nemar-cli 0.10.10-dev.2999 → 0.10.10
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
|
@@ -99,18 +99,18 @@ ${t}`,jSe,qSe,MSe=(e,t,r)=>{let n=r===""?"":`with ${r.trim()}() `,o=NSe.bind(nul
|
|
|
99
99
|
`)}var mE=!1;var{spawn:FLe}=globalThis.Bun;async function C(e,t={}){let r={...process.env,GIT_TERMINAL_PROMPT:"0",...t.env};for(let u of t.unsetEnv??[])delete r[u];let n=FLe({cmd:e,cwd:t.cwd,...t.stdin===void 0?{}:{stdin:new TextEncoder().encode(t.stdin)},stdout:"pipe",stderr:"pipe",env:r}),o=!1,i;if(t.timeout)i=setTimeout(()=>{o=!0,n.kill()},t.timeout);if(hE()){let u=t.cwd?` (cwd=${t.cwd})`:"";Tf(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(hE()){if(s.trim())Tf(l.dim(s.trimEnd()));if(a.trim())Tf(l.yellow(a.trimEnd()));Tf(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 vt=O(()=>{Xe()});function ILe(){if(process.platform==="darwin")return"macos";if(process.platform==="win32")return"windows";return"linux"}function dY(e,t=ILe()){return e.installInstructions[t]}function TLe(e){let t=e.match(/(\d+\.\d+(?:\.\d+)?)/);return t?t[1]:void 0}function jLe(){let e=Number(process.env.TEST_PROBE_TIMEOUT_MS);return Number.isFinite(e)&&e>0?e:NLe}async function fY(e){try{let{exitCode:t,stdout:r,timedOut:n}=await C(e.cmd,{timeout:jLe()});if(n)return{available:!1,timedOut:!0};if(t!==0)return{available:!1};return{available:!0,version:TLe(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 Nf(){let e=Object.entries(uY);return Promise.all(e.map(async([t,r])=>{let{available:n,version:o,timedOut:i}=await fY(r);return{key:t,name:r.name,purpose:r.purpose,required:r.required,available:n,version:o,timedOut:i,installInstruction:dY(r)}}))}async function pY(){let t=(await Nf()).filter((r)=>r.required&&!r.available);if(t.length===0)return[];console.warn(`
|
|
100
100
|
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 Pa(e){let r=PLe[e].map((s)=>uY[s]).filter(Boolean),n=await Promise.all(r.map(async(s)=>{let a=await fY(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:dY(s.check)}));if(o.length===0)return;let i=[`
|
|
101
101
|
Missing required tools:`];for(let s of o)i.push(` ${s.tool} not installed`),i.push(` Install: ${s.installInstruction}`);throw Error(i.join(`
|
|
102
|
-
`))}var uY,PLe,NLe=4000;var jf=O(()=>{vt();uY={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)"}}},PLe={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 hY;var mY=O(()=>{hY={name:"nemar-cli",version:"0.10.10
|
|
102
|
+
`))}var uY,PLe,NLe=4000;var jf=O(()=>{vt();uY={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)"}}},PLe={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 hY;var mY=O(()=>{hY={name:"nemar-cli",version:"0.10.10",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 Si;var qf=O(()=>{mY();Si=hY.version});import{mkdirSync as MLe,readdirSync as LLe,unlinkSync as BLe,writeFileSync as ULe}from"fs";import{join as gE}from"path";function vY(){Fl=!0}function Ia(){return Fl}function wY(e,t=process.env){return e.includes("--debug")||t.NEMAR_DEBUG==="1"}function Lf(e){_Y=e,$r(`Step: ${e}`)}function Bf(){bY=!0}function DY(){return bY}function bE(){xY=!0}function EY(){return xY}function $r(e){if(Fl)process.stderr.write(`[debug] ${e}
|
|
103
103
|
`)}function HLe(e){let t={};for(let[r,n]of Object.entries(e))t[r]=GLe.has(r.toLowerCase())?"[REDACTED]":n;return t}function $Y(e){let t=e.indexOf("@");if(t<=0)return"***";return`${e[0]}***${e.slice(t)}`}function yE(e,t,r=0){if(r>KLe)return"[REDACTED: depth]";if(Array.isArray(t))return t.map((n)=>yE(e,n,r+1));if(t&&typeof t==="object"){let n={};for(let[o,i]of Object.entries(t))n[o]=yE(o,i,r+1);return n}if(typeof t==="string"){if(WLe.test(e))return"[REDACTED]";return t.replace(SY,$Y)}return t}function xE(e){return e.replace(YLe,"Bearer [REDACTED]").replace(JLe,"[REDACTED_AWS_KEY]").replace(XLe,"$1[REDACTED]").replace(ZLe,"$1$2=[REDACTED]").replace(SY,$Y)}function QLe(e){return xE(e)}function gY(e,t=VLe){if(e===void 0)return;let r=e;try{let n=JSON.parse(e);r=JSON.stringify(yE("",n))}catch{}if(r=xE(r),Buffer.byteLength(r,"utf8")>t)r=`${Buffer.from(r,"utf8").subarray(0,t).toString("utf8")}... [truncated]`;return r}function I0(e){if(!Fl)return;let t=QLe(e.url);try{let r={...e,url:t,requestHeaders:e.requestHeaders?HLe(e.requestHeaders):void 0,requestBody:gY(e.requestBody),responseBody:gY(e.responseBody)};P0.push(r),$r(`${e.method} ${t} -> ${e.status??"ERROR"} (${e.durationMs}ms)`)}catch(r){let n=N(r);P0.push({method:e.method,url:t,status:e.status,durationMs:e.durationMs,note:`redaction failed: ${n}`}),$r(`redaction failed for ${e.method} ${t}: ${n}`)}}async function eBe(){let e=[];try{let t=process.versions.bun?`Bun ${process.versions.bun}`:`Node ${process.version}`;e.push(`CLI version: ${Si}`),e.push(`OS/Arch: ${process.platform}/${process.arch}`),e.push(`Runtime: ${t}`)}catch(t){e.push(`(could not read CLI/OS/runtime info: ${N(t)})`)}e.push(""),e.push("Active account:");try{let t=ot();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: ${N(t)})`)}e.push(""),e.push("External tools:");try{let t=await Nf();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: ${N(t)})`)}return e}async function _E(){return(await eBe()).join(`
|
|
104
104
|
`)}async function CY(){if(!Fl||F0!==void 0)return;try{F0=await _E()}catch(e){let t=N(e);F0=`(could not build environment report: ${t})`,$r(`environment snapshot failed: ${t}`)}}function kY(e){if(yY.has(e))return{flag:e};for(let t of yY){if(!e.startsWith(t)||e.length<=t.length)continue;if(t.length===2)return{flag:t,kind:"short-attached"};if(e[t.length]==="=")return{flag:t,kind:"long-eq"}}return null}function tBe(e){let t=[];for(let r=0;r<e.length;r++){let n=e[r],o=kY(n);if(!o){t.push(n);continue}if(o.kind==="long-eq")t.push(`${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 rBe(e){let t=[];for(let r=0;r<e.length;r++){let n=e[r],o=kY(n);if(!o){t.push(n);continue}if(!o.kind&&r+1<e.length)r++}return t}function nBe(e){let t=[];for(let n of rBe(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 oBe(e,t){let r=[];if(r.push("NEMAR CLI Debug Log"),r.push(`Generated: ${new Date().toISOString()}`),r.push(`Command: nemar ${xE(tBe(e).join(" "))}`),r.push(""),r.push(F0??"(environment snapshot unavailable)"),r.push(""),r.push("HTTP requests:"),P0.length===0)r.push(" (none)");else P0.forEach((n,o)=>{if(r.push(` [${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: ${_Y??"(none recorded)"}`),r.push(`Exit code: ${t}`),`${r.join(`
|
|
105
105
|
`)}
|
|
106
106
|
