nemar-cli 0.10.2-dev.2460 → 0.10.2
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 +3 -3
- package/package.json +1 -1
package/dist/index.js
CHANGED
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@@ -99,18 +99,18 @@ ${t}`,WDe,KDe,YDe=(e,t,r)=>{let n=r===""?"":`with ${r.trim()}() `,o=HDe.bind(nul
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`)}var fD=!1;var{spawn:k9e}=globalThis.Bun;async function A(e,t={}){let r={...process.env,GIT_TERMINAL_PROMPT:"0",...t.env};for(let u of t.unsetEnv??[])delete r[u];let n=k9e({cmd:e,cwd:t.cwd,stdout:"pipe",stderr:"pipe",env:r}),o=!1,i;if(t.timeout)i=setTimeout(()=>{o=!0,n.kill()},t.timeout);if(pD()){let u=t.cwd?` (cwd=${t.cwd})`:"";sf(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(pD()){if(s.trim())sf(l.dim(s.trimEnd()));if(a.trim())sf(l.yellow(a.trimEnd()));sf(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 sr=F(()=>{Xe()});function O9e(){if(process.platform==="darwin")return"macos";if(process.platform==="win32")return"windows";return"linux"}function BW(e,t=O9e()){return e.installInstructions[t]}function F9e(e){let t=e.match(/(\d+\.\d+(?:\.\d+)?)/);return t?t[1]:void 0}function P9e(){let e=Number(process.env.TEST_PROBE_TIMEOUT_MS);return Number.isFinite(e)&&e>0?e:I9e}async function UW(e){try{let{exitCode:t,stdout:r,timedOut:n}=await A(e.cmd,{timeout:P9e()});if(n)return{available:!1,timedOut:!0};if(t!==0)return{available:!1};return{available:!0,version:F9e(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 af(){let e=Object.entries(LW);return Promise.all(e.map(async([t,r])=>{let{available:n,version:o,timedOut:i}=await UW(r);return{key:t,name:r.name,purpose:r.purpose,required:r.required,available:n,version:o,timedOut:i,installInstruction:BW(r)}}))}async function VW(){let t=(await af()).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 aa(e){let r=A9e[e].map((s)=>LW[s]).filter(Boolean),n=await Promise.all(r.map(async(s)=>{let a=await UW(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:BW(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 LW,A9e,I9e=4000;var cf=F(()=>{sr();LW={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)"}}},A9e={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 GW;var zW=F(()=>{GW={name:"nemar-cli",version:"0.10.2
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`))}var LW,A9e,I9e=4000;var cf=F(()=>{sr();LW={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)"}}},A9e={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 GW;var zW=F(()=>{GW={name:"nemar-cli",version:"0.10.2",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 ai;var lf=F(()=>{zW();ai=GW.version});import{mkdirSync as N9e,readdirSync as q9e,unlinkSync as j9e,writeFileSync as M9e}from"fs";import{join as mD}from"path";function JW(){nl=!0}function ca(){return nl}function XW(e,t=process.env){return e.includes("--debug")||t.NEMAR_DEBUG==="1"}function df(e){YW=e,vr(`Step: ${e}`)}function ff(){KW=!0}function ZW(){return KW}function vr(e){if(nl)process.stderr.write(`[debug] ${e}
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`)}function V9e(e){let t={};for(let[r,n]of Object.entries(e))t[r]=U9e.has(r.toLowerCase())?"