nemar-cli 0.10.4-dev.2519 → 0.10.4-dev.2542
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}`,XDe,ZDe,QDe=(e,t,r)=>{let n=r===""?"":`with ${r.trim()}() `,o=JDe.bind(nul
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`)}var pD=!1;var{spawn:I9e}=globalThis.Bun;async function A(e,t={}){let r={...process.env,GIT_TERMINAL_PROMPT:"0",...t.env};for(let u of t.unsetEnv??[])delete r[u];let n=I9e({cmd:e,cwd:t.cwd,stdout:"pipe",stderr:"pipe",env:r}),o=!1,i;if(t.timeout)i=setTimeout(()=>{o=!0,n.kill()},t.timeout);if(mD()){let u=t.cwd?` (cwd=${t.cwd})`:"";sf(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(mD()){if(s.trim())sf(l.dim(s.trimEnd()));if(a.trim())sf(l.yellow(a.trimEnd()));sf(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 sr=F(()=>{Xe()});function T9e(){if(process.platform==="darwin")return"macos";if(process.platform==="win32")return"windows";return"linux"}function VW(e,t=T9e()){return e.installInstructions[t]}function N9e(e){let t=e.match(/(\d+\.\d+(?:\.\d+)?)/);return t?t[1]:void 0}function j9e(){let e=Number(process.env.TEST_PROBE_TIMEOUT_MS);return Number.isFinite(e)&&e>0?e:q9e}async function zW(e){try{let{exitCode:t,stdout:r,timedOut:n}=await A(e.cmd,{timeout:j9e()});if(n)return{available:!1,timedOut:!0};if(t!==0)return{available:!1};return{available:!0,version:N9e(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 af(){let e=Object.entries(UW);return Promise.all(e.map(async([t,r])=>{let{available:n,version:o,timedOut:i}=await zW(r);return{key:t,name:r.name,purpose:r.purpose,required:r.required,available:n,version:o,timedOut:i,installInstruction:VW(r)}}))}async function GW(){let t=(await af()).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 aa(e){let r=P9e[e].map((s)=>UW[s]).filter(Boolean),n=await Promise.all(r.map(async(s)=>{let a=await zW(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:VW(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 UW,P9e,q9e=4000;var cf=F(()=>{sr();UW={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)"}}},P9e={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 WW;var HW=F(()=>{WW={name:"nemar-cli",version:"0.10.4-dev.
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`))}var UW,P9e,q9e=4000;var cf=F(()=>{sr();UW={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)"}}},P9e={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 WW;var HW=F(()=>{WW={name:"nemar-cli",version:"0.10.4-dev.2542",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 ci;var lf=F(()=>{HW();ci=WW.version});import{mkdirSync as L9e,readdirSync as B9e,unlinkSync as U9e,writeFileSync as V9e}from"fs";import{join as hD}from"path";function QW(){nl=!0}function ca(){return nl}function eK(e,t=process.env){return e.includes("--debug")||t.NEMAR_DEBUG==="1"}function df(e){ZW=e,vr(`Step: ${e}`)}function ff(){JW=!0}function tK(){return JW}function yD(){XW=!0}function rK(){return XW}function vr(e){if(nl)process.stderr.write(`[debug] ${e}
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`)}function W9e(e){let t={};for(let[r,n]of Object.entries(e))t[r]=H9e.has(r.toLowerCase())?"[REDACTED]":n;return t}function oK(e){let t=e.indexOf("@");if(t<=0)return"***";return`${e[0]}***${e.slice(t)}`}function gD(e,t,r=0){if(r>Y9e)return"[REDACTED: depth]";if(Array.isArray(t))return t.map((n)=>gD(e,n,r+1));if(t&&typeof t==="object"){let n={};for(let[o,i]of Object.entries(t))n[o]=gD(o,i,r+1);return n}if(typeof t==="string"){if(K9e.test(e))return"[REDACTED]";return t.replace(nK,oK)}return t}function xD(e){return e.replace(J9e,"Bearer [REDACTED]").replace(X9e,"[REDACTED_AWS_KEY]").replace(Z9e,"$1[REDACTED]").replace(Q9e,"$1$2=[REDACTED]").replace(nK,oK)}function e7e(e){return xD(e)}function KW(e,t=G9e){if(e===void 0)return;let r=e;try{let n=JSON.parse(e);r=JSON.stringify(gD("",n))}catch{}if(r=xD(r),Buffer.byteLength(r,"utf8")>t)r=`${Buffer.from(r,"utf8").subarray(0,t).toString("utf8")}... [truncated]`;return r}function W0(e){if(!nl)return;let t=e7e(e.url);try{let r={...e,url:t,requestHeaders:e.requestHeaders?W9e(e.requestHeaders):void 0,requestBody:KW(e.requestBody),responseBody:KW(e.responseBody)};H0.push(r),vr(`${e.method} ${t} -> ${e.status??"ERROR"} (${e.durationMs}ms)`)}catch(r){let n=P(r);H0.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 t7e(){let e=[];try{let t=process.versions.bun?`Bun ${process.versions.bun}`:`Node ${process.version}`;e.push(`CLI version: ${ci}`),e.push(`OS/Arch: ${process.platform}/${process.arch}`),e.push(`Runtime: ${t}`)}catch(t){e.push(`(could not read CLI/OS/runtime info: ${P(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: ${P(t)})`)}e.push(""),e.push("External tools:");try{let t=await af();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: ${P(t)})`)}return e}async function bD(){return(await t7e()).join(`
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`)}async function iK(){if(!nl||G0!==void 0)return;try{G0=await bD()}catch(e){let t=P(e);G0=`(could not build environment report: ${t})`,vr(`environment snapshot failed: ${t}`)}}function sK(e){if(YW.has(e))return{flag:e};for(let t of YW){if(!e.startsWith(t)||e.length<=t.length)continue;if(t.length===2)return{flag:t,kind:"short-attached"};if(e[t.length]==="=")return{flag:t,kind:"long-eq"}}return null}function r7e(e){let t=[];for(let r=0;r<e.length;r++){let n=e[r],o=sK(n);if(!o){t.push(n);continue}if(o.kind==="long-eq")t.push(`${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 n7e(e){let t=[];for(let r=0;r<e.length;r++){let n=e[r],o=sK(n);if(!o){t.push(n);continue}if(!o.kind&&r+1<e.length)r++}return t}function o7e(e){let t=[];for(let n of n7e(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 i7e(e,t){let r=[];if(r.push("NEMAR CLI Debug Log"),r.push(`Generated: ${new Date().toISOString()}`),r.push(`Command: nemar ${xD(r7e(e).join(" "))}`),r.push(""),r.push(G0??"(environment snapshot unavailable)"),r.push(""),r.push("HTTP requests:"),H0.length===0)r.push(" (none)");else H0.forEach((n,o)=>{if(r.push(` [${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: ${ZW??"(none recorded)"}`),r.push(`Exit code: ${t}`),`${r.join(`
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package/package.json
CHANGED