`}function iBe(e,t){let r;try{r=LLe(e).filter((o)=>o.startsWith("nemar-")&&o.endsWith(".log"))}catch(o){if(o.code!=="ENOENT")$r(`could not list ${e} for log rotation: ${N(o)}`);return}r.sort();let n=r.length-t;for(let o=0;o<n;o++)try{BLe(gE(e,r[o]))}catch(i){if(i.code!=="ENOENT")$r(`could not remove old log ${r[o]}: ${N(i)}`)}}function RY(){return Mf}function AY(e,t){if(!Fl)return null;let r=gE(vE(),"logs");try{MLe(r,{recursive:!0})}catch(s){return Mf=N(s),$r(`could not create log directory ${r}: ${Mf}`),null}let o=`nemar-${new Date().toISOString().replace(/[:.]/g,"-")}-${nBe(e)}.log`,i=gE(r,o);try{ULe(i,oBe(e,t),"utf8")}catch(s){return Mf=N(s),$r(`could not write log file ${i}: ${Mf}`),null}return iBe(r,zLe),i}var zLe=10,VLe=2048,Fl=!1,bY=!1,xY=!1,_Y,F0,P0,GLe,WLe,SY,KLe=32,YLe,JLe,XLe,ZLe,yY,Mf;var jo=O(()=>{It();qo();jf();qf();P0=[];GLe=new Set(["authorization","cookie","set-cookie","x-api-key"]);WLe=/^(api[_-]?key|apikey|password|token|secret|access[_-]?key(_id)?|secret[_-]?access[_-]?key|session|session[_-]?token|authorization|ssh[_-]?key|private[_-]?key|device[_-]?code)$/i,SY=/[a-zA-Z0-9._%+-]+@[a-zA-Z0-9.-]+\.[a-zA-Z]{2,}/g;YLe=/Bearer\s+[A-Za-z0-9\-._~+/=]+/gi,JLe=/\b(?:AKIA|ASIA)[0-9A-Z]{16}\b/g,XLe=/((?:aws_)?secret_access_key["']?\s*[:=]\s*["']?)[A-Za-z0-9/+=]{20,}/gi,ZLe=/([?&])(X-Amz-Signature|X-Amz-Security-Token|X-Amz-Credential|Signature|AWSAccessKeyId)=[^&\s"']+/gi;yY=new Set(["-k","--key","--password","--api-key"])});import{chmodSync as sBe,copyFileSync as aBe,existsSync as wE,mkdirSync as cBe,statSync as lBe}from"fs";import{homedir as T0}from"os";import{join as Pl}from"path";function dBe(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 vE(){return process.env.NEMAR_CONFIG_DIR||Pl(T0(),".config","nemar")}function pBe(e){if(process.env.NEMAR_CONFIG_DIR)return;let t=Pl(e,"config.json");if(wE(t))return;let r=[];if(process.platform==="darwin")r.push(Pl(T0(),"Library","Preferences","nemar-nodejs","config.json"));if(process.platform==="win32"){let n=process.env.APPDATA||Pl(T0(),"AppData","Roaming");r.push(Pl(n,"nemar-nodejs","config.json"))}r.push(Pl(T0(),".config","nemar-nodejs","config.json"));for(let n of r)if(wE(n))try{cBe(e,{recursive:!0}),aBe(n,t),console.error(`[nemar] Config migrated from ${n} to ${t}
|
|
107
107
|
[nemar] You can safely remove the old file.`);return}catch(o){console.error(`[nemar] Failed to migrate config from ${n}:`,o,`
|
|
108
|
-
[nemar] You can manually copy ${n} to ${t}`)}}function Sn(){let e=vE();if(Uf&&OY===e)return Uf;if(pBe(e),Uf=new O0({projectName:"nemar",configFileMode:DE,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}),OY=e,!FY.has(e))FY.add(e),mBe(Uf.path),gBe(),yBe();return Uf}function mBe(e){if(process.platform==="win32")return;if(!wE(e))return;try{if((lBe(e).mode&511)!==DE)sBe(e,DE)}catch(t){console.error(`[nemar] could not secure config file permissions for ${e}:`,t)}}function gBe(){let e=Sn(),t=e.get("accounts");if(t&&Object.keys(t).length>0)return;let r=e.get("apiKey"),n=e.get("username");if(!r&&!n)return;try{let o=n||"default",i={};for(let s of hBe){let a=e.get(s);if(a!==void 0)i[s]=a}e.store={activeAccount:o,accounts:{[o]:i}}}catch(o){console.error("Config migration failed (legacy config preserved):",o)}}function yBe(){let e=Sn(),t=e.store,r=t.accounts,n=!1;if(r)for(let[i,s]of Object.entries(r)){let a=s?.apiUrl;if(!a)continue;if(uBe.has(dBe(a)))r[i]={...s,apiUrl:Il},console.error(`[nemar] migrated stored apiUrl for account "${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: ${o})`),n=!1}catch(a){console.error("API URL cleanup failed (config file unchanged):",a)}}if(n)try{e.store={...e.store,accounts:r}}catch(i){console.error("API URL migration failed (config file unchanged):",i)}}function zf(){return Sn().get("activeAccount")}function Ts(){return Sn().get("accounts")||{}}function ot(){let e={apiUrl:Il},t=zf();if(!t)return e;return Ts()[t]||e}function wt(e,t){let r=Sn(),n=r.get("activeAccount")||"default",o=r.get("accounts")||{};if(!o[n])o[n]={apiUrl:Il};o[n][e]=t,r.store={...r.store,accounts:o,activeAccount:n}}function Vf(e){let t=zf();if(!t)return;let r=Ts();if(r[t])delete r[t][e],Sn().set("accounts",r)}function PY(){let e=Sn(),t=zf();if(!t){e.clear();return}let r=Ts();delete r[t];let n=Object.keys(r);if(n.length>0)e.store={...e.store,accounts:r,activeAccount:n[0]};else e.clear()}function IY(){Sn().clear()}function je(){return!!ot().apiKey}function EE(){return Sn().path}function Gf(){let e=Ts(),t=zf();return Object.entries(e).map(([r,n])=>({key:r,username:n.username,email:n.email,githubUsername:n.githubUsername,active:r===t,keySource:n.keySource}))}function TY(e){return e.username?.trim()||e.email}function bBe(e){let t=e.trim().toLowerCase();if(!t)return;let r=Object.entries(Ts()).filter(([,n])=>n.email&&n.email.toLowerCase()===t).map(([n])=>n);if(r.length>1){$r(`findAccountKeyByEmail: ${r.length} accounts share email ${t}: ${r.join(", ")}`);return}return r[0]}function NY(e,t){let r=Sn(),n=Ts(),o;if(n[e])o=e;else if(t.email)o=bBe(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 jY(e){let t=e.trim();if(!t)return"unchanged";let r=Sn(),n=zf();if(!n||n===t)return"unchanged";let o=Ts(),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 SE(e){let t=Sn(),r=Ts();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://
|
|
108
|
+
[nemar] You can manually copy ${n} to ${t}`)}}function Sn(){let e=vE();if(Uf&&OY===e)return Uf;if(pBe(e),Uf=new O0({projectName:"nemar",configFileMode:DE,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}),OY=e,!FY.has(e))FY.add(e),mBe(Uf.path),gBe(),yBe();return Uf}function mBe(e){if(process.platform==="win32")return;if(!wE(e))return;try{if((lBe(e).mode&511)!==DE)sBe(e,DE)}catch(t){console.error(`[nemar] could not secure config file permissions for ${e}:`,t)}}function gBe(){let e=Sn(),t=e.get("accounts");if(t&&Object.keys(t).length>0)return;let r=e.get("apiKey"),n=e.get("username");if(!r&&!n)return;try{let o=n||"default",i={};for(let s of hBe){let a=e.get(s);if(a!==void 0)i[s]=a}e.store={activeAccount:o,accounts:{[o]:i}}}catch(o){console.error("Config migration failed (legacy config preserved):",o)}}function yBe(){let e=Sn(),t=e.store,r=t.accounts,n=!1;if(r)for(let[i,s]of Object.entries(r)){let a=s?.apiUrl;if(!a)continue;if(uBe.has(dBe(a)))r[i]={...s,apiUrl:Il},console.error(`[nemar] migrated stored apiUrl for account "${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: ${o})`),n=!1}catch(a){console.error("API URL cleanup failed (config file unchanged):",a)}}if(n)try{e.store={...e.store,accounts:r}}catch(i){console.error("API URL migration failed (config file unchanged):",i)}}function zf(){return Sn().get("activeAccount")}function Ts(){return Sn().get("accounts")||{}}function ot(){let e={apiUrl:Il},t=zf();if(!t)return e;return Ts()[t]||e}function wt(e,t){let r=Sn(),n=r.get("activeAccount")||"default",o=r.get("accounts")||{};if(!o[n])o[n]={apiUrl:Il};o[n][e]=t,r.store={...r.store,accounts:o,activeAccount:n}}function Vf(e){let t=zf();if(!t)return;let r=Ts();if(r[t])delete r[t][e],Sn().set("accounts",r)}function PY(){let e=Sn(),t=zf();if(!t){e.clear();return}let r=Ts();delete r[t];let n=Object.keys(r);if(n.length>0)e.store={...e.store,accounts:r,activeAccount:n[0]};else e.clear()}function IY(){Sn().clear()}function je(){return!!ot().apiKey}function EE(){return Sn().path}function Gf(){let e=Ts(),t=zf();return Object.entries(e).map(([r,n])=>({key:r,username:n.username,email:n.email,githubUsername:n.githubUsername,active:r===t,keySource:n.keySource}))}function TY(e){return e.username?.trim()||e.email}function bBe(e){let t=e.trim().toLowerCase();if(!t)return;let r=Object.entries(Ts()).filter(([,n])=>n.email&&n.email.toLowerCase()===t).map(([n])=>n);if(r.length>1){$r(`findAccountKeyByEmail: ${r.length} accounts share email ${t}: ${r.join(", ")}`);return}return r[0]}function NY(e,t){let r=Sn(),n=Ts(),o;if(n[e])o=e;else if(t.email)o=bBe(t.email);let i=o?n[o]:void 0,s={...i??