jbrowse-plugin-msaview 5.3.0 → 5.4.0

package/dist/chunks/chunk-F726IWCW.js

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+import{a as S}from"./chunk-J6KYLXRD.js";import{b as x}from"./chunk-FY3BTKY4.js";function A(t){try{return new URL(t).host}catch{return t}}var p=class extends Error{constructor(r,o){super(r);this.status=o}};async function b(t,e){let r;try{r=await fetch(t,e)}catch(o){throw o instanceof TypeError?new Error(`Could not reach ${A(t)} \u2014 the request failed at the network level. This is usually a CORS restriction (the server refused to let this site read the response), an offline connection, or a blocked request.`,{cause:o}):o}if(!r.ok)throw new p(`HTTP ${r.status} fetching ${t} ${(await r.text()).slice(0,500)}`,r.status);return r}async function c(t,e){return(await b(t,e)).text()}async function v(t,e){return(await b(t,e)).json()}function l(t,e){return new Promise((r,o)=>{if(e?.aborted){o(new DOMException("Aborted","AbortError"));return}let s=()=>{clearTimeout(n),o(new DOMException("Aborted","AbortError"))},n=setTimeout(()=>{e?.removeEventListener("abort",s),r()},t);e?.addEventListener("abort",s,{once:!0})})}function h(t){return t instanceof Error&&t.name==="AbortError"}var f=x(S());function u(t,e){try{let r=globalThis.localStorage.getItem(t);return r===null?e:JSON.parse(r)}catch(r){return console.error(r),e}}function O(t,e){let[r,o]=(0,f.useState)(()=>u(t,e));return[r,n=>{o(n);try{globalThis.localStorage.setItem(t,JSON.stringify(n))}catch(a){console.error(a)}}]}async function d({check:t,intervalSeconds:e,onCountdown:r,signal:o}){for(;;){if(o?.throwIfAborted(),await t())return;for(let s=e;s>0;s--)r(s),await l(1e3,o)}}var m="https://www.ebi.ac.uk/Tools/services/rest",y="msa-ebiContactEmail",g="jbrowse2@berkeley.edu";function T(){return u(y,g).trim()||g}var B=new Set(["ERROR","FAILURE","NOT_FOUND"]);async function I({tool:t,params:e,signal:r}){return(await c(`${m}/${t}/run`,{method:"POST",body:new URLSearchParams({email:T(),...e}),signal:r})).trim()}var w=900*1e3;async function P({tool:t,jobId:e,intervalSeconds:r=10,onCountdown:o,signal:s}){let n;await d({intervalSeconds:r,onCountdown:o,signal:s,check:async()=>{let a;try{a=(await c(`${m}/${t}/status/${e}`,{signal:s})).trim()}catch(i){if(h(i))throw i;if(n??=Date.now(),Date.now()-n>=w)throw new Error(`Could not reach EBI to check ${t} job ${e} for ${Math.round(w/6e4)} minutes`,{cause:i});return console.warn("[msaview] EBI status check failed, retrying:",i),!1}if(n=void 0,a==="FINISHED")return!0;if(B.has(a))throw new Error(`EBI ${t} job ${e} returned status ${a}`);return!1}})}async function H({tool:t,label:e,params:r,onProgress:o,onRid:s,signal:n}){o(`Submitting ${e} to EBI...`);let a=await I({tool:t,params:r,signal:n});return s?.(a),await P({tool:t,jobId:a,signal:n,onCountdown:i=>{o(`Re-checking ${e} status in... ${i}`)}}),{jobId:a,result:i=>c(`${m}/${t}/result/${a}/${i}`,{signal:n})}}var N="https://blast.ncbi.nlm.nih.gov/Blast.cgi",R=["clustalo","muscle","kalign","mafft"],V=[...R,"browser"],G={clustalo:"Clustal Omega (EBI)",muscle:"MUSCLE (EBI)",kalign:"Kalign (EBI)",mafft:"MAFFT (EBI)",browser:"in browser, query-anchored"},D=["uniprotkb_swissprot","uniprotkb","pan_proteomes","uniprotkb_trembl"],L="uniprotkb_swissprot",Y=["blastp","phmmer"],z={blastp:"blastp (sequence search)",phmmer:"phmmer (profile HMM search)"},$=["swissprot","uniprotkb","uniprotrefprot","rp75","rp55","rp35","rp15"],_="swissprot",E=[5,10,20,50,100,150,200,250,500,750,1e3],Q=100;function W(t){return E.find(e=>e>=t)??E.at(-1)}function X(t){return t==="phmmer"?{program:t,database:_}:{program:t,database:L}}function Z(t){return t==="phmmer"?$:D}var k={uniprotkb_swissprot:"UniProtKB/Swiss-Prot (curated)",swissprot:"UniProtKB/Swiss-Prot (curated)",uniprotkb:"UniProtKB (all entries)",uniprotkb_trembl:"UniProtKB/TrEMBL (unreviewed)",pan_proteomes:"Pan-proteomes",uniprotrefprot:"UniProt reference proteomes",rp75:"Representative proteomes, 75%",rp55:"Representative proteomes, 55%",rp35:"Representative proteomes, 35%",rp15:"Representative proteomes, 15% (widest spread)"};function tt(t){return k[t]}export{p as a,b,c,v as d,l as e,h as f,O as g,y as h,g as i,H as j,N as k,V as l,G as m,Y as n,z as o,Q as p,W as q,X as r,Z as s,tt as t};
