nemar-cli 0.10.4-PR1405.ba5371f → 0.10.4-PR1405.e3fdbed

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Files changed (2) hide show
  1. package/dist/index.js +2 -2
  2. package/package.json +1 -1
package/dist/index.js CHANGED
@@ -99,7 +99,7 @@ ${t}`,dSe,fSe,pSe=(e,t,r)=>{let n=r===""?"":`with ${r.trim()}() `,o=uSe.bind(nul
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  `)}var cE=!1;var{spawn:W7e}=globalThis.Bun;async function C(e,t={}){let r={...process.env,GIT_TERMINAL_PROMPT:"0",...t.env};for(let u of t.unsetEnv??[])delete r[u];let n=W7e({cmd:e,cwd:t.cwd,...t.stdin===void 0?{}:{stdin:new TextEncoder().encode(t.stdin)},stdout:"pipe",stderr:"pipe",env:r}),o=!1,i;if(t.timeout)i=setTimeout(()=>{o=!0,n.kill()},t.timeout);if(lE()){let u=t.cwd?` (cwd=${t.cwd})`:"";Tf(l.dim(`$ ${e.join(" ")}${u}`))}let s=await new Response(n.stdout).text(),a=await new Response(n.stderr).text(),c=await n.exited;if(i)clearTimeout(i);if(lE()){if(s.trim())Tf(l.dim(s.trimEnd()));if(a.trim())Tf(l.yellow(a.trimEnd()));Tf(l.dim(`(exit ${c})`))}if(o)return{stdout:s,stderr:a||`Command timed out after ${Math.round(t.timeout/1000)}s`,exitCode:c??1,timedOut:!0};return{stdout:s,stderr:a,exitCode:c,timedOut:!1}}var vt=O(()=>{Xe()});function Y7e(){if(process.platform==="darwin")return"macos";if(process.platform==="win32")return"windows";return"linux"}function YK(e,t=Y7e()){return e.installInstructions[t]}function J7e(e){let t=e.match(/(\d+\.\d+(?:\.\d+)?)/);return t?t[1]:void 0}function Z7e(){let e=Number(process.env.TEST_PROBE_TIMEOUT_MS);return Number.isFinite(e)&&e>0?e:X7e}async function JK(e){try{let{exitCode:t,stdout:r,timedOut:n}=await C(e.cmd,{timeout:Z7e()});if(n)return{available:!1,timedOut:!0};if(t!==0)return{available:!1};return{available:!0,version:J7e(r)}}catch(t){let r=t instanceof Error?t.message:String(t);if(!r.includes("ENOENT")&&!r.includes("not found"))console.error(` Warning: ${e.name} check failed unexpectedly: ${r}`);return{available:!1}}}async function Nf(){let e=Object.entries(KK);return Promise.all(e.map(async([t,r])=>{let{available:n,version:o,timedOut:i}=await JK(r);return{key:t,name:r.name,purpose:r.purpose,required:r.required,available:n,version:o,timedOut:i,installInstruction:YK(r)}}))}async function XK(){let t=(await Nf()).filter((r)=>r.required&&!r.available);if(t.length===0)return[];console.warn(`
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  Heads up: some tools NEMAR needs for uploading/validating aren't installed yet:`);for(let r of t)console.warn(` - ${r.name} (${r.purpose})`),console.warn(` Install: ${r.installInstruction}`);return console.warn("Run `nemar doctor` anytime to re-check. You can finish signup without them.\n"),t}async function Ra(e){let r=K7e[e].map((s)=>KK[s]).filter(Boolean),n=await Promise.all(r.map(async(s)=>{let a=await JK(s);return{check:s,available:a.available,timedOut:a.timedOut}}));for(let s of n)if(s.timedOut&&s.check.required)console.warn(`Warning: ${s.check.name} did not respond to a version check in time; continuing anyway.`);let o=n.filter((s)=>!s.available&&!s.timedOut&&s.check.required).map((s)=>({tool:s.check.name,installInstruction:YK(s.check)}));if(o.length===0)return;let i=[`
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  Missing required tools:`];for(let s of o)i.push(` ${s.tool} not installed`),i.push(` Install: ${s.installInstruction}`);throw Error(i.join(`
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- `))}var KK,K7e,X7e=4000;var jf=O(()=>{vt();KK={git:{name:"git",purpose:"version control for dataset metadata",cmd:["git","--version"],required:!0,installInstructions:{macos:"brew install git (or install Xcode Command Line Tools)",linux:"sudo apt-get install git OR sudo dnf install git",windows:"winget install Git.Git (or https://git-scm.com/download/win)"}},"git-annex":{name:"git-annex",purpose:"large-file data transfer (upload/download)",cmd:["git-annex","version"],required:!0,installInstructions:{macos:"brew install git-annex",linux:"sudo apt-get install git-annex OR sudo dnf install git-annex",windows:"Download the installer from https://git-annex.branchable.com/install/Windows/"}},gh:{name:"GitHub CLI (gh)",purpose:"GitHub authentication + repository operations",cmd:["gh","--version"],required:!0,installInstructions:{macos:"brew install gh",linux:"See https://cli.github.com/manual/installation",windows:"winget install GitHub.cli (or: scoop install gh)"}},aws:{name:"AWS CLI",purpose:"S3 data upload/download",cmd:["aws","--version"],required:!0,installInstructions:{macos:"brew install awscli",linux:"pip install awscli OR sudo snap install aws-cli --classic",windows:"winget install Amazon.AWSCLI (or the MSI from https://aws.amazon.com/cli/)"}},deno:{name:"Deno",purpose:"BIDS validation",cmd:["deno","--version"],required:!0,installInstructions:{macos:"brew install deno (or: curl -fsSL https://deno.land/install.sh | sh)",linux:"curl -fsSL https://deno.land/install.sh | sh",windows:"winget install DenoLand.Deno (or: irm https://deno.land/install.ps1 | iex)"}}},K7e={upload:["git-annex","gh","aws","deno"],download:["gh"],clone:["git","gh"],push:["git-annex","gh"],publish:["gh","aws"],update:["git","gh"],release:["git","gh"]}});var QK;var ZK=O(()=>{QK={name:"nemar-cli",version:"0.10.4-PR1405.ba5371f",description:"CLI for NEMAR (Neuroelectromagnetic Data Archive and Tools Resource) dataset management",type:"module",main:"dist/index.js",bin:{nemar:"dist/index.js"},scripts:{dev:"bun run src/index.ts",build:"bun build src/index.ts --outdir dist --target bun --minify && sed '1s|#!