{apiUrl:Il},...t};if(o&&o!==e)delete n[o];return n[e]=s,r.store={...r.store,accounts:n,activeAccount:e},{key:e,previous:i}}function jY(e){let t=e.trim();if(!t)return"unchanged";let r=Sn(),n=zf();if(!n||n===t)return"unchanged";let o=Ts(),i=o[n];if(!i)return"unchanged";if(o[t])return"key_taken";return delete o[n],o[t]={...i,username:t},r.store={...r.store,accounts:o,activeAccount:t},"renamed"}function SE(e){let t=Sn(),r=Ts();if(r[e])return t.store={...t.store,activeAccount:e},r[e];for(let[n,o]of Object.entries(r))if(o.githubUsername===e)return t.store={...t.store,activeAccount:n},o;return null}var Il="https://api.nemar.org",DE=384,uBe,fBe,ght,Uf=null,OY=null,FY,hBe;var qo=O(()=>{cY();en();Cd();jo();uBe=new Set(["https://api.osc.earth/nemar","https://nemar-api.neuromechanist.workers.dev","https://nemar-api-dev.shirazi-10f.workers.dev"]);fBe=U({field:w(),blocks:te(w()).optional(),set_on:te(w()).optional()}).passthrough(),ght=U({apiKey:w().optional(),apiUrl:w().url().default(Il),username:w().optional(),email:w().email().optional(),githubUsername:w().optional(),sandboxCompleted:be().optional(),sandboxDatasetId:w().optional(),dismissedNoticeIds:te(k()).optional(),serviceAccess:be().optional(),profileGaps:te(fBe).optional(),orcidVerified:be().optional(),role:w().optional(),accountKind:$d.optional(),pendingEmailChange:w().email().optional()});FY=new Set;hBe=["apiKey","apiUrl","username","email","githubUsername","sandboxCompleted","sandboxDatasetId","dismissedNoticeIds"]});function N0(e){if(qY)return;qY=!0;let t=l.yellow("\u2500".repeat(60)),r=l.yellow.bold("[MAINTENANCE]"),n=l.dim(`mode: ${e.mode}`),o=e.eta?`
|
|
109
109
|
${l.dim(`eta: ${e.eta}`)}`:"";process.stderr.write(`${t}
|
|
110
110
|
${r} ${e.message}
|
|
111
111
|
${n}${o}
|
|
112
112
|
${t}
|
|
113
|
-
`)}var qY=!1;var $E=O(()=>{Xe()});function j0(){if(process.env.TEST_API_URL)return process.env.TEST_API_URL;if(kE)return CE;return ot().apiUrl||CE}async function F(e,t={},r=!1,n){let o=`${j0()}${e}`,i={"Content-Type":"application/json","X-CLI-Version":Si,...t.headers};if(r){let m=ot();if(!m.apiKey&&r===!0)throw new L(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(Ia())I0({method:s,url:o,status:null,durationMs:Date.now()-c,requestHeaders:i,requestBody:a,error:m instanceof Error?m.message:String(m)});throw new L(0,`Network error: Could not connect to ${j0()}`,{originalError:m instanceof Error?m.message:String(m)})}let d;try{d=await u.text()}catch(m){if(Ia())I0({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 L(0,"Failed to read response body",{httpStatus:u.status,originalError:m instanceof Error?m.message:String(m)})}if(Ia())I0({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 L(u.status,`Invalid response from server (status ${u.status})`)}if(!u.ok){if(u.status===503&&(f.mode==="read-only"||f.mode==="full")){let R=typeof f.message==="string"?f.message:"NEMAR is in maintenance mode. Please retry shortly.",E=typeof f.eta==="string"?f.eta:null,P=new Is(f.mode,R,E,f.details);throw N0(P),P}let m=typeof f.block_reason==="string",p=Array.isArray(f.missing)?f.missing.filter((R)=>typeof R==="string"):void 0,h=typeof f.error==="string"&&(Iq.includes(f.error)||Bq.includes(f.error)),g=typeof f.error==="string"&&(jh.options.includes(f.error)||Hq.includes(f.error)),b=typeof f.error==="string"&&kq.includes(f.error),v=m||h||g||b||p!==void 0&&typeof f.error==="string"&&Pq.includes(f.error)?f.message||f.error:f.error||f.message;if(u.status===404&&f.error==="Not Found"&&typeof f.message==="string")v=`${f.message}. This NEMAR backend does not support this command yet.`;let S=new L(u.status,v||"Request failed",f.details,typeof f.step==="string"?f.step:void 0,m?f.block_reason:void 0,p);if(typeof f.error==="string")S.code=f.error;if(typeof f.reason==="string")S.reason=f.reason;throw S.rawBody=f,S}if(n){let m=n.safeParse(f);if(!m.success)throw new L(u.status,`Response for ${e} did not match the expected NEMAR contract`,{issues:m.error.issues});return m.data}return f}var CE="https://nemar-api-dev.sccn-org.workers.dev",kE;var $i=O(()=>{Lh();kw();Cd();qo();jo();$E();qf();It();kE=CE.includes("workers.dev")});function q0(e){if(e.service_access===void 0||e.service_access===null)return"unknown";return e.service_access?"upload":"browse"}async function MY(e,t,r,n){let o=new URLSearchParams;if(e)o.set("status",e);if(t)o.set("role",t);if(r)o.set("awaiting_approval","1");if(n)o.set("kind",n);let i=o.toString()?`?${o.toString()}`:"";return F(`/admin/users${i}`,{},!0,Oq)}async function LY(e){return F(`/admin/approve/${e}`,{method:"POST"},!0)}async function BY(e){return F(`/admin/approve/by-id/${e}`,{method:"POST"},!0)}async function UY(e){return F(`/admin/revoke/${e}`,{method:"POST"},!0)}async function zY(e){return F(`/admin/revoke/by-id/${e}`,{method:"POST"},!0)}async function VY(e,t){return F(`/admin/users/${e}/role`,{method:"POST",body:JSON.stringify({role:t})},!0)}async function GY(e,t){return F(`/admin/users/${e}/kind`,{method:"POST",body:JSON.stringify({kind:t})},!0)}async function HY(e){return F(`/admin/users/${e}`,{},!0)}async function WY(e,t){return F(`/admin/users/${e}/keys`,{method:"POST",body:JSON.stringify({name:t})},!0,Mh)}async function KY(e){return F(`/admin/users/${e}/keys`,{},!0,qh)}async function YY(e,t){return F(`/admin/users/${e}/keys/${t}`,{method:"DELETE"},!0)}async function RE(e,t){return F(`/admin/datasets/${e}/visibility`,{method:"PATCH",body:JSON.stringify({visibility:t})},!0)}async function JY(e){return F(`/datasets/${e}/publish`,{method:"POST"},!0)}async function XY(e){return F(`/admin/datasets/${e}/ci`,{},!0)}async function Ci(e){return F(`/admin/datasets/${e}/ci`,{method:"POST"},!0)}async function AE(e){return F(`/admin/datasets/${e}/ci/validate`,{method:"POST"},!0)}async function OE(e){return F(`/admin/datasets/${e}/ci/sync`,{method:"POST"},!0)}async function ZY(e,t){return F(`/admin/datasets/${e}/doi/concept`,{method:"POST",body:JSON.stringify(t)},!0)}async function Hf(e){return F(`/admin/datasets/${e}/doi`,{},!0)}async function FE(e,t){return F(`/admin/datasets/${e}/doi/update`,{method:"POST",body:JSON.stringify(t)},!0)}async function QY(e,t){return F(`/admin/datasets/${e}/withdraw`,{method:"POST",body:JSON.stringify({reason:t.reason,dry_run:t.dryRun})},!0)}async function eJ(e,t){return F(`/admin/datasets/${e}/restore`,{method:"POST",body:JSON.stringify({dry_run:t.dryRun})},!0)}async function tJ(e){return F(`/admin/datasets/${e}/reset`,{method:"POST"},!0)}async function rJ(e,t=!1){return F(`/admin/datasets/${e}`,{method:"DELETE",headers:{"Content-Type":"application/json"},body:JSON.stringify({force:t})},!0)}async function nJ(e){return F("/admin/datasets/bulk-delete",{method:"POST",headers:{"Content-Type":"application/json"},body:JSON.stringify({dataset_ids:e})},!0)}async function oJ(e){return F("/admin/datasets/import",{method:"POST",body:JSON.stringify(e)},!0)}async function iJ(e){return F("/admin/datasets/exemplar",{method:"POST",body:JSON.stringify(e)},!0)}async function sJ(e){return F(`/admin/datasets/${e}/exemplar/remint-dois`,{method:"POST"},!0)}async function PE(e,t){let r=new URLSearchParams;if(e)r.set("status",e);if(t!