nemar-cli 0.10.27-dev.4105 → 0.10.27-dev.4110
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 +1 -1
- 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.4110",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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`)}async function vB(){if(!Ds||cc!==void 0)return;try{cc=await EV()}catch(e){let t=dr(e);cc=`(could not build environment report: ${t})`,pr(`environment snapshot failed: ${t}`)}}function Ab(e){if(Sb.has(e))return{flag:e};for(let t of Sb){if(!e.startsWith(t)||e.length<=t.length)continue;if(t.length===2)return{flag:t,kind:"short-attached"};if(e[t.length]==="=")return{flag:t,kind:"long-eq"}}return null}function wV(e){let t=[];for(let r=0;r<e.length;r++){let n=e[r],s=Ab(n);if(!s){t.push(n);continue}if(s.kind==="long-eq")t.push(`${s.flag}=[REDACTED]`);else if(s.kind==="short-attached")t.push(`${s.flag}[REDACTED]`);else if(t.push(n),r+1<e.length)t.push("[REDACTED]"),r++}return t}function bV(e){let t=[];for(let r=0;r<e.length;r++){let n=e[r],s=Ab(n);if(!s){t.push(n);continue}if(!s.kind&&r+1<e.length)r++}return t}function SV(e){let t=[];for(let n of bV(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 xV(e,t){let r=[];if(r.push("NEMAR CLI Debug Log"),r.push(`Generated: ${new Date().toISOString()}`),r.push(`Command: nemar ${Wl(wV(e).join(" "))}`),r.push(""),r.push(cc??"(environment snapshot unavailable)"),r.push(""),r.push("HTTP requests:"),uc.length===0)r.push(" (none)");else uc.forEach((n,s)=>{if(r.push(` [${s+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: ${Tb??"(none recorded)"}`),r.push(`Exit code: ${t}`),`${r.join(`
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package/dist/index.js
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`)}var nN=!1;var{spawn:vpt}=globalThis.Bun;function Bf(e,t=[]){let n=e.replace(kpt,'("$1","<redacted>")');for(let r of t)if(r.length>=Ept)n=n.split(r).join("<redacted>");return n}function CS(e){let t=["AWS_SESSION_TOKEN","AWS_SECRET_ACCESS_KEY","AWS_ACCESS_KEY_ID"],n=new Set;for(let r of[process.env,e??{}])for(let o of t){let s=r[o];if(typeof s==="string"&&s.length>0)n.add(s)}return[...n]}async function Bfe(e,t){let n=e.getReader(),r=new TextDecoder,o="";while(!0){let{done:s,value:i}=await n.read();if(s)break;if(i.byteLength===0)continue;t(),o+=r.decode(i,{stream:!0})}return o+r.decode()}async function R(e,t={}){let n={...process.env,GIT_TERMINAL_PROMPT:"0",...t.env};for(let y of t.unsetEnv??[])delete n[y];let r=vpt({cmd:e,cwd:t.cwd,...t.stdin===void 0?{}:{stdin:new TextEncoder().encode(t.stdin)},stdout:"pipe",stderr:"pipe",env:n}),o=!1,s,i,a=performance.now(),c=()=>{if(i!==void 0)clearTimeout(i),i=void 0},l=()=>{if(!t.onInactivityWarning)return;c(),i=setTimeout(()=>{i=void 0;try{t.onInactivityWarning?.(performance.now()-a)}catch{console.error("Could not display subprocess inactivity warning; the child result is unaffected.")}},t.inactivityWarningAfterMs??Spt)};if(l(),t.timeout)s=setTimeout(()=>{o=!0,c(),r.kill()},t.timeout);let d=ig()?[...CS(n),...t.redact??[]]:[];if(ig()){let y=t.cwd?` (cwd=${t.cwd})`:"";hd(u.dim(Bf(`$ ${e.join(" ")}${y}`,d)))}let f=()=>{a=performance.now(),l()},p,m,h,g=r.exited.then((y)=>(c(),y));try{[p,m,h]=await Promise.all([Bfe(r.stdout,f),Bfe(r.stderr,f),g])}finally{if(c(),s)clearTimeout(s)}if(ig()){if(t.sensitiveOutput)hd(u.dim("[sensitive subprocess output suppressed]"));else{if(p.trim())hd(u.dim(Bf(p.trimEnd(),d)));if(m.trim())hd(u.yellow(Bf(m.trimEnd(),d)))}hd(u.dim(`(exit ${h})`))}if(o)return{stdout:p,stderr:m||`Command timed out after ${Math.round(t.timeout/1000)}s`,exitCode:h??1,timedOut:!0};return{stdout:p,stderr:m,exitCode:h,timedOut:!1}}var kpt,Ept=8,Spt=120000;var qt=z(()=>{He();kpt=/\(\s*"((?:x-amz-)[^"]*|authorization|proxy-authorization)"\s*,\s*"[^"]*"\s*\)/gi});function Dpt(){if(process.platform==="darwin")return"macos";if(process.platform==="win32")return"windows";return"linux"}function Hfe(e,t=Dpt()){return e.installInstructions[t]}function Rpt(e){let t=e.match(/(\d+\.\d+(?:\.\d+)?)