/usr/bin/env node|#!/usr/bin/env bun|' dist/index.js > dist/index.js.tmp && mv dist/index.js.tmp dist/index.js",test:"bun test",lint:"biome check src/","migrations:d1-check":"bun run scripts/d1-migration-check.ts","zarr:geometry-check":"bun run backend/scripts/zarr-geometry-conformance.ts","lint:fix":"biome check --fix src/",format:"biome format --write src/",typecheck:"tsc --noEmit && tsc --noEmit -p backend","generate-openapi":"bun run scripts/generate-openapi.ts",prepublishOnly:"bun run build",prepare:"husky",postinstall:"bun scripts/postinstall-check.mjs",deploy:"wrangler deploy",preview:"wrangler dev"},keywords:["nemar","bids","neuroimaging","eeg","emg","datalad","cli"],author:"NEMAR Team",license:"CC-BY-NC-ND-4.0",repository:{type:"git",url:"git+https://github.com/nemarOrg/nemar-cli.git"},bugs:{url:"https://github.com/nemarOrg/nemar-cli/issues"},homepage:"https://docs.nemar.org",engines:{bun:">=1.0.0"},files:["dist","scripts/postinstall-check.mjs","scripts/recover-datasets.json","scripts/withdrawn-datasets.json","README.md","LICENSE"],dependencies:{chalk:"^5.3.0",commander:"^12.1.0",conf:"^13.0.1",inquirer:"^9.2.15",ora:"^8.0.1",semver:"^7.8.5",zod:"^3.23.8"},"lint-staged":{"src/**/*.{ts,tsx}":["biome check --fix"],"backend/src/**/*.{ts,tsx}":["biome check --fix"]},devDependencies:{"@asteasolutions/zod-to-openapi":"^7.3.4","@biomejs/biome":"1.9.4","@types/bun":"latest","@types/inquirer":"^9.0.7","@types/semver":"^7.8.0",ajv:"^8.20.0","ajv-formats":"^3.0.1",bcryptjs:"^3.0.3",husky:"^9.1.7","lint-staged":"^16.3.2",typescript:"^5.5.4",wrangler:"^4.70.0",yaml:"^2.8.4"}}});var wi;var qf=O(()=>{ZK();wi=QK.version});import{mkdirSync as eLe,readdirSync as tLe,unlinkSync as rLe,writeFileSync as nLe}from"fs";import{join as uE}from"path";function iY(){Al=!0}function Aa(){return Al}function sY(e,t=process.env){return e.includes("--debug")||t.NEMAR_DEBUG==="1"}function Lf(e){oY=e,$r(`Step: ${e}`)}function Bf(){rY=!0}function aY(){return rY}function fE(){nY=!0}function cY(){return nY}function $r(e){if(Al)process.stderr.write(`[debug] ${e}
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+ `))}var KK,K7e,X7e=4000;var jf=O(()=>{vt();KK={git:{name:"git",purpose:"version control for dataset metadata",cmd:["git","--version"],required:!0,installInstructions:{macos:"brew install git (or install Xcode Command Line Tools)",linux:"sudo apt-get install git OR sudo dnf install git",windows:"winget install Git.Git (or https://git-scm.com/download/win)"}},"git-annex":{name:"git-annex",purpose:"large-file data transfer (upload/download)",cmd:["git-annex","version"],required:!0,installInstructions:{macos:"brew install git-annex",linux:"sudo apt-get install git-annex OR sudo dnf install git-annex",windows:"Download the installer from https://git-annex.branchable.com/install/Windows/"}},gh:{name:"GitHub CLI (gh)",purpose:"GitHub authentication + repository operations",cmd:["gh","--version"],required:!0,installInstructions:{macos:"brew install gh",linux:"See https://cli.github.com/manual/installation",windows:"winget install GitHub.cli (or: scoop install gh)"}},aws:{name:"AWS CLI",purpose:"S3 data upload/download",cmd:["aws","--version"],required:!0,installInstructions:{macos:"brew install awscli",linux:"pip install awscli OR sudo snap install aws-cli --classic",windows:"winget install Amazon.AWSCLI (or the MSI from https://aws.amazon.com/cli/)"}},deno:{name:"Deno",purpose:"BIDS validation",cmd:["deno","--version"],required:!0,installInstructions:{macos:"brew install deno (or: curl -fsSL https://deno.land/install.sh | sh)",linux:"curl -fsSL https://deno.land/install.sh | sh",windows:"winget install DenoLand.Deno (or: irm https://deno.land/install.ps1 | iex)"}}},K7e={upload:["git-annex","gh","aws","deno"],download:["gh"],clone:["git","gh"],push:["git-annex","gh"],publish:["gh","aws"],update:["git","gh"],release:["git","gh"]}});var QK;var ZK=O(()=>{QK={name:"nemar-cli",version:"0.10.4-PR1405.e3fdbed",description:"CLI for NEMAR (Neuroelectromagnetic Data Archive and Tools Resource) dataset management",type:"module",main:"dist/index.js",bin:{nemar:"dist/index.js"},scripts:{dev:"bun run src/index.ts",build:"bun build src/index.ts --outdir dist --target bun --minify && sed '1s|#!