nemar-cli 0.10.4-dev.2601 → 0.10.4-dev.2605
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}`,a2e,c2e,l2e=(e,t,r)=>{let n=r===""?"":`with ${r.trim()}() `,o=s2e.bind(nul
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`)}var HD=!1;var{spawn:z7e}=globalThis.Bun;async function C(e,t={}){let r={...process.env,GIT_TERMINAL_PROMPT:"0",...t.env};for(let u of t.unsetEnv??[])delete r[u];let n=z7e({cmd:e,cwd:t.cwd,...t.stdin===void 0?{}:{stdin:new TextEncoder().encode(t.stdin)},stdout:"pipe",stderr:"pipe",env:r}),o=!1,i;if(t.timeout)i=setTimeout(()=>{o=!0,n.kill()},t.timeout);if(WD()){let u=t.cwd?` (cwd=${t.cwd})`:"";kf(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(WD()){if(s.trim())kf(l.dim(s.trimEnd()));if(a.trim())kf(l.yellow(a.trimEnd()));kf(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(()=>{Qe()});function G7e(){if(process.platform==="darwin")return"macos";if(process.platform==="win32")return"windows";return"linux"}function CK(e,t=G7e()){return e.installInstructions[t]}function H7e(e){let t=e.match(/(\d+\.\d+(?:\.\d+)?)/);return t?t[1]:void 0}function K7e(){let e=Number(process.env.TEST_PROBE_TIMEOUT_MS);return Number.isFinite(e)&&e>0?e:W7e}async function kK(e){try{let{exitCode:t,stdout:r,timedOut:n}=await C(e.cmd,{timeout:K7e()});if(n)return{available:!1,timedOut:!0};if(t!==0)return{available:!1};return{available:!0,version:H7e(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: ${r}`);return{available:!1}}}async function Rf(){let e=Object.entries($K);return Promise.all(e.map(async([t,r])=>{let{available:n,version:o,timedOut:i}=await kK(r);return{key:t,name:r.name,purpose:r.purpose,required:r.required,available:n,version:o,timedOut:i,installInstruction:CK(r)}}))}async function RK(){let t=(await Rf()).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: ${r.installInstruction}`);return console.warn("Run `nemar doctor` anytime to re-check. You can finish signup without them.\n"),t}async function Da(e){let r=V7e[e].map((s)=>$K[s]).filter(Boolean),n=await Promise.all(r.map(async(s)=>{let a=await kK(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 $K,V7e,W7e=4000;var Af=O(()=>{At();$K={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)"}}},V7e={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 OK;var AK=O(()=>{OK={name:"nemar-cli",version:"0.10.4-dev.
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`))}var $K,V7e,W7e=4000;var Af=O(()=>{At();$K={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)"}}},V7e={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 OK;var AK=O(()=>{OK={name:"nemar-cli",version:"0.10.4-dev.2605",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 yi;var Of=O(()=>{AK();yi=OK.version});import{mkdirSync as J7e,readdirSync as X7e,unlinkSync as Z7e,writeFileSync as Q7e}from"fs";import{join as KD}from"path";function jK(){wl=!0}function Ea(){return wl}function qK(e,t=process.env){return e.includes("--debug")||t.NEMAR_DEBUG==="1"}function If(e){NK=e,$r(`Step: ${e}`)}function Pf(){PK=!0}function MK(){return PK}function JD(){TK=!0}function LK(){return TK}function $r(e){if(wl)process.stderr.write(`[debug] ${e}
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`)}function nMe(e){let t={};for(let[r,n]of Object.entries(e))t[r]=rMe.has(r.toLowerCase())?"[REDACTED]":n;return t}function UK(e){let t=e.indexOf("@");if(t<=0)return"***";return`${e[0]}***${e.slice(t)}`}function YD(e,t,r=0){if(r>iMe)return"[REDACTED: depth]";if(Array.isArray(t))return t.map((n)=>YD(e,n,r+1));if(t&&typeof t==="object"){let n={};for(let[o,i]of Object.entries(t))n[o]=YD(o,i,r+1);return n}if(typeof t==="string"){if(oMe.test(e))return"[REDACTED]";return t.replace(BK,UK)}return t}function XD(e){return e.replace(sMe,"Bearer [REDACTED]").replace(aMe,"[REDACTED_AWS_KEY]").replace(cMe,"$1[REDACTED]").replace(lMe,"$1$2=[REDACTED]").replace(BK,UK)}function uMe(e){return XD(e)}function FK(e,t=tMe){if(e===void 0)return;let r=e;try{let n=JSON.parse(e);r=JSON.stringify(YD("",n))}catch{}if(r=XD(r),Buffer.byteLength(r,"utf8")>t)r=`${Buffer.from(r,"utf8").subarray(0,t).toString("utf8")}... [truncated]`;return r}function b0(e){if(!wl)return;let t=uMe(e.url);try{let r={...e,url:t,requestHeaders:e.requestHeaders?nMe(e.requestHeaders):void 0,requestBody:FK(e.requestBody),responseBody:FK(e.responseBody)};x0.push(r),$r(`${e.method} ${t} -> ${e.status??"ERROR"} (${e.durationMs}ms)`)}catch(r){let n=T(r);x0.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 dMe(){let e=[];try{let t=process.versions.bun?`Bun ${process.versions.bun}`:`Node ${process.version}`;e.push(`CLI version: ${yi}`),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 Rf();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 ZD(){return(await dMe()).join(`
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`)}async function zK(){if(!wl||y0!==void 0)return;try{y0=await ZD()}catch(e){let t=T(e);y0=`(could not build environment report: ${t})`,$r(`environment snapshot failed: ${t}`)}}function VK(e){if(IK.has(e))return{flag:e};for(let t of IK){if(!e.startsWith(t)||e.length<=t.length)continue;if(t.length===2)return{flag:t,kind:"short-attached"};if(e[t.length]==="=")return{flag:t,kind:"long-eq"}}return null}function fMe(e){let t=[];for(let r=0;r<e.length;r++){let n=e[r],o=VK(n);if(!o){t.push(n);continue}if(o.kind==="long-eq")t.push(`${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 pMe(e){let t=[];for(let r=0;r<e.length;r++){let n=e[r],o=VK(n);if(!o){t.push(n);continue}if(!o.kind&&r+1<e.length)r++}return t}function mMe(e){let t=[];for(let n of pMe(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 hMe(e,t){let r=[];if(r.push("NEMAR CLI Debug Log"),r.push(`Generated: ${new Date().toISOString()}`),r.push(`Command: nemar ${XD(fMe(e).join(" "))}`),r.push(""),r.push(y0??"(environment snapshot unavailable)"),r.push(""),r.push("HTTP requests:"),x0.length===0)r.push(" (none)");else x0.forEach((n,o)=>{if(r.push(` [${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: ${NK??"(none recorded)"}`),r.push(`Exit code: ${t}`),`${r.join(`
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`)}
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package/package.json
CHANGED