nemar-cli 0.10.18-dev.3426 → 0.10.18-dev.3427
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}`,eIe,tIe,rIe=(e,t,r)=>{let n=r===""?"":`with ${r.trim()}() `,i=Q6e.bind(nul
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`)}var R2=!1;var{spawn:jJe}=globalThis.Bun;function Vl(e,t=[]){let r=e.replace(MJe,'("$1","<redacted>")');for(let n of t)if(n.length>=qJe)r=r.split(n).join("<redacted>");return r}function rw(e){let t=["AWS_SESSION_TOKEN","AWS_SECRET_ACCESS_KEY","AWS_ACCESS_KEY_ID"],r=new Set;for(let n of[process.env,e??{}])for(let i of t){let o=n[i];if(typeof o==="string"&&o.length>0)r.add(o)}return[...r]}async function Xte(e,t){let r=e.getReader(),n=new TextDecoder,i="";while(!0){let{done:o,value:s}=await r.read();if(o)break;if(s.byteLength===0)continue;t(),i+=n.decode(s,{stream:!0})}return i+n.decode()}async function k(e,t={}){let r={...process.env,GIT_TERMINAL_PROMPT:"0",...t.env};for(let b of t.unsetEnv??[])delete r[b];let n=jJe({cmd:e,cwd:t.cwd,...t.stdin===void 0?{}:{stdin:new TextEncoder().encode(t.stdin)},stdout:"pipe",stderr:"pipe",env:r}),i=!1,o,s,a=performance.now(),c=()=>{if(s!==void 0)clearTimeout(s),s=void 0},u=()=>{if(!t.onInactivityWarning)return;c(),s=setTimeout(()=>{s=void 0;try{t.onInactivityWarning?.(performance.now()-a)}catch{console.error("Could not display subprocess inactivity warning; the child result is unaffected.")}},t.inactivityWarningAfterMs??LJe)};if(u(),t.timeout)o=setTimeout(()=>{i=!0,c(),n.kill()},t.timeout);let d=tw()?[...rw(r),...t.redact??[]]:[];if(tw()){let b=t.cwd?` (cwd=${t.cwd})`:"";Ic(l.dim(Vl(`$ ${e.join(" ")}${b}`,d)))}let f=()=>{a=performance.now(),u()},m,p,g,h=n.exited.then((b)=>(c(),b));try{[m,p,g]=await Promise.all([Xte(n.stdout,f),Xte(n.stderr,f),h])}finally{if(c(),o)clearTimeout(o)}if(tw()){if(t.sensitiveOutput)Ic(l.dim("[sensitive subprocess output suppressed]"));else{if(m.trim())Ic(l.dim(Vl(m.trimEnd(),d)));if(p.trim())Ic(l.yellow(Vl(p.trimEnd(),d)))}Ic(l.dim(`(exit ${g})`))}if(i)return{stdout:m,stderr:p||`Command timed out after ${Math.round(t.timeout/1000)}s`,exitCode:g??1,timedOut:!0};return{stdout:m,stderr:p,exitCode:g,timedOut:!1}}var MJe,qJe=8,LJe=120000;var It=I(()=>{Ze();MJe=/\(\s*"((?:x-amz-)[^"]*|authorization|proxy-authorization)"\s*,\s*"[^"]*"\s*\)/gi});function UJe(){if(process.platform==="darwin")return"macos";if(process.platform==="win32")return"windows";return"linux"}function Qte(e,t=UJe()){return e.installInstructions[t]}function zJe(e){let t=e.match(/(\d+\.\d+(?:\.\d+)?)/);return t?t[1]:void 0}function HJe(){let e=Number(process.env.TEST_PROBE_TIMEOUT_MS);return Number.isFinite(e)&&e>0?e:VJe}async function ere(e){try{let{exitCode:t,stdout:r,timedOut:n}=await k(e.cmd,{timeout:HJe()});if(n)return{available:!1,timedOut:!0};if(t!==0)return{available:!1};return{available:!0,version:zJe(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 ph(){let e=Object.entries(Zte);return Promise.all(e.map(async([t,r])=>{let{available:n,version:i,timedOut:o}=await ere(r);return{key:t,name:r.name,purpose:r.purpose,required:r.required,available:n,version:i,timedOut:o,installInstruction:Qte(r)}}))}async function tre(){let t=(await ph()).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 Hl(e){let r=BJe[e].map((s)=>Zte[s]).filter(Boolean),n=await Promise.all(r.map(async(s)=>{let a=await ere(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:Qte(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 Zte,BJe,VJe=4000;var mh=I(()=>{It();Zte={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)"}}},BJe={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 nre;var rre=I(()=>{nre={name:"nemar-cli",packageManager:"bun@1.4.3",version:"0.10.18-dev.