==void 0)r.set("blocklisted",t?"1":"0");let n=r.toString();return F(`/admin/imports${n?`?${n}`:""}`,{},!0)}async function aJ(e){return F(`/admin/imports/${e}/rollback`,{method:"POST"},!0)}async function cJ(e){return F(`/admin/imports/${e}/retry`,{method:"POST"},!0)}async function IE(e){return F(`/admin/imports/${e}/verify`,{method:"POST"},!0)}async function lJ(e){return F("/admin/imports/dispatch-cooldown",{method:"POST",headers:{"Content-Type":"application/json"},body:JSON.stringify({dataset_ids:e})},!0)}async function Tl(e,t){return F(`/admin/datasets/${e}/reindex`,{method:"POST",headers:{"Content-Type":"application/json"},body:JSON.stringify(t??{})},!0)}async function uJ(e,t){return F("/admin/datasets/reindex/bulk",{method:"POST",headers:{"Content-Type":"application/json"},body:JSON.stringify({filter:e,...t??{}})},!0)}async function dJ(e){let t=e?.limit??15;return F(`/admin/datasets/hed-sweep?limit=${encodeURIComponent(String(t))}`,{method:"POST",headers:{"Content-Type":"application/json"}},!0)}async function fJ(){return F("/admin/datasets/hed-sweep?reset=1",{method:"POST",headers:{"Content-Type":"application/json"}},!0)}async function pJ(e){let t=e?.limit??50;return F(`/admin/datasets/recording-stats-sweep?limit=${encodeURIComponent(String(t))}`,{method:"POST",headers:{"Content-Type":"application/json"}},!0)}async function mJ(){return F("/admin/datasets/recording-stats-sweep?reset=1",{method:"POST",headers:{"Content-Type":"application/json"}},!0)}async function hJ(e){let t=e?.limit??15;return F(`/admin/datasets/signal-defaults-sweep?limit=${encodeURIComponent(String(t))}`,{method:"POST",headers:{"Content-Type":"application/json"}},!0)}async function gJ(){return F("/admin/datasets/signal-defaults-sweep?reset=1",{method:"POST",headers:{"Content-Type":"application/json"}},!0)}async function yJ(e){let t=e?.limit??15,r=new URLSearchParams({limit:String(t)});if(e?.olderThan!=null)r.set("older-than",String(e.olderThan));if(e?.before!=null)r.set("before",e.before);return F(`/admin/datasets/data-integrity-sweep?${r.toString()}`,{method:"POST",headers:{"Content-Type":"application/json"}},!0)}async function bJ(){return F("/admin/datasets/data-integrity-sweep?reset=1",{method:"POST",headers:{"Content-Type":"application/json"}},!0)}async function xJ(e,t){let r=t?.write?"":"?dry_run=1";return F(`/admin/datasets/${e}/availability-report${r}`,{method:"POST",headers:{"Content-Type":"application/json"}},!0)}async function _J(e){let t=e?.limit??30,r=new URLSearchParams({limit:String(t)});if(e?.missingOnly)r.set("missing-only","1");return F(`/admin/datasets/availability-report-sweep?${r.toString()}`,{method:"POST",headers:{"Content-Type":"application/json"}},!0)}async function vJ(){return F("/admin/datasets/availability-report-sweep?reset=1",{method:"POST",headers:{"Content-Type":"application/json"}},!0)}async function wJ(e){let t=new URLSearchParams;if(e?.prefix)t.set("prefix",e.prefix);if(e?.visibility)t.set("visibility",e.visibility);if(e?.limit)t.set("limit",String(e.limit));let r=t.toString()?`?${t.toString()}`:"";return F(`/admin/fleet/drift${r}`,{},!0)}async function Nl(e,t){return F(`/admin/datasets/${e}/enforce`,{method:"POST",body:JSON.stringify({dry_run:t})},!0)}async function DJ(e){return F("/admin/datasets/enforce/bulk",{method:"POST",body:JSON.stringify({prefix:e.prefix,visibility:e.visibility,limit:e.limit,dry_run:e.dryRun})},!0)}async function EJ(e,t=!1){return F(`/admin/datasets/${e}/revalidate${t?"?force=true":""}`,{method:"POST"},!0)}async function SJ(e){let t=e?`?user=${encodeURIComponent(e)}`:"";return F(`/admin/email-preferences${t}`,{},!0)}async function $J(e,t){let r=t?`?user=${encodeURIComponent(t)}`:"";return F(`/admin/email-preferences${r}`,{method:"PUT",headers:{"Content-Type":"application/json"},body:JSON.stringify(e)},!0)}async function TE(e){return F("/admin/notify",{method:"POST",body:JSON.stringify(e)},!0)}async function CJ(){return F("/admin/summary/coverage",{},!0)}async function kJ(e,t,r){return F("/admin/manifest/dispatch",{method:"POST",body:JSON.stringify({dataset_id:e,version:t,skip_canary:r?.skipCanary??!1})},!0)}async function NE(e){return F("/admin/doctor/scan",{method:"POST",body:JSON.stringify({...e?.check&&{check:e.check},...e?.datasetId&&{dataset_id:e.datasetId}})},!0)}async function jE(e){return F("/admin/doctor/fix",{method:"POST",body:JSON.stringify({check:e.check,...e.datasetId&&{dataset_id:e.datasetId},...e.dryRun&&{dry_run:!0}})},!0)}async function RJ(){return F("/admin/zarr-catalog/publish",{method:"POST"},!0)}async function AJ(e){let t=new URLSearchParams;if(e?.limit!=null)t.set("limit",String(e.limit));let r=t.toString()?`?${t.toString()}`:"";return F(`/admin/datasets/zarr-fidelity-sweep${r}`,{method:"POST",headers:{"Content-Type":"application/json"}},!0)}async function OJ(e){let t=new URLSearchParams;if(e?.limit!=null)t.set("limit",String(e.limit));if(e?.apply)t.set("apply","1");let r=t.toString()?`?${t.toString()}`:"";return F(`/admin/imports/issue-triage${r}`,{method:"POST",headers:{"Content-Type":"application/json"}},!0)}async function FJ(e){let t=e?.apply?"?apply=1":"";return F(`/admin/imports/coverage-sweep${t}`,{method:"POST",headers:{"Content-Type":"application/json"}},!0)}async function PJ(e){let t=e?.apply?"?apply=1":"";return F(`/admin/imports/weekly-summary${t}`,{method:"POST",headers:{"Content-Type":"application/json"}},!0)}async function IJ(e){return F("/admin/users/backfill-names",{method:"POST",headers:{"Content-Type":"application/json"},body:JSON.stringify({apply:e?.apply??!1,...e?.limit!=null?{limit:e.limit}:{}})},!0)}async function TJ(e){return F("/admin/users/backfill-usernames",{method:"POST",headers:{"Content-Type":"application/json"},body:JSON.stringify({apply:e?.apply??!1,...e?.limit!=null?{limit:e.limit}:{}})},!0)}async function NJ(){return F("/admin/users/duplicates",{},!0,Uq)}async function jJ(e){return F(`/admin/users/${e}/clear-identity-conflict`,{method:"POST"},!0,zq)}async function qJ(e){let t=new URLSearchParams;if(e?.limit!=null)t.set("limit",String(e.limit));let r=t.toString()?`?${t.toString()}`:"";return F(`/admin/datasets/anonymity-sweep${r}`,{method:"POST",headers:{"Content-Type":"application/json"}},!0)}async function MJ(){return F("/admin/datasets/anonymity-sweep?reset=1",{method:"POST",headers:{"Content-Type":"application/json"}},!0)}var jl=O(()=>{sl();$i()});async function dr(e,t){return F(`/datasets/${e}/upload-credentials`,{method:"POST",body:JSON.stringify({duration_seconds:t})},!0)}async function qE(e,t){return F(`/datasets/${e}/download-credentials`,{method:"POST",body:JSON.stringify({duration_seconds:t})},!0)}async function LJ(e){return F(`/admin/datasets/${e}/files`,{},!0)}async function BJ(e){let t,r=0,n=[],o=!0;while(o){let i=await F(`/admin/datasets/${e}/s3-lock`,{method:"POST",headers:{"Content-Type":"application/json"},body:JSON.stringify({continuation_token:t})},!0);if(r+=i.locked,i.failed?.length)n.push(...i.failed);if(o=i.hasMore,t=i.continuation_token,o&&!t)throw new L(500,"S3 lock paginated response missing continuation_token; aborting to avoid infinite loop")}return{locked:r,failed:n}}var ki=O(()=>{$i();It()});async function L0(e){return F(`/datasets/${e}/ci/status`,{},!0)}async function UJ(e){return F(`/datasets/${e}/manifest`,{},!0)}async function B0(e,t){return F(`/datasets/${e}/manifest/${t}`,{},!0)}function zJ(e){let t=e;if(!t.status)t.status="active";else if(!