npm - nemar-cli - Versions diffs - 0.10.1-PR1333.6f5d7fe → 0.10.1-PR1333.9a5fdee - Mend

nemar-cli 0.10.1-PR1333.6f5d7fe → 0.10.1-PR1333.9a5fdee

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Files changed (2) hide show

package/dist/index.js +2 -2
package/package.json +1 -1

package/dist/index.js CHANGED Viewed

@@ -99,7 +99,7 @@ ${t}`,ADe,ODe,FDe=(e,t,r)=>{let n=r===""?"":`with ${r.trim()}() `,o=kDe.bind(nul
 `)}var Qw=!1;var{spawn:q9e}=globalThis.Bun;async function k(e,t={}){let r={...process.env,GIT_TERMINAL_PROMPT:"0",...t.env};for(let u of t.unsetEnv??[])delete r[u];let n=q9e({cmd:e,cwd:t.cwd,stdout:"pipe",stderr:"pipe",env:r}),o=!1,i;if(t.timeout)i=setTimeout(()=>{o=!0,n.kill()},t.timeout);if(Zw()){let u=t.cwd?` (cwd=${t.cwd})`:"";ef(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(Zw()){if(s.trim())ef(l.dim(s.trimEnd()));if(a.trim())ef(l.yellow(a.trimEnd()));ef(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 ir=F(()=>{We()});function M9e(){if(process.platform==="darwin")return"macos";if(process.platform==="win32")return"windows";return"linux"}function EW(e,t=M9e()){return e.installInstructions[t]}function L9e(e){let t=e.match(/(\d+\.\d+(?:\.\d+)?)/);return t?t[1]:void 0}function U9e(){let e=Number(process.env.TEST_PROBE_TIMEOUT_MS);return Number.isFinite(e)&&e>0?e:B9e}async function SW(e){try{let{exitCode:t,stdout:r,timedOut:n}=await k(e.cmd,{timeout:U9e()});if(n)return{available:!1,timedOut:!0};if(t!==0)return{available:!1};return{available:!0,version:L9e(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 tf(){let e=Object.entries(DW);return Promise.all(e.map(async([t,r])=>{let{available:n,version:o,timedOut:i}=await SW(r);return{key:t,name:r.name,purpose:r.purpose,required:r.required,available:n,version:o,timedOut:i,installInstruction:EW(r)}}))}async function $W(){let t=(await tf()).filter((r)=>r.required&&!r.available);if(t.length===0)return[];console.warn(`
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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(`
-`))}var DW,j9e,B9e=4000;var rf=F(()=>{ir();DW={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)"}}},j9e={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 RW;var CW=F(()=>{RW={name:"nemar-cli",version:"0.10.1-PR1333.6f5d7fe",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","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 nf=F(()=>{CW();si=RW.version});import{mkdirSync as G9e,readdirSync as z9e,unlinkSync as H9e,writeFileSync as W9e}from"fs";import{join as eD}from"path";function PW(){tl=!0}function aa(){return tl}function IW(e,t=process.env){return e.includes("--debug")||t.NEMAR_DEBUG==="1"}function sf(e){FW=e,br(`Step: ${e}`)}function TW(){OW=!0}function NW(){return OW}function br(e){if(tl)process.stderr.write(`[debug] ${e}
+`))}var DW,j9e,B9e=4000;var rf=F(()=>{ir();DW={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)"}}},j9e={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 RW;var CW=F(()=>{RW={name:"nemar-cli",version:"0.10.1-PR1333.9a5fdee",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","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 nf=F(()=>{CW();si=RW.version});import{mkdirSync as G9e,readdirSync as z9e,unlinkSync as H9e,writeFileSync as W9e}from"fs";import{join as eD}from"path";function PW(){tl=!0}function aa(){return tl}function IW(e,t=process.env){return e.includes("--debug")||t.NEMAR_DEBUG==="1"}function sf(e){FW=e,br(`Step: ${e}`)}function TW(){OW=!0}function NW(){return OW}function br(e){if(tl)process.stderr.write(`[debug] ${e}