[REDACTED]":n;return t}function eK(e){let t=e.indexOf("@");if(t<=0)return"***";return`${e[0]}***${e.slice(t)}`}function hD(e,t,r=0){if(r>G9e)return"[REDACTED: depth]";if(Array.isArray(t))return t.map((n)=>hD(e,n,r+1));if(t&&typeof t==="object"){let n={};for(let[o,i]of Object.entries(t))n[o]=hD(o,i,r+1);return n}if(typeof t==="string"){if(z9e.test(e))return"[REDACTED]";return t.replace(QW,eK)}return t}function gD(e){return e.replace(H9e,"Bearer [REDACTED]").replace(W9e,"[REDACTED_AWS_KEY]").replace(K9e,"$1[REDACTED]").replace(Y9e,"$1$2=[REDACTED]").replace(QW,eK)}function J9e(e){return gD(e)}function HW(e,t=B9e){if(e===void 0)return;let r=e;try{let n=JSON.parse(e);r=JSON.stringify(hD("",n))}catch{}if(r=gD(r),Buffer.byteLength(r,"utf8")>t)r=`${Buffer.from(r,"utf8").subarray(0,t).toString("utf8")}... [truncated]`;return r}function W0(e){if(!nl)return;let t=J9e(e.url);try{let r={...e,url:t,requestHeaders:e.requestHeaders?V9e(e.requestHeaders):void 0,requestBody:HW(e.requestBody),responseBody:HW(e.responseBody)};H0.push(r),vr(`${e.method} ${t} -> ${e.status??"ERROR"} (${e.durationMs}ms)`)}catch(r){let n=P(r);H0.push({method:e.method,url:t,status:e.status,durationMs:e.durationMs,note:`redaction failed: ${n}`}),vr(`redaction failed for ${e.method} ${t}: ${n}`)}}async function X9e(){let e=[];try{let t=process.versions.bun?`Bun ${process.versions.bun}`:`Node ${process.version}`;e.push(`CLI version: ${ai}`),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=nt();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 af();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 yD(){return(await X9e()).join(`
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`)}async function tK(){if(!nl||G0!==void 0)return;try{G0=await yD()}catch(e){let t=P(e);G0=`(could not build environment report: ${t})`,vr(`environment snapshot failed: ${t}`)}}function rK(e){if(WW.has(e))return{flag:e};for(let t of WW){if(!e.startsWith(t)||e.length<=t.length)continue;if(t.length===2)return{flag:t,kind:"short-attached"};if(e[t.length]==="=")return{flag:t,kind:"long-eq"}}return null}function Z9e(e){let t=[];for(let r=0;r<e.length;r++){let n=e[r],o=rK(n);if(!o){t.push(n);continue}if(o.kind==="long-eq")t.push(`${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 Q9e(e){let t=[];for(let r=0;r<e.length;r++){let n=e[r],o=rK(n);if(!o){t.push(n);continue}if(!o.kind&&r+1<e.length)r++}return t}function e7e(e){let t=[];for(let n of Q9e(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 t7e(e,t){let r=[];if(r.push("NEMAR CLI Debug Log"),r.push(`Generated: ${new Date().toISOString()}`),r.push(`Command: nemar ${gD(Z9e(e).join(" "))}`),r.push(""),r.push(G0??"(environment snapshot unavailable)"),r.push(""),r.push("HTTP requests:"),H0.length===0)r.push(" (none)");else H0.forEach((n,o)=>{if(r.push(` [${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: ${YW??"(none recorded)"}`),r.push(`Exit code: ${t}`),`${r.join(`
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`}function r7e(e,t){let r;try{r=q9e(e).filter((o)=>o.startsWith("nemar-")&&o.endsWith(".log"))}catch(o){if(o.code!=="ENOENT")vr(`could not list ${e} for log rotation: ${P(o)}`);return}r.sort();let n=r.length-t;for(let o=0;o<n;o++)try{j9e(mD(e,r[o]))}catch(i){if(i.code!=="ENOENT")vr(`could not remove old log ${r[o]}: ${P(i)}`)}}function nK(){return uf}function oK(e,t){if(!nl)return null;let r=mD(xD(),"logs");try{N9e(r,{recursive:!0})}catch(s){return uf=P(s),vr(`could not create log directory ${r}: ${uf}`),null}let o=`nemar-${new Date().toISOString().replace(/[:.]/g,"-")}-${e7e(e)}.log`,i=mD(r,o);try{M9e(i,t7e(e,t),"utf8")}catch(s){return uf=P(s),vr(`could not write log file ${i}: ${uf}`),null}return r7e(r,L9e),i}var L9e=10,B9e=2048,nl=!1,KW=!1,YW,G0,H0,U9e,z9e,QW,G9e=32,H9e,W9e,K9e,Y9e,WW,uf;var ci=F(()=>{kt();$o();cf();lf();H0=[];U9e=new Set(["authorization","cookie","set-cookie","x-api-key"]);z9e=/^(api[_-]?key|apikey|password|token|secret|access[_-]?key(_id)?|secret[_-]?access[_-]?key|session[_-]?token|authorization|ssh[_-]?key|private[_-]?key|device[_-]?code)$/i,QW=/[a-zA-Z0-9._%+-]+@[a-zA-Z0-9.-]+\.[a-zA-Z]{2,}/g;H9e=/Bearer\s+[A-Za-z0-9\-._~+/=]+/gi,W9e=/\b(?:AKIA|ASIA)[0-9A-Z]{16}\b/g,K9e=/((?:aws_)?secret_access_key["']?