/);return t?t[1]:void 0}function Apt(){let e=Number(process.env.TEST_PROBE_TIMEOUT_MS);return Number.isFinite(e)&&e>0?e:Cpt}async function Vfe(e){try{let{exitCode:t,stdout:n,timedOut:r}=await R(e.cmd,{timeout:Apt()});if(r)return{available:!1,timedOut:!0};if(t!==0)return{available:!1};return{available:!0,version:Rpt(n)}}catch(t){let n=t instanceof Error?t.message:String(t);if(!n.includes("ENOENT")&&!n.includes("not found"))console.error(` Warning: ${e.name} check failed unexpectedly: ${n}`);return{available:!1}}}async function jb(){let e=Object.entries(Ufe);return Promise.all(e.map(async([t,n])=>{let{available:r,version:o,timedOut:s}=await Vfe(n);return{key:t,name:n.name,purpose:n.purpose,required:n.required,available:r,version:o,timedOut:s,installInstruction:Hfe(n)}}))}async function zfe(){let t=(await jb()).filter((n)=>n.required&&!n.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 n of t)console.warn(` - ${n.name} (${n.purpose})`),console.warn(` Install: ${n.installInstruction}`);return console.warn("Run `nemar doctor` anytime to re-check. You can finish signup without them.\n"),t}async function Uf(e){let n=$pt[e].map((i)=>Ufe[i]).filter(Boolean),r=await Promise.all(n.map(async(i)=>{let a=await Vfe(i);return{check:i,available:a.available,timedOut:a.timedOut}}));for(let i of r)if(i.timedOut&&i.check.required)console.warn(`Warning: ${i.check.name} did not respond to a version check in time; continuing anyway.`);let o=r.filter((i)=>!i.available&&!i.timedOut&&i.check.required).map((i)=>({tool:i.check.name,installInstruction:Hfe(i.check)}));if(o.length===0)return;let s=[`
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Missing required tools:`];for(let i of o)s.push(` ${i.tool} not installed`),s.push(` Install: ${i.installInstruction}`);throw Error(s.join(`
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`))}var Ufe,$pt,Cpt=4000;var Lb=z(()=>{qt();Ufe={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)"}}},$pt={upload:["git-annex","gh","aws","deno"],download:["gh"],clone:["git","gh"],push:["git-annex","gh"],publish:["gh","aws"],update:["git","gh"],release:["git","gh"]}});var Wfe;var Gfe=z(()=>{Wfe={name:"nemar-cli",packageManager:"bun@1.4.3",version:"0.10.27-dev.
|
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102
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+
`))}var Ufe,$pt,Cpt=4000;var Lb=z(()=>{qt();Ufe={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)"}}},$pt={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 Wfe;var Gfe=z(()=>{Wfe={name:"nemar-cli",packageManager:"bun@1.4.3",version:"0.10.27-dev.4110",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 Ds;var Hf=z(()=>{Gfe();Ds=Wfe.version});import{mkdirSync as Tpt,readdirSync as Ppt,unlinkSync as Ipt,writeFileSync as Npt}from"fs";import{join as rN}from"path";function Zfe(){ag=!0}function ul(){return ag}function epe(e,t=process.env){return e.includes("--debug")||t.NEMAR_DEBUG==="1"}function Bb(e){Qfe=e,$n(`Step: ${e}`)}function Io(){Yfe=!0}function tpe(){return Yfe}function ce(){if(Xfe)return;sN=!0}function Ub(){sN=!1,Xfe=!0}function npe(){return sN}function $n(e){if(ag)process.stderr.write(`[debug] ${e}
|
|
103
103
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`)}function Lpt(e){let t={};for(let[n,r]of Object.entries(e))t[n]=jpt.has(n.toLowerCase())?"[REDACTED]":r;return t}function ope(e){let t=e.indexOf("@");if(t<=0)return"***";return`${e[0]}***${e.slice(t)}`}function oN(e,t,n=0){if(n>Bpt)return"[REDACTED: depth]";if(Array.isArray(t))return t.map((r)=>oN(e,r,n+1));if(t&&typeof t==="object"){let r={};for(let[o,s]of Object.entries(t))r[o]=oN(o,s,n+1);return r}if(typeof t==="string"){if(qpt.test(e))return"[REDACTED]";return t.replace(rpe,ope)}return t}function iN(e){return e.replace(Upt,"Bearer [REDACTED]").replace(Hpt,"[REDACTED_AWS_KEY]").replace(Vpt,"$1[REDACTED]").replace(zpt,"$1$2=[REDACTED]").replace(rpe,ope)}function Gpt(e){return iN(e)}function Kfe(e,t=Mpt){if(e===void 0)return;let n=e;try{let