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 `)}async function MW(){if(!tl||T0!==void 0)return;try{T0=await nD()}catch(e){let t=P(e);T0=`(could not build environment report: ${t})`,br(`environment snapshot failed: ${t}`)}}function LW(e){if(AW.has(e))return{flag:e};for(let t of AW){if(!e.startsWith(t)||e.length<=t.length)continue;if(t.length===2)return{flag:t,kind:"short-attached"};if(e[t.length]==="=")return{flag:t,kind:"long-eq"}}return null}function sje(e){let t=[];for(let r=0;r<e.length;r++){let n=e[r],o=LW(n);if(!o){t.push(n);continue}if(o.kind==="long-eq")t.push(`${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 aje(e){let t=[];for(let r=0;r<e.length;r++){let n=e[r],o=LW(n);if(!o){t.push(n);continue}if(!o.kind&&r+1<e.length)r++}return t}function cje(e){let t=[];for(let n of aje(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 lje(e,t){let r=[];if(r.push("NEMAR CLI Debug Log"),r.push(`Generated: ${new Date().toISOString()}`),r.push(`Command: nemar ${rD(sje(e).join(" "))}`),r.push(""),r.push(T0??"(environment snapshot unavailable)"),r.push(""),r.push("HTTP requests:"),N0.length===0)r.push("  (none)");else N0.forEach((n,o)=>{if(r.push(`  [${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: ${FW??"(none recorded)"}`),r.push(`Exit code: ${t}`),`${r.join(`
 `)}
@@ -496,7 +496,7 @@ ${o} finding(s). Preview the remediation with: nemar admin doctor fix <check> --
 ${l.bold(e)}: ${l.green(`${s.fixed} fixed`)}, ${s.skipped} skipped, ${s.failed>0?l.red(`${s.failed} failed`):"0 failed"}${c}`)}if(s.failed>0)process.exit(1)});async function KUe(e,t,r){let n={fixed:0,skipped:0,failed:0,resolved:0},o=[];for(let[i,s]of e.entries()){let a;try{let c=await t(s,i);if(a=c.results,a.length===0)n.resolved++;else n.fixed+=c.fixed,n.skipped+=c.skipped,n.failed+=c.failed}catch(c){n.failed++,a=[{dataset_id:s,status:"failed",message:P(c)}]}o.push(...a),r?.onDataset?.(s,a)}return{totals:n,results:o}}Ng.command("kinds").description("Check that operational accounts carry their expected account kind (read-only)").action(async()=>{if(!Z())return;let e=Object.entries(J5),t=w(`Checking ${e.length} operational account kind(s)...`).start(),r=[],n=[];try{for(let[o,i]of e)try{let{user:s}=await iK(o);if(s.account_kind!==i)r.push(`${o}: expected '${i}', found '${s.account_kind??"unknown"}'`)}catch(s){if(s instanceof q&&s.statusCode===404)n.push(o);else throw s}if(t.stop(),r.length===0&&n.length===0){console.log(l.green(`All ${e.length} operational account(s) carry their expected kind.`));return}for(let o of r)console.log(`  ${l.yellow("kind mismatch")}  ${o}`);for(let o of n)console.log(`  ${l.yellow("account absent")} ${o}`);console.log(l.yellow(`
 ${r.length+n.length} finding(s). Fix a mismatch with \`nemar admin kind <username> <kind>\`.`))}catch(o){t.fail("Doctor kinds check failed"),console.error(l.red(P(o))),process.exit(1)}});le.addCommand(Ng);var S2=new ie("email-preferences").description("Manage email notification preferences");S2.command("show").description("Show email notification preferences").option("--user <username>","(owner only) show another user's preferences").action(async(e)=>{if(!Pe())console.error(l.red("Not authenticated. Run: nemar auth login")),process.exit(1);let t=w("Fetching email preferences...").start();try{let r=await jK(e.user),n=r.username?`${r.username}'s`:"Your";t.succeed(`${n} email notification preferences:`),console.log();let o=[{key:"user_approval",label:"User approval notifications"},{key:"publication_request",label:"Publication request notifications"},{key:"announcements",label:"Announcement emails"}];for(let i of o){let a=r[i.key]?l.green("enabled"):l.dim("disabled");console.log(`  ${i.label.padEnd(40)} ${a}`)}console.log(),console.log(l.dim("  Use 'nemar admin email-preferences update' to change settings."))