\s*[:=]\s*["']?)[A-Za-z0-9/+=]{20,}/gi,Y9e=/([?&])(X-Amz-Signature|X-Amz-Security-Token|X-Amz-Credential|Signature|AWSAccessKeyId)=[^&\s"']+/gi;WW=new Set(["-k","--key","--password","--api-key"])});import{chmodSync as n7e,copyFileSync as o7e,existsSync as bD,mkdirSync as i7e,statSync as s7e}from"fs";import{homedir as K0}from"os";import{join as ol}from"path";function c7e(e){let t=e.trim().replace(/\/+$/,"");try{let r=new URL(t);return r.protocol=r.protocol.toLowerCase(),r.host=r.host.toLowerCase(),r.toString().replace(/\/+$/,"")}catch{return console.error(`[nemar] could not parse stored apiUrl ${JSON.stringify(e)}; leaving as-is`),t}}function xD(){return process.env.NEMAR_CONFIG_DIR||ol(K0(),".config","nemar")}function u7e(e){if(process.env.NEMAR_CONFIG_DIR)return;let t=ol(e,"config.json");if(bD(t))return;let r=[];if(process.platform==="darwin")r.push(ol(K0(),"Library","Preferences","nemar-nodejs","config.json"));if(process.platform==="win32"){let n=process.env.APPDATA||ol(K0(),"AppData","Roaming");r.push(ol(n,"nemar-nodejs","config.json"))}r.push(ol(K0(),".config","nemar-nodejs","config.json"));for(let n of r)if(bD(n))try{i7e(e,{recursive:!0}),o7e(n,t),console.error(`[nemar] Config migrated from ${n} to ${t}
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[nemar] You can safely remove the old file.`);return}catch(o){console.error(`[nemar] Failed to migrate config from ${n}:`,o,`
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[nemar] You can manually copy ${n} to ${t}`)}}function bn(){let e=xD();if(pf&&iK===e)return pf;if(u7e(e),pf=new z0({projectName:"nemar",configFileMode:_D,schema:{activeAccount:{type:"string"},accounts:{type:"object"},apiKey:{type:"string"},apiUrl:{type:"string"},username:{type:"string"},email:{type:"string"},githubUsername:{type:"string"},sandboxCompleted:{type:"boolean"},sandboxDatasetId:{type:"string"}},cwd:e}),iK=e,!sK.has(e))sK.add(e),d7e(pf.path),p7e(),m7e();return pf}function d7e(e){if(process.platform==="win32")return;if(!bD(e))return;try{if((s7e(e).mode&511)!==_D)n7e(e,_D)}catch(t){console.error(`[nemar] could not secure config file permissions for ${e}:`,t)}}function p7e(){let e=bn(),t=e.get("accounts");if(t&&Object.keys(t).length>0)return;let r=e.get("apiKey"),n=e.get("username");if(!r&&!n)return;try{let o=n||"default",i={};for(let s of f7e){let a=e.get(s);if(a!==void 0)i[s]=a}e.store={activeAccount:o,accounts:{[o]:i}}}catch(o){console.error("Config migration failed (legacy config preserved):",o)}}function m7e(){let e=bn(),t=e.store,r=t.accounts,n=!1;if(r)for(let[i,s]of Object.entries(r)){let a=s?.apiUrl;if(!a)continue;if(a7e.has(c7e(a)))r[i]={...s,apiUrl:il},console.error(`[nemar] migrated stored apiUrl for account "${i}": ${a} -> ${il}`),n=!0}let o=t.apiUrl;if(r&&Object.keys(r).length>0&&o!==void 0){let{apiUrl:i,...s}=t;try{e.store=s,console.error(`[nemar] removed stale top-level apiUrl from config (was: ${o})`),n=!1}catch(a){console.error("API URL cleanup failed (config file unchanged):",a)}}if(n)try{e.store={...e.store,accounts:r}}catch(i){console.error("API URL migration failed (config file unchanged):",i)}}function mf(){return bn().get("activeAccount")}function us(){return bn().get("accounts")||{}}function nt(){let e={apiUrl:il},t=mf();if(!t)return e;return us()[t]||e}function _t(e,t){let r=bn(),n=r.get("activeAccount")||"default",o=r.get("accounts")||{};if(!o[n])o[n]={apiUrl:il};o[n][e]=t,r.store={...r.store,accounts:o,activeAccount:n}}function hf(e){let t=mf();if(!t)return;let r=us();if(r[t])delete r[t][e],bn().set("accounts",r)}function aK(){let e=bn(),t=mf();if(!t){e.clear();return}let