/usr/bin/env node|#!/usr/bin/env bun|' dist/index.js > dist/index.js.tmp && mv dist/index.js.tmp dist/index.js",test:"bun test",lint:"biome check src/","migrations:d1-check":"bun run scripts/d1-migration-check.ts","zarr:geometry-check":"bun run backend/scripts/zarr-geometry-conformance.ts","lint:fix":"biome check --fix src/",format:"biome format --write src/",typecheck:"tsc --noEmit && tsc --noEmit -p backend","generate-openapi":"bun run scripts/generate-openapi.ts",prepublishOnly:"bun run build",prepare:"husky",postinstall:"bun scripts/postinstall-check.mjs",deploy:"wrangler deploy",preview:"wrangler dev"},keywords:["nemar","bids","neuroimaging","eeg","emg","datalad","cli"],author:"NEMAR Team",license:"CC-BY-NC-ND-4.0",repository:{type:"git",url:"git+https://github.com/nemarOrg/nemar-cli.git"},bugs:{url:"https://github.com/nemarOrg/nemar-cli/issues"},homepage:"https://docs.nemar.org",engines:{bun:">=1.0.0"},files:["dist","scripts/postinstall-check.mjs","scripts/recover-datasets.json","scripts/withdrawn-datasets.json","README.md","LICENSE"],dependencies:{chalk:"^5.3.0",commander:"^12.1.0",conf:"^13.0.1",inquirer:"^9.2.15",ora:"^8.0.1",semver:"^7.8.5",zod:"^3.23.8"},"lint-staged":{"src/**/*.{ts,tsx}":["biome check --fix"],"backend/src/**/*.{ts,tsx}":["biome check --fix"]},devDependencies:{"@asteasolutions/zod-to-openapi":"^7.3.4","@biomejs/biome":"1.9.4","@types/bun":"latest","@types/inquirer":"^9.0.7","@types/semver":"^7.8.0",ajv:"^8.20.0","ajv-formats":"^3.0.1",bcryptjs:"^3.0.3",husky:"^9.1.7","lint-staged":"^16.3.2",typescript:"^5.5.4",wrangler:"^4.70.0",yaml:"^2.8.4"}}});var wi;var qf=O(()=>{ZK();wi=QK.version});import{mkdirSync as eLe,readdirSync as tLe,unlinkSync as rLe,writeFileSync as nLe}from"fs";import{join as uE}from"path";function iY(){Al=!0}function Aa(){return Al}function sY(e,t=process.env){return e.includes("--debug")||t.NEMAR_DEBUG==="1"}function Lf(e){oY=e,$r(`Step: ${e}`)}function Bf(){rY=!0}function aY(){return rY}function fE(){nY=!0}function cY(){return nY}function $r(e){if(Al)process.stderr.write(`[debug] ${e}
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  `)}function aLe(e){let t={};for(let[r,n]of Object.entries(e))t[r]=sLe.has(r.toLowerCase())?"[REDACTED]":n;return t}function uY(e){let t=e.indexOf("@");if(t<=0)return"***";return`${e[0]}***${e.slice(t)}`}function dE(e,t,r=0){if(r>lLe)return"[REDACTED: depth]";if(Array.isArray(t))return t.map((n)=>dE(e,n,r+1));if(t&&typeof t==="object"){let n={};for(let[o,i]of Object.entries(t))n[o]=dE(o,i,r+1);return n}if(typeof t==="string"){if(cLe.test(e))return"[REDACTED]";return t.replace(lY,uY)}return t}function pE(e){return e.replace(uLe,"Bearer [REDACTED]").replace(dLe,"[REDACTED_AWS_KEY]").replace(fLe,"$1[REDACTED]").replace(pLe,"$1$2=[REDACTED]").replace(lY,uY)}function mLe(e){return pE(e)}function eY(e,t=iLe){if(e===void 0)return;let r=e;try{let n=JSON.parse(e);r=JSON.stringify(dE("",n))}catch{}if(r=pE(r),Buffer.byteLength(r,"utf8")>t)r=`${Buffer.from(r,"utf8").subarray(0,t).toString("utf8")}... [truncated]`;return r}function A0(e){if(!Al)return;let t=mLe(e.url);try{let r={...e,url:t,requestHeaders:e.requestHeaders?aLe(e.requestHeaders):void 0,requestBody:eY(e.requestBody),responseBody:eY(e.responseBody)};R0.push(r),$r(`${e.method} ${t} -> ${e.status??"ERROR"} (${e.durationMs}ms)`)}catch(r){let n=T(r);R0.push({method:e.method,url:t,status:e.status,durationMs:e.durationMs,note:`redaction failed: ${n}`}),$r(`redaction failed for ${e.method} ${t}: ${n}`)}}async function hLe(){let e=[];try{let t=process.versions.bun?`Bun ${process.versions.bun}`:`Node ${process.version}`;e.push(`CLI version: ${wi}`),e.push(`OS/Arch: ${process.platform}/${process.arch}`),e.push(`Runtime: ${t}`)}catch(t){e.push(`(could not read CLI/OS/runtime info: ${T(t)})`)}e.push(""),e.push("Active account:");try{let t=ot();if(t.apiKey){if(t.username)e.push(` Username: ${t.username}`);if(e.push(` API URL: ${t.apiUrl}`),t.role)e.push(` Role: ${t.role}`);e.push(` Sandbox completed: ${!!t.sandboxCompleted}`)}else e.push(" (not authenticated)")}catch(t){e.push(` (could not read account config: ${T(t)})`)}e.push(""),e.push("External tools:");try{let t=await Nf();for(let r of t){let n=r.available?r.version??"installed":r.timedOut?"(timed out)":"not installed";e.push(` ${r.name}: ${n}`)}}catch(t){e.push(` (could not probe external tools: ${T(t)})`)}return e}async function mE(){return(await hLe()).join(`
