nemar-cli 0.10.2-dev.2453 → 0.10.2-dev.2454
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 +1 -1
package/dist/index.js
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@@ -99,7 +99,7 @@ ${t}`,qDe,jDe,MDe=(e,t,r)=>{let n=r===""?"":`with ${r.trim()}() `,i=NDe.bind(nul
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`)}var lD=!1;var{spawn:b9e}=globalThis.Bun;async function A(e,t={}){let r={...process.env,GIT_TERMINAL_PROMPT:"0",...t.env};for(let u of t.unsetEnv??[])delete r[u];let n=b9e({cmd:e,cwd:t.cwd,stdout:"pipe",stderr:"pipe",env:r}),i=!1,o;if(t.timeout)o=setTimeout(()=>{i=!0,n.kill()},t.timeout);if(uD()){let u=t.cwd?` (cwd=${t.cwd})`:"";of(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(o)clearTimeout(o);if(uD()){if(s.trim())of(l.dim(s.trimEnd()));if(a.trim())of(l.yellow(a.trimEnd()));of(l.dim(`(exit ${c})`))}if(i)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 sr=O(()=>{Xe()});function v9e(){if(process.platform==="darwin")return"macos";if(process.platform==="win32")return"windows";return"linux"}function jW(e,t=v9e()){return e.installInstructions[t]}function w9e(e){let t=e.match(/(\d+\.\d+(?:\.\d+)?)/);return t?t[1]:void 0}function E9e(){let e=Number(process.env.TEST_PROBE_TIMEOUT_MS);return Number.isFinite(e)&&e>0?e:D9e}async function MW(e){try{let{exitCode:t,stdout:r,timedOut:n}=await A(e.cmd,{timeout:E9e()});if(n)return{available:!1,timedOut:!0};if(t!==0)return{available:!1};return{available:!0,version:w9e(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 sf(){let e=Object.entries(qW);return Promise.all(e.map(async([t,r])=>{let{available:n,version:i,timedOut:o}=await MW(r);return{key:t,name:r.name,purpose:r.purpose,required:r.required,available:n,version:i,timedOut:o,installInstruction:jW(r)}}))}async function LW(){let t=(await sf()).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 sa(e){let r=_9e[e].map((s)=>qW[s]).filter(Boolean),n=await Promise.all(r.map(async(s)=>{let a=await MW(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:jW(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 qW,_9e,D9e=4000;var af=O(()=>{sr();qW={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)"}}},_9e={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 UW;var BW=O(()=>{UW={name:"nemar-cli",version:"0.10.2-dev.
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`))}var qW,_9e,D9e=4000;var af=O(()=>{sr();qW={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)"}}},_9e={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 UW;var BW=O(()=>{UW={name:"nemar-cli",version:"0.10.2-dev.2454",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 so;var cf=O(()=>{BW();so=UW.version});import{mkdirSync as $9e,readdirSync as C9e,unlinkSync as R9e,writeFileSync as k9e}from"fs";import{join as dD}from"path";function WW(){rl=!0}function aa(){return rl}function KW(e,t=process.env){return e.includes("--debug")||t.NEMAR_DEBUG==="1"}function uf(e){HW=e,vr(`Step: ${e}`)}function YW(){GW=!0}function JW(){return GW}function vr(e){if(rl)process.stderr.write(`[debug] ${e}
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`)}function I9e(e){let t={};for(let[r,n]of Object.entries(e))t[r]=F9e.has(r.toLowerCase())?"[REDACTED]":n;return t}function ZW(e){let t=e.indexOf("@");if(t<=0)return"***";return`${e[0]}***${e.slice(t)}`}function fD(e,t,r=0){if(r>T9e)return"[REDACTED: depth]";if(Array.isArray(t))return t.map((n)=>fD(e,n,r+1));if(t&&typeof t==="object"){let n={};for(let[i,o]of Object.entries(t))n[i]=fD(i,o,r+1);return n}if(typeof t==="string"){if(P9e.test(e))return"[REDACTED]";return t.replace(XW,ZW)}return t}function pD(e){return e.replace(N9e,"Bearer [REDACTED]").replace(q9e,"[REDACTED_AWS_KEY]").replace(j9e,"$1[REDACTED]").replace(M9e,"$1$2=[REDACTED]").replace(XW,ZW)}function L9e(e){return pD(e)}function VW(e,t=O9e){if(e===void 0)return;let r=e;try{let n=JSON.parse(e);r=JSON.stringify(fD("",n))}catch{}if(r=pD(r),Buffer.byteLength(r,"utf8")>t)r=`${Buffer.from(r,"utf8").subarray(0,t).toString("utf8")}... [truncated]`;return r}function G0(e){if(!rl)return;let t=L9e(e.url);try{let r={...e,url:t,requestHeaders:e.requestHeaders?I9e(e.requestHeaders):void 0,requestBody:VW(e.requestBody),responseBody:VW(e.responseBody)};z0.push(r),vr(`${e.method} ${t} -> ${e.status??"ERROR"} (${e.durationMs}ms)`)}catch(r){let n=N(r);z0.push({method:e.method,url:t,status:e.status,durationMs:e.durationMs,note:`redaction failed: ${n}`}),vr(`redaction failed for ${e.method} ${t}: ${n}`)}}async function B9e(){let e=[];try{let t=process.versions.bun?`Bun ${process.versions.bun}`:`Node ${process.version}`;e.push(`CLI version: ${so}`),e.push(`OS/Arch: ${process.platform}/${process.arch}`),e.push(`Runtime: ${t}`)}catch(t){e.push(`(could not read CLI/OS/runtime info: ${N(t)})`)}e.push(""),e.push("Active account:");try{let t=nt();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: ${N(t)})`)}e.push(""),e.push("External tools:");try{let t=await sf();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: ${N(t)})`)}return e}async function mD(){return(await B9e()).join(`
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`)}async function QW(){if(!rl||V0!==void 0)return;try{V0=await mD()}catch(e){let t=N(e);V0=`(could not build environment report: ${t})`,vr(`environment snapshot failed: ${t}`)}}function eK(e){if(zW.has(e))return{flag:e};for(let t of zW){if(!e.startsWith(t)||e.length<=t.length)continue;if(t.length===2)return{flag:t,kind:"short-attached"};if(e[t.length]==="=")return{flag:t,kind:"long-eq"}}return null}function U9e(e){let t=[];for(let r=0;r<e.length;r++){let n=e[r],i=eK(n);if(!i){t.push(n);continue}if(i.kind==="long-eq")t.push(`${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 V9e(e){let t=[];for(let r=0;r<e.length;r++){let n=e[r],i=eK(n);if(!i){t.push(n);continue}if(!i.kind&&r+1<e.length)r++}return t}function z9e(e){let t=[];for(let n of V9e(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 G9e(e,t){let r=[];if(r.push("NEMAR CLI Debug Log"),r.push(`Generated: ${new Date().toISOString()}`),r.push(`Command: nemar ${pD(U9e(e).join(" "))}`),r.push(""),r.push(V0??"(environment snapshot unavailable)"),r.push(""),r.push("HTTP requests:"),z0.length===0)r.push(" (none)");else z0.forEach((n,i)=>{if(r.push(` [${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: ${HW??"(none recorded)"}`),r.push(`Exit code: ${t}`),`${r.join(`
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package/package.json
CHANGED