r=us();delete r[t];let n=Object.keys(r);if(n.length>0)e.store={...e.store,accounts:r,activeAccount:n[0]};else e.clear()}function cK(){bn().clear()}function Te(){return!!nt().apiKey}function vD(){return bn().path}function gf(){let e=us(),t=mf();return Object.entries(e).map(([r,n])=>({key:r,username:n.username,email:n.email,githubUsername:n.githubUsername,active:r===t,keySource:n.keySource}))}function lK(e){return e.username?.trim()||e.email}function h7e(e){let t=e.trim().toLowerCase();if(!t)return;let r=Object.entries(us()).filter(([,n])=>n.email&&n.email.toLowerCase()===t).map(([n])=>n);if(r.length>1){vr(`findAccountKeyByEmail: ${r.length} accounts share email ${t}: ${r.join(", ")}`);return}return r[0]}function uK(e,t){let r=bn(),n=us(),o;if(n[e])o=e;else if(t.email)o=h7e(t.email);let i=o?n[o]:void 0,s={...i??{apiUrl:il},...t};if(o&&o!==e)delete n[o];return n[e]=s,r.store={...r.store,accounts:n,activeAccount:e},{key:e,previous:i}}function dK(e){let t=e.trim();if(!t)return"unchanged";let r=bn(),n=mf();if(!n||n===t)return"unchanged";let o=us(),i=o[n];if(!i)return"unchanged";if(o[t])return"key_taken";return delete o[n],o[t]={...i,username:t},r.store={...r.store,accounts:o,activeAccount:t},"renamed"}function wD(e){let t=bn(),r=us();if(r[e])return t.store={...t.store,activeAccount:e},r[e];for(let[n,o]of Object.entries(r))if(o.githubUsername===e)return t.store={...t.store,activeAccount:n},o;return null}var il="https://
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[nemar] You can manually copy ${n} to ${t}`)}}function bn(){let e=xD();if(pf&&iK===e)return pf;if(u7e(e),pf=new z0({projectName:"nemar",configFileMode:_D,schema:{activeAccount:{type:"string"},accounts:{type:"object"},apiKey:{type:"string"},apiUrl:{type:"string"},username:{type:"string"},email:{type:"string"},githubUsername:{type:"string"},sandboxCompleted:{type:"boolean"},sandboxDatasetId:{type:"string"}},cwd:e}),iK=e,!sK.has(e))sK.add(e),d7e(pf.path),p7e(),m7e();return pf}function d7e(e){if(process.platform==="win32")return;if(!bD(e))return;try{if((s7e(e).mode&511)!==_D)n7e(e,_D)}catch(t){console.error(`[nemar] could not secure config file permissions for ${e}:`,t)}}function p7e(){let e=bn(),t=e.get("accounts");if(t&&Object.keys(t).length>0)return;let r=e.get("apiKey"),n=e.get("username");if(!r&&!n)return;try{let o=n||"default",i={};for(let s of f7e){let a=e.get(s);if(a!==void 0)i[s]=a}e.store={activeAccount:o,accounts:{[o]:i}}}catch(o){console.error("Config migration failed (legacy config preserved):",o)}}function m7e(){let e=bn(),t=e.store,r=t.accounts,n=!1;if(r)for(let[i,s]of Object.entries(r)){let a=s?.apiUrl;if(!a)continue;if(a7e.has(c7e(a)))r[i]={...s,apiUrl:il},console.error(`[nemar] migrated stored apiUrl for account "${i}": ${a} -> ${il}`),n=!0}let o=t.apiUrl;if(r&&Object.keys(r).length>0&&o!==void 0){let{apiUrl:i,...s}=t;try{e.store=s,console.error(`[nemar] removed stale top-level apiUrl from config (was: ${o})`),n=!1}catch(a){console.error("API URL cleanup failed (config file unchanged):",a)}}if(n)try{e.store={...e.store,accounts:r}}catch(i){console.error("API URL migration failed (config file unchanged):",i)}}function mf(){return bn().get("activeAccount")}function us(){return bn().get("accounts")||{}}function nt(){let e={apiUrl:il},t=mf();if(!t)return e;return us()[t]||e}function _t(e,t){let r=bn(),n=r.get("activeAccount")||"default",o=r.get("accounts")||{};if(!o[n])o[n]={apiUrl:il};o[n][e]=t,r.store={...r.store,accounts:o,activeAccount:n}}function hf(e){let t=mf();if(!t)return;let r=us();if(r[t])delete r[t][e],bn().set("accounts",r)}function aK(){let e=bn(),t=mf();if(!t){e.clear();return}let r=us();delete r[t];let