+//# sourceMappingURL=chunk-F726IWCW.js.map

package/dist/chunks/chunk-F726IWCW.js.map

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+{
+  "version": 3,
+  "sources": ["../../src/utils/fetch.ts", "../../src/utils/useLocalStorage.ts", "../../src/utils/poll.ts", "../../src/utils/ebiJobDispatcher.ts", "../../src/LaunchMsaView/components/BlastQuery/consts.ts"],
+  "sourcesContent": ["function hostOf(url: string) {\n  try {\n    return new URL(url).host\n  } catch {\n    // a relative url, e.g. a same-origin proxy path\n    return url\n  }\n}\n\nexport class HttpError extends Error {\n  constructor(\n    message: string,\n    readonly status: number,\n  ) {\n    super(message)\n  }\n}\n\nexport async function handleFetch(url: string, args?: RequestInit) {\n  let response: Response\n  try {\n    response = await fetch(url, args)\n  } catch (e) {\n    // fetch rejects with a bare \"TypeError: Failed to fetch\" for every network\n    // level failure, including a cross-origin response the browser refused to\n    // hand over. That is not a hypothetical: NCBI's Blast.cgi stopped sending\n    // Access-Control-Allow-Origin to third-party origins, and the raw TypeError\n    // told users nothing at all about why. See docs/blast.md.\n    if (e instanceof TypeError) {\n      throw new Error(\n        `Could not reach ${hostOf(url)} \u2014 the request failed at the network level. This is usually a CORS restriction (the server refused to let this site read the response), an offline connection, or a blocked request.`,\n        { cause: e },\n      )\n    }\n    throw e\n  }\n\n  if (!response.ok) {\n    throw new HttpError(\n      `HTTP ${response.status} fetching ${url} ${(await response.text()).slice(0, 500)}`,\n      response.status,\n    )\n  }\n\n  return response\n}\n\nexport async function textfetch(url: string, args?: RequestInit) {\n  const response = await handleFetch(url, args)\n  return response.text()\n}\n\nexport async function jsonfetch<T>(url: string, args?: RequestInit) {\n  const response = await handleFetch(url, args)\n  return response.json() as Promise<T>\n}\n\nexport function timeout(time: number, signal?: AbortSignal) {\n  return new Promise<void>((resolve, reject) => {\n    if (signal?.aborted) {\n      reject(new DOMException('Aborted', 'AbortError'))\n      return\n    }\n    // the listener is removed on the natural path too: one signal serves every\n    // tick of a poll, and a 10-minute job is ~600 sleeps -- leaving each\n    // listener behind accumulates them all on that one signal\n    const onAbort = () => {\n      clearTimeout(id)\n      reject(new DOMException('Aborted', 'AbortError'))\n    }\n    const id = setTimeout(() => {\n      signal?.removeEventListener('abort', onAbort)\n      resolve()\n    }, time)\n    signal?.addEventListener('abort', onAbort, { once: true })\n  })\n}\n\n/**\n * A cancelled launch has to be told apart from a failed one: it must not render\n * the \"failed\" panel, and it must not touch a model that may already be gone.\n * `fetch` and the sleep above both reject with a DOMException named AbortError,\n * which subclasses Error.\n */\nexport function isAbortError(e: unknown) {\n  return e instanceof Error && e.name === 'AbortError'\n}\n", "import { useState } from 'react'\n\n// Vendored rather than imported from `@jbrowse/core/util`: that barrel is\n// host-provided, and a barrel split dropped this export, making the BLAST panel\n// throw \"(0, PR.useLocalStorage) is not a function\" on hosts built during that\n// window. Same failure mode as `defaultCodonTable`; keeping our own copy takes\n// this plugin out of the whack-a-mole.