["active","archived","deleted"].includes(t.status))throw Error(`Invalid dataset status: ${t.status}`);if(!t.visibility)t.visibility="private";else if(!["public","private"].includes(t.visibility))throw Error(`Invalid dataset visibility: ${t.visibility}`);return t}async function Ns(e={}){let t=new URLSearchParams;if(e.mine)t.set("mine","true");if(e.search)t.set("search",e.search);if(e.modality)t.set("modality",e.modality);if(e.author)t.set("author",e.author);if(e.task)t.set("task",e.task);if(e.license)t.set("license",e.license);if(e.hasDoi)t.set("has_doi","true");if(e.hasHed)t.set("has_hed","1");if(e.hasZarr)t.set("has_zarr","1");if(e.hasZarrVerified)t.set("has_zarr_verified","1");if(e.dataComplete)t.set("data_complete","1");if(e.recent)t.set("recent",String(e.recent));if(e.sort)t.set("sort",e.sort);if(e.limit!=null)t.set("limit",String(e.limit));if(e.offset!=null)t.set("offset",String(e.offset));if(e.owner)t.set("owner",e.owner);if(e.facets)for(let[o,i]of Object.entries(e.facets))t.set(o,i);if(e.includeUnknown)t.set("include_unknown","1");let r=t.toString()?`?${t.toString()}`:"",n=await F(`/datasets${r}`,{},e.mine?!0:"optional");return n.datasets=n.datasets.map(zJ),n}async function VJ(e){return F(`/datasets/resolve/${e}`,{},"optional")}async function GJ(){return F("/datasets/facets",{signal:AbortSignal.timeout(5000)},"optional",Nh)}async function HJ(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 F(`/datasets/search?${r.toString()}`,{},"optional",Mq)}async function Tt(e){let t=await F(`/datasets/${e}`,{},"optional");return zJ(t.dataset)}async function WJ(e){return F(`/datasets/${e}/versions`,{},!0)}async function U0(e){return F("/datasets",{method:"POST",body:JSON.stringify(e)},!0)}async function z0(e){return F(`/datasets/${e}/finalize`,{method:"POST"},!0)}async function ME(e){return F(`/datasets/${e}/request-access`,{method:"POST"},!0)}async function KJ(e,t){let r=t?`?status=${t}`:"";return F(`/datasets/${e}/access-requests${r}`,{},!0)}async function YJ(e,t){return F(`/datasets/${e}/access-requests/${t}/approve`,{method:"POST"},!0)}async function JJ(e,t){return F(`/datasets/${e}/access-requests/${t}/deny`,{method:"POST"},!0)}async function XJ(e,t){return F(`/datasets/${e}/invite`,{method:"POST",body:JSON.stringify({username:t})},!0)}async function ZJ(e){return F(`/datasets/${e}/collaborators`,{},!0)}async function QJ(e,t){return F(`/admin/datasets/${e}/enrichment`,{method:"POST",body:JSON.stringify(t)},!0)}var M0;var js=O(()=>{sl();$i();M0=/^\d{4}-\d{4}-\d{4}-\d{3}[\dX]$/});async function ql(e,t={}){return F(`/datasets/${e}/publish/request`,t.anonymous?{method:"POST",headers:{"Content-Type":"application/json"},body:JSON.stringify({anonymous:!0})}:{method:"POST"},!0)}async function V0(e){return F(`/datasets/${e}/publish/status`,{},!0)}async function iX(e){return F(`/datasets/${e}/publish/resend`,{method:"POST"},!0)}async function sX(e){let t=e?`?status=${e}`:"";return F(`/admin/publish/requests${t}`,{},!0)}async function aX(e,t){return F(`/admin/publish/${e}/deny`,{method:"POST",headers:{"Content-Type":"application/json"},body:JSON.stringify({reason:t})},!0)}function xBe(e,t=[]){if(e){let r=xs.indexOf(e);if(r>=0)return r+1}return Math.min(t.length+1,xs.length)}function _Be(e){if(!(e instanceof L))return!1;if(e.statusCode===0)return!0;if(e.statusCode===429)return!0;if(e.statusCode>=500&&e.statusCode<600)return!0;if(e.statusCode===403&&/repository has been locked/i.test(e.message))return!0;return!1}async function Ml(e,t=!1,r=!1,n=!1,o,i){let c,u,d=0,f=!1,m,p=t,h=[],g;function b(x,v,S,R){if(!i)return;i({step:x,stepIndex:xBe(x,v),stepTotal:xs.length,s3LockLocked:S,s3LockTotal:R,s3LockResumed:x==="s3_lock"&&f?!0:void 0})}for(let x=1;x<=5;x++)try{let v,S=!0;do{if(v=await F(`/admin/publish/${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,v.step_results)h.push(...v.step_results);if(v.s3_lock_total!==void 0)u=v.s3_lock_total;if(v.s3_lock_batch_count!==void 0)d+=v.s3_lock_batch_count;let R=v.step??v.step_results?.[v.step_results.length-1]?.step;if(R&&(R!==m||R==="s3_lock"))b(R,v.steps_completed??[],R==="s3_lock"?d:void 0,R==="s3_lock"?u:void 0),m=R;if(v.hasMore&&v.s3_lock_continuation_token!==void 0)c=v.s3_lock_continuation_token;else break}while(v.hasMore);if(h.length>0)v.step_results=oX(h);return v}catch(v){if(g=v,x===5||!_Be(v)){if(v instanceof L&&h.length>0)v.stepResults=oX(h);throw v}let R=v;if(o?.({attempt:x,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 g}function oX(e){let t=new Map;for(let r of e)t.set(r.step,r);return Array.from(t.values())}var Wf=O(()=>{Jh();$i();It()});function RX(e,t){return e.filter((r)=>r.visibility==="public").map((r)=>r.dataset_id).filter((r)=>r.startsWith("nm")||r.startsWith("on")).filter((r)=>r!=="nm099999"&&!Ri.has(r)).filter((r)=>t.prefix?r.startsWith(t.prefix):!0).sort()}var Ri;var K0=O(()=>{Ri=new Set(["nm000103","nm000104","nm000105","nm000106","nm000107"])});async function $Be(){try{let{exitCode:e,stderr:t}=await C(["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 Ta(){try{let{stdout:e,exitCode:t,stderr:r}=await C(["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 Y0(e){try{let{stdout:t,exitCode:r,stderr:n}=await C(["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: ${r}`}}}async function J0(e){if(!/^[a-zA-Z0-9_.-]+\/[a-zA-Z0-9_.-]+$/.test(e))return{accepted:!1,error:`Invalid repository format: ${e}`};let{stdout:t,exitCode:r,stderr:n}=await C(["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: ${c}`}}if(!o){let{exitCode:a}=await C(["gh","api",`/repos/${e}`,"--silent"]);if(a===0)return{accepted:!0,alreadyCollaborator:!0};return{accepted:!1,error:`No pending invitation found for ${e}. You may need to accept it manually via GitHub.`}}let{exitCode:i,stderr:s}=await C(["gh","api","--method","PATCH",`/user/repository_invitations/${o}`]);if(i!==0)return{accepted:!1,error:`Failed to accept invitation: ${s.trim()||"unknown error"}`};return{accepted:!0}}async function Mo(e,t,r="origin"){let n=t;if(process.env.GH_TOKEN&&t.startsWith("git@github.com:")){let o=process.env.GH_TOKEN.trim();if(!o||/\s/.test(o))return{success:!1,error:"GH_TOKEN environment variable is set but appears malformed (empty or contains whitespace)"};n=`https://github.com/${t.replace("git@github.com:","")}`,await C(["git","config","credential.https://github.com.helper",`!printf 'username=x-access-token\\npassword=${o}'`],{cwd:e})}else if(t.startsWith("git@github.com:")){let o=t.replace("git@github.com:",""),i=await Ta();if(i.token)n=`https://github.com/${o}`,await C(["git","config","credential.https://github.com.helper",`!printf 'username=x-access-token\\npassword=${i.token}'`],{cwd:e});else{let s=await $Be();if(s.works)n=t;else return{success:!1,error:`GitHub authentication not configured.