}catch(r){t.fail("Failed to fetch preferences"),console.error(l.red(P(r)))}});S2.command("update").description("Update email notification preferences").option("--user-approval <bool>","Enable/disable user approval notifications").option("--publication-request <bool>","Enable/disable publication request notifications").option("--announcements <bool>","Enable/disable announcement emails").option("--all <bool>","Enable/disable all notifications").option("--user <username>","(owner only) update another user's preferences").action(async(e)=>{if(!Pe())console.error(l.red("Not authenticated. Run: nemar auth login")),process.exit(1);function t(o){if(o===void 0)return;let i=o.toLowerCase();if(i==="true"||i==="1"||i==="on"||i==="yes")return!0;if(i==="false"||i==="0"||i==="off"||i==="no")return!1;console.error(l.red(`Invalid boolean value: "${o}". Use true/false, on/off, yes/no.`)),process.exit(1)}let r={};if(e.all!==void 0){let o=t(e.all);r.user_approval=o,r.publication_request=o,r.announcements=o}else{let o=t(e.userApproval),i=t(e.publicationRequest),s=t(e.announcements);if(o===void 0&&i===void 0&&s===void 0)console.error(l.red("No preferences specified.")),console.log("  --user-approval <bool>        User approval notifications"),console.log("  --publication-request <bool>   Publication request notifications"),console.log("  --announcements <bool>         Announcement emails"),console.log("  --all <bool>                   All notifications"),process.exit(1);if(o!==void 0)r.user_approval=o;if(i!==void 0)r.publication_request=i;if(s!==void 0)r.announcements=s}let n=w("Updating email preferences...").start();try{let o=await MK(r,e.user),i=o.username?`${o.username}'s`:"Your";n.succeed(`${i} email preferences updated:`),console.log(),console.log(`  User approval:        ${o.user_approval?l.green("enabled"):l.dim("disabled")}`),console.log(`  Publication request:   ${o.publication_request?l.green("enabled"):l.dim("disabled")}`),console.log(`  Announcements:         ${o.announcements?l.green("enabled"):l.dim("disabled")}`)}catch(o){n.fail("Failed to update preferences"),console.error(l.red(P(o)))}});le.addCommand(S2);var qg=new ie("notice").description("Manage system notices displayed to CLI users");qg.command("list").description("List all notices (including expired)").action(async()=>{if(!Pe())console.error(l.red("Not authenticated. 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-Nothing to dispatch.`));return}let c=o?` (scoped to ${o})`:"",u=await Se(`Dispatch generate-manifest for ${a.length} version(s)${c}? Each dispatch queues a runner job on nemarDatasets/.github.`,e);if(u!=="confirmed"){console.log(l.dim(u==="declined"?"Skipped":"Cancelled"));return}let d=0,f=0;console.log();for(let[m,p]of a.entries()){let g=`${p.dataset_id}@${p.version}`,y=w(`[${m+1}/${a.length}] dispatching ${g}...`).start();try{await BK(p.dataset_id,p.version),y.succeed(`[${m+1}/${a.length}] dispatched ${g}`),d++}catch(x){y.fail(`[${m+1}/${a.length}] ${g}: ${P(x)}`),f++}if(m<a.length-1)await new Promise((x)=>setTimeout(x,YUe))}if(console.log(),console.log(f===0?l.green(`All ${d} dispatches succeeded.`):l.yellow(`${d} succeeded, ${f} failed.`)),console.log(l.dim("Workflow runs will appear on https://github.com/nemarDatasets/.github/actions. 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Re-run with --apply."));console.log(l.cyan(`scanned=${o.scanned} ${o.apply?"filled":"would_fill"}=${o.apply?o.filled:o.would_fill} no_public_name=${o.no_public_name} lookup_failed=${o.lookup_failed} write_failed=${o.write_failed??0} remaining=${o.remaining??"unknown"}`));for(let i of o.results){let s=i.username??