\nexport function readLocalStorage<T>(key: string, initialValue: T): T {\n  try {\n    const item = globalThis.localStorage.getItem(key)\n    return item === null ? initialValue : (JSON.parse(item) as T)\n  } catch (error) {\n    console.error(error)\n    return initialValue\n  }\n}\n\nexport function useLocalStorage<T>(key: string, initialValue: T) {\n  const [storedValue, setStoredValue] = useState<T>(() =>\n    readLocalStorage(key, initialValue),\n  )\n  const setValue = (value: T) => {\n    setStoredValue(value)\n    try {\n      globalThis.localStorage.setItem(key, JSON.stringify(value))\n    } catch (error) {\n      console.error(error)\n    }\n  }\n  return [storedValue, setValue] as const\n}\n", "import { timeout } from './fetch'\n\n/**\n * Poll a remote job until it reports done. `check` returns true when finished,\n * false when still pending, and throws on failure. Between checks it counts down\n * `intervalSeconds`, calling `onCountdown` each second so the UI can show\n * progress.\n *\n * `signal` ends the loop with an AbortError: the countdown rejects on the tick\n * it is aborted rather than at the end of the interval, so a cancelled launch\n * stops within a second instead of running for the job's lifetime.\n */\nexport async function pollLoop({\n  check,\n  intervalSeconds,\n  onCountdown,\n  signal,\n}: {\n  check: () => Promise<boolean>\n  intervalSeconds: number\n  onCountdown: (secondsRemaining: number) => void\n  signal?: AbortSignal\n}) {\n  // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition\n  while (true) {\n    signal?.throwIfAborted()\n    if (await check()) {\n      return\n    }\n    for (let i = intervalSeconds; i > 0; i--) {\n      onCountdown(i)\n      await timeout(1000, signal)\n    }\n  }\n}\n", "import { isAbortError, textfetch } from './fetch'\nimport { pollLoop } from './poll'\nimport { readLocalStorage } from './useLocalStorage'\n\n/**\n * EBI's Job Dispatcher REST services (clustalo, muscle, ncbiblast, ...) all\n * speak the same run/status/result protocol, so the transport lives here and\n * each tool only supplies its own parameters and result types.\n *\n * Unlike NCBI's Blast.cgi these endpoints send `Access-Control-Allow-Origin: *`,\n * which is why the BLAST backend moved here \u2014 see docs/blast.md.\n */\nexport const EBI_BASE = 'https://www.ebi.ac.uk/Tools/services/rest'\n\n/**\n * EBI asks for a contact address on every submission so they can reach whoever\n * is generating the load. The default is the project's mailbox; a deployment\n * that sends real volume should name its own maintainer in the BLAST settings\n * dialog.\n */\nexport const EBI_EMAIL_STORAGE_KEY = 'msa-ebiContactEmail'\nexport const DEFAULT_EBI_EMAIL = 'jbrowse2@berkeley.edu'\n\nexport function getEbiEmail() {\n  const configured = readLocalStorage(\n    EBI_EMAIL_STORAGE_KEY,\n    DEFAULT_EBI_EMAIL,\n  ).trim()\n  return configured || DEFAULT_EBI_EMAIL\n}\n\n/** Statuses that mean the job is over and produced no result. */\nconst FAILED_STATUSES = new Set(['ERROR', 'FAILURE', 'NOT_FOUND'])\n\nasync function submitEbiJob({\n  tool,\n  params,\n  signal,\n}: {\n  tool: string\n  params: Record<string, string>\n  signal?: AbortSignal\n}) {\n  const jobId = await textfetch(`${EBI_BASE}/${tool}/run`, {\n    method: 'POST',\n    body: new URLSearchParams({ email: getEbiEmail(), ...params }),\n    signal,\n  })\n  return jobId.trim()\n}\n\n/**\n * A status check that could not reach EBI at all says nothing about the job, so\n * it is not a reason to abandon one. A job the server has accepted keeps running\n * whatever happens to the poller's connection, and EBI's cluster has answered\n * status checks with a 502 for ten minutes on jobs that then finished (see\n * docs/blast.md).\n *\n * So the poll gives up only once checks have failed without a break for this\n * long: an endpoint that has genuinely gone away must not be polled forever.