nemar-cli 0.10.3 → 0.10.4-dev.2510
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}`,XDe,ZDe,QDe=(e,t,r)=>{let n=r===""?"":`with ${r.trim()}() `,o=JDe.bind(nul
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`)}var pD=!1;var{spawn:I9e}=globalThis.Bun;async function A(e,t={}){let r={...process.env,GIT_TERMINAL_PROMPT:"0",...t.env};for(let u of t.unsetEnv??[])delete r[u];let n=I9e({cmd:e,cwd:t.cwd,stdout:"pipe",stderr:"pipe",env:r}),o=!1,i;if(t.timeout)i=setTimeout(()=>{o=!0,n.kill()},t.timeout);if(mD()){let u=t.cwd?` (cwd=${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(mD()){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 T9e(){if(process.platform==="darwin")return"macos";if(process.platform==="win32")return"windows";return"linux"}function VW(e,t=T9e()){return e.installInstructions[t]}function N9e(e){let t=e.match(/(\d+\.\d+(?:\.\d+)?)/);return t?t[1]:void 0}function j9e(){let e=Number(process.env.TEST_PROBE_TIMEOUT_MS);return Number.isFinite(e)&&e>0?e:q9e}async function zW(e){try{let{exitCode:t,stdout:r,timedOut:n}=await A(e.cmd,{timeout:j9e()});if(n)return{available:!1,timedOut:!0};if(t!==0)return{available:!1};return{available:!0,version:N9e(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(UW);return Promise.all(e.map(async([t,r])=>{let{available:n,version:o,timedOut:i}=await zW(r);return{key:t,name:r.name,purpose:r.purpose,required:r.required,available:n,version:o,timedOut:i,installInstruction:VW(r)}}))}async function GW(){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=P9e[e].map((s)=>UW[s]).filter(Boolean),n=await Promise.all(r.map(async(s)=>{let a=await zW(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:VW(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 UW,P9e,q9e=4000;var cf=F(()=>{sr();UW={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)"}}},P9e={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 WW;var HW=F(()=>{WW={name:"nemar-cli",version:"0.10.
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`))}var UW,P9e,q9e=4000;var cf=F(()=>{sr();UW={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)"}}},P9e={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 WW;var HW=F(()=>{WW={name:"nemar-cli",version:"0.10.4-dev.2510",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 ci;var lf=F(()=>{HW();ci=WW.version});import{mkdirSync as L9e,readdirSync as B9e,unlinkSync as U9e,writeFileSync as V9e}from"fs";import{join as hD}from"path";function QW(){nl=!0}function ca(){return nl}function eK(e,t=process.env){return e.includes("--debug")||t.NEMAR_DEBUG==="1"}function df(e){ZW=e,vr(`Step: ${e}`)}function ff(){JW=!0}function tK(){return JW}function yD(){XW=!0}function rK(){return XW}function vr(e){if(nl)process.stderr.write(`[debug] ${e}
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`)}function W9e(e){let t={};for(let[r,n]of Object.entries(e))t[r]=H9e.has(r.toLowerCase())?"[REDACTED]":n;return t}function oK(e){let t=e.indexOf("@");if(t<=0)return"***";return`${e[0]}***${e.slice(t)}`}function gD(e,t,r=0){if(r>Y9e)return"[REDACTED: depth]";if(Array.isArray(t))return t.map((n)=>gD(e,n,r+1));if(t&&typeof t==="object"){let n={};for(let[o,i]of Object.entries(t))n[o]=gD(o,i,r+1);return n}if(typeof t==="string"){if(K9e.test(e))return"[REDACTED]";return t.replace(nK,oK)}return t}function xD(e){return e.replace(J9e,"Bearer [REDACTED]").replace(X9e,"[REDACTED_AWS_KEY]").replace(Z9e,"$1[REDACTED]").replace(Q9e,"$1$2=[REDACTED]").replace(nK,oK)}function e7e(e){return xD(e)}function KW(e,t=G9e){if(e===void 0)return;let r=e;try{let n=JSON.parse(e);r=JSON.stringify(gD("",n))}catch{}if(r=xD(r),Buffer.byteLength(r,"utf8")>t)r=`${Buffer.from(r,"utf8").subarray(0,t).toString("utf8")}... [truncated]`;return r}function W0(e){if(!nl)return;let t=e7e(e.url);try{let r={...e,url:t,requestHeaders:e.requestHeaders?W9e(e.requestHeaders):void 0,requestBody:KW(e.requestBody),responseBody:KW(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 t7e(){let e=[];try{let t=process.versions.bun?`Bun ${process.versions.bun}`:`Node ${process.version}`;e.push(`CLI version: ${ci}`),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 bD(){return(await t7e()).join(`