|
|
113
|
+
`)}var qY=!1;var $E=O(()=>{Xe()});function j0(){if(process.env.TEST_API_URL)return process.env.TEST_API_URL;if(kE)return CE;return ot().apiUrl||CE}async function F(e,t={},r=!1,n){let o=`${j0()}${e}`,i={"Content-Type":"application/json","X-CLI-Version":Si,...t.headers};if(r){let m=ot();if(!m.apiKey&&r===!0)throw new L(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(Ia())I0({method:s,url:o,status:null,durationMs:Date.now()-c,requestHeaders:i,requestBody:a,error:m instanceof Error?m.message:String(m)});throw new L(0,`Network error: Could not connect to ${j0()}`,{originalError:m instanceof Error?m.message:String(m)})}let d;try{d=await u.text()}catch(m){if(Ia())I0({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 L(0,"Failed to read response body",{httpStatus:u.status,originalError:m instanceof Error?m.message:String(m)})}if(Ia())I0({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 L(u.status,`Invalid response from server (status ${u.status})`)}if(!u.ok){if(u.status===503&&(f.mode==="read-only"||f.mode==="full")){let R=typeof f.message==="string"?f.message:"NEMAR is in maintenance mode. Please retry shortly.",E=typeof f.eta==="string"?f.eta:null,P=new Is(f.mode,R,E,f.details);throw N0(P),P}let m=typeof f.block_reason==="string",p=Array.isArray(f.missing)?f.missing.filter((R)=>typeof R==="string"):void 0,h=typeof f.error==="string"&&(Iq.includes(f.error)||Bq.includes(f.error)),g=typeof f.error==="string"&&(jh.options.includes(f.error)||Hq.includes(f.error)),b=typeof f.error==="string"&&kq.includes(f.error),v=m||h||g||b||p!==void 0&&typeof f.error==="string"&&Pq.includes(f.error)?f.message||f.error:f.error||f.message;if(u.status===404&&f.error==="Not Found"&&typeof f.message==="string")v=`${f.message}. This NEMAR backend does not support this command yet.`;let S=new L(u.status,v||"Request failed",f.details,typeof f.step==="string"?f.step:void 0,m?f.block_reason:void 0,p);if(typeof f.error==="string")S.code=f.error;if(typeof f.reason==="string")S.reason=f.reason;throw S.rawBody=f,S}if(n){let m=n.safeParse(f);if(!m.success)throw new L(u.status,`Response for ${e} did not match the expected NEMAR contract`,{issues:m.error.issues});return m.data}return f}var CE="https://api.nemar.org",kE;var $i=O(()=>{Lh();kw();Cd();qo();jo();$E();qf();It();kE=CE.includes("workers.dev")});function q0(e){if(e.service_access===void 0||e.service_access===null)return"unknown";return e.service_access?"upload":"browse"}async function MY(e,t,r,n){let o=new URLSearchParams;if(e)o.set("status",e);if(t)o.set("role",t);if(r)o.set("awaiting_approval","1");if(n)o.set("kind",n);let i=o.toString()?`?${o.toString()}`:"";return F(`/admin/users${i}`,{},!0,Oq)}async function LY(e){return F(`/admin/approve/${e}`,{method:"POST"},!0)}async function BY(e){return F(`/admin/approve/by-id/${e}`,{method:"POST"},!0)}async function UY(e){return F(`/admin/revoke/${e}`,{method:"POST"},!0)}async function zY(e){return F(`/admin/revoke/by-id/${e}`,{method:"POST"},!0)}async function VY(e,t){return F(`/admin/users/${e}/role`,{method:"POST",body:JSON.stringify({role:t})},!0)}async function GY(e,t){return F(`/admin/users/${e}/kind`,{method:"POST",body:JSON.stringify({kind:t})},!0)}async function HY(e){return F(`/admin/users/${e}`,{},!0)}async function WY(e,t){return F(`/admin/users/${e}/keys`,{method:"POST",body:JSON.stringify({name:t})},!0,Mh)}async function KY(e){return F(`/admin/users/${e}/keys`,{},!0,qh)}async function YY(e,t){return F(`/admin/users/${e}/keys/${t}`,{method:"DELETE"},!0)}async function RE(e,t){return F(`/admin/datasets/${e}/visibility`,{method:"PATCH",body:JSON.stringify({visibility:t})},!0)}async function JY(e){return F(`/datasets/${e}/publish`,{method:"POST"},!0)}async function XY(e){return F(`/admin/datasets/${e}/ci`,{},!0)}async function Ci(e){return F(`/admin/datasets/${e}/ci`,{method:"POST"},!0)}async function AE(e){return F(`/admin/datasets/${e}/ci/validate`,{method:"POST"},!0)}async function OE(e){return F(`/admin/datasets/${e}/ci/sync`,{method:"POST"},!0)}async function ZY(e,t){return F(`/admin/datasets/${e}/doi/concept`,{method:"POST",body:JSON.stringify(t)},!0)}async function Hf(e){return F(`/admin/datasets/${e}/doi`,{},!0)}async function FE(e,t){return F(`/admin/datasets/${e}/doi/update`,{method:"POST",body:JSON.stringify(t)},!0)}async function QY(e,t){return F(`/admin/datasets/${e}/withdraw`,{method:"POST",body:JSON.stringify({reason:t.reason,dry_run:t.dryRun})},!0)}async function eJ(e,t){return F(`/admin/datasets/${e}/restore`,{method:"POST",body:JSON.stringify({dry_run:t.dryRun})},!0)}async function tJ(e){return F(`/admin/datasets/${e}/reset`,{method:"POST"},!0)}async function rJ(e,t=!1){return F(`/admin/datasets/${e}`,{method:"DELETE",headers:{"Content-Type":"application/json"},body:JSON.stringify({force:t})},!0)}async function nJ(e){return F("/admin/datasets/bulk-delete",{method:"POST",headers:{"Content-Type":"application/json"},body:JSON.stringify({dataset_ids:e})},!0)}async function oJ(e){return F("/admin/datasets/import",{method:"POST",body:JSON.stringify(e)},!0)}async function iJ(e){return F("/admin/datasets/exemplar",{method:"POST",body:JSON.stringify(e)},!0)}async function sJ(e){return F(`/admin/datasets/${e}/exemplar/remint-dois`,{method:"POST"},!0)}async function PE(e,t){let r=new URLSearchParams;if(e)r.set("status",e);if(t!==void 0)r.set("blocklisted",t?"1":"0");let n=r.toString();return F(`/admin/imports${n?`?${n}`:""}`,{},!0)}async function aJ(e){return F(`/admin/imports/${e}/rollback`,{method:"POST"},!0)}async function cJ(e){return F(`/admin/imports/${e}/retry`,{method:"POST"},!0)}async function IE(e){return F(`/admin/imports/${e}/verify`,{method:"POST"},!0)}async function lJ(e){return F("/admin/imports/dispatch-cooldown",{method:"POST",headers:{"Content-Type":"application/json"},body:JSON.stringify({dataset_ids:e})},!0)}async function Tl(e,t){return F(`/admin/datasets/${e}/reindex`,{method:"POST",headers:{"Content-Type":"application/json"},body:JSON.stringify(t??{})},!0)}async function uJ(e,t){return F("/admin/datasets/reindex/bulk",{method:"POST",headers:{"Content-Type":"application/json"},body:JSON.stringify({filter:e,...t??