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  `)}async function dY(){if(!Al||k0!==void 0)return;try{k0=await mE()}catch(e){let t=T(e);k0=`(could not build environment report: ${t})`,$r(`environment snapshot failed: ${t}`)}}function fY(e){if(tY.has(e))return{flag:e};for(let t of tY){if(!e.startsWith(t)||e.length<=t.length)continue;if(t.length===2)return{flag:t,kind:"short-attached"};if(e[t.length]==="=")return{flag:t,kind:"long-eq"}}return null}function gLe(e){let t=[];for(let r=0;r<e.length;r++){let n=e[r],o=fY(n);if(!o){t.push(n);continue}if(o.kind==="long-eq")t.push(`${o.flag}=[REDACTED]`);else if(o.kind==="short-attached")t.push(`${o.flag}[REDACTED]`);else if(t.push(n),r+1<e.length)t.push("[REDACTED]"),r++}return t}function yLe(e){let t=[];for(let r=0;r<e.length;r++){let n=e[r],o=fY(n);if(!o){t.push(n);continue}if(!o.kind&&r+1<e.length)r++}return t}function bLe(e){let t=[];for(let n of yLe(e)){if(n.startsWith("-"))continue;if(t.push(n),t.length===2)break}return(t.length>0?t.join("-"):"nemar").replace(/[^a-zA-Z0-9_-]/g,"_")}function xLe(e,t){let r=[];if(r.push("NEMAR CLI Debug Log"),r.push(`Generated: ${new Date().toISOString()}`),r.push(`Command: nemar ${pE(gLe(e).join(" "))}`),r.push(""),r.push(k0??"(environment snapshot unavailable)"),r.push(""),r.push("HTTP requests:"),R0.length===0)r.push(" (none)");else R0.forEach((n,o)=>{if(r.push(` [${o+1}] ${n.method} ${n.url} -> ${n.status??"ERROR"} (${n.durationMs}ms)`),n.error)r.push(` Error: ${n.error}`);if(n.note)r.push(` Note: ${n.note}`);if(n.requestHeaders)r.push(` Request headers: ${JSON.stringify(n.requestHeaders)}`);if(n.requestBody)r.push(` Request body: ${n.requestBody}`);if(n.responseBody)r.push(` Response body: ${n.responseBody}`)});return r.push(""),r.push(`Failing step: ${oY??"(none recorded)"}`),r.push(`Exit code: ${t}`),`${r.join(`
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@@ -193,7 +193,7 @@ Exemplar clone + publish complete: ${i} -> ${o}`)),console.log(l.dim(` GitHub:
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  `).filter(Boolean))].sort()}async function NHe(e,t=mp){let{stdout:r,exitCode:n}=await C(["git","show","git-annex:remote.log"],{cwd:e});if(n!==0)return null;for(let o of r.split(`
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  `)){let i=o.trim().split(/\s+/);if(!i.some((a)=>a===`name=${t}`))continue;let s=i[0];if(s)return s}return null}async function jHe(e,t,r,n=mp){let o=await NHe(t,n),i=await THe(t);if(!o)return{datasetId:e,remoteUuid:null,annexed:i,registered:[],inBucket:[],toRegister:[],missingContent:[],falselyClaimed:[]};let s=await Jee(t,o),a=await r(e),c=new Set(s),u=i.filter((d)=>nn(d,a));return{datasetId:e,remoteUuid:o,annexed:i,registered:s,inBucket:u,toRegister:u.filter((d)=>!c.has(d)),missingContent:i.filter((d)=>!nn(d,a)),falselyClaimed:i.filter((d)=>c.has(d)&&!nn(d,a))}}async function qHe(e,t,r){let n=r.remoteName??mp;if(!PHe.test(e))return{datasetId:e,action:"failed",pushed:!1,notes:[],error:`"${e}" is not a dataset id, and it would become a directory this deletes`};let o=FHe(r.workRoot,e),i=[];q2(o,{recursive:!0,force:!0});let s=r.originUrl??`https://github.com/nemarDatasets/${e}.git`,a=await M2(s,o);if(a)return q2(o,{recursive:!0,force:!0}),{datasetId:e,action:"failed",pushed:!1,notes:i,error:a};try{let c=await jHe(e,o,t,n);if(!c.remoteUuid)return{datasetId:e,action:"skipped-no-remote",state:c,pushed:!1,notes:[`no ${n} remote in the git-annex branch; nothing to register against`]};if(r.retractFalseClaims&&c.falselyClaimed.length>0){if(!r.apply)return{datasetId:e,action:"would-repair",state:c,pushed:!1,notes:[`${c.falselyClaimed.length} key(s) are advertised at ${n} and not in the bucket; would withdraw`]};let p=await BQ(o,c.falselyClaimed,c.remoteUuid);if(p.failed>0)return{datasetId:e,action:"failed",state:c,pushed:!1,notes:i,error:`${p.failed} claim(s) still stand after setpresentkey 0: ${p.missing.join(", ")}`};i.push(`withdrew ${p.success} claim(s) the bucket cannot back`);let h=Yee(await Tt(o,"origin"));if(h)return{datasetId:e,action:"failed",state:c,pushed:!1,notes:i,error:`the retraction did not reach GitHub: ${h}. The claims are still advertised; re-run to redo it.`};return{datasetId:e,action:"repaired",state:c,pushed:!0,notes:i}}if(c.missingContent.length>0&&!r.includeIncomplete)return{datasetId:e,action:"skipped-missing-content",state:c,pushed:!1,notes:[`${c.missingContent.length} of ${c.annexed.length} annexed key(s) have no object in the bucket${c.falselyClaimed.length>0?`, ${c.falselyClaimed.length} of them advertised at ${n} anyway (rerun with retractFalseClaims to withdraw)`:""}, so this is missing content (#1396) rather than a lost registration; first: ${c.missingContent[0]}`]};if(c.toRegister.length===0){if(c.missingContent.length>0)return{datasetId:e,action:"skipped-missing-content",state:c,pushed:!1,notes:[`nothing to register: the bucket holds none of the ${c.missingContent.length} key(s) still outstanding (#1396)`]};return{datasetId:e,action:"compliant",state:c,pushed:!1,notes:i}}if(!r.apply)return{datasetId:e,action:"would-repair",state:c,pushed:!1,notes:[`${c.toRegister.length} key(s) are in the bucket and not in the log`]};let u=await Ms(o,c.toRegister,c.remoteUuid),d=new Set(await Jee(o,c.remoteUuid)),f=c.toRegister.filter((p)=>!d.has(p));if(f.length>0)return{datasetId:e,action:"failed",state:c,pushed:!1,notes:i,error:`registered ${u.success} of ${c.toRegister.length}, and the location log still does not record ${f.length} of them (first: ${f[0]}). Nothing pushed.