nemar-cli 0.10.15-dev.3217 → 0.10.15-dev.3218

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Files changed (2) hide show
  1. package/dist/index.js +1 -1
  2. package/package.json +1 -1
package/dist/index.js CHANGED
@@ -99,7 +99,7 @@ ${t}`,oAe,sAe,aAe=(e,t,r)=>{let n=r===""?"":`with ${r.trim()}() `,i=iAe.bind(nul
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  `)}var JS=!1;var{spawn:iHe}=globalThis.Bun;async function k(e,t={}){let r={...process.env,GIT_TERMINAL_PROMPT:"0",...t.env};for(let u of t.unsetEnv??[])delete r[u];let n=iHe({cmd:e,cwd:t.cwd,...t.stdin===void 0?{}:{stdin:new TextEncoder().encode(t.stdin)},stdout:"pipe",stderr:"pipe",env:r}),i=!1,o;if(t.timeout)o=setTimeout(()=>{i=!0,n.kill()},t.timeout);if(XS()){let u=t.cwd?` (cwd=${t.cwd})`:"";$p(l.dim(`$ ${e.join(" ")}${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(XS()){if(s.trim())$p(l.dim(s.trimEnd()));if(a.trim())$p(l.yellow(a.trimEnd()));$p(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 Dt=P(()=>{Xe()});function sHe(){if(process.platform==="darwin")return"macos";if(process.platform==="win32")return"windows";return"linux"}function FX(e,t=sHe()){return e.installInstructions[t]}function aHe(e){let t=e.match(/(\d+\.\d+(?:\.\d+)?)/);return t?t[1]:void 0}function lHe(){let e=Number(process.env.TEST_PROBE_TIMEOUT_MS);return Number.isFinite(e)&&e>0?e:cHe}async function PX(e){try{let{exitCode:t,stdout:r,timedOut:n}=await k(e.cmd,{timeout:lHe()});if(n)return{available:!1,timedOut:!0};if(t!==0)return{available:!1};return{available:!0,version:aHe(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 kp(){let e=Object.entries(OX);return Promise.all(e.map(async([t,r])=>{let{available:n,version:i,timedOut:o}=await PX(r);return{key:t,name:r.name,purpose:r.purpose,required:r.required,available:n,version:i,timedOut:o,installInstruction:FX(r)}}))}async function TX(){let t=(await kp()).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 fc(e){let r=oHe[e].map((s)=>OX[s]).filter(Boolean),n=await Promise.all(r.map(async(s)=>{let a=await PX(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:FX(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 OX,oHe,cHe=4000;var Cp=P(()=>{Dt();OX={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)"}}},oHe={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 NX;var IX=P(()=>{NX={name:"nemar-cli",version:"0.10.15-dev.3217",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/","lint:scrub":"biome check scripts/scrub shared/identifier-scrub.ts test/scrub","test:scrub":"bun test --preload ./test/scrub/helpers/temp-dirs-preload.ts --path-ignore-patterns='__run_every_scrub_suite__' test/scrub test/identifier-scan.test.ts test/identifier-scrub.test.ts test/identifier-dates.test.ts test/identifier-fleet.test.ts","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 Di;var mu=P(()=>{IX();Di=NX.version});import{mkdirSync as dHe,readdirSync as fHe,unlinkSync as pHe,writeFileSync as mHe}from"fs";import{join as ZS}from"path";function UX(){hu=!0}function pc(){return hu}function zX(e,t=process.env){return e.includes("--debug")||t.NEMAR_DEBUG==="1"}function Ap(e){BX=e,Kt(`Step: ${e}`)}function Op(){qX=!0}function VX(){return qX}function so(){LX=!0}function HX(){return LX}function Kt(e){if(hu)process.stderr.write(`[debug] ${e}
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+ `))}var OX,oHe,cHe=4000;var Cp=P(()=>{Dt();OX={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)"}}},oHe={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 NX;var IX=P(()=>{NX={name:"nemar-cli",version:"0.10.15-dev.3218",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/","lint:scrub":"biome check scripts/scrub shared/identifier-scrub.ts test/scrub","test:scrub":"bun test --preload ./test/scrub/helpers/temp-dirs-preload.ts --path-ignore-patterns='__run_every_scrub_suite__' test/scrub test/identifier-scan.test.ts test/identifier-scrub.test.ts test/identifier-dates.test.ts test/identifier-fleet.test.ts","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 Di;var mu=P(()=>{IX();Di=NX.version});import{mkdirSync as dHe,readdirSync as fHe,unlinkSync as pHe,writeFileSync as mHe}from"fs";import{join as ZS}from"path";function UX(){hu=!0}function pc(){return hu}function zX(e,t=process.env){return e.includes("--debug")||t.NEMAR_DEBUG==="1"}function Ap(e){BX=e,Kt(`Step: ${e}`)}function Op(){qX=!0}function VX(){return qX}function so(){LX=!0}function HX(){return LX}function Kt(e){if(hu)process.stderr.write(`[debug] ${e}
