nemar-cli 0.10.16-dev.3335 → 0.10.16-dev.3338
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/dist/index.js +1 -1
- package/package.json +2 -1
package/dist/index.js
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@@ -99,7 +99,7 @@ ${t}`,hPe,gPe,yPe=(e,t,r)=>{let n=r===""?"":`with ${r.trim()}() `,i=mPe.bind(nul
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`)}var h2=!1;var{spawn:ZKe}=globalThis.Bun;function Ml(e,t=[]){let r=e.replace(QKe,'("$1","<redacted>")');for(let n of t)if(n.length>=eJe)r=r.split(n).join("<redacted>");return r}function Wx(e){let t=["AWS_SESSION_TOKEN","AWS_SECRET_ACCESS_KEY","AWS_ACCESS_KEY_ID"],r=new Set;for(let n of[process.env,e??{}])for(let i of t){let o=n[i];if(typeof o==="string"&&o.length>0)r.add(o)}return[...r]}async function Ste(e,t){let r=e.getReader(),n=new TextDecoder,i="";while(!0){let{done:o,value:s}=await r.read();if(o)break;if(s.byteLength===0)continue;t(),i+=n.decode(s,{stream:!0})}return i+n.decode()}async function k(e,t={}){let r={...process.env,GIT_TERMINAL_PROMPT:"0",...t.env};for(let b of t.unsetEnv??[])delete r[b];let n=ZKe({cmd:e,cwd:t.cwd,...t.stdin===void 0?{}:{stdin:new TextEncoder().encode(t.stdin)},stdout:"pipe",stderr:"pipe",env:r}),i=!1,o,s,a=performance.now(),c=()=>{if(s!==void 0)clearTimeout(s),s=void 0},u=()=>{if(!t.onInactivityWarning)return;c(),s=setTimeout(()=>{s=void 0;try{t.onInactivityWarning?.(performance.now()-a)}catch{console.error("Could not display subprocess inactivity warning; the child result is unaffected.")}},t.inactivityWarningAfterMs??tJe)};if(u(),t.timeout)o=setTimeout(()=>{i=!0,c(),n.kill()},t.timeout);let d=Gx()?Wx(r):[];if(Gx()){let b=t.cwd?` (cwd=${t.cwd})`:"";_f(l.dim(Ml(`$ ${e.join(" ")}${b}`,d)))}let f=()=>{a=performance.now(),u()},p,m,g,h=n.exited.then((b)=>(c(),b));try{[p,m,g]=await Promise.all([Ste(n.stdout,f),Ste(n.stderr,f),h])}finally{if(c(),o)clearTimeout(o)}if(Gx()){if(t.sensitiveOutput)_f(l.dim("[sensitive subprocess output suppressed]"));else{if(p.trim())_f(l.dim(Ml(p.trimEnd(),d)));if(m.trim())_f(l.yellow(Ml(m.trimEnd(),d)))}_f(l.dim(`(exit ${g})`))}if(i)return{stdout:p,stderr:m||`Command timed out after ${Math.round(t.timeout/1000)}s`,exitCode:g??1,timedOut:!0};return{stdout:p,stderr:m,exitCode:g,timedOut:!1}}var QKe,eJe=8,tJe=120000;var Nt=P(()=>{Ze();QKe=/\(\s*"((?:x-amz-)[^"]*|authorization|proxy-authorization)"\s*,\s*"[^"]*"\s*\)/gi});function nJe(){if(process.platform==="darwin")return"macos";if(process.platform==="win32")return"windows";return"linux"}function kte(e,t=nJe()){return e.installInstructions[t]}function iJe(e){let t=e.match(/(\d+\.\d+(?:\.\d+)?)/);return t?t[1]:void 0}function sJe(){let e=Number(process.env.TEST_PROBE_TIMEOUT_MS);return Number.isFinite(e)&&e>0?e:oJe}async function Cte(e){try{let{exitCode:t,stdout:r,timedOut:n}=await k(e.cmd,{timeout:sJe()});if(n)return{available:!1,timedOut:!0};if(t!==0)return{available:!1};return{available:!0,version:iJe(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: ${r}`);return{available:!1}}}async function ah(){let e=Object.entries($te);return Promise.all(e.map(async([t,r])=>{let{available:n,version:i,timedOut:o}=await Cte(r);return{key:t,name:r.name,purpose:r.purpose,required:r.required,available:n,version:i,timedOut:o,installInstruction:kte(r)}}))}async function Rte(){let t=(await ah()).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: ${r.installInstruction}`);return console.warn("Run `nemar doctor` anytime to re-check. You can finish signup without them.\n"),t}async function ql(e){let r=rJe[e].map((s)=>$te[s]).filter(Boolean),n=await Promise.all(r.map(async(s)=>{let a=await Cte(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 i=n.filter((s)=>!s.available&&!s.timedOut&&s.check.required).map((s)=>({tool:s.check.name,installInstruction:kte(s.check)}));if(i.length===0)return;let o=[`
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Missing required tools:`];for(let s of i)o.push(` ${s.tool} not installed`),o.push(` Install: ${s.installInstruction}`);throw Error(o.join(`
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`))}var $te,rJe,oJe=4000;var ch=P(()=>{Nt();$te={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)"}}},rJe={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 Ote;var Ate=P(()=>{Ote={name:"nemar-cli",version:"0.10.16-dev.