`};if(i.push(`registered ${c.toRegister.length} key(s), all confirmed in the location log`),r.push===!1)return{datasetId:e,action:"repaired",state:c,pushed:!1,notes:i};let m=Yee(await Tt(o,"origin"));if(m)return{datasetId:e,action:"failed",state:c,pushed:!1,notes:i,error:`the git-annex branch did not push: ${m}. The registration is local only; re-run to redo it.`};return{datasetId:e,action:"repaired",state:c,pushed:!0,notes:i}}finally{q2(o,{recursive:!0,force:!0})}}async function hp(e,t,r){let n=Array(e.length),o=0,i=!1,s=Array.from({length:Math.max(1,Math.min(t,e.length))},async()=>{while(!i){let u=o++;if(u>=e.length)return;try{n[u]=await r(e[u],u)}catch(d){throw i=!0,d}}}),c=(await Promise.allSettled(s)).find((u)=>u.status==="rejected");if(c?.status==="rejected")throw c.reason;return n}async function Xee(e,t,r){let n=[...new Set(e)],o=0,i=await hp(n,r.concurrency??4,async(c)=>{let u;try{u=await qHe(c,t,r)}catch(d){u={datasetId:c,action:"failed",pushed:!1,notes:[],error:d instanceof Error?d.message:String(d)}}return r.onDataset?.(u,++o,n.length),u}),s={compliant:0,repaired:0,"would-repair":0,"skipped-missing-content":0,"skipped-no-remote":0,failed:0},a=0;for(let c of i)if(s[c.action]++,c.action==="repaired")a+=c.state?.toRegister.length??0;return{outcomes:i,tally:s,keysRegistered:a}}var mp="nemar-s3",PHe;var gp=O(()=>{Si();Ul();Bo();Mo();vt();kn();Oi();Oi();PHe=/^[a-z]{2}[0-9]{6}$/});function ete(e){let t=Ia(e),r=/^([A-Z0-9]+)-s\d+(?:-[SC]\d+)*--(.+)$/.exec(e);if(t===null||!r)return null;let[,n,o]=r,i=VHe[n],s=i&&o.length>=i?o.slice(0,i).toLowerCase():null;return{backend:n,size:t,hashHex:s&&/^[0-9a-f]+$/.test(s)?s:null}}function U2(e){let t=new Map;for(let r of e.split(`
195
195
  `)){let n=r.trim().split(/\s+/),o=n[0];if(!o||n.length<2)continue;let i=(a)=>n.find((c)=>c.startsWith(`${a}=`))?.slice(a.length+1),s=i("name");if(!s)continue;t.set(o,{uuid:o,name:s,bucket:i("bucket"),fileprefix:i("fileprefix")})}return t}function GHe(e){if(!e.startsWith("!"))return e;let t=e.slice(1),r=Buffer.from(t,"base64");if(r.toString("base64").replace(/=+$/,"")!==t.replace(/=+$/,""))return e;return r.toString("utf8")}function tte(e,t){let r=[];for(let o of e.split(`
196
- `)){let i=/^(\S+?)s?\s+([0-9a-f-]{36}):V\s+([+-])(\S+)$/.exec(o.trim());if(!i)continue;let s=t.get(i[2]);if(!s?.bucket)continue;let a=GHe(i[4]),c=a.indexOf("#");if(c<=0)continue;let u=Number.parseFloat(i[1])||0;r.push({stamp:u,retracted:i[3]==="-",value:a,pin:{bucket:s.bucket,object:a.slice(c+1),version:a.slice(0,c),remoteName:s.name}})}r.sort((o,i)=>o.stamp-i.stamp);let n=new Map;for(let o of r)if(o.retracted)n.delete(o.value);else n.set(o.value,o.pin);return[...n.values()]}async function rte(e){let t=["aws","s3api","list-object-versions","--bucket",e.bucket,"--prefix",e.prefix,"--output","json","--query","Versions[].[Key,VersionId,Size,ETag]","--page-size","1000"];if(!e.signed)t.push("--no-sign-request");let{stdout:r,stderr:n,exitCode:o,timedOut:i}=await C(t,{unsetEnv:B2,timeout:L2});if(o!==0||i)throw Error(`listing s3://${e.bucket}/${e.prefix} failed: ${i?"timed out":n.trim()||`exit ${o}`}`);return HHe(r)}function HHe(e){let t=new Map,r=e.trim()?JSON.parse(e):[];for(let[n,o,i,s]of r??[]){let a=t.get(n)??[];a.push({object:n,version:o,size:i,etag:(s??"").replace(/"/g,"")}),t.set(n,a)}return t}function nte(e){let t=ete(e.key);if(!t)return{key:e.key,size:0,reason:"not a parseable annex key"};let r={key:e.key,size:t.size},n=e.pins[e.pins.length-1],o=e.upstream?WHe(t.size,e):null;if(n){let i=o&&o.version!==n.version?[o]:void 0;return{...r,source:{...n,origin:"pinned",size:t.size},alternatives:i}}if(!e.upstream)return{...r,reason:"no upstream remote to recover from"};if(o)return{...r,source:o};return{...r,reason:KHe(t.size,e)}}function WHe(e,t){let r=t.upstream;if(!r)return null;let n=t.paths.flatMap((s)=>r.index.get(`${r.prefix}${s}`)?.filter((a)=>a.size===e)??[]),o=new Map(n.map((s)=>[s.etag,s]));if(o.size!==1)return null;let[i]=o.values();return{bucket:r.bucket,object:i.object,version:i.version,etag:i.etag,origin:"version-match",size:e}}function KHe(e,t){let r=t.upstream;if(!r)return"no upstream remote to recover from";let n=t.paths.flatMap((i)=>r.index.get(`${r.prefix}${i}`)?.filter((s)=>s.size===e)??[]),o=new Set(n.map((i)=>i.etag));return o.size>1?