`id ${i.id} <${i.email}>`;if(i.outcome==="filled"||i.outcome==="would_fill"){let a=i.outcome==="filled"?l.green("filled  "):l.cyan("would fill");console.log(`  ${a} ${s}: ${i.given_name} ${i.family_name}  (${i.orcid})`)}else if(i.outcome==="no_public_name")console.log(`  ${l.yellow("no name ")} ${s}: ORCID ${i.orcid} does not publish a full name`);else if(i.outcome==="write_failed")console.log(`  ${l.red("write   ")} ${s}: ${i.error}; retry the batch`);else console.log(`  ${l.red("error   ")} ${s}: ${i.error}`)}if(o.warning)console.log(l.yellow(`  Warning: ${o.warning}`));if(o.no_public_name>0)console.log(),console.log(l.dim("These accounts must make their name public on their ORCID record and sign in again; NEMAR cannot type a name in for an ORCID-linked account, because the record is re-read on every sign-in and would overwrite it. 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Drift, not a gap.`));if(a!==n.discovered)console.log(l.yellow(`  Counts do not balance (${a} accounted for vs ${n.discovered} discovered): this run did not get a complete view, so treat the verdict as unreliable.`));if(o.neverAttempted.length>0){let c=o.neverAttempted.slice(0,Ag).join(", "),u=o.neverAttempted.length-Ag;console.log(l.dim(`  never attempted: ${c}${u>0?` ... and ${u} more`:""}`))}if(o.untracked.length>0){let c=o.untracked.slice(0,Ag).join(", "),u=o.untracked.length-Ag;console.log(l.dim(`  stale row nothing owns: ${c}${u>0?` ... and ${u} more`:""}`))}for(let c of n.errors){let u=`${c.stage}: ${c.error}`;console.log(c.stage==="anomaly"?`${l.yellow("ANOMALY".padEnd(12))} ${u}`:`${l.red("ERROR".padEnd(12))} ${u}`)}if(n.issue){let c=n.applied?n.issue.action:`would ${tVe[n.issue.action]??n.issue.action}`,u=n.issue.number===null?"":` #${n.issue.number}`;if(console.log(l.dim(`  Issue: ${c}${u} on nemarDatasets/.github`)),n.issue.labelError)console.log(l.yellow(`  The body was updated but its labels were not: ${n.issue.labelError}`));if(n.issue.commentError)console.log(l.yellow(`  The issue changed but its comment failed: ${n.issue.commentError}`))}if(n.audit_failed)console.log(l.yellow(`  Changes applied but the audit row failed to write: ${n.audit_failed}`));if(!n.applied&&n.issue)console.log(l.dim("  Re-run with --apply to perform this change."))});le.addCommand(lZ);var uZ=new ie("import-weekly").description("Read this week's import summary (dry run by default; 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Re-run with --apply."));console.log(l.cyan(`scanned=${o.scanned} ${o.apply?"filled":"would_fill"}=${o.apply?o.filled:o.would_fill} no_public_name=${o.no_public_name} lookup_failed=${o.lookup_failed} write_failed=${o.write_failed??0} remaining=${o.remaining??"unknown"}`));for(let i of o.results){let s=i.username??`id ${i.id} <${i.email}>`;if(i.outcome==="filled"||i.outcome==="would_fill"){let a=i.outcome==="filled"?l.green("filled  "):l.cyan("would fill");console.log(`  ${a} ${s}: ${i.given_name} ${i.family_name}  (${i.orcid})`)}else if(i.outcome==="no_public_name")console.log(`  ${l.yellow("no name ")} ${s}: ORCID ${i.orcid} does not publish a full name`);else if(i.outcome==="write_failed")console.log(`  ${l.red("write   ")} ${s}: ${i.error}; retry the batch`);else console.log(`  ${l.red("error   ")} ${s}: ${i.error}`)}if(o.warning)console.log(l.yellow(`  Warning: ${o.warning}`));if(o.no_public_name>0)console.log(),console.log(l.dim("These accounts must make their name public on their ORCID record and sign in again; NEMAR cannot type a name in for an ORCID-linked account, because the record is re-read on every sign-in and would overwrite it. An account with no verified ORCID can set its name in Settings (ADR 0042)."))});le.addCommand(aZ);function ZUe(e){return typeof e==="object"&&e!==null&&Array.isArray(e.errors)}function eVe(e){return typeof e==="object"&&e!