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`))}var $te,rJe,oJe=4000;var ch=P(()=>{Nt();$te={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)"}}},rJe={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 Ote;var Ate=P(()=>{Ote={name:"nemar-cli",packageManager:"bun@1.4.3",version:"0.10.16-dev.3338",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/","lint:scrub":"biome check scripts/scrub shared/identifier-scrub.ts test/scrub","test:scrub":"bun test --preload ./test/scrub/helpers/temp-dirs-preload.ts --path-ignore-patterns='__run_every_scrub_suite__' test/scrub test/identifier-scan.test.ts test/identifier-scrub.test.ts test/identifier-dates.test.ts test/identifier-fleet.test.ts","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:{"@anthropic-ai/sdk":"^0.132.1","@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",husky:"^9.1.7","lint-staged":"^16.3.2",typescript:"^5.5.4",wrangler:"^4.70.0",yaml:"^2.8.4"}}});var Ji;var Df=P(()=>{Ate();Ji=Ote.version});import{mkdirSync as cJe,readdirSync as lJe,unlinkSync as uJe,writeFileSync as dJe}from"fs";import{join as g2}from"path";function jte(){Ef=!0}function Ll(){return Ef}function Mte(e,t=process.env){return e.includes("--debug")||t.NEMAR_DEBUG==="1"}function uh(e){Nte=e,Zt(`Step: ${e}`)}function dh(){Pte=!0}function qte(){return Pte}function Pr(){Ite=!0}function Lte(){return Ite}function Zt(e){if(Ef)process.stderr.write(`[debug] ${e}
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`)}function hJe(e){let t={};for(let[r,n]of Object.entries(e))t[r]=mJe.has(r.toLowerCase())?"[REDACTED]":n;return t}function Ute(e){let t=e.indexOf("@");if(t<=0)return"***";return`${e[0]}***${e.slice(t)}`}function y2(e,t,r=0){if(r>yJe)return"[REDACTED: depth]";if(Array.isArray(t))return t.map((n)=>y2(e,n,r+1));if(t&&typeof t==="object"){let n={};for(let[i,o]of Object.entries(t))n[i]=y2(i,o,r+1);return n}if(typeof t==="string"){if(gJe.test(e))return"[REDACTED]";return t.replace(Bte,Ute)}return t}function b2(e){return e.replace(bJe,"Bearer [REDACTED]").replace(xJe,"[REDACTED_AWS_KEY]").replace(wJe,"$1[REDACTED]").replace(vJe,"$1$2=[REDACTED]").replace(Bte,Ute)}function _Je(e){return b2(e)}function Tte(e,t=pJe){if(e===void 0)return;let r=e;try{let n=JSON.parse(e);r=JSON.stringify(y2("",n))}catch{}if(r=b2(r),Buffer.byteLength(r,"utf8")>t)r=`${Buffer.from(r,"utf8").subarray(0,t).toString("utf8")}... [truncated]`;return r}function Yx(e){if(!Ef)return;let t=_Je(e.url);try{let r={...e,url:t,requestHeaders:e.requestHeaders?hJe(e.requestHeaders):void 0,requestBody:Tte(e.requestBody),responseBody:Tte(e.responseBody)};Jx.push(r),Zt(`${e.method} ${t} -> ${e.status??"ERROR"} (${e.durationMs}ms)`)}catch(r){let n=q(r);Jx.push({method:e.method,url:t,status:e.status,durationMs:e.durationMs,note:`redaction failed: ${n}`}),Zt(`redaction failed for ${e.method} ${t}: ${n}`)}}async function DJe(){let e=[];try{let t=process.versions.bun?`Bun ${process.versions.bun}`:`Node ${process.version}`;e.push(`CLI version: ${Ji}`),e.push(`OS/Arch: ${process.platform}/${process.arch}`),e.push(`Runtime: ${t}`)}catch(t){e.push(`(could not read CLI/OS/runtime info: ${q(t)})`)}e.push(""),e.push("Active account:");try{let t=Ft();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: ${q(t)})`)}e.push(""),e.push("External tools:");try{let t=await ah();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: ${q(t)})`)}return e}async function x2(){return(await DJe()).join(`
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`)}async function zte(){if(!Ef||Kx!==void 0)return;try{Kx=await x2()}catch(e){let t=q(e);Kx=`(could not build environment report: ${t})`,Zt(`environment snapshot failed: ${t}`)}}function Vte(e){if(Fte.has(e))return{flag:e};for(let t of Fte){if(!e.startsWith(t)||e.length<=t.length)continue;if(t.length===2)return{flag:t,kind:"short-attached"};if(e[t.length]==="=")return{flag:t,kind:"long-eq"}}return null}function EJe(e){let t=[];for(let r=0;r<e.length;r++){let n=e[r],i=Vte(n);if(!i){t.push(n);continue}if(i.kind==="long-eq")t.push(`${i.flag}=[REDACTED]`);else if(i.kind==="short-attached")t.push(`${i.flag}[REDACTED]`);else if(t.push(n),r+1<e.length)t.push("[REDACTED]"),r++}return t}function SJe(e){let t=[];for(let r=0;r<e.length;r++){let n=e[r],i=Vte(n);if(!i){t.push(n);continue}if(!i.kind&&r+1<e.length)r++}return t}function $Je(e){let t=[];for(let n of SJe(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 kJe(e,t){let r=[];if(r.push("NEMAR CLI Debug Log"),r.push(`Generated: ${new Date().toISOString()}`),r.push(`Command: nemar ${b2(EJe(e).join(" "))}`),r.push(""),r.push(Kx??"(environment snapshot unavailable)"),r.push(""),r.push("HTTP requests:"),Jx.length===0)r.push(" (none)");else Jx.forEach((n,i)=>{if(r.push(` [${i+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: ${Nte??"(none recorded)"}`),r.push(`Exit code: ${t}`),`${r.join(`
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package/package.json
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{
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"name": "nemar-cli",
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"packageManager": "bun@1.4.3",
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"version": "0.10.16-dev.3338",
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"description": "CLI for NEMAR (Neuroelectromagnetic Data Archive and Tools Resource) dataset management",
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"type": "module",
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"main": "dist/index.js",
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