nemar-cli 0.10.4-PR1402.32d1e4a → 0.10.4-PR1402.ea255a8
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 +2 -11
- package/package.json +1 -1
package/dist/index.js
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@@ -99,7 +99,7 @@ ${t}`,i2e,s2e,a2e=(e,t,r)=>{let n=r===""?"":`with ${r.trim()}() `,o=o2e.bind(nul
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`)}var MD=!1;var{spawn:B7e}=globalThis.Bun;async function k(e,t={}){let r={...process.env,GIT_TERMINAL_PROMPT:"0",...t.env};for(let u of t.unsetEnv??[])delete r[u];let n=B7e({cmd:e,cwd:t.cwd,stdout:"pipe",stderr:"pipe",env:r}),o=!1,i;if(t.timeout)i=setTimeout(()=>{o=!0,n.kill()},t.timeout);if(LD()){let u=t.cwd?` (cwd=${t.cwd})`:"";_f(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(LD()){if(s.trim())_f(l.dim(s.trimEnd()));if(a.trim())_f(l.yellow(a.trimEnd()));_f(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(()=>{Ye()});function z7e(){if(process.platform==="darwin")return"macos";if(process.platform==="win32")return"windows";return"linux"}function gK(e,t=z7e()){return e.installInstructions[t]}function V7e(e){let t=e.match(/(\d+\.\d+(?:\.\d+)?)/);return t?t[1]:void 0}function H7e(){let e=Number(process.env.TEST_PROBE_TIMEOUT_MS);return Number.isFinite(e)&&e>0?e:G7e}async function yK(e){try{let{exitCode:t,stdout:r,timedOut:n}=await k(e.cmd,{timeout:H7e()});if(n)return{available:!1,timedOut:!0};if(t!==0)return{available:!1};return{available:!0,version:V7e(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 vf(){let e=Object.entries(hK);return Promise.all(e.map(async([t,r])=>{let{available:n,version:o,timedOut:i}=await yK(r);return{key:t,name:r.name,purpose:r.purpose,required:r.required,available:n,version:o,timedOut:i,installInstruction:gK(r)}}))}async function xK(){let t=(await vf()).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 ba(e){let r=U7e[e].map((s)=>hK[s]).filter(Boolean),n=await Promise.all(r.map(async(s)=>{let a=await yK(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:gK(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 hK,U7e,G7e=4000;var wf=O(()=>{Pt();hK={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)"}}},U7e={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 _K;var bK=O(()=>{_K={name:"nemar-cli",version:"0.10.4-PR1402.
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`))}var hK,U7e,G7e=4000;var wf=O(()=>{Pt();hK={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)"}}},U7e={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 _K;var bK=O(()=>{_K={name:"nemar-cli",version:"0.10.4-PR1402.ea255a8",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 hi;var Df=O(()=>{bK();hi=_K.version});import{mkdirSync as K7e,readdirSync as Y7e,unlinkSync as J7e,writeFileSync as X7e}from"fs";import{join as BD}from"path";function $K(){hl=!0}function _a(){return hl}function CK(e,t=process.env){return e.includes("--debug")||t.NEMAR_DEBUG==="1"}function Sf(e){SK=e,Er(`Step: ${e}`)}function $f(){DK=!0}function kK(){return DK}function zD(){EK=!0}function RK(){return EK}function Er(e){if(hl)process.stderr.write(`[debug] ${e}
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`)}function tMe(e){let t={};for(let[r,n]of Object.entries(e))t[r]=eMe.has(r.toLowerCase())?"[REDACTED]":n;return t}function OK(e){let t=e.indexOf("@");if(t<=0)return"***";return`${e[0]}***${e.slice(t)}`}function UD(e,t,r=0){if(r>nMe)return"[REDACTED: depth]";if(Array.isArray(t))return t.map((n)=>UD(e,n,r+1));if(t&&typeof t==="object"){let n={};for(let[o,i]of Object.entries(t))n[o]=UD(o,i,r+1);return n}if(typeof t==="string"){if(rMe.test(e))return"[REDACTED]";return t.replace(AK,OK)}return t}function VD(e){return e.replace(oMe,"Bearer [REDACTED]").replace(iMe,"[REDACTED_AWS_KEY]").replace(sMe,"$1[REDACTED]").replace(aMe,"$1$2=[REDACTED]").replace(AK,OK)}function cMe(e){return VD(e)}function vK(e,t=Q7e){if(e===void 0)return;let r=e;try{let n=JSON.parse(e);r=JSON.stringify(UD("",n))}catch{}if(r=VD(r),Buffer.byteLength(r,"utf8")>t)r=`${Buffer.from(r,"utf8").subarray(0,t).toString("utf8")}... [truncated]`;return r}function gg(e){if(!hl)return;let t=cMe(e.url);try{let r={...e,url:t,requestHeaders:e.requestHeaders?tMe(e.requestHeaders):void 0,requestBody:vK(e.requestBody),responseBody:vK(e.responseBody)};hg.push(r),Er(`${e.method} ${t} -> ${e.status??"ERROR"} (${e.durationMs}ms)`)}catch(r){let n=P(r);hg.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 lMe(){let e=[];try{let t=process.versions.bun?`Bun ${process.versions.bun}`:`Node ${process.version}`;e.push(`CLI version: ${hi}`),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 vf();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 GD(){return(await lMe()).join(`