n=Object.keys(r);if(n.length>0)e.store={...e.store,accounts:r,activeAccount:n[0]};else e.clear()}function cK(){bn().clear()}function Te(){return!!nt().apiKey}function vD(){return bn().path}function gf(){let e=us(),t=mf();return Object.entries(e).map(([r,n])=>({key:r,username:n.username,email:n.email,githubUsername:n.githubUsername,active:r===t,keySource:n.keySource}))}function lK(e){return e.username?.trim()||e.email}function h7e(e){let t=e.trim().toLowerCase();if(!t)return;let r=Object.entries(us()).filter(([,n])=>n.email&&n.email.toLowerCase()===t).map(([n])=>n);if(r.length>1){vr(`findAccountKeyByEmail: ${r.length} accounts share email ${t}: ${r.join(", ")}`);return}return r[0]}function uK(e,t){let r=bn(),n=us(),o;if(n[e])o=e;else if(t.email)o=h7e(t.email);let i=o?n[o]:void 0,s={...i??{apiUrl:il},...t};if(o&&o!==e)delete n[o];return n[e]=s,r.store={...r.store,accounts:n,activeAccount:e},{key:e,previous:i}}function dK(e){let t=e.trim();if(!t)return"unchanged";let r=bn(),n=mf();if(!n||n===t)return"unchanged";let o=us(),i=o[n];if(!i)return"unchanged";if(o[t])return"key_taken";return delete o[n],o[t]={...i,username:t},r.store={...r.store,accounts:o,activeAccount:t},"renamed"}function wD(e){let t=bn(),r=us();if(r[e])return t.store={...t.store,activeAccount:e},r[e];for(let[n,o]of Object.entries(r))if(o.githubUsername===e)return t.store={...t.store,activeAccount:n},o;return null}var il="https://api.nemar.org",_D=384,a7e,l7e,Cut,pf=null,iK=null,sK,f7e;var $o=F(()=>{jW();dn();Zu();ci();a7e=new Set(["https://api.osc.earth/nemar","https://nemar-api.neuromechanist.workers.dev","https://nemar-api-dev.shirazi-10f.workers.dev"]);l7e=M({field:v(),blocks:te(v()).optional(),set_on:te(v()).optional()}).passthrough(),Cut=M({apiKey:v().optional(),apiUrl:v().url().default(il),username:v().optional(),email:v().email().optional(),githubUsername:v().optional(),sandboxCompleted:De().optional(),sandboxDatasetId:v().optional(),dismissedNoticeIds:te(C()).optional(),serviceAccess:De().optional(),profileGaps:te(l7e).optional(),orcidVerified:De().optional(),role:v().optional(),accountKind:Xu.optional(),pendingEmailChange:v().email().optional()});sK=new Set;f7e=["apiKey","apiUrl","username","email","githubUsername","sandboxCompleted","sandboxDatasetId","dismissedNoticeIds"]});function Y0(e){if(fK)return;fK=!0;let t=l.yellow("\u2500".repeat(60)),r=l.yellow.bold("[MAINTENANCE]"),n=l.dim(`mode: ${e.mode}`),o=e.eta?`
|
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109
109
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${l.dim(`eta: ${e.eta}`)}`:"";process.stderr.write(`${t}
|
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110
110
|
${r} ${e.message}
|
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111
111
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${n}${o}
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112
112
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${t}
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-
`)}var fK=!1;var DD=F(()=>{Xe()});function pK(){if(process.env.TEST_API_URL)return process.env.TEST_API_URL;if(SD)return ED;return nt().apiUrl||ED}async function O(e,t={},r=!1,n){let o=`${pK()}${e}`,i={"Content-Type":"application/json","X-CLI-Version":ai,...t.headers};if(r){let m=nt();if(!m.apiKey&&r===!0)throw new j(401,"Not authenticated. Run 'nemar auth login' first.");if(m.apiKey)i.Authorization=`Bearer ${m.apiKey}`}let s=t.method||"GET",a=typeof t.body==="string"?t.body:void 0,c=Date.now(),u;try{u=await fetch(o,{...t,headers:i})}catch(m){if(ca())W0({method:s,url:o,status:null,durationMs:Date.now()-c,requestHeaders:i,requestBody:a,error:m instanceof