nemar-cli 0.10.27-dev.4103 → 0.10.27-dev.4109
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/git-annex-remote-nemar.js +1 -1
- package/dist/index.js +469 -457
- package/package.json +1 -1
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@@ -23,7 +23,7 @@ ${t}`,zM,GM,KM=(e,t,r)=>{let n=r===""?"":`with ${r.trim()}() `,s=VM.bind(null,n,
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`)}var Fl=!1;var{spawn:WF}=globalThis.Bun;function Vl(e,t=[]){let r=e.replace(YF,'("$1","<redacted>")');for(let n of t)if(n.length>=XF)r=r.split(n).join("<redacted>");return r}function QF(e){let t=["AWS_SESSION_TOKEN","AWS_SECRET_ACCESS_KEY","AWS_ACCESS_KEY_ID"],r=new Set;for(let n of[process.env,e??{}])for(let s of t){let o=n[s];if(typeof o==="string"&&o.length>0)r.add(o)}return[...r]}async function hb(e,t){let r=e.getReader(),n=new TextDecoder,s="";while(!0){let{done:o,value:i}=await r.read();if(o)break;if(i.byteLength===0)continue;t(),s+=n.decode(i,{stream:!0})}return s+n.decode()}async function mb(e,t={}){let r={...process.env,GIT_TERMINAL_PROMPT:"0",...t.env};for(let y of t.unsetEnv??[])delete r[y];let n=WF({cmd:e,cwd:t.cwd,...t.stdin===void 0?{}:{stdin:new TextEncoder().encode(t.stdin)},stdout:"pipe",stderr:"pipe",env:r}),s=!1,o,i,a=performance.now(),c=()=>{if(i!==void 0)clearTimeout(i),i=void 0},u=()=>{if(!t.onInactivityWarning)return;c(),i=setTimeout(()=>{i=void 0;try{t.onInactivityWarning?.(performance.now()-a)}catch{console.error("Could not display subprocess inactivity warning; the child result is unaffected.")}},t.inactivityWarningAfterMs??JF)};if(u(),t.timeout)o=setTimeout(()=>{s=!0,c(),n.kill()},t.timeout);let d=ic()?[...QF(r),...t.redact??[]]:[];if(ic()){let y=t.cwd?` (cwd=${t.cwd})`:"";qs(Nt.dim(Vl(`$ ${e.join(" ")}${y}`,d)))}let l=()=>{a=performance.now(),u()},p,f,h,m=n.exited.then((y)=>(c(),y));try{[p,f,h]=await Promise.all([hb(n.stdout,l),hb(n.stderr,l),m])}finally{if(c(),o)clearTimeout(o)}if(ic()){if(t.sensitiveOutput)qs(Nt.dim("[sensitive subprocess output suppressed]"));else{if(p.trim())qs(Nt.dim(Vl(p.trimEnd(),d)));if(f.trim())qs(Nt.yellow(Vl(f.trimEnd(),d)))}qs(Nt.dim(`(exit ${h})`))}if(s)return{stdout:p,stderr:f||`Command timed out after ${Math.round(t.timeout/1000)}s`,exitCode:h??1,timedOut:!0};return{stdout:p,stderr:f,exitCode:h,timedOut:!1}}var YF,XF=8,JF=120000;var gb=F(()=>{Ul();YF=/\(\s*"((?:x-amz-)[^"]*|authorization|proxy-authorization)"\s*,\s*"[^"]*"\s*\)/gi});function eV(){if(process.platform==="darwin")return"macos";if(process.platform==="win32")return"windows";return"linux"}function _b(e,t=eV()){return e.installInstructions[t]}function tV(e){let t=e.match(/(\d+\.\d+(?:\.\d+)?)/);return t?t[1]:void 0}function nV(){let e=Number(process.env.TEST_PROBE_TIMEOUT_MS);return Number.isFinite(e)&&e>0?e:rV}async function vb(e){try{let{exitCode:t,stdout:r,timedOut:n}=await mb(e.cmd,{timeout:nV()});if(n)return{available:!1,timedOut:!0};if(t!==0)return{available:!1};return{available:!0,version:tV(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 zl(){let e=Object.entries(yb);return Promise.all(e.map(async([t,r])=>{let{available:n,version:s,timedOut:o}=await vb(r);return{key:t,name:r.name,purpose:r.purpose,required:r.required,available:n,version:s,timedOut:o,installInstruction:_b(r)}}))}async function Z3(){let t=(await zl()).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 eB(e){let r=ZF[e].map((i)=>yb[i]).filter(Boolean),n=await Promise.all(r.map(async(i)=>{let a=await vb(i);return{check:i,available:a.available,timedOut:a.timedOut}}));for(let i of n)if(i.timedOut&&i.check.required)console.warn(`Warning: ${i.check.name} did not respond to a version check in time; continuing anyway.`);let s=n.filter((i)=>!i.available&&!i.timedOut&&i.check.required).map((i)=>({tool:i.check.name,installInstruction:_b(i.check)}));if(s.length===0)return;let o=[`
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Missing required tools:`];for(let i of s)o.push(` ${i.tool} not installed`),o.push(` Install: ${i.installInstruction}`);throw Error(o.join(`
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`))}var yb,ZF,rV=4000;var $b=F(()=>{gb();yb={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)"}}},ZF={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 wb;var Eb=F(()=>{wb={name:"nemar-cli",packageManager:"bun@1.4.3",version:"0.10.27-dev.