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`)}async function FK(){if(!hl||mg!==void 0)return;try{mg=await GD()}catch(e){let t=P(e);mg=`(could not build environment report: ${t})`,Er(`environment snapshot failed: ${t}`)}}function IK(e){if(wK.has(e))return{flag:e};for(let t of wK){if(!e.startsWith(t)||e.length<=t.length)continue;if(t.length===2)return{flag:t,kind:"short-attached"};if(e[t.length]==="=")return{flag:t,kind:"long-eq"}}return null}function uMe(e){let t=[];for(let r=0;r<e.length;r++){let n=e[r],o=IK(n);if(!o){t.push(n);continue}if(o.kind==="long-eq")t.push(`${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 dMe(e){let t=[];for(let r=0;r<e.length;r++){let n=e[r],o=IK(n);if(!o){t.push(n);continue}if(!o.kind&&r+1<e.length)r++}return t}function fMe(e){let t=[];for(let n of dMe(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 pMe(e,t){let r=[];if(r.push("NEMAR CLI Debug Log"),r.push(`Generated: ${new Date().toISOString()}`),r.push(`Command: nemar ${VD(uMe(e).join(" "))}`),r.push(""),r.push(mg??"(environment snapshot unavailable)"),r.push(""),r.push("HTTP requests:"),hg.length===0)r.push(" (none)");else hg.forEach((n,o)=>{if(r.push(` [${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: ${SK??"(none recorded)"}`),r.push(`Exit code: ${t}`),`${r.join(`
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@@ -991,18 +991,10 @@ Description:
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always downloaded.)
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Requirements:
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- git-annex installed (NEMAR datasets only)
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- git-annex installed (NEMAR datasets only)
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- NEMAR account (for private datasets)
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- AWS CLI recommended for OpenNeuro downloads (falls back to HTTPS)
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Without git-annex:
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--http downloads over plain HTTP with no git, git-annex or GitHub account,
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and is used automatically when git-annex is missing. It honours the same
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filters and writes the same BIDS tree, but the result is a file snapshot,
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not a repository: 'commit', 'push' and 'update' need a git-annex clone.
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Re-running resumes, since a file already present at its declared size is
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skipped.
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Examples:
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$ nemar dataset download nm000104 # Download NEMAR dataset (skips stimuli/derivatives)
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$ nemar dataset download nm000104 -o ./data # Custom output directory
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@@ -1011,7 +1003,6 @@ Examples:
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$ nemar dataset download nm000104 --resume # Resume partial download
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$ nemar dataset download nm000104 --update # Pull only the version diff
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$ nemar dataset download nm000104 --update --prune # Plus drop orphan objects
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$ nemar dataset download nm000104 --http # No git-annex needed (snapshot)
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$ nemar dataset download nm000104 --subjects sub-01,02 # Only these subjects
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$ nemar dataset download nm000104 --tasks rest --datatypes eeg # Subset
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$ nemar dataset download nm000104 --stimuli # Also download stimuli/
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package/package.json
CHANGED