Error?m.message:String(m)});throw new j(0,`Network error: Could not connect to ${pK()}`,{originalError:m instanceof Error?m.message:String(m)})}let d;try{d=await u.text()}catch(m){if(ca())W0({method:s,url:o,status:u.status,durationMs:Date.now()-c,requestHeaders:i,requestBody:a,error:m instanceof Error?m.message:String(m)});throw new j(0,"Failed to read response body",{httpStatus:u.status,originalError:m instanceof Error?m.message:String(m)})}if(ca())W0({method:s,url:o,status:u.status,durationMs:Date.now()-c,requestHeaders:i,requestBody:a,responseBody:d});let f;try{f=JSON.parse(d)}catch{throw new j(u.status,`Invalid response from server (status ${u.status})`)}if(!u.ok){if(u.status===503&&(f.mode==="read-only"||f.mode==="full")){let R=typeof f.message==="string"?f.message:"NEMAR is in maintenance mode. 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O(`/admin/approve/${e}`,{method:"POST"},!0)}async function gK(e){return O(`/admin/approve/by-id/${e}`,{method:"POST"},!0)}async function yK(e){return O(`/admin/revoke/${e}`,{method:"POST"},!0)}async function xK(e){return O(`/admin/revoke/by-id/${e}`,{method:"POST"},!0)}async function bK(e,t){return O(`/admin/users/${e}/role`,{method:"POST",body:JSON.stringify({role:t})},!0)}async function _K(e,t){return O(`/admin/users/${e}/kind`,{method:"POST",body:JSON.stringify({kind:t})},!0)}async function vK(e){return O(`/admin/users/${e}`,{},!0)}async function wK(e,t){return O(`/admin/users/${e}/keys`,{method:"POST",body:JSON.stringify({name:t})},!0,th)}async function DK(e){return O(`/admin/users/${e}/keys`,{},!0,eh)}async function EK(e,t){return O(`/admin/users/${e}/keys/${t}`,{method:"DELETE"},!0)}async function $D(e,t){return O(`/admin/datasets/${e}/visibility`,{method:"PATCH",body:JSON.stringify({visibility:t})},!0)}async function SK(e){return O(`/datasets/${e}/publish`,{method:"POST"},!0)}async function $K(e){return O(`/admin/datasets/${e}/ci`,{},!0)}async function li(e){return O(`/admin/datasets/${e}/ci`,{method:"POST"},!0)}async function CD(e){return O(`/admin/datasets/${e}/ci/validate`,{method:"POST"},!0)}async function RD(e){return O(`/admin/datasets/${e}/ci/sync`,{method:"POST"},!0)}async function CK(e,t){return O(`/admin/datasets/${e}/doi/concept`,{method:"POST",body:JSON.stringify(t)},!0)}async function yf(e){return O(`/admin/datasets/${e}/doi`,{},!0)}async function kD(e,t){return O(`/admin/datasets/${e}/doi/update`,{method:"POST",body:JSON.stringify(t)},!0)}async function RK(e,t){return O(`/admin/datasets/${e}/withdraw`,{method:"POST",body:JSON.stringify({reason:t.reason,dry_run:t.dryRun})},!0)}async function kK(e,t){return O(`/admin/datasets/${e}/restore`,{method:"POST",body:JSON.stringify({dry_run:t.dryRun})},!0)}async function AK(e){return O(`/admin/datasets/${e}/reset`,{method:"POST"},!0)}async function 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t=await O(`/datasets/${e}`,{},"optional");return gY(t.dataset)}async function _Y(e){return O(`/datasets/${e}/versions`,{},!0)}async function eg(e){return O("/datasets",{method:"POST",body:JSON.stringify(e)},!0)}async function tg(e){return O(`/datasets/${e}/finalize`,{method:"POST"},!0)}async function ND(e){return O(`/datasets/${e}/request-access`,{method:"POST"},!0)}async function vY(e,t){let r=t?`?status=${t}`:"";return O(`/datasets/${e}/access-requests${r}`,{},!0)}async function wY(e,t){return O(`/datasets/${e}/access-requests/${t}/approve`,{method:"POST"},!0)}async function DY(e,t){return O(`/datasets/${e}/access-requests/${t}/deny`,{method:"POST"},!0)}async function EY(e,t){return O(`/datasets/${e}/invite`,{method:"POST",body:JSON.stringify({username:t})},!0)}async function SY(e){return O(`/datasets/${e}/collaborators`,{},!0)}async function $Y(e,t){return O(`/admin/datasets/${e}/enrichment`,{method:"POST",body:JSON.stringify(t)},!0)}var X0;var 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|
