nemar-cli 0.10.4-dev.2575 → 0.10.4-dev.2576
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}`,OEe,FEe,IEe=(e,t,r)=>{let n=r===""?"":`with ${r.trim()}() `,o=AEe.bind(nul
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`)}var FD=!1;var{spawn:p7e}=globalThis.Bun;async function k(e,t={}){let r={...process.env,GIT_TERMINAL_PROMPT:"0",...t.env};for(let u of t.unsetEnv??[])delete r[u];let n=p7e({cmd:e,cwd:t.cwd,stdout:"pipe",stderr:"pipe",env:r}),o=!1,i;if(t.timeout)i=setTimeout(()=>{o=!0,n.kill()},t.timeout);if(ID()){let u=t.cwd?` (cwd=${t.cwd})`:"";bf(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(ID()){if(s.trim())bf(l.dim(s.trimEnd()));if(a.trim())bf(l.yellow(a.trimEnd()));bf(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 Pt=O(()=>{Xe()});function h7e(){if(process.platform==="darwin")return"macos";if(process.platform==="win32")return"windows";return"linux"}function cK(e,t=h7e()){return e.installInstructions[t]}function g7e(e){let t=e.match(/(\d+\.\d+(?:\.\d+)?)/);return t?t[1]:void 0}function x7e(){let e=Number(process.env.TEST_PROBE_TIMEOUT_MS);return Number.isFinite(e)&&e>0?e:y7e}async function lK(e){try{let{exitCode:t,stdout:r,timedOut:n}=await k(e.cmd,{timeout:x7e()});if(n)return{available:!1,timedOut:!0};if(t!==0)return{available:!1};return{available:!0,version:g7e(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 _f(){let e=Object.entries(aK);return Promise.all(e.map(async([t,r])=>{let{available:n,version:o,timedOut:i}=await lK(r);return{key:t,name:r.name,purpose:r.purpose,required:r.required,available:n,version:o,timedOut:i,installInstruction:cK(r)}}))}async function uK(){let t=(await _f()).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 xa(e){let r=m7e[e].map((s)=>aK[s]).filter(Boolean),n=await Promise.all(r.map(async(s)=>{let a=await lK(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:cK(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 aK,m7e,y7e=4000;var vf=O(()=>{Pt();aK={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)"}}},m7e={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 fK;var dK=O(()=>{fK={name:"nemar-cli",version:"0.10.4-dev.
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`))}var aK,m7e,y7e=4000;var vf=O(()=>{Pt();aK={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)"}}},m7e={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 fK;var dK=O(()=>{fK={name:"nemar-cli",version:"0.10.4-dev.2576",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 pi;var wf=O(()=>{dK();pi=fK.version});import{mkdirSync as _7e,readdirSync as v7e,unlinkSync as w7e,writeFileSync as D7e}from"fs";import{join as PD}from"path";function xK(){ml=!0}function ba(){return ml}function bK(e,t=process.env){return e.includes("--debug")||t.NEMAR_DEBUG==="1"}function Ef(e){yK=e,Er(`Step: ${e}`)}function Sf(){hK=!0}function _K(){return hK}function ND(){gK=!0}function vK(){return gK}function Er(e){if(ml)process.stderr.write(`[debug] ${e}
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`)}function C7e(e){let t={};for(let[r,n]of Object.entries(e))t[r]=$7e.has(r.toLowerCase())?"[REDACTED]":n;return t}function DK(e){let t=e.indexOf("@");if(t<=0)return"***";return`${e[0]}***${e.slice(t)}`}function TD(e,t,r=0){if(r>R7e)return"[REDACTED: depth]";if(Array.isArray(t))return t.map((n)=>TD(e,n,r+1));if(t&&typeof t==="object"){let n={};for(let[o,i]of Object.entries(t))n[o]=TD(o,i,r+1);return n}if(typeof t==="string"){if(k7e.test(e))return"[REDACTED]";return t.replace(wK,DK)}return t}function qD(e){return e.replace(A7e,"Bearer [REDACTED]").replace(O7e,"[REDACTED_AWS_KEY]").replace(F7e,"$1[REDACTED]").replace(I7e,"$1$2=[REDACTED]").replace(wK,DK)}function P7e(e){return qD(e)}function pK(e,t=S7e){if(e===void 0)return;let r=e;try{let n=JSON.parse(e);r=JSON.stringify(TD("",n))}catch{}if(r=qD(r),Buffer.byteLength(r,"utf8")>t)r=`${Buffer.from(r,"utf8").subarray(0,t).toString("utf8")}... [truncated]`;return r}function dg(e){if(!ml)return;let t=P7e(e.url);try{let r={...e,url:t,requestHeaders:e.requestHeaders?C7e(e.requestHeaders):void 0,requestBody:pK(e.requestBody),responseBody:pK(e.responseBody)};ug.push(r),Er(`${e.method} ${t} -> ${e.status??"ERROR"} (${e.durationMs}ms)`)}catch(r){let n=P(r);ug.push({method:e.method,url:t,status:e.status,durationMs:e.durationMs,note:`redaction failed: ${n}`}),Er(`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: ${pi}`),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=rt();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 _f();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 jD(){return(await T7e()).join(`
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`)}async function EK(){if(!ml||lg!==void 0)return;try{lg=await jD()}catch(e){let t=P(e);lg=`(could not build environment report: ${t})`,Er(`environment snapshot failed: ${t}`)}}function SK(e){if(mK.has(e))return{flag:e};for(let t of mK){if(!e.startsWith(t)||e.length<=t.length)continue;if(t.length===2)return{flag:t,kind:"short-attached"};if(e[t.length]==="=")return{flag:t,kind:"long-eq"}}return null}function N7e(e){let t=[];for(let r=0;r<e.length;r++){let n=e[r],o=SK(n);if(!o){t.push(n);continue}if(o.kind==="long-eq")t.push(`${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 q7e(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 j7e(e){let t=[];for(let n of q7e(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 M7e(e,t){let r=[];if(r.push("NEMAR CLI Debug Log"),r.push(`Generated: ${new Date().toISOString()}`),r.push(`Command: nemar ${qD(N7e(e).join(" "))}`),r.push(""),r.push(lg??"(environment snapshot unavailable)"),r.push(""),r.push("HTTP requests:"),ug.length===0)r.push(" (none)");else ug.forEach((n,o)=>{if(r.push(` [${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: ${yK??"(none recorded)"}`),r.push(`Exit code: ${t}`),`${r.join(`
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package/package.json
CHANGED