==null&&Array.isArray(e.errors)}var cZ=new ie("import-issue-triage").description("Close recovered import-failure issues and retire stale cause labels (dry run by default)");cZ.option("--apply","Perform the changes (without this flag, only report what would change)").option("--limit <n>","Issues per batch (server clamps to [1,30])","15").option("--json","Output raw JSON instead of the human summary").action(async(e)=>{if(!Z())return;let t=e.limit??"15",r=t.trim()===""?Number.NaN:Number(t);if(!Number.isInteger(r)||r<1){console.error(l.red(`Invalid --limit ${JSON.stringify(t)}: expected an integer >= 1.`)),process.exitCode=1;return}let n=e.apply===!0,o=w(n?"Triaging import-failure issues...":"Checking import-failure issues...").start(),i;try{i=await GK({apply:n,limit:r}),o.stop()}catch(s){o.fail("Import-failure issue triage failed"),console.error(l.red(P(s)));let a=s instanceof q?s.details:void 0,c=ZUe(a)?a.errors:[];if(e.json)console.log(JSON.stringify(s instanceof q?s.rawBody??{errors:c}:{errors:c},null,2));else for(let u of c)console.error(`${l.red("ERROR".padEnd(15))} #${u.issue} ${u.dataset_id??""}  ${u.stage}: ${u.error}`);process.exitCode=1;return}if(i.errors.length>0)process.exitCode=1;if(e.json){console.log(JSON.stringify(i,null,2));return}if(console.log(),!i.applied)console.log(l.yellow("DRY RUN \u2014 nothing was written. Re-run with --apply."));for(let s of i.plan){let a=s.failed?"FAILED ":i.applied?"":"WOULD ",c=`#${s.issueNumber} ${s.datasetId??"(unknown)"}`;if(s.kind==="close"){let u=`${a}CLOSE`.padEnd(15);console.log(`${s.failed?l.red(u):l.green(u)} ${c}  ${l.dim(s.reason)}`)}else if(s.kind==="relabel"){let u=`${a}RELABEL`.padEnd(15);console.log(`${s.failed?l.red(u):l.yellow(u)} ${c}  ${l.dim(s.reason)}`)}else console.log(`${l.dim("KEEP".padEnd(15))} ${c}  ${l.dim(s.reason)}`)}for(let s of i.rollups){let c=(s.outcome==="failed"?"FAILED RELEASE":s.outcome==="released"?"RELEASE":i.mode==="per-dataset"?"WOULD RELEASE":"ROLLUP").padEnd(15);console.log(`${s.outcome==="failed"?l.red(c):l.magenta(c)} #${s.number} ${l.dim(s.title)}`)}for(let s of i.errors)console.log(`${l.red("ERROR".padEnd(15))} #${s.issue} ${s.dataset_id??""}  ${s.stage}: ${s.error}`);if(console.log(),console.log(l.cyan(`open=${i.openIssues} mode=${i.mode} examined=${i.examined} attempted=${i.attempted} ${i.applied?"closed":"would_close"}=${i.closed} ${i.applied?"relabelled":"would_relabel"}=${i.relabelled} kept=${i.kept} errors=${i.errors.length} remaining=${i.remaining}`)),i.remaining>0)console.log(l.dim(`  ${i.remaining} candidate(s) outside this run's window; the window rotates daily.`));if(i.mode==="rollup")console.log(l.dim("  Rollup mode: new failures with a cause that already has a rollup join it instead of opening their own issue."));if(i.rollupsReleased>0)console.log(l.dim(`  ${i.applied?"Released":"Would release"} ${i.rollupsReleased} rollup(s): the backlog has drained, so per-dataset filing resumes.`));if(i.audit_failed)console.log(l.yellow(`  Changes were applied but the audit row failed to write: ${i.audit_failed}`));if(!i.applied&&(i.closed>0||i.relabelled>0||i.rollupsReleased>0))console.log(l.dim("  Re-run with --apply to perform these changes."))});le.addCommand(cZ);var lZ=new ie("import-coverage").description("Check whether the import pipeline is keeping up with OpenNeuro (dry run by default)"),Ag=20,zQ=5,tVe={created:"create",refreshed:"refresh",relabelled:"relabel",closed:"close"};lZ.option("--apply","File, update or close the tracking issue (production only)").option("--json","Output raw JSON instead of the human summary").action(async(e)=>{if(!Z())return;let t=e.apply===!0,r=w("Checking import coverage...").start(),n;try{n=await zK({apply:t}),r.stop()}catch(c){r.fail("Import coverage check failed"),console.error(l.red(P(c)));let u=c instanceof q?c.details:void 0,d=eVe(u)?u.errors:[];if(e.json)console.log(JSON.stringify(c instanceof q?c.rawBody??