\n */\nexport const STATUS_FAILURE_BUDGET_MS = 15 * 60 * 1000\n\nexport async function waitForEbiJob({\n  tool,\n  jobId,\n  intervalSeconds = 10,\n  onCountdown,\n  signal,\n}: {\n  tool: string\n  jobId: string\n  intervalSeconds?: number\n  onCountdown: (secondsRemaining: number) => void\n  signal?: AbortSignal\n}) {\n  let failingSince: number | undefined\n  await pollLoop({\n    intervalSeconds,\n    onCountdown,\n    signal,\n    check: async () => {\n      let status: string\n      try {\n        status = (\n          await textfetch(`${EBI_BASE}/${tool}/status/${jobId}`, { signal })\n        ).trim()\n      } catch (e) {\n        // a cancelled request is the caller giving up, not EBI being\n        // unreachable, so it must end the poll rather than be retried\n        if (isAbortError(e)) {\n          throw e\n        }\n        failingSince ??= Date.now()\n        if (Date.now() - failingSince >= STATUS_FAILURE_BUDGET_MS) {\n          throw new Error(\n            `Could not reach EBI to check ${tool} job ${jobId} for ${Math.round(STATUS_FAILURE_BUDGET_MS / 60_000)} minutes`,\n            { cause: e },\n          )\n        }\n        console.warn('[msaview] EBI status check failed, retrying:', e)\n        return false\n      }\n      failingSince = undefined\n      // exact match, not includes(): a job whose status is ERROR must not be\n      // able to poll forever waiting for a FINISHED that will never arrive\n      if (status === 'FINISHED') {\n        return true\n      }\n      if (FAILED_STATUSES.has(status)) {\n        throw new Error(`EBI ${tool} job ${jobId} returned status ${status}`)\n      }\n      // RUNNING, QUEUED, PENDING and anything else EBI adds later\n      return false\n    },\n  })\n}\n\nexport async function runEbiJob({\n  tool,\n  label,\n  params,\n  onProgress,\n  onRid,\n  signal,\n}: {\n  tool: string\n  label: string\n  params: Record<string, string>\n  onProgress: (arg: string) => void\n  onRid?: (jobId: string) => void\n  signal?: AbortSignal\n}) {\n  onProgress(`Submitting ${label} to EBI...`)\n  const jobId = await submitEbiJob({ tool, params, signal })\n  onRid?.(jobId)\n  await waitForEbiJob({\n    tool,\n    jobId,\n    signal,\n    onCountdown: s => {\n      onProgress(`Re-checking ${label} status in... ${s}`)\n    },\n  })\n  return {\n    jobId,\n    result: (type: string) =>\n      textfetch(`${EBI_BASE}/${tool}/result/${jobId}/${type}`, { signal }),\n  }\n}\n", "/**\n * Only used to build the link-out on the manual panel, which sends the user to\n * NCBI's own site to run BLAST there. Nothing fetches this url: NCBI stopped\n * sending Access-Control-Allow-Origin to third-party origins, so a browser\n * cannot read a response from it at all. See docs/blast.md.\n */\nexport const BASE_BLAST_URL = 'https://blast.ncbi.nlm.nih.gov/Blast.cgi'\n\n/** The aligners EBI's Job Dispatcher runs, each a tool name at their REST api. */\nexport const ebiMsaAlgorithms = [\n  'clustalo',\n  'muscle',\n  'kalign',\n  'mafft',\n] as const\nexport type EbiMsaAlgorithm = (typeof ebiMsaAlgorithms)[number]\n\n/**\n * `browser` is no job at all: each sequence is aligned to the query in the\n * page and the rows merged on the query (utils/browserAlign.ts), with the tree\n * built by react-msaview's neighbour joining. It is the aligner for a launch\n * that must not depend on EBI, and for one that wants to be quick -- a\n * hundred 400-residue rows take under a second, and a hundred 1400-residue\n * rows eight, against a Job Dispatcher queue that has been measured at\n * anything from ten seconds to fifteen minutes. Past the per-sequence limit in\n * browserAlign.ts it refuses and names an EBI aligner instead.\n */\nexport const msaAlgorithms = [...ebiMsaAlgorithms, 'browser'] as const\nexport type MsaAlgorithm = (typeof msaAlgorithms)[number]\n\nexport const msaAlgorithmLabels: Record<MsaAlgorithm, string> = {\n  clustalo: 'Clustal Omega (EBI)',\n  muscle: 'MUSCLE (EBI)',\n  kalign: 'Kalign (EBI)',\n  mafft: 'MAFFT (EBI)',\n  browser: 'in browser, query-anchored',\n}\n\n/**\n * EBI rejects a submission naming a database outside its own list with a 400,\n * so every value here has to appear in\n * https://www.ebi.ac.uk/Tools/services/rest/ncbiblast/parameterdetails/database\n * -- `uniprotkb_reference_proteomes` did not, and 3.0.0 shipped it as a dead\n * menu entry.