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`))}var Zte,BJe,VJe=4000;var mh=I(()=>{It();Zte={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)"}}},BJe={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 nre;var rre=I(()=>{nre={name:"nemar-cli",packageManager:"bun@1.4.3",version:"0.10.18-dev.3427",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:{"@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 eo;var kf=I(()=>{rre();eo=nre.version});import{mkdirSync as WJe,readdirSync as KJe,unlinkSync as JJe,writeFileSync as YJe}from"fs";import{join as A2}from"path";function lre(){Cf=!0}function Gl(){return Cf}function ure(e,t=process.env){return e.includes("--debug")||t.NEMAR_DEBUG==="1"}function gh(e){cre=e,Zt(`Step: ${e}`)}function yh(){sre=!0}function dre(){return sre}function Qt(){are=!0}function fre(){return are}function Zt(e){if(Cf)process.stderr.write(`[debug] ${e}
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`)}function eYe(e){let t={};for(let[r,n]of Object.entries(e))t[r]=QJe.has(r.toLowerCase())?"[REDACTED]":n;return t}function mre(e){let t=e.indexOf("@");if(t<=0)return"***";return`${e[0]}***${e.slice(t)}`}function O2(e,t,r=0){if(r>rYe)return"[REDACTED: depth]";if(Array.isArray(t))return t.map((n)=>O2(e,n,r+1));if(t&&typeof t==="object"){let n={};for(let[i,o]of Object.entries(t))n[i]=O2(i,o,r+1);return n}if(typeof t==="string"){if(tYe.test(e))return"[REDACTED]";return t.replace(pre,mre)}return t}function T2(e){return e.replace(nYe,"Bearer [REDACTED]").replace(iYe,"[REDACTED_AWS_KEY]").replace(oYe,"$1[REDACTED]").replace(sYe,"$1$2=[REDACTED]").replace(pre,mre)}function aYe(e){return T2(e)}function ire(e,t=ZJe){if(e===void 0)return;let r=e;try{let n=JSON.parse(e);r=JSON.stringify(O2("",n))}catch{}if(r=T2(r),Buffer.byteLength(r,"utf8")>t)r=`${Buffer.from(r,"utf8").subarray(0,t).toString("utf8")}... [truncated]`;return r}function ow(e){if(!Cf)return;let t=aYe(e.url);try{let r={...e,url:t,requestHeaders:e.requestHeaders?eYe(e.requestHeaders):void 0,requestBody:ire(e.requestBody),responseBody:ire(e.responseBody)};iw.push(r),Zt(`${e.method} ${t} -> ${e.status??"ERROR"} (${e.durationMs}ms)`)}catch(r){let n=q(r);iw.push({method:e.method,url:t,status:e.status,durationMs:e.durationMs,note:`redaction failed: ${n}`}),Zt(`redaction failed for ${e.method} ${t}: ${n}`)}}async function cYe(){let e=[];try{let t=process.versions.bun?`Bun ${process.versions.bun}`:`Node ${process.version}`;e.push(`CLI version: ${eo}`),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=Ft();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 ph();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 F2(){return(await cYe()).join(`
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`)}async function hre(){if(!Cf||nw!==void 0)return;try{nw=await F2()}catch(e){let t=q(e);nw=`(could not build environment report: ${t})`,Zt(`environment snapshot failed: ${t}`)}}function gre(e){if(ore.has(e))return{flag:e};for(let t of ore){if(!e.startsWith(t)||e.length<=t.length)continue;if(t.length===2)return{flag:t,kind:"short-attached"};if(e[t.length]==="=")return{flag:t,kind:"long-eq"}}return null}function lYe(e){let t=[];for(let r=0;r<e.length;r++){let n=e[r],i=gre(n);if(!i){t.push(n);continue}if(i.kind==="long-eq")t.push(`${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 uYe(e){let t=[];for(let r=0;r<e.length;r++){let n=e[r],i=gre(n);if(!i){t.push(n);continue}if(!i.kind&&r+1<e.length)r++}return t}function dYe(e){let t=[];for(let n of uYe(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 fYe(e,t){let r=[];if(r.push("NEMAR CLI Debug Log"),r.push(`Generated: ${new Date().toISOString()}`),r.push(`Command: nemar ${T2(lYe(e).join(" "))}`),r.push(""),r.push(nw??"(environment snapshot unavailable)"),r.push(""),r.push("HTTP requests:"),iw.length===0)r.push(" (none)");else iw.forEach((n,i)=>{if(r.push(` [${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: ${cre??"(none recorded)"}`),r.push(`Exit code: ${t}`),`${r.join(`
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package/package.json
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{
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"name": "nemar-cli",
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"packageManager": "bun@1.4.3",
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"version": "0.10.18-dev.
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"version": "0.10.18-dev.3427",
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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",
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