{errors:d}:{errors:d},null,2));else for(let f of d)console.error(`${l.red("ERROR".padEnd(12))} ${f.stage}: ${f.error}`);process.exitCode=c instanceof q&&c.statusCode===502?2:1;return}if(n.status==="unknown")process.exitCode=2;else if(n.status!=="healthy"||n.errors.length>0)process.exitCode=1;if(e.json){console.log(JSON.stringify(n,null,2));return}let o=n.backlog,i=o.neverAttempted.length+o.untracked.length;console.log();let s=`${n.status.toUpperCase()}${n.kind?` (${n.kind})`:""}`;console.log(n.status==="healthy"?l.green(s):l.red(l.bold(s))),console.log(n.reason),console.log(),console.log(l.cyan(`auto_import=${n.enabled?"enabled":l.red("DISABLED")} last_dispatch=${n.dispatchAgeHours===null?"never":n.dispatchAgeHours<0?"dated in the future":`${n.dispatchAgeHours}h ago`}${n.lastDispatchSourceId?` (${n.lastDispatchSourceId})`:""} dispatch_lost=${n.dispatchLost}`));let a=n.importedInScan+n.inFlight+n.terminal+i+o.tracked.length+o.blocklisted.length;if(console.log(l.cyan(`discovered=${n.discovered} in_scan=${n.importedInScan} in_flight=${n.inFlight} terminal=${n.terminal} tracked=${o.tracked.length} blocklisted=${o.blocklisted.length}`)),console.log(l.cyan(`outstanding=${i} (never_attempted=${o.neverAttempted.length} untracked=${o.untracked.length})`)),n.importedNotInScan>0)console.log(l.dim(`  ${n.importedNotInScan} of ${n.imported} mirror(s) are no longer in the scan (upstream removal, unreadable snapshot, or a modality retag). 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Re-run with --apply."));console.log(l.cyan(`scanned=${o.scanned} ${o.apply?"assigned":"would_assign"}=${o.apply?o.assigned:o.would_assign} single_name=${o.single_name} no_name=${o.no_name} lookup_failed=${o.lookup_failed} conflict=${o.conflict} exhausted=${o.exhausted??0} write_failed=${o.write_failed??0} verify_sent=${o.verify_sent} verify_failed=${o.verify_failed??0} verify_rate_limited=${o.verify_rate_limited??0} remaining=${o.remaining??"unknown"}`));for(let i of o.results){let s=`id ${i.id} <${i.email}>`,a=[i.given_name,i.family_name].filter(Boolean).join(" ");if(i.outcome==="assigned"||i.outcome==="would_assign"){let c=i.outcome==="assigned"?l.green("assigned  "):l.cyan("would give"),u=i.outcome==="assigned"?`  [verify: ${i.verify}]`:"";console.log(`  ${c} ${s}: ${l.cyan(i.username??"?")}  (${a})${u}`)}else if(i.outcome==="single_name")console.log(`  ${l.yellow("one name  ")} ${s}: only "${a}" on record; pick a username by hand`);else if(i.outcome==="no_name")console.log(`  ${l.yellow("no name   ")} ${s}: run 'nemar admin backfill-names --apply' first`);else if(i.outcome==="conflict")console.log(`  ${l.yellow("conflict  ")} ${s}: ${i.error}`);else if(i.outcome==="exhausted")console.log(`  ${l.yellow("exhausted ")} ${s}: ${i.error}; pick a username by hand`);else if(i.outcome==="write_failed")console.log(`  ${l.red("write     ")} ${s}: ${i.error}; retry the batch`);else console.log(`  ${l.red("error     ")} ${s}: ${i.error}`)}for(let i of o.verify_retries??[]){let s=i.verify==="sent"?l.green("re-sent  "):i.verify==="not_attempted"?l.cyan("would send"):l.yellow(`verify ${i.verify}`);console.log(`  ${s} id ${i.id} <${i.email}>`)}if(o.warning)console.log(l.yellow(`  Warning: ${o.warning}`));if(o.single_name>0||o.no_name>0)console.log(),console.log(l.dim("Accounts with one name or none are listed, never guessed at: a username derived from an email address is a handle the person never chose."))});le.addCommand(dZ);var fZ=new ie("duplicates").description("Report live accounts sharing an ORCID iD, email, or GitHub handle");function nVe(e){let t=e.username??l.dim("(no username)"),r=[];if(e.canonical)r.push(l.green("canonical"));if(e.identity_conflict===1)r.push(l.yellow("flagged"));if(e.has_oauth_identity)r.push(l.dim("orcid-login"));let n=r.length>0?