\n */\nexport const blastDatabaseOptions = [\n  'uniprotkb_swissprot',\n  'uniprotkb',\n  'pan_proteomes',\n  'uniprotkb_trembl',\n] as const\nexport type BlastDatabase = (typeof blastDatabaseOptions)[number]\n\n// curated, so it returns roughly one good sequence per species rather than the\n// many near-identical TrEMBL entries an alignment reads poorly\nconst defaultBlastDatabase: BlastDatabase = 'uniprotkb_swissprot'\n\nexport const searchPrograms = ['blastp', 'phmmer'] as const\nexport type SearchProgram = (typeof searchPrograms)[number]\n\nexport const searchProgramLabels: Record<SearchProgram, string> = {\n  blastp: 'blastp (sequence search)',\n  phmmer: 'phmmer (profile HMM search)',\n}\n\n/**\n * phmmer offers PDB, AlphaFold, Ensembl Genomes, MEROPS and ChEMBL too, but\n * targets outside UniProt carry no species in their description, so those rows\n * would lose their species and common name. Only the databases that label their\n * hits are offered.\n *\n * rp15..rp75 are the Representative Proteomes: UniProt's reference proteomes\n * thinned so that no two are more than 15% (35%, 55%, 75%) similar, which is\n * the widest taxonomic spread per hit that any of these databases gives. rp15\n * is the one to reach for when the question is \"what is this like across all\n * of life\"; swissprot when it is \"what is this like in the curated set\".\n */\nexport const phmmerDatabaseOptions = [\n  'swissprot',\n  'uniprotkb',\n  'uniprotrefprot',\n  'rp75',\n  'rp55',\n  'rp35',\n  'rp15',\n] as const\nexport type PhmmerDatabase = (typeof phmmerDatabaseOptions)[number]\n\nconst defaultPhmmerDatabase: PhmmerDatabase = 'swissprot'\n\n/**\n * The hit counts EBI's ncbiblast accepts for `alignments` and `scores`. A value\n * off this list is a 400 at submit time, so a request is rounded up to the next\n * one on it.\n */\nconst blastHitCounts = [5, 10, 20, 50, 100, 150, 200, 250, 500, 750, 1000]\n\nexport const defaultMaxHits = 100\n\nexport function snapBlastHitCount(maxHits: number) {\n  return blastHitCounts.find(n => n >= maxHits) ?? blastHitCounts.at(-1)!\n}\n\n/**\n * A program together with a database that program actually has.\n *\n * The pair travels as one value because neither service knows the other's\n * database names \u2014 `swissprot` is a phmmer database and `uniprotkb_swissprot` a\n * blastp one \u2014 so a program held apart from its database can drift into a\n * combination EBI answers with a 400, minutes after the user pressed Submit.\n */\nexport type SearchChoice =\n  | { program: 'blastp'; database: BlastDatabase }\n  | { program: 'phmmer'; database: PhmmerDatabase }\n\nexport function defaultSearchFor(program: SearchProgram): SearchChoice {\n  return program === 'phmmer'\n    ? { program, database: defaultPhmmerDatabase }\n    : { program, database: defaultBlastDatabase }\n}\n\nexport function databaseOptionsFor(program: SearchProgram) {\n  return program === 'phmmer' ? phmmerDatabaseOptions : blastDatabaseOptions\n}\n\n/**\n * What each database is called in the menu. The keys are what EBI is sent and\n * are not negotiable; `uniprotkb_swissprot` and `swissprot` are the same\n * collection under each service's own name, so they read the same here.\n */\nconst databaseLabels: Record<BlastDatabase | PhmmerDatabase, string> = {\n  uniprotkb_swissprot: 'UniProtKB/Swiss-Prot (curated)',\n  swissprot: 'UniProtKB/Swiss-Prot (curated)',\n  uniprotkb: 'UniProtKB (all entries)',\n  uniprotkb_trembl: 'UniProtKB/TrEMBL (unreviewed)',\n  pan_proteomes: 'Pan-proteomes',\n  uniprotrefprot: 'UniProt reference proteomes',\n  rp75: 'Representative proteomes, 75%',\n  rp55: 'Representative proteomes, 55%',\n  rp35: 'Representative proteomes, 35%',\n  rp15: 'Representative proteomes, 15% (widest spread)',\n}\n\nexport function databaseLabel(database: BlastDatabase | PhmmerDatabase) {\n  return databaseLabels[database]\n}\n"],
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+}