r=JSON.parse(e);n=JSON.stringify(oN("",r))}catch{}if(n=iN(n),Buffer.byteLength(n,"utf8")>t)n=`${Buffer.from(n,"utf8").subarray(0,t).toString("utf8")}... [truncated]`;return n}function TS(e){if(!ag)return;let t=Gpt(e.url);try{let n={...e,url:t,requestHeaders:e.requestHeaders?Lpt(e.requestHeaders):void 0,requestBody:Kfe(e.requestBody),responseBody:Kfe(e.responseBody)};OS.push(n),$n(`${e.method} ${t} -> ${e.status??"ERROR"} (${e.durationMs}ms)`)}catch(n){let r=G(n);OS.push({method:e.method,url:t,status:e.status,durationMs:e.durationMs,note:`redaction failed: ${r}`}),$n(`redaction failed for ${e.method} ${t}: ${r}`)}}async function Wpt(){let e=[];try{let t=process.versions.bun?`Bun ${process.versions.bun}`:`Node ${process.version}`;e.push(`CLI version: ${Ds}`),e.push(`OS/Arch: ${process.platform}/${process.arch}`),e.push(`Runtime: ${t}`)}catch(t){e.push(`(could not read CLI/OS/runtime info: ${G(t)})`)}e.push(""),e.push("Active account:");try{let t=zt();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: ${G(t)})`)}e.push(""),e.push("External tools:");try{let t=await jb();for(let n of t){let r=n.available?n.version??"installed":n.timedOut?"(timed out)":"not installed";e.push(` ${n.name}: ${r}`)}}catch(t){e.push(` (could not probe external tools: ${G(t)})`)}return e}async function aN(){return(await Wpt()).join(`
|
|
104
104
|
`)}async function spe(){if(!ag||AS!==void 0)return;try{AS=await aN()}catch(e){let t=G(e);AS=`(could not build environment report: ${t})`,$n(`environment snapshot failed: ${t}`)}}function ipe(e){if(Jfe.has(e))return{flag:e};for(let t of Jfe){if(!e.startsWith(t)||e.length<=t.length)continue;if(t.length===2)return{flag:t,kind:"short-attached"};if(e[t.length]==="=")return{flag:t,kind:"long-eq"}}return null}function Kpt(e){let t=[];for(let n=0;n<e.length;n++){let r=e[n],o=ipe(r);if(!o){t.push(r);continue}if(o.kind==="long-eq")t.push(`${o.flag}=[REDACTED]`);else if(o.kind==="short-attached")t.push(`${o.flag}[REDACTED]`);else if(t.push(r),n+1<e.length)t.push("[REDACTED]"),n++}return t}function Jpt(e){let t=[];for(let n=0;n<e.length;n++){let r=e[n],o=ipe(r);if(!o){t.push(r);continue}if(!o.kind&&n+1<e.length)n++}return t}function Ypt(e){let t=[];for(let r of Jpt(e)){if(r.startsWith("-"))continue;if(t.push(r),t.length===2)break}return(t.length>0?t.join("-"):"nemar").replace(/[^a-zA-Z0-9_-]/g,"_")}function Xpt(e,t){let n=[];if(n.push("NEMAR CLI Debug Log"),n.push(`Generated: ${new Date().toISOString()}`),n.push(`Command: nemar ${iN(Kpt(e).join(" "))}`),n.push(""),n.push(AS??"(environment snapshot unavailable)"),n.push(""),n.push("HTTP requests:"),OS.length===0)n.push(" (none)");else OS.forEach((r,o)=>{if(n.push(` [${o+1}] ${r.method} ${r.url} -> ${r.status??"ERROR"} (${r.durationMs}ms)`),r.error)n.push(` Error: ${r.error}`);if(r.note)n.push(` Note: ${r.note}`);if(r.requestHeaders)n.push(` Request headers: ${JSON.stringify(r.requestHeaders)}`);if(r.requestBody)n.push(` Request body: ${r.requestBody}`);if(r.responseBody)n.push(` Response body: ${r.responseBody}`)});return n.push(""),n.push(`Failing step: ${Qfe??"(none recorded)"}`),n.push(`Exit code: ${t}`),`${n.join(`
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105
105
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`)}
|
package/package.json
CHANGED
|
@@ -1,7 +1,7 @@
|
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1
1
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{
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2
2
|
"name": "nemar-cli",
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3
|
"packageManager": "bun@1.4.3",
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|
4
|
-
"version": "0.10.27-dev.
|
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4
|
+
"version": "0.10.27-dev.4110",
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5
|
"description": "CLI for NEMAR (Neuroelectromagnetic Data Archive and Tools Resource) dataset management",
|
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6
6
|
"type": "module",
|
|
7
7
|
"main": "dist/index.js",
|