|
113
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+
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r=t.toString()?`?${t.toString()}`:"",n=await O(`/datasets${r}`,{},e.mine?!0:"optional");return n.datasets=n.datasets.map(gY),n}async function yY(e){return O(`/datasets/resolve/${e}`,{},"optional")}async function xY(){return O("/datasets/facets",{signal:AbortSignal.timeout(5000)},"optional",Zm)}async function bY(e,t={}){let r=new URLSearchParams({q:e});if(t.modality)r.set("modality",t.modality);if(t.limit)r.set("limit",String(t.limit));if(t.hasHed)r.set("has_hed","1");if(t.hasZarr)r.set("has_zarr","1");if(t.hasZarrVerified)r.set("has_zarr_verified","1");if(t.author)r.set("author",t.author);if(t.task)r.set("task",t.task);if(t.license)r.set("license",t.license);if(t.hasDoi)r.set("has_doi","true");if(t.dataComplete)r.set("data_complete","1");if(t.recent)r.set("recent",String(t.recent));if(t.facets)for(let[o,i]of Object.entries(t.facets))r.set(o,i);if(t.includeUnknown)r.set("include_unknown","1");return await O(`/datasets/search?${r.toString()}`,{},"optional",bq)}async function At(e){let t=await O(`/datasets/${e}`,{},"optional");return gY(t.dataset)}async function _Y(e){return O(`/datasets/${e}/versions`,{},!0)}async function eg(e){return O("/datasets",{method:"POST",body:JSON.stringify(e)},!0)}async function tg(e){return O(`/datasets/${e}/finalize`,{method:"POST"},!0)}async function ND(e){return O(`/datasets/${e}/request-access`,{method:"POST"},!0)}async function vY(e,t){let r=t?`?status=${t}`:"";return O(`/datasets/${e}/access-requests${r}`,{},!0)}async function wY(e,t){return O(`/datasets/${e}/access-requests/${t}/approve`,{method:"POST"},!0)}async function DY(e,t){return O(`/datasets/${e}/access-requests/${t}/deny`,{method:"POST"},!0)}async function EY(e,t){return O(`/datasets/${e}/invite`,{method:"POST",body:JSON.stringify({username:t})},!0)}async function SY(e){return O(`/datasets/${e}/collaborators`,{},!0)}async function $Y(e,t){return O(`/admin/datasets/${e}/enrichment`,{method:"POST",body:JSON.stringify(t)},!0)}var X0;var fs=F(()=>{Oc();ds();X0=/^\d{4}-\d{4}-\d{4}-\d{3}[\dX]$/});var dl;var OY=F(()=>{dl=["ci_check","enrichment_check","s3_public_read","repo_public","tag_protect","doi_create","update_metadata","update_readme","create_tag","create_release","upload_to_zenodo","publish_doi","version_doi","s3_lock","sync_nemar","notify_user"]});async function fl(e){return O(`/datasets/${e}/publish/request`,{method:"POST"},!0)}async function IY(e){return O(`/datasets/${e}/publish/status`,{},!0)}async function PY(e){return O(`/datasets/${e}/publish/resend`,{method:"POST"},!0)}async function TY(e){let t=e?`?status=${e}`:"";return O(`/admin/publish/requests${t}`,{},!0)}async function NY(e,t){return O(`/admin/publish/${e}/deny`,{method:"POST",headers:{"Content-Type":"application/json"},body:JSON.stringify({reason:t})},!0)}function g7e(e,t=[]){if(e){let r=dl.indexOf(e);if(r>=0)return r+1}return Math.min(t.length+1,dl.length)}function y7e(e){if(!(e instanceof 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bf(){try{let{stdout:e,exitCode:t,stderr:r}=await A(["gh","auth","token"]);if(t!