{}})},!0)}async function dJ(e){let t=e?.limit??15;return F(`/admin/datasets/hed-sweep?limit=${encodeURIComponent(String(t))}`,{method:"POST",headers:{"Content-Type":"application/json"}},!0)}async function fJ(){return F("/admin/datasets/hed-sweep?reset=1",{method:"POST",headers:{"Content-Type":"application/json"}},!0)}async function pJ(e){let t=e?.limit??50;return F(`/admin/datasets/recording-stats-sweep?limit=${encodeURIComponent(String(t))}`,{method:"POST",headers:{"Content-Type":"application/json"}},!0)}async function mJ(){return F("/admin/datasets/recording-stats-sweep?reset=1",{method:"POST",headers:{"Content-Type":"application/json"}},!0)}async function hJ(e){let t=e?.limit??15;return F(`/admin/datasets/signal-defaults-sweep?limit=${encodeURIComponent(String(t))}`,{method:"POST",headers:{"Content-Type":"application/json"}},!0)}async function gJ(){return F("/admin/datasets/signal-defaults-sweep?reset=1",{method:"POST",headers:{"Content-Type":"application/json"}},!0)}async function yJ(e){let t=e?.limit??15,r=new URLSearchParams({limit:String(t)});if(e?.olderThan!=null)r.set("older-than",String(e.olderThan));if(e?.before!=null)r.set("before",e.before);return F(`/admin/datasets/data-integrity-sweep?${r.toString()}`,{method:"POST",headers:{"Content-Type":"application/json"}},!0)}async function bJ(){return F("/admin/datasets/data-integrity-sweep?reset=1",{method:"POST",headers:{"Content-Type":"application/json"}},!0)}async function xJ(e,t){let r=t?.write?"":"?dry_run=1";return F(`/admin/datasets/${e}/availability-report${r}`,{method:"POST",headers:{"Content-Type":"application/json"}},!0)}async function _J(e){let t=e?.limit??30,r=new URLSearchParams({limit:String(t)});if(e?.missingOnly)r.set("missing-only","1");return F(`/admin/datasets/availability-report-sweep?${r.toString()}`,{method:"POST",headers:{"Content-Type":"application/json"}},!0)}async function vJ(){return F("/admin/datasets/availability-report-sweep?reset=1",{method:"POST",headers:{"Content-Type":"application/json"}},!0)}async function wJ(e){let t=new URLSearchParams;if(e?.prefix)t.set("prefix",e.prefix);if(e?.visibility)t.set("visibility",e.visibility);if(e?.limit)t.set("limit",String(e.limit));let r=t.toString()?`?${t.toString()}`:"";return F(`/admin/fleet/drift${r}`,{},!0)}async function Nl(e,t){return F(`/admin/datasets/${e}/enforce`,{method:"POST",body:JSON.stringify({dry_run:t})},!0)}async function DJ(e){return F("/admin/datasets/enforce/bulk",{method:"POST",body:JSON.stringify({prefix:e.prefix,visibility:e.visibility,limit:e.limit,dry_run:e.dryRun})},!0)}async function EJ(e,t=!1){return F(`/admin/datasets/${e}/revalidate${t?"?force=true":""}`,{method:"POST"},!0)}async function SJ(e){let t=e?`?user=${encodeURIComponent(e)}`:"";return F(`/admin/email-preferences${t}`,{},!0)}async function $J(e,t){let r=t?`?user=${encodeURIComponent(t)}`:"";return F(`/admin/email-preferences${r}`,{method:"PUT",headers:{"Content-Type":"application/json"},body:JSON.stringify(e)},!0)}async function TE(e){return F("/admin/notify",{method:"POST",body:JSON.stringify(e)},!0)}async function CJ(){return F("/admin/summary/coverage",{},!0)}async function kJ(e,t,r){return F("/admin/manifest/dispatch",{method:"POST",body:JSON.stringify({dataset_id:e,version:t,skip_canary:r?.skipCanary??!1})},!0)}async function NE(e){return F("/admin/doctor/scan",{method:"POST",body:JSON.stringify({...e?.check&&{check:e.check},...e?.datasetId&&{dataset_id:e.datasetId}})},!0)}async function jE(e){return F("/admin/doctor/fix",{method:"POST",body:JSON.stringify({check:e.check,...e.datasetId&&{dataset_id:e.datasetId},...e.dryRun&&{dry_run:!0}})},!0)}async function RJ(){return F("/admin/zarr-catalog/publish",{method:"POST"},!0)}async function AJ(e){let t=new URLSearchParams;if(e?.limit!=null)t.set("limit",String(e.limit));let r=t.toString()?`?${t.toString()}`:"";return F(`/admin/datasets/zarr-fidelity-sweep${r}`,{method:"POST",headers:{"Content-Type":"application/json"}},!0)}async function OJ(e){let t=new URLSearchParams;if(e?.limit!=null)t.set("limit",String(e.limit));if(e?.apply)t.set("apply","1");let r=t.toString()?`?${t.toString()}`:"";return F(`/admin/imports/issue-triage${r}`,{method:"POST",headers:{"Content-Type":"application/json"}},!0)}async function FJ(e){let t=e?.apply?"?apply=1":"";return F(`/admin/imports/coverage-sweep${t}`,{method:"POST",headers:{"Content-Type":"application/json"}},!0)}async function PJ(e){let t=e?.apply?"?apply=1":"";return F(`/admin/imports/weekly-summary${t}`,{method:"POST",headers:{"Content-Type":"application/json"}},!0)}async function IJ(e){return F("/admin/users/backfill-names",{method:"POST",headers:{"Content-Type":"application/json"},body:JSON.stringify({apply:e?.apply??!1,...e?.limit!=null?{limit:e.limit}:{}})},!0)}async function TJ(e){return F("/admin/users/backfill-usernames",{method:"POST",headers:{"Content-Type":"application/json"},body:JSON.stringify({apply:e?.apply??!1,...e?.limit!=null?{limit:e.limit}:{}})},!0)}async function NJ(){return F("/admin/users/duplicates",{},!0,Uq)}async function jJ(e){return F(`/admin/users/${e}/clear-identity-conflict`,{method:"POST"},!0,zq)}async function qJ(e){let t=new URLSearchParams;if(e?.limit!=null)t.set("limit",String(e.limit));let r=t.toString()?`?${t.toString()}`:"";return F(`/admin/datasets/anonymity-sweep${r}`,{method:"POST",headers:{"Content-Type":"application/json"}},!0)}async function MJ(){return F("/admin/datasets/anonymity-sweep?reset=1",{method:"POST",headers:{"Content-Type":"application/json"}},!0)}var jl=O(()=>{sl();$i()});async function dr(e,t){return F(`/datasets/${e}/upload-credentials`,{method:"POST",body:JSON.stringify({duration_seconds:t})},!0)}async function qE(e,t){return F(`/datasets/${e}/download-credentials`,{method:"POST",body:JSON.stringify({duration_seconds:t})},!0)}async function LJ(e){return F(`/admin/datasets/${e}/files`,{},!0)}async function BJ(e){let t,r=0,n=[],o=!0;while(o){let i=await F(`/admin/datasets/${e}/s3-lock`,{method:"POST",headers:{"Content-Type":"application/json"},body:JSON.stringify({continuation_token:t})},!0);if(r+=i.locked,i.failed?.length)n.push(...i.failed);if(o=i.hasMore,t=i.continuation_token,o&&!t)throw new L(500,"S3 lock paginated response missing continuation_token; aborting to avoid infinite loop")}return{locked:r,failed:n}}var ki=O(()=>{$i();It()});async function L0(e){return F(`/datasets/${e}/ci/status`,{},!0)}async function UJ(e){return F(`/datasets/${e}/manifest`,{},!0)}async function B0(e,t){return F(`/datasets/${e}/manifest/${t}`,{},!0)}function zJ(e){let t=e;if(!t.status)t.status="active";else if(!["active","archived","deleted"].includes(t.status))throw Error(`Invalid dataset status: ${t.status}`);if(!t.visibility)t.visibility="private";else if(!