nemar-cli 0.10.4-dev.2608 → 0.10.4-dev.2609
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}`,T2e,N2e,j2e=(e,t,r)=>{let n=r===""?"":`with ${r.trim()}() `,o=I2e.bind(nul
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`)}var ZD=!1;var{spawn:yMe}=globalThis.Bun;async function C(e,t={}){let r={...process.env,GIT_TERMINAL_PROMPT:"0",...t.env};for(let u of t.unsetEnv??[])delete r[u];let n=yMe({cmd:e,cwd:t.cwd,...t.stdin===void 0?{}:{stdin:new TextEncoder().encode(t.stdin)},stdout:"pipe",stderr:"pipe",env:r}),o=!1,i;if(t.timeout)i=setTimeout(()=>{o=!0,n.kill()},t.timeout);if(QD()){let u=t.cwd?` (cwd=${t.cwd})`:"";Af(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(QD()){if(s.trim())Af(l.dim(s.trimEnd()));if(a.trim())Af(l.yellow(a.trimEnd()));Af(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 At=O(()=>{Xe()});function bMe(){if(process.platform==="darwin")return"macos";if(process.platform==="win32")return"windows";return"linux"}function PK(e,t=bMe()){return e.installInstructions[t]}function _Me(e){let t=e.match(/(\d+\.\d+(?:\.\d+)?)/);return t?t[1]:void 0}function wMe(){let e=Number(process.env.TEST_PROBE_TIMEOUT_MS);return Number.isFinite(e)&&e>0?e:vMe}async function IK(e){try{let{exitCode:t,stdout:r,timedOut:n}=await C(e.cmd,{timeout:wMe()});if(n)return{available:!1,timedOut:!0};if(t!==0)return{available:!1};return{available:!0,version:_Me(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 Of(){let e=Object.entries(FK);return Promise.all(e.map(async([t,r])=>{let{available:n,version:o,timedOut:i}=await IK(r);return{key:t,name:r.name,purpose:r.purpose,required:r.required,available:n,version:o,timedOut:i,installInstruction:PK(r)}}))}async function TK(){let t=(await Of()).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=xMe[e].map((s)=>FK[s]).filter(Boolean),n=await Promise.all(r.map(async(s)=>{let a=await IK(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:PK(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 FK,xMe,vMe=4000;var Ff=O(()=>{At();FK={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)"}}},xMe={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 jK;var NK=O(()=>{jK={name:"nemar-cli",version:"0.10.4-dev.
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`))}var FK,xMe,vMe=4000;var Ff=O(()=>{At();FK={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)"}}},xMe={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 jK;var NK=O(()=>{jK={name:"nemar-cli",version:"0.10.4-dev.2609",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 bi;var Pf=O(()=>{NK();bi=jK.version});import{mkdirSync as EMe,readdirSync as SMe,unlinkSync as $Me,writeFileSync as CMe}from"fs";import{join as eE}from"path";function zK(){El=!0}function $a(){return El}function VK(e,t=process.env){return e.includes("--debug")||t.NEMAR_DEBUG==="1"}function Tf(e){UK=e,$r(`Step: ${e}`)}function Nf(){LK=!0}function GK(){return LK}function rE(){BK=!0}function HK(){return BK}function $r(e){if(El)process.stderr.write(`[debug] ${e}
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`)}function OMe(e){let t={};for(let[r,n]of Object.entries(e))t[r]=AMe.has(r.toLowerCase())?"[REDACTED]":n;return t}function KK(e){let t=e.indexOf("@");if(t<=0)return"***";return`${e[0]}***${e.slice(t)}`}function tE(e,t,r=0){if(r>PMe)return"[REDACTED: depth]";if(Array.isArray(t))return t.map((n)=>tE(e,n,r+1));if(t&&typeof t==="object"){let n={};for(let[o,i]of Object.entries(t))n[o]=tE(o,i,r+1);return n}if(typeof t==="string"){if(FMe.test(e))return"[REDACTED]";return t.replace(WK,KK)}return t}function nE(e){return e.replace(IMe,"Bearer [REDACTED]").replace(TMe,"[REDACTED_AWS_KEY]").replace(NMe,"$1[REDACTED]").replace(jMe,"$1$2=[REDACTED]").replace(WK,KK)}function qMe(e){return nE(e)}function qK(e,t=RMe){if(e===void 0)return;let r=e;try{let n=JSON.parse(e);r=JSON.stringify(tE("",n))}catch{}if(r=nE(r),Buffer.byteLength(r,"utf8")>t)r=`${Buffer.from(r,"utf8").subarray(0,t).toString("utf8")}... [truncated]`;return r}function w0(e){if(!El)return;let t=qMe(e.url);try{let r={...e,url:t,requestHeaders:e.requestHeaders?OMe(e.requestHeaders):void 0,requestBody:qK(e.requestBody),responseBody:qK(e.responseBody)};v0.push(r),$r(`${e.method} ${t} -> ${e.status??"ERROR"} (${e.durationMs}ms)`)}catch(r){let n=T(r);v0.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 MMe(){let e=[];try{let t=process.versions.bun?`Bun ${process.versions.bun}`:`Node ${process.version}`;e.push(`CLI version: ${bi}`),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 Of();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 oE(){return(await MMe()).join(`
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`)}async function YK(){if(!El||_0!==void 0)return;try{_0=await oE()}catch(e){let t=T(e);_0=`(could not build environment report: ${t})`,$r(`environment snapshot failed: ${t}`)}}function JK(e){if(MK.has(e))return{flag:e};for(let t of MK){if(!e.startsWith(t)||e.length<=t.length)continue;if(t.length===2)return{flag:t,kind:"short-attached"};if(e[t.length]==="=")return{flag:t,kind:"long-eq"}}return null}function LMe(e){let t=[];for(let r=0;r<e.length;r++){let n=e[r],o=JK(n);if(!o){t.push(n);continue}if(o.kind==="long-eq")t.push(`${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 BMe(e){let t=[];for(let r=0;r<e.length;r++){let n=e[r],o=JK(n);if(!o){t.push(n);continue}if(!o.kind&&r+1<e.length)r++}return t}function UMe(e){let t=[];for(let n of BMe(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 zMe(e,t){let r=[];if(r.push("NEMAR CLI Debug Log"),r.push(`Generated: ${new Date().toISOString()}`),r.push(`Command: nemar ${nE(LMe(e).join(" "))}`),r.push(""),r.push(_0??"(environment snapshot unavailable)"),r.push(""),r.push("HTTP requests:"),v0.length===0)r.push(" (none)");else v0.forEach((n,o)=>{if(r.push(` [${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: ${UK??"(none recorded)"}`),r.push(`Exit code: ${t}`),`${r.join(`
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package/package.json
CHANGED