`${o.size} distinct upstream objects carry this key's size; refusing to guess`:"no upstream object of this key's size at any of its paths"}function ote(e){return e==="pinned"}function YHe(e){let t=ete(e.key);if(!t)return{ok:!1,method:"unparseable-key",detail:"unparseable key"};if(e.checksumSha256&&t.backend.startsWith("SHA256")&&t.hashHex){let n=Buffer.from(t.hashHex,"hex").toString("base64");return e.checksumSha256===n?{ok:!0,method:"checksum"}:{ok:!1,method:"checksum",detail:`S3 hashed the object to ${e.checksumSha256}, the key says ${n}`}}let r=e.etag?.replace(/"/g,"");if(r&&!r.includes("-")&&t.backend.startsWith("MD5")&&t.hashHex)return r===t.hashHex?{ok:!0,method:"etag"}:{ok:!1,method:"etag",detail:`the object's MD5 is ${r}, the key says ${t.hashHex}`};if(e.size==null)return{ok:!1,method:"unmeasured",detail:"the bucket did not answer for the copy, so nothing about it was checked"};if(e.size!==t.size)return{ok:!1,method:"size",detail:`the object is ${e.size} bytes, the key says ${t.size}`};if(!ote(e.origin))return{ok:!1,method:"size-and-pin",detail:"only the size could be checked, and nothing pins this source to this key"};if(e.sourceCrc64&&e.crc64)return e.sourceCrc64===e.crc64?{ok:!0,method:"crc64-of-source"}:{ok:!1,method:"crc64-of-source",detail:`the copy's CRC64 is ${e.crc64}, the source reads ${e.sourceCrc64}`};return{ok:!0,method:"size-and-pin"}}function ite(e){let t=`${e.bucket}/${e.object}`;return e.version?`${t}?versionId=${e.version}`:t}function XHe(e){return JHe.test(e)}async function Ii(e,t){let r=await C(["aws",...e],{env:t,unsetEnv:B2,timeout:L2});for(let n=1;n<=ZHe;n++){if(r.exitCode===0||!XHe(r.stderr))return r;let o=QHe*2**(n-1)*(1+Math.random());await new Promise((i)=>setTimeout(i,o)),r=await C(["aws",...e],{env:t,unsetEnv:B2,timeout:L2})}return r}async function eWe(e){if(e.source.size>Qee)return{...await rWe(e),multipart:!0};let{stdout:t,stderr:r,exitCode:n,timedOut:o}=await Ii(["s3api","copy-object","--bucket",e.destBucket,"--key",e.destKey,"--copy-source",ite(e.source),"--tagging-directive","REPLACE","--tagging","","--checksum-algorithm","SHA256","--output","json"],e.env);if(n!==0)throw Error(`copy-object failed: ${o?"timed out":r.trim()||`exit ${n}`}`);let i=JSON.parse(t||"{}");return{checksumSha256:i.CopyObjectResult?.ChecksumSHA256??null,etag:i.CopyObjectResult?.ETag?.replace(/"/g,"")??null,multipart:!1}}function tWe(e,t){let r=[];for(let n=0,o=1;n<e;n+=t,o++)r.push({part:o,offset:n,end:Math.min(n+t,e)-1});return r}async function rWe(e){let t=await Ii(["s3api","create-multipart-upload","--bucket",e.destBucket,"--key",e.destKey,"--checksum-algorithm","CRC64NVME","--checksum-type","FULL_OBJECT","--output","json"],e.env);if(t.exitCode!==0)throw Error(`create-multipart-upload failed: ${t.stderr.trim()||`exit ${t.exitCode}`}`);let r=JSON.parse(t.stdout||"{}").UploadId;if(!r)throw Error("create-multipart-upload returned no UploadId");let n=tWe(e.source.size,UHe);try{let o=await hp(n,zHe,async(a)=>{let c=await Ii(["s3api","upload-part-copy","--bucket",e.destBucket,"--key",e.destKey,"--upload-id",r,"--part-number",String(a.part),"--copy-source",ite(e.source),"--copy-source-range",`bytes=${a.offset}-${a.end}`,"--output","json"],e.env);if(c.exitCode!==0)throw Error(`upload-part-copy ${a.part} failed: ${c.stderr.trim()||`exit ${c.exitCode}`}`);let u=JSON.parse(c.stdout||"{}").CopyPartResult?.ETag;if(!u)throw Error(`upload-part-copy ${a.part} returned no ETag`);return{ETag:u,PartNumber:a.part}}),i=await Ii(["s3api","complete-multipart-upload","--bucket",e.destBucket,"--key",e.destKey,"--upload-id",r,"--multipart-upload",JSON.stringify({Parts:o}),"--output","json"],e.env);if(i.exitCode!==0)throw Error(`complete-multipart-upload failed: ${i.stderr.trim()||`exit ${i.exitCode}`}`);return{checksumSha256:null,etag:JSON.parse(i.stdout||"{}").ETag??null}}catch(o){let i=await Ii(["s3api","abort-multipart-upload","--bucket",e.destBucket,"--key",e.destKey,"--upload-id",r],e.env).catch(()=>({exitCode:1,stderr:"abort-multipart-upload could not be invoked"}));if(i.exitCode!==0)console.warn([`[content-recovery] FAILED to abort multipart upload ${r}`,`for ${e.destBucket}/${e.destKey}: ${i.stderr.trim().slice(0,300)}.`,"It is billable storage invisible to every object listing; clear it with",`aws s3api abort-multipart-upload --bucket ${e.destBucket}`,`--key ${e.destKey} --upload-id ${r}`].join(" "));throw o}}async function nWe(e){let{stdout:t,stderr:r,exitCode:n,timedOut:o}=await Ii(["s3api","head-object","--bucket",e.bucket,"--key",e.key,"--checksum-mode","ENABLED","--output","json"],e.env);if(n!==0){let s=o?"timed out":r.trim()||`exit ${n}`;return LHe.test(r)?