["public","private"].includes(t.visibility))throw Error(`Invalid dataset visibility: ${t.visibility}`);return t}async function Ns(e={}){let t=new URLSearchParams;if(e.mine)t.set("mine","true");if(e.search)t.set("search",e.search);if(e.modality)t.set("modality",e.modality);if(e.author)t.set("author",e.author);if(e.task)t.set("task",e.task);if(e.license)t.set("license",e.license);if(e.hasDoi)t.set("has_doi","true");if(e.hasHed)t.set("has_hed","1");if(e.hasZarr)t.set("has_zarr","1");if(e.hasZarrVerified)t.set("has_zarr_verified","1");if(e.dataComplete)t.set("data_complete","1");if(e.recent)t.set("recent",String(e.recent));if(e.sort)t.set("sort",e.sort);if(e.limit!=null)t.set("limit",String(e.limit));if(e.offset!=null)t.set("offset",String(e.offset));if(e.owner)t.set("owner",e.owner);if(e.facets)for(let[o,i]of Object.entries(e.facets))t.set(o,i);if(e.includeUnknown)t.set("include_unknown","1");let r=t.toString()?`?${t.toString()}`:"",n=await F(`/datasets${r}`,{},e.mine?!0:"optional");return n.datasets=n.datasets.map(zJ),n}async function VJ(e){return F(`/datasets/resolve/${e}`,{},"optional")}async function GJ(){return F("/datasets/facets",{signal:AbortSignal.timeout(5000)},"optional",Nh)}async function HJ(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 F(`/datasets/search?${r.toString()}`,{},"optional",Mq)}async function Tt(e){let t=await F(`/datasets/${e}`,{},"optional");return zJ(t.dataset)}async function WJ(e){return F(`/datasets/${e}/versions`,{},!0)}async function U0(e){return F("/datasets",{method:"POST",body:JSON.stringify(e)},!0)}async function z0(e){return F(`/datasets/${e}/finalize`,{method:"POST"},!0)}async function ME(e){return F(`/datasets/${e}/request-access`,{method:"POST"},!0)}async function KJ(e,t){let r=t?`?status=${t}`:"";return F(`/datasets/${e}/access-requests${r}`,{},!0)}async function YJ(e,t){return F(`/datasets/${e}/access-requests/${t}/approve`,{method:"POST"},!0)}async function JJ(e,t){return F(`/datasets/${e}/access-requests/${t}/deny`,{method:"POST"},!0)}async function XJ(e,t){return F(`/datasets/${e}/invite`,{method:"POST",body:JSON.stringify({username:t})},!0)}async function ZJ(e){return F(`/datasets/${e}/collaborators`,{},!0)}async function QJ(e,t){return F(`/admin/datasets/${e}/enrichment`,{method:"POST",body:JSON.stringify(t)},!0)}var M0;var js=O(()=>{sl();$i();M0=/^\d{4}-\d{4}-\d{4}-\d{3}[\dX]$/});async function ql(e,t={}){return F(`/datasets/${e}/publish/request`,t.anonymous?{method:"POST",headers:{"Content-Type":"application/json"},body:JSON.stringify({anonymous:!0})}:{method:"POST"},!0)}async function V0(e){return F(`/datasets/${e}/publish/status`,{},!0)}async function iX(e){return F(`/datasets/${e}/publish/resend`,{method:"POST"},!0)}async function sX(e){let t=e?`?status=${e}`:"";return F(`/admin/publish/requests${t}`,{},!0)}async function aX(e,t){return F(`/admin/publish/${e}/deny`,{method:"POST",headers:{"Content-Type":"application/json"},body:JSON.stringify({reason:t})},!0)}function xBe(e,t=[]){if(e){let r=xs.indexOf(e);if(r>=0)return r+1}return Math.min(t.length+1,xs.length)}function _Be(e){if(!(e instanceof L))return!1;if(e.statusCode===0)return!0;if(e.statusCode===429)return!0;if(e.statusCode>=500&&e.statusCode<600)return!0;if(e.statusCode===403&&/repository has been locked/i.test(e.message))return!0;return!1}async function Ml(e,t=!1,r=!1,n=!1,o,i){let c,u,d=0,f=!1,m,p=t,h=[],g;function b(x,v,S,R){if(!i)return;i({step:x,stepIndex:xBe(x,v),stepTotal:xs.length,s3LockLocked:S,s3LockTotal:R,s3LockResumed:x==="s3_lock"&&f?!0:void 0})}for(let x=1;x<=5;x++)try{let v,S=!0;do{if(v=await F(`/admin/publish/${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,v.step_results)h.push(...v.step_results);if(v.s3_lock_total!==void 0)u=v.s3_lock_total;if(v.s3_lock_batch_count!==void 0)d+=v.s3_lock_batch_count;let R=v.step??v.step_results?.[v.step_results.length-1]?.step;if(R&&(R!==m||R==="s3_lock"))b(R,v.steps_completed??[],R==="s3_lock"?d:void 0,R==="s3_lock"?u:void 0),m=R;if(v.hasMore&&v.s3_lock_continuation_token!==void 0)c=v.s3_lock_continuation_token;else break}while(v.hasMore);if(h.length>0)v.step_results=oX(h);return v}catch(v){if(g=v,x===5||!_Be(v)){if(v instanceof L&&h.length>0)v.stepResults=oX(h);throw v}let R=v;if(o?.({attempt:x,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 g}function oX(e){let t=new Map;for(let r of e)t.set(r.step,r);return Array.from(t.values())}var Wf=O(()=>{Jh();$i();It()});function RX(e,t){return e.filter((r)=>r.visibility==="public").map((r)=>r.dataset_id).filter((r)=>r.startsWith("nm")||r.startsWith("on")).filter((r)=>r!=="nm099999"&&!Ri.has(r)).filter((r)=>t.prefix?r.startsWith(t.prefix):!0).sort()}var Ri;var K0=O(()=>{Ri=new Set(["nm000103","nm000104","nm000105","nm000106","nm000107"])});async function $Be(){try{let{exitCode:e,stderr:t}=await C(["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 Ta(){try{let{stdout:e,exitCode:t,stderr:r}=await C(["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 Y0(e){try{let{stdout:t,exitCode:r,stderr:n}=await C(["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: ${r}`}}}async function J0(e){if(!/^[a-zA-Z0-9_.-]+\/[a-zA-Z0-9_.-]+$/.test(e))return{accepted:!1,error:`Invalid repository format: ${e}`};let{stdout:t,exitCode:r,stderr:n}=await C(["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: ${c}`}}if(!o){let{exitCode:a}=await C(["gh","api",`/repos/${e}`,"--silent"]);if(a===0)return{accepted:!0,alreadyCollaborator:!0};return{accepted:!1,error:`No pending invitation found for ${e}. You may need to accept it manually via GitHub.`}}let{exitCode:i,stderr:s}=await C(["gh","api","--method","PATCH",`/user/repository_invitations/${o}`]);if(i!==0)return{accepted:!1,error:`Failed to accept invitation: ${s.trim()||"unknown error"}`};return{accepted:!0}}async function Mo(e,t,r="origin"){let n=t;if(process.env.GH_TOKEN&&t.startsWith("git@github.com:")){let o=process.env.GH_TOKEN.trim();if(!o||/\s/.test(o))return{success:!1,error:"GH_TOKEN environment variable is set but appears malformed (empty or contains whitespace)"};n=`https://github.com/${t.replace("git@github.com:","")}`,await C(["git","config","credential.https://github.com.helper",`!printf 'username=x-access-token\\npassword=${o}'`],{cwd:e})}else if(t.startsWith("git@github.com:")){let o=t.replace("git@github.com:",""),i=await Ta();if(i.token)n=`https://github.com/${o}`,await C(["git","config","credential.https://github.com.helper",`!printf 'username=x-access-token\\npassword=${i.token}'`],{cwd:e});else{let s=await $Be();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"}
|