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`)}async function iK(){if(!nl||G0!==void 0)return;try{G0=await bD()}catch(e){let t=P(e);G0=`(could not build environment report: ${t})`,vr(`environment snapshot failed: ${t}`)}}function sK(e){if(YW.has(e))return{flag:e};for(let t of YW){if(!e.startsWith(t)||e.length<=t.length)continue;if(t.length===2)return{flag:t,kind:"short-attached"};if(e[t.length]==="=")return{flag:t,kind:"long-eq"}}return null}function r7e(e){let t=[];for(let r=0;r<e.length;r++){let n=e[r],o=sK(n);if(!o){t.push(n);continue}if(o.kind==="long-eq")t.push(`${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 n7e(e){let t=[];for(let r=0;r<e.length;r++){let n=e[r],o=sK(n);if(!o){t.push(n);continue}if(!o.kind&&r+1<e.length)r++}return t}function o7e(e){let t=[];for(let n of n7e(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 i7e(e,t){let r=[];if(r.push("NEMAR CLI Debug Log"),r.push(`Generated: ${new Date().toISOString()}`),r.push(`Command: nemar ${xD(r7e(e).join(" "))}`),r.push(""),r.push(G0??"(environment snapshot unavailable)"),r.push(""),r.push("HTTP requests:"),H0.length===0)r.push(" (none)");else H0.forEach((n,o)=>{if(r.push(` [${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: ${ZW??"(none recorded)"}`),r.push(`Exit code: ${t}`),`${r.join(`
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`}function s7e(e,t){let r;try{r=B9e(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{U9e(hD(e,r[o]))}catch(i){if(i.code!=="ENOENT")vr(`could not remove old log ${r[o]}: ${P(i)}`)}}function aK(){return uf}function cK(e,t){if(!nl)return null;let r=hD(_D(),"logs");try{L9e(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,"-")}-${o7e(e)}.log`,i=hD(r,o);try{V9e(i,i7e(e,t),"utf8")}catch(s){return uf=P(s),vr(`could not write log file ${i}: ${uf}`),null}return s7e(r,z9e),i}var z9e=10,G9e=2048,nl=!1,JW=!1,XW=!1,ZW,G0,H0,H9e,K9e,nK,Y9e=32,J9e,X9e,Z9e,Q9e,YW,uf;var $o=F(()=>{kt();Co();cf();lf();H0=[];H9e=new Set(["authorization","cookie","set-cookie","x-api-key"]);K9e=/^(api[_-]?key|apikey|password|token|secret|access[_-]?key(_id)?|secret[_-]?access[_-]?key|session[_-]?token|authorization|ssh[_-]?key|private[_-]?key|device[_-]?code)$/i,nK=/[a-zA-Z0-9._%+-]+@[a-zA-Z0-9.-]+\.[a-zA-Z]{2,}/g;J9e=/Bearer\s+[A-Za-z0-9\-._~+/=]+/gi,X9e=/\b(?:AKIA|ASIA)[0-9A-Z]{16}\b/g,Z9e=/((?:aws_)?secret_access_key["']?\s*[:=]\s*["']?)[A-Za-z0-9/+=]{20,}/gi,Q9e=/([?&])(X-Amz-Signature|X-Amz-Security-Token|X-Amz-Credential|Signature|AWSAccessKeyId)=[^&\s"']+/gi;YW=new Set(["-k","--key","--password","--api-key"])});import{chmodSync as a7e,copyFileSync as c7e,existsSync as vD,mkdirSync as l7e,statSync as u7e}from"fs";import{homedir as K0}from"os";import{join as ol}from"path";function f7e(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 _D(){return process.env.NEMAR_CONFIG_DIR||ol(K0(),".config","nemar")}function m7e(e){if(process.env.NEMAR_CONFIG_DIR)return;let t=ol(e,"config.json");if(vD(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(vD(n))try{l7e(e,{recursive:!0}),c7e(n,t),console.error(`[nemar] Config migrated from ${n} to ${t}