{object:null,failed:null}:{object:null,failed:s}}let i=JSON.parse(t||"{}");return{object:{size:i.ContentLength??0,etag:i.ETag?.replace(/"/g,"")??null,checksumSha256:i.ChecksumSHA256??null,crc64:i.ChecksumType==="FULL_OBJECT"?i.ChecksumCRC64NVME??null:null},failed:null}}async function Zee(e,t){let r=["s3api","head-object","--no-sign-request","--bucket",e.bucket,"--key",e.object];if(e.version)r.push("--version-id",e.version);let{stderr:n,exitCode:o,timedOut:i}=await Ii(r,t);if(o===0)return{readable:!0,refusedByUpstream:!1,detail:null};let s=i?"timed out":n.trim()||`exit ${o}`;return{readable:!1,refusedByUpstream:BHe.test(n),detail:s}}async function oWe(e,t){let r=["s3api","head-object","--no-sign-request","--checksum-mode","ENABLED","--bucket",e.bucket,"--key",e.object,"--output","json"];if(e.version)r.push("--version-id",e.version);let{stdout:n,stderr:o,exitCode:i,timedOut:s}=await Ii(r,t);if(i!==0)return{crc64:null,failed:s?"timed out":o.trim()||`exit ${i}`};let a=JSON.parse(n||"{}");return{crc64:a.ChecksumType==="FULL_OBJECT"?a.ChecksumCRC64NVME??null:null,failed:null}}async function iWe(e){let{stderr:t,exitCode:r,timedOut:n}=await Ii(["s3api","delete-object","--bucket",e.bucket,"--key",e.key],e.env);if(r===0)return{deleted:!0,detail:null};return{deleted:!1,detail:n?"timed out":t.trim()||`exit ${r}`}}async function ste(e){let{entry:t}=e;if(!t.source)return{key:t.key,size:t.size,action:"unrecoverable",detail:t.reason};let r=t.source.origin,n=(u)=>t.size>Qee&&!ote(u.origin),o="above CopyObject's 5 GB limit; a multipart copy cannot carry the key's SHA-256, and matching the source's CRC64 would only prove we faithfully copied a guess";if(n(t.source)&&(t.alternatives??[]).every(n))return{key:t.key,size:t.size,action:"unrecoverable",origin:r,detail:o};if(!e.apply){for(let u of[t.source,...t.alternatives??[]]){if(n(u))continue;if((await Zee(u,e.env)).readable)return{key:t.key,size:t.size,action:"would-recover",origin:u.origin}}return{key:t.key,size:t.size,action:"unrecoverable",origin:r,detail:"every recorded source for this key is unreadable"}}let i=[t.source,...t.alternatives??[]].filter((u)=>!n(u)),s=[];for(let u of i){let d;try{d=await eWe({source:u,destBucket:e.destBucket,destKey:e.destKey,env:e.env})}catch(b){let x=b instanceof Error?b.message:String(b);if(s.push(x),MHe.test(x))continue;return{key:t.key,size:t.size,action:"failed",origin:u.origin,detail:x}}let f=await nWe({bucket:e.destBucket,key:e.destKey,env:e.env}),m=d.checksumSha256??f.object?.checksumSha256??null,p=!m&&f.object?.crc64?await oWe(u,e.env):null;if(p?.failed)s.push(`could not read the source's CRC64: ${p.failed}`);let h=YHe({key:t.key,origin:u.origin,checksumSha256:m,etag:d.etag??f.object?.etag??null,size:f.object?.size??null,crc64:f.object?.crc64??null,sourceCrc64:p?.crc64??null});if(h.ok)return{key:t.key,size:t.size,action:"recovered",origin:u.origin,verification:h.method};let y=await iWe({bucket:e.destBucket,key:e.destKey,env:e.env});return{key:t.key,size:t.size,action:"failed",detail:[`refused by ${h.method}: ${h.detail}`,y.deleted?"the object was deleted":`the object was LEFT IN THE BUCKET (delete failed: ${y.detail})`].join("; "),origin:u.origin,leftInBucket:!y.deleted}}let a=await Zee(t.source,e.env),c=s[s.length-1]??"no candidate source could be copied";if(a.refusedByUpstream)return{key:t.key,size:t.size,action:"unrecoverable",origin:t.source.origin,detail:`upstream will not serve any recorded source for this key (${a.detail}): ${c.slice(0,160)}`};return{key:t.key,size:t.size,action:"failed",origin:t.source.origin,detail:a.readable?c:`the source could not be probed (${a.detail}), so whether upstream serves it is unknown: ${c.slice(0,160)}`}}var MHe,LHe,BHe,Qee=5368709120,UHe=1073741824,zHe=8,L2=1800000,B2,VHe,JHe,ZHe=4,QHe=750;var ate=O(()=>{gp();vt();Oi();MHe=/\((?:AccessDenied|NoSuchVersion|NoSuchKey|NotFound|Forbidden|InvalidArgument|403|404)\)/i,LHe=/\((?:404|NoSuchKey|NotFound)\)/i,BHe=/\((?:403|404|AccessDenied|Forbidden|NoSuchKey|NotFound|NoSuchVersion|InvalidArgument)\)/i,B2=["AWS_ENDPOINT_URL","AWS_ENDPOINT_URL_S3"],VHe={SHA256:64,SHA256E:64,MD5:32,MD5E:32};JHe=/\((?:429|503|SlowDown|Throttling\w*|ThrottledException|RequestTimeout|RequestTimeoutException|InternalError|ServiceUnavailable)\)|Rate exceeded/i});import{rmSync as z2}from"fs";import{join as sWe}from"path";async function cWe(e){let t=await Yl(e),r=new Map;for(let[n,o]of t){let i=r.get(o)??[];i.push(n),r.set(o,i)}return r}function lte(e){return/does not exist in/.test(e)}async function lWe(e,t,r){let n=new Map;if(r.length===0)return n;let o=Bun.spawn({cmd:["git","cat-file","--batch"],cwd:e,stdin:new TextEncoder().encode(r.map((u)=>`${t}:${u}
196