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  `)}function bHe(e){let t={};for(let[r,n]of Object.entries(e))t[r]=yHe.has(r.toLowerCase())?"[REDACTED]":n;return t}function WX(e){let t=e.indexOf("@");if(t<=0)return"***";return`${e[0]}***${e.slice(t)}`}function QS(e,t,r=0){if(r>_He)return"[REDACTED: depth]";if(Array.isArray(t))return t.map((n)=>QS(e,n,r+1));if(t&&typeof t==="object"){let n={};for(let[i,o]of Object.entries(t))n[i]=QS(i,o,r+1);return n}if(typeof t==="string"){if(xHe.test(e))return"[REDACTED]";return t.replace(GX,WX)}return t}function e$(e){return e.replace(vHe,"Bearer [REDACTED]").replace(wHe,"[REDACTED_AWS_KEY]").replace(DHe,"$1[REDACTED]").replace(EHe,"$1$2=[REDACTED]").replace(GX,WX)}function SHe(e){return e$(e)}function jX(e,t=gHe){if(e===void 0)return;let r=e;try{let n=JSON.parse(e);r=JSON.stringify(QS("",n))}catch{}if(r=e$(r),Buffer.byteLength(r,"utf8")>t)r=`${Buffer.from(r,"utf8").subarray(0,t).toString("utf8")}... [truncated]`;return r}function By(e){if(!hu)return;let t=SHe(e.url);try{let r={...e,url:t,requestHeaders:e.requestHeaders?bHe(e.requestHeaders):void 0,requestBody:jX(e.requestBody),responseBody:jX(e.responseBody)};Ly.push(r),Kt(`${e.method} ${t} -> ${e.status??"ERROR"} (${e.durationMs}ms)`)}catch(r){let n=q(r);Ly.push({method:e.method,url:t,status:e.status,durationMs:e.durationMs,note:`redaction failed: ${n}`}),Kt(`redaction failed for ${e.method} ${t}: ${n}`)}}async function $He(){let e=[];try{let t=process.versions.bun?`Bun ${process.versions.bun}`:`Node ${process.version}`;e.push(`CLI version: ${Di}`),e.push(`OS/Arch: ${process.platform}/${process.arch}`),e.push(`Runtime: ${t}`)}catch(t){e.push(`(could not read CLI/OS/runtime info: ${q(t)})`)}e.push(""),e.push("Active account:");try{let t=mt();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: ${q(t)})`)}e.push(""),e.push("External tools:");try{let t=await kp();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: ${q(t)})`)}return e}async function t$(){return(await $He()).join(`
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  `)}async function KX(){if(!hu||qy!==void 0)return;try{qy=await t$()}catch(e){let t=q(e);qy=`(could not build environment report: ${t})`,Kt(`environment snapshot failed: ${t}`)}}function YX(e){if(MX.has(e))return{flag:e};for(let t of MX){if(!e.startsWith(t)||e.length<=t.length)continue;if(t.length===2)return{flag:t,kind:"short-attached"};if(e[t.length]==="=")return{flag:t,kind:"long-eq"}}return null}function kHe(e){let t=[];for(let r=0;r<e.length;r++){let n=e[r],i=YX(n);if(!i){t.push(n);continue}if(i.kind==="long-eq")t.push(`${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 CHe(e){let t=[];for(let r=0;r<e.length;r++){let n=e[r],i=YX(n);if(!i){t.push(n);continue}if(!i.kind&&r+1<e.length)r++}return t}function RHe(e){let t=[];for(let n of CHe(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 AHe(e,t){let r=[];if(r.push("NEMAR CLI Debug Log"),r.push(`Generated: ${new Date().toISOString()}`),r.push(`Command: nemar ${e$(kHe(e).join(" "))}`),r.push(""),r.push(qy??"(environment snapshot unavailable)"),r.push(""),r.push("HTTP requests:"),Ly.length===0)r.push(" (none)");else Ly.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: ${BX??"(none recorded)"}`),r.push(`Exit code: ${t}`),`${r.join(`
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  `)}
package/package.json CHANGED
@@ -1,6 +1,6 @@
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  {
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  "name": "nemar-cli",
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- "version": "0.10.15-dev.3217",
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+ "version": "0.10.15-dev.3218",
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  "description": "CLI for NEMAR (Neuroelectromagnetic Data Archive and Tools Resource) dataset management",
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  "type": "module",
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  "main": "dist/index.js",