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[nemar] You can manually copy ${n} to ${t}`)}}function bn(){let e=_D();if(pf&&lK===e)return pf;if(m7e(e),pf=new z0({projectName:"nemar",configFileMode:wD,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}),lK=e,!uK.has(e))uK.add(e),h7e(pf.path),y7e(),x7e();return pf}function h7e(e){if(process.platform==="win32")return;if(!vD(e))return;try{if((u7e(e).mode&511)!==wD)a7e(e,wD)}catch(t){console.error(`[nemar] could not secure config file permissions for ${e}:`,t)}}function y7e(){let e=bn(),t=e.get("accounts");if(t&&Object.keys(t).length>0)return;let r=e.get("apiKey"),n=e.get("username");if(!r&&!n)return;try{let o=n||"default",i={};for(let s of g7e){let a=e.get(s);if(a!==void 0)i[s]=a}e.store={activeAccount:o,accounts:{[o]:i}}}catch(o){console.error("Config migration failed (legacy config preserved):",o)}}function x7e(){let e=bn(),t=e.store,r=t.accounts,n=!1;if(r)for(let[i,s]of Object.entries(r)){let a=s?.apiUrl;if(!a)continue;if(d7e.has(f7e(a)))r[i]={...s,apiUrl:il},console.error(`[nemar] migrated stored apiUrl for account "${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 dK(){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 fK(){bn().clear()}function Te(){return!!nt().apiKey}function DD(){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 pK(e){return e.username?.trim()||e.email}function b7e(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 mK(e,t){let r=bn(),n=us(),o;if(n[e])o=e;else if(t.email)o=b7e(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 hK(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 ED(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.
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[nemar] You can manually copy ${n} to ${t}`)}}function bn(){let e=_D();if(pf&&lK===e)return pf;if(m7e(e),pf=new z0({projectName:"nemar",configFileMode:wD,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}),lK=e,!uK.has(e))uK.add(e),h7e(pf.path),y7e(),x7e();return pf}function h7e(e){if(process.platform==="win32")return;if(!vD(e))return;try{if((u7e(e).mode&511)!==wD)a7e(e,wD)}catch(t){console.error(`[nemar] could not secure config file permissions for ${e}:`,t)}}function y7e(){let e=bn(),t=e.get("accounts");if(t&&Object.keys(t).length>0)return;let r=e.get("apiKey"),n=e.get("username");if(!r&&!n)return;try{let o=n||"default",i={};for(let s of g7e){let a=e.get(s);if(a!==void 0)i[s]=a}e.store={activeAccount:o,accounts:{[o]:i}}}catch(o){console.error("Config migration failed (legacy config preserved):",o)}}function x7e(){let e=bn(),t=e.store,r=t.accounts,n=!1;if(r)for(let[i,s]of Object.entries(r)){let a=s?.apiUrl;if(!a)continue;if(d7e.has(f7e(a)))r[i]={...s,apiUrl:il},console.error(`[nemar] migrated stored apiUrl for account "${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 dK(){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 fK(){bn().clear()}function Te(){return!!nt().apiKey}function DD(){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 pK(e){return e.username?.trim()||e.email}function b7e(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}: ${r.join(", ")}`);return}return r[0]}function mK(e,t){let r=bn(),n=us(),o;if(n[e])o=e;else if(t.email)o=b7e(t.email);let i=o?n[o]:void 0,s={...i??{apiUrl:il},...t};if(o&&o!==e)delete n[o];return n[e]=s,r.store={...r.store,accounts:n,activeAccount:e},{key:e,previous:i}}function hK(e){let t=e.trim();if(!t)return"unchanged";let r=bn(),n=mf();if(!n||n===t)return"unchanged";let o=us(),i=o[n];if(!i)return"unchanged";if(o[t])return"key_taken";return delete o[n],o[t]={...i,username:t},r.store={...r.store,accounts:o,activeAccount:t},"renamed"}function ED(e){let t=bn(),r=us();if(r[e])return t.store={...t.store,activeAccount:e},r[e];for(let[n,o]of Object.entries(r))if(o.githubUsername===e)return t.store={...t.store,activeAccount:n},o;return null}var il="https://nemar-api-dev.sccn-org.workers.dev",wD=384,d7e,p7e,Out,pf=null,lK=null,uK,g7e;var Co=F(()=>{LW();dn();Zu();$o();d7e=new Set(["https://api.osc.earth/nemar","https://nemar-api.neuromechanist.workers.dev","https://nemar-api-dev.shirazi-10f.workers.dev"]);p7e=M({field:v(),blocks:te(v()).optional(),set_on:te(v()).optional()}).passthrough(),Out=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(p7e).optional(),orcidVerified:De().optional(),role:v().optional(),accountKind:Xu.optional(),pendingEmailChange:v().email().optional()});uK=new Set;g7e=["apiKey","apiUrl","username","email","githubUsername","sandboxCompleted","sandboxDatasetId","dismissedNoticeIds"]});function Y0(e){if(gK)return;gK=!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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${r} ${e.message}