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`))}var yb,ZF,rV=4000;var $b=F(()=>{gb();yb={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)"}}},ZF={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 wb;var Eb=F(()=>{wb={name:"nemar-cli",packageManager:"bun@1.4.3",version:"0.10.27-dev.4109",description:"CLI for NEMAR (Neuroelectromagnetic Data Archive and Tools Resource) dataset management",type:"module",main:"dist/index.js",bin:{nemar:"dist/index.js","git-annex-remote-nemar":"dist/git-annex-remote-nemar.js"},scripts:{dev:"bun run src/index.ts",build:"bun build src/index.ts src/git-annex-remote-nemar.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"]},trustedDependencies:["@biomejs/biome"],devDependencies:{"@anthropic-ai/sdk":"^0.132.1","@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",husky:"^9.1.7","lint-staged":"^16.3.2",typescript:"^5.5.4",wrangler:"^4.70.0",yaml:"^2.8.4"}}});var ac;var Gl=F(()=>{Eb();ac=wb.version});import{mkdirSync as oV,readdirSync as iV,unlinkSync as aV,writeFileSync as cV}from"fs";import{join as Kl}from"path";function dB(){Ds=!0}function lc(){return Ds}function fB(e,t=process.env){return e.includes("--debug")||t.NEMAR_DEBUG==="1"}function pB(e){Tb=e,pr(`Step: ${e}`)}function hB(){xb=!0}function mB(){return xb}function gB(){if(Rb)return;Bl=!0}function yB(){Bl=!1,Rb=!0}function _B(){return Bl}function pr(e){if(Ds)process.stderr.write(`[debug] ${e}
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`)}function fV(e){let t={};for(let[r,n]of Object.entries(e))t[r]=dV.has(r.toLowerCase())?"[REDACTED]":n;return t}function Ob(e){let t=e.indexOf("@");if(t<=0)return"***";return`${e[0]}***${e.slice(t)}`}function Hl(e,t,r=0){if(r>hV)return"[REDACTED: depth]";if(Array.isArray(t))return t.map((n)=>Hl(e,n,r+1));if(t&&typeof t==="object"){let n={};for(let[s,o]of Object.entries(t))n[s]=Hl(s,o,r+1);return n}if(typeof t==="string"){if(pV.test(e))return"[REDACTED]";return t.replace(kb,Ob)}return t}function Wl(e){return e.replace(mV,"Bearer [REDACTED]").replace(gV,"[REDACTED_AWS_KEY]").replace(yV,"$1[REDACTED]").replace(_V,"$1$2=[REDACTED]").replace(kb,Ob)}function vV(e){return Wl(e)}function bb(e,t=lV){if(e===void 0)return;let r=e;try{let n=JSON.parse(e);r=JSON.stringify(Hl("",n))}catch{}if(r=Wl(r),Buffer.byteLength(r,"utf8")>t)r=`${Buffer.from(r,"utf8").subarray(0,t).toString("utf8")}... [truncated]`;return r}function dc(e){if(!Ds)return;let t=vV(e.url);try{let r={...e,url:t,requestHeaders:e.requestHeaders?fV(e.requestHeaders):void 0,requestBody:bb(e.requestBody),responseBody:bb(e.responseBody)};uc.push(r),pr(`${e.method} ${t} -> ${e.status??"ERROR"} (${e.durationMs}ms)`)}catch(r){let n=dr(r);uc.push({method:e.method,url:t,status:e.status,durationMs:e.durationMs,note:`redaction failed: ${n}`}),pr(`redaction failed for ${e.method} ${t}: ${n}`)}}async function $V(){let e=[];try{let t=process.versions.bun?`Bun ${process.versions.bun}`:`Node ${process.version}`;e.push(`CLI version: ${ac}`),e.push(`OS/Arch: ${process.platform}/${process.arch}`),e.push(`Runtime: ${t}`)}catch(t){e.push(`(could not read CLI/OS/runtime info: ${dr(t)})`)}e.push(""),e.push("Active account:");try{let t=hn();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: ${dr(t)})`)}e.push(""),e.push("External tools:");try{let t=await zl();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: ${dr(t)})`)}return e}async function EV(){return(await $V()).join(`
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`)}
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