1b52cdf1e311e74356823747d581ee9b0662825"

removed `/files/.gitignore`

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{
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"55864e479f655e166053f5e6bcd9b1b8f7239fb82f27a2c8104ed450dd701ce1"

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"e867df32928212c16043bd46f8c5402c21e5b8aac31fc2f6b2d471f7516a1b02"

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{
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  "size": 58280
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"1a0fd9492a125ceacdbea8238188e38958a8818a564fdf86f5aa238487a7f1e9"

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  "sha256": "4e7ec88f42c0d7ecd9c1cc27f55a94b4cbaca03c58e6f85b9516e4d9f51c86d5",
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  "size": 911
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{
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  "size": 46302
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  "size": 19051
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{
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  "size": 103826
}

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{
  "sha256": "58145c876d1c63023f446f6ea671364eb0e5aa02044e06205fa1b2ab8f8bde04",
  "size": 1751
}

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{
  "sha256": "1072359d24f7760cdad5c2c112308e7ba93ddc60bbe00c839e623eaca6aa1d69",
  "size": 1560
}

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{
  "sha256": "82b0b206e4c0f159e6e2a83dddbd0f92d6bf7af677b54154f7668c314a96e260",
  "size": 2606
}

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{
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{
  "sha256": "a530059cba6c7389c6c97af8283baf6a659d891460fe42a90179d30bcf8b3d9b",
  "size": 1715
}

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{
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  "size": 1902
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  "size": 98648
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{
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  "size": 112
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{
  "sha256": "72f2966d9a29a1a0ce63233186f45295cf7e199a09c0a2d0ce6bc1c04b31fb30",
  "size": 2444
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{
  "sha256": "c5d5376ad8a0f3310132379271bc0f330c18dc1f59391439d2506125c7da79ba",
  "size": 2487
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{
  "sha256": "b4398cf2ebc2913f1c3cbc652bbd8df68424ab67770732832072a15187e2462c",
  "size": 3556
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  "sha256": "b95fc8f5d13c7e8f5959ac378d1bf853743584df459ff64021e378578cf5fa02",
  "size": 3810
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{
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  "size": 1782
}

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{
  "sha256": "07889d260a5ce9ac81afba6427201beb1f42efd76ae72b1b9cc8cf7d9c2d9b4b",
  "size": 5459
}

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{
  "sha256": "80248f4908950241fefef3deebdfe981cae5a664b81540770643b58db5cd5000",
  "size": 4963
}

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{
  "sha256": "fa80589aee3f4c5deeaca7f0984e334231680b763de63a78b1a0d1e512acc885",
  "size": 966
}

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{
  "sha256": "f659593e9679cb0ed6b9c47226785a8d1b2a292589b0d121d16512be859fc65e",
  "size": 7795
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{
  "sha256": "b3f7991d9c59749c5ce53e2f937d764c0af7e3cb8b034ebe224df7feaed2b221",
  "size": 926
}

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{
  "sha256": "e7fa243ae3d5eeb7319a2282e0959de0bf6d0bd2d62b3f2813132391e788325b",
  "size": 12639
}

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{
  "sha256": "bbd9f3d2c3ad86ab1e9d2e54f06c6eb09db41116b61cd47966171b24c84e351a",
  "size": 3780
}

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{
  "sha256": "bbc7e66f8d3847a7e8f8662162297c5f5fbb2d5c7d516146abaa024993da62c1",
  "size": 3131
}

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{
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  "size": 20539
}

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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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Full snapshot data

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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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src/public-example-acquisition.ts

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removed `/files/smoke-fixtures~1alignment.pir`

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removed `/files/smoke-fixtures~1clustal-consensus.aln`

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removed `/files/smoke-fixtures~1equal-width-ungapped-ambiguous.fasta`

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