|
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111
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${n}${o}
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${t}
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-
`)}var gK=!1;var SD=F(()=>{Xe()});function yK(){if(process.env.TEST_API_URL)return process.env.TEST_API_URL;if(CD)return $D;return nt().apiUrl||$D}async function O(e,t={},r=!1,n){let o=`${yK()}${e}`,i={"Content-Type":"application/json","X-CLI-Version":ci,...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 ${yK()}`,{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 ${u.status})`)}if(!u.ok){if(u.status===503&&(f.mode==="read-only"||f.mode==="full")){let R=typeof f.message==="string"?f.message:"NEMAR is in maintenance mode. 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O(`/datasets/${e}/publish`,{method:"POST"},!0)}async function AK(e){return O(`/admin/datasets/${e}/ci`,{},!0)}async function li(e){return O(`/admin/datasets/${e}/ci`,{method:"POST"},!0)}async function kD(e){return O(`/admin/datasets/${e}/ci/validate`,{method:"POST"},!0)}async function AD(e){return O(`/admin/datasets/${e}/ci/sync`,{method:"POST"},!0)}async function OK(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 OD(e,t){return O(`/admin/datasets/${e}/doi/update`,{method:"POST",body:JSON.stringify(t)},!0)}async function FK(e,t){return O(`/admin/datasets/${e}/withdraw`,{method:"POST",body:JSON.stringify({reason:t.reason,dry_run:t.dryRun})},!0)}async function IK(e,t){return O(`/admin/datasets/${e}/restore`,{method:"POST",body:JSON.stringify({dry_run:t.dryRun})},!0)}async function PK(e){return O(`/admin/datasets/${e}/reset`,{method:"POST"},!0)}async function 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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(_Y),n}async function vY(e){return O(`/datasets/resolve/${e}`,{},"optional")}async function wY(){return O("/datasets/facets",{signal:AbortSignal.timeout(5000)},"optional",Zm)}async function DY(e,t={}){let r=new URLSearchParams({q:e});if(t.modality)r.set("modality",t.modality);if(t.limit)r.set("limit",String(t.limit));if(t.hasHed)r.set("has_hed","1");if(t.hasZarr)r.set("has_zarr","1");if(t.hasZarrVerified)r.set("has_zarr_verified","1");if(t.author)r.set("author",t.author);if(t.task)r.set("task",t.task);if(t.license)r.set("license",t.license);if(t.hasDoi)r.set("has_doi","true");if(t.dataComplete)r.set("data_complete","1");if(t.recent)r.set("recent",String(t.recent));if(t.facets)for(let[o,i]of Object.entries(t.facets))r.set(o,i);if(t.includeUnknown)r.set("include_unknown","1");return await O(`/datasets/search?${r.toString()}`,{},"optional",vq)}async function At(e){let t=await O(`/datasets/${e}`,{},"optional");return _Y(t.dataset)}async function EY(e){return O(`/datasets/${e}/versions`,{},!0)}async function eg(e){return O("/datasets",{method:"POST",body:JSON.stringify(e)},!0)}async function tg(e){return O(`/datasets/${e}/finalize`,{method:"POST"},!0)}async function jD(e){return O(`/datasets/${e}/request-access`,{method:"POST"},!0)}async function SY(e,t){let r=t?