==0)return console.warn("gh CLI returned non-zero exit code:",t),console.warn("stderr:",r),{token:null,error:`gh auth token failed: ${r.trim()||"unknown error"}`};if(!e.trim())return console.warn("gh auth token returned empty output"),{token:null,error:"gh CLI returned empty token"};return{token:e.trim()}}catch(e){let t=e instanceof Error?e.message:String(e);if(console.error("Failed to get GitHub token from gh CLI:",t),t.includes("ENOENT")||t.includes("not found"))return{token:null,error:"gh CLI not installed (command not found)"};return{token:null,error:`gh CLI error: ${t}`}}}async function rg(e){try{let{stdout:t,exitCode:r,stderr:n}=await A(["gh","api","user","--jq",".login"]);if(r!==0){if(n.includes("not logged in")||n.includes("auth login"))return{authenticated:!1,error:"gh CLI not authenticated. Run 'gh auth login' to authenticate."};return{authenticated:!1,error:`gh CLI error: ${n.trim()||"unknown error"}`}}let o=t.trim();if(!o)return{authenticated:!1,error:"gh CLI returned empty username"};if(e){let i=o.toLowerCase()===e.toLowerCase();return{authenticated:!0,username:o,matches:i,error:i?void 0:`gh CLI authenticated as '${o}', expected '${e}'`}}return{authenticated:!0,username:o}}catch(t){let r=t instanceof Error?t.message:String(t);if(r.includes("ENOENT")||r.includes("not found"))return{authenticated:!1,error:"gh CLI not installed. Install from https://cli.github.com/"};return{authenticated:!1,error:`Failed to verify gh CLI: ${r}`}}}async function ng(e){if(!/^[a-zA-Z0-9_.-]+\/[a-zA-Z0-9_.-]+$/.test(e))return{accepted:!1,error:`Invalid repository format: ${e}`};let{stdout:t,exitCode:r,stderr:n}=await A(["gh","api","/user/repository_invitations"]);if(r!==0){if(n.includes("not logged in")||n.includes("auth login"))return{accepted:!1,error:"gh CLI not authenticated. Run 'gh auth login' to authenticate."};if(n.includes("API rate limit")||n.includes("403"))return{accepted:!1,error:"GitHub API rate limit exceeded. Please try again in a few minutes."};if(n.includes("ENOENT")||n.includes("not found"))return{accepted:!1,error:"gh CLI not installed. Install from https://cli.github.com/"};return{accepted:!1,error:`Failed to list invitations: ${n.trim()||"unknown error"}`}}let o=null;try{o=JSON.parse(t||"[]").find((u)=>u.repository.full_name===e)?.id??null}catch(a){let c=a instanceof Error?a.message:String(a);return console.error("Failed to parse GitHub invitations response:",c),console.error(" Raw response (first 500 chars):",(t||"").slice(0,500)),{accepted:!1,error:`Failed to parse GitHub API response: ${c}`}}if(!o){let{exitCode:a}=await A(["gh","api",`/repos/${e}`,"--silent"]);if(a===0)return{accepted:!0,alreadyCollaborator:!0};return{accepted:!1,error:`No pending invitation found for ${e}. You may need to accept it manually via GitHub.`}}let{exitCode:i,stderr:s}=await A(["gh","api","--method","PATCH",`/user/repository_invitations/${o}`]);if(i!==0)return{accepted:!1,error:`Failed to accept invitation: ${s.trim()||"unknown error"}`};return{accepted:!0}}async function Ro(e,t,r="origin"){let n=t;if(process.env.GH_TOKEN&&t.startsWith("git@github.com:")){let o=process.env.GH_TOKEN.trim();if(!o||/\s/.test(o))return{success:!1,error:"GH_TOKEN environment variable is set but appears malformed (empty or contains whitespace)"};n=`https://github.com/${t.replace("git@github.com:","")}`,await A(["git","config","credential.https://github.com.helper",`!printf 'username=x-access-token\\npassword=${o}'`],{cwd:e})}else if(t.startsWith("git@github.com:")){let o=t.replace("git@github.com:",""),i=await bf();if(i.token)n=`https://github.com/${o}`,await A(["git","config","credential.https://github.com.helper",`!printf 'username=x-access-token\\npassword=${i.token}'`],{cwd:e});else{let s=await x7e();if(s.works)n=t;else return{success:!1,error:`GitHub authentication not configured.
|
|
114
114
|
|
|
115
115
|
gh CLI failed: ${i.error||"could not get token"}
|
|
116
116
|
SSH failed: ${s.error||"could not connect"}
|