+ `)){let i=/^(\S+?)s?\s+([0-9a-f-]{36}):V\s+([+-])(\S+)$/.exec(o.trim());if(!i)continue;let s=t.get(i[2]);if(!s?.bucket)continue;let a=GHe(i[4]),c=a.indexOf("#");if(c<=0)continue;let u=Number.parseFloat(i[1])||0;r.push({stamp:u,retracted:i[3]==="-",value:a,pin:{bucket:s.bucket,object:a.slice(c+1),version:a.slice(0,c),remoteName:s.name}})}r.sort((o,i)=>o.stamp-i.stamp);let n=new Map;for(let o of r)if(o.retracted)n.delete(o.value);else n.set(o.value,o.pin);return[...n.values()]}async function rte(e){let t=["aws","s3api","list-object-versions","--bucket",e.bucket,"--prefix",e.prefix,"--output","json","--query","Versions[].[Key,VersionId,Size,ETag]","--page-size","1000"];if(!e.signed)t.push("--no-sign-request");let{stdout:r,stderr:n,exitCode:o,timedOut:i}=await C(t,{unsetEnv:B2,timeout:L2});if(o!==0||i)throw Error(`listing s3://${e.bucket}/${e.prefix} failed: ${i?"timed out":n.trim()||`exit ${o}`}`);return HHe(r)}function HHe(e){let t=new Map,r=e.trim()?JSON.parse(e):[];for(let[n,o,i,s]of r??[]){let a=t.get(n)??[];a.push({object:n,version:o,size:i,etag:(s??"").replace(/"/g,"")}),t.set(n,a)}return t}function nte(e){let t=ete(e.key);if(!t)return{key:e.key,size:0,reason:"not a parseable annex key"};let r={key:e.key,size:t.size},n=e.pins[e.pins.length-1],o=e.upstream?WHe(t.size,e):null;if(n){let i=o&&o.version!==n.version?[o]:void 0;return{...r,source:{...n,origin:"pinned",size:t.size},alternatives:i}}if(!e.upstream)return{...r,reason:"no upstream remote to recover from"};if(o)return{...r,source:o};return{...r,reason:KHe(t.size,e)}}function WHe(e,t){let r=t.upstream;if(!r)return null;let n=t.paths.flatMap((s)=>r.index.get(`${r.prefix}${s}`)?.filter((a)=>a.size===e)??[]),o=new Map(n.map((s)=>[s.etag,s]));if(o.size!==1)return null;let[i]=o.values();return{bucket:r.bucket,object:i.object,version:i.version,remoteName:"upstream",origin:"version-match",size:e}}function KHe(e,t){let r=t.upstream;if(!r)return"no upstream remote to recover from";let n=t.paths.flatMap((i)=>r.index.get(`${r.prefix}${i}`)?.filter((s)=>s.size===e)??[]),o=new Set(n.map((i)=>i.etag));return o.size>1?`${o.size} distinct upstream objects carry this key's size; 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a multipart copy cannot carry the key's SHA-256, and matching the source's CRC64 would only prove we faithfully copied a guess";if(n(t.source)&&(t.alternatives??[]).every(n))return{key:t.key,size:t.size,action:"unrecoverable",origin:r,detail:o};if(!e.apply){for(let u of[t.source,...t.alternatives??[]]){if(n(u))continue;if((await Zee(u,e.env)).readable)return{key:t.key,size:t.size,action:"would-recover",origin:u.origin}}return{key:t.key,size:t.size,action:"unrecoverable",origin:r,detail:"every recorded source for this key is unreadable"}}let i=[t.source,...t.alternatives??[]].filter((u)=>!n(u)),s=[];for(let u of i){let d;try{d=await eWe({source:u,destBucket:e.destBucket,destKey:e.destKey,env:e.env})}catch(b){let x=b instanceof Error?b.message:String(b);if(s.push(x),MHe.test(x))continue;return{key:t.key,size:t.size,action:"failed",origin:u.origin,detail:x}}let f=await nWe({bucket:e.destBucket,key:e.destKey,env:e.env}),m=d.checksumSha256??f.object?.checksumSha256??null,p=!m&&f.object?.crc64?await oWe(u,e.env):null;if(p?.failed)s.push(`could not read the source's CRC64: ${p.failed}`);let h=YHe({key:t.key,origin:u.origin,checksumSha256:m,etag:d.etag??f.object?.etag??null,size:f.object?.size??null,crc64:f.object?.crc64??null,sourceCrc64:p?.crc64??null});if(h.ok)return{key:t.key,size:t.size,action:"recovered",origin:u.origin,verification:h.method};let y=await iWe({bucket:e.destBucket,key:e.destKey,env:e.env});return{key:t.key,size:t.size,action:"failed",detail:[`refused by ${h.method}: ${h.detail}`,y.deleted?"the object was deleted":`the object was LEFT IN THE BUCKET (delete failed: ${y.detail})`].join("; 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198
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PYe,IYe,NYe="https://api.datacite.org/application/vnd.datacite.datacite+json",vne=5;var Ene=O(()=>{xne();PYe=/^10\.\d{4,}\/[^\s]+$/,IYe=/^\d{4}-\d{4}-\d{4}-[\dX]{4}$/});Xe();var $b={};IS($b,{program:()=>a$,createCommand:()=>c$,createOption:()=>l$,createArgument:()=>u$,Command:()=>d$,Option:()=>f$,Argument:()=>p$,Help:()=>m$,CommanderError:()=>h$,InvalidArgumentError:()=>g$,InvalidOptionArgumentError:()=>y$},{program:(iXe)=>a$=iXe,createCommand:(iXe)=>c$=iXe,createOption:(iXe)=>l$=iXe,createArgument:(iXe)=>u$=iXe,Command:(iXe)=>d$=iXe,Option:(iXe)=>f$=iXe,Argument:(iXe)=>p$=iXe,Help:(iXe)=>m$=iXe,CommanderError:(iXe)=>h$=iXe,InvalidArgumentError:(iXe)=>g$=iXe,InvalidOptionArgumentError:(iXe)=>y$=iXe});var{Argument:o$}=Pp(),{Command:Sb}=n$(),{CommanderError:wie,InvalidArgumentError:i$}=au(),{Help:Die}=xb(),{Option:s$}=_b();var a$=new Sb,c$=(e)=>new Sb(e),l$=(e,t)=>new s$(e,t),u$=(e,t)=>new 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199
199
  Run with --help-all for examples and detailed descriptions.
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "nemar-cli",
3
- "version": "0.10.4-PR1405.ba5371f",
3
+ "version": "0.10.4-PR1405.e3fdbed",
4
4
  "description": "CLI for NEMAR (Neuroelectromagnetic Data Archive and Tools Resource) dataset management",
5
5
  "type": "module",
6
6
  "main": "dist/index.js",