`?status=${t}`:"";return O(`/datasets/${e}/access-requests${r}`,{},!0)}async function $Y(e,t){return O(`/datasets/${e}/access-requests/${t}/approve`,{method:"POST"},!0)}async function CY(e,t){return O(`/datasets/${e}/access-requests/${t}/deny`,{method:"POST"},!0)}async function RY(e,t){return O(`/datasets/${e}/invite`,{method:"POST",body:JSON.stringify({username:t})},!0)}async function kY(e){return O(`/datasets/${e}/collaborators`,{},!0)}async function AY(e,t){return O(`/admin/datasets/${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]$/});var dl;var TY=F(()=>{dl=["ci_check","enrichment_check","s3_public_read","repo_public","tag_protect","doi_create","update_metadata","update_readme","create_tag","create_release","upload_to_zenodo","publish_doi","version_doi","s3_lock","sync_nemar","notify_user"]});async function fl(e){return O(`/datasets/${e}/publish/request`,{method:"POST"},!0)}async function qY(e){return O(`/datasets/${e}/publish/status`,{},!0)}async function jY(e){return O(`/datasets/${e}/publish/resend`,{method:"POST"},!0)}async function MY(e){let t=e?`?status=${e}`:"";return O(`/admin/publish/requests${t}`,{},!0)}async function LY(e,t){return O(`/admin/publish/${e}/deny`,{method:"POST",headers:{"Content-Type":"application/json"},body:JSON.stringify({reason:t})},!0)}function _7e(e,t=[]){if(e){let r=dl.indexOf(e);if(r>=0)return r+1}return Math.min(t.length+1,dl.length)}function v7e(e){if(!(e instanceof j))return!1;if(e.statusCode===0)return!0;if(e.statusCode===429)return!0;if(e.statusCode>=500&&e.statusCode<600)return!0;if(e.statusCode===403&&/repository has been locked/i.test(e.message))return!0;return!1}async function pl(e,t=!1,r=!1,n=!1,o,i){let c,u,d=0,f=!1,m,p=t,g=[],y;function x(_,w,S,R){if(!i)return;i({step:_,stepIndex:_7e(_,w),stepTotal:dl.length,s3LockLocked:S,s3LockTotal:R,s3LockResumed:_==="s3_lock"&&f?!0:void 0})}for(let _=1;_<=5;_++)try{let w,S=!0;do{if(w=await O(`/admin/publish/${e}/approve`,{method:"POST",headers:{"Content-Type":"application/json"},body:JSON.stringify({resume:S?p:!0,sandbox:r,s3_lock_continuation_token:c,s3_lock_total:u,skip_ci_check:n})},!0),S=!1,w.step_results)g.push(...w.step_results);if(w.s3_lock_total!==void 0)u=w.s3_lock_total;if(w.s3_lock_batch_count!==void 0)d+=w.s3_lock_batch_count;let R=w.step??w.step_results?.[w.step_results.length-1]?.step;if(R&&(R!==m||R==="s3_lock"))x(R,w.steps_completed??[],R==="s3_lock"?d:void 0,R==="s3_lock"?u:void 0),m=R;if(w.hasMore&&w.s3_lock_continuation_token!==void 0)c=w.s3_lock_continuation_token;else break}while(w.hasMore);if(g.length>0)w.step_results=NY(g);return w}catch(w){if(y=w,_===5||!v7e(w)){if(w instanceof j&&g.length>0)w.stepResults=NY(g);throw w}let R=w;if(o?.({attempt:_,maxAttempts:5,delayMs:1e4,step:R.step,error:R.message}),await new Promise((E)=>setTimeout(E,1e4)),p=!0,c!==void 0)f=!0}throw y}function NY(e){let t=new Map;for(let r of e)t.set(r.step,r);return Array.from(t.values())}var xf=F(()=>{TY();ds();kt()});async function w7e(){try{let{exitCode:e,stderr:t}=await A(["ssh","-T","-o","BatchMode=yes","-o","ConnectTimeout=5","git@github.com"]),r=t.includes("successfully authenticated");if(!r)console.warn("SSH test to github.com failed:",{exitCode:e,stderr:t.trim().slice(0,500)});return{works:r,error:r?void 0:t.trim().slice(0,500)}}catch(e){let t=e instanceof Error?e.message:String(e);return console.warn("SSH test exception:",t),{works:!1,error:t}}}async function 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: ${s.trim()||"unknown error"}`};return{accepted:!0}}async function ko(e,t,r="origin"){let n=t;if(process.env.GH_TOKEN&&t.startsWith("git@github.com:")){let o=process.env.GH_TOKEN.trim();if(!o||/\s/.test(o))return{success:!1,error:"GH_TOKEN environment variable is set but appears malformed (empty or contains whitespace)"};n=`https://github.com/${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 w7e();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"}
|