`  [${r.join(", ")}]`:"",o=`created ${e.created_at}  datasets=${e.dataset_count}`;console.log(`    id ${String(e.id).padEnd(5)} ${t}  <${e.email}>  ${o}${n}`)}fZ.option("--json","Output raw JSON instead of the human report").option("--clear <id>","Clear one account's identity-conflict flag (refuses while the collision remains)").action(async(e)=>{if(!Z())return;if(e.clear!==void 0){let n=Number.parseInt(e.clear,10);if(!Number.isInteger(n)||n<=0){console.error(l.red(`Invalid user id: ${e.clear}`)),process.exit(1);return}let o=w(`Clearing identity-conflict flag on user ${n}...`).start();try{let i=await JK(n);if(o.stop(),e.json){console.log(JSON.stringify(i,null,2));return}console.log(i.cleared?l.green(`Cleared the identity-conflict flag on user ${n}.`):l.dim(`User ${n} was not flagged; nothing to clear.`))}catch(i){o.fail(i instanceof q&&i.statusCode===409?"Still colliding; flag not cleared":"Failed to clear the identity-conflict flag"),console.error(l.red(P(i))),process.exit(1)}return}let t=w("Checking for duplicate accounts...").start(),r;try{r=await YK(),t.stop()}catch(n){t.fail("Duplicate report failed"),console.error(l.red(P(n))),process.exit(1);return}if(e.json){console.log(JSON.stringify(r,null,2));return}if(console.log(),r.groups.length===0){if(console.log(l.green("No duplicate accounts.")),r.flagged_count>0)console.log(l.yellow(`${r.flagged_count} account(s) still carry an identity-conflict flag with no remaining collision.`)),console.log(l.dim("  Clear each with 'nemar admin duplicates --clear <id>'."));return}console.log(l.cyan(`${r.group_count} duplicate group(s); ${r.flagged_count} account(s) flagged`));for(let n of r.groups){console.log(),console.log(`  ${l.bold(n.kind)}  ${n.value}`);for(let o of n.accounts)nVe(o)}console.log(),console.log(l.dim("The fix is self-service on the surviving account: change its email or GitHub username, or unlink/re-link its ORCID iD, in Settings on nemar.org. Merging two accounts is manual.")),process.exitCode=1});le.addCommand(fZ);We();lo();Rn();$c();Rc();Ku();We();$c();Rc();var oVe=Dt["cli.gaps.section.title"];function pZ(e){if(e.gaps===void 0)return[e.unknownReason??Dt["cli.gaps.unknown"]];let t=Qm(e.gaps,{orcidVerified:e.orcidVerified}).map(Dq);if(e.sandboxCompleted===!1)t.push(Zm());return t.length>0?t:[Dt["gaps.none"]]}function iVe(e){let t=pZ(e);return t.length===1&&t[0]===Dt["gaps.none"]}function Pf(e){let t=e.gaps===void 0||iVe(e);console.log(),console.log(l.bold(oVe));for(let r of pZ(e))console.log(`  ${t?l.dim(r):l.yellow(r)}`)}function jg(e,t,r={}){let n=r.indent??"  ";console.log(),console.log(`${n}${e}`);for(let o of t)console.log(`${n}  ${l.yellow(o.label)} ${vv(o)}`)}kc();us();Ct();async function $2(e){return A("/auth/login",{method:"POST",body:JSON.stringify({api_key:e})})}async function mZ(e){return A("/auth/resend-verification",{method:"POST",body:JSON.stringify({email:e})})}async function hZ(e,t){return A("/auth/retrieve-key",{method:"POST",body:JSON.stringify({email:e,password:t})})}async function gZ(e){return A("/auth/request-key-regeneration",{method:"POST",body:JSON.stringify({email:e})})}async function Hn(){return(await A("/users/me",{},!0,Z5)).user}async function yZ(e){return A("/sandbox/complete",{method:"POST",body:JSON.stringify({dataset_id:e})},!0)}async function xZ(){return A("/sandbox/reset",{method:"POST"},!0)}async function Mg(){return A("/sandbox/status",{},!0)}async function bZ(e){return A("/users/me/upload-access/request",{method:"POST",body:JSON.stringify({why:e})},!0)}async function _Z(e){return A("/auth/email/change/request",{method:"POST",body:JSON.stringify({email:e})},!0)}async function vZ(e,t){return A("/auth/email/change/verify",{method:"POST",body:JSON.stringify({email:e,code:t})},!0)}async function C2(e){return A("/auth/profile",{method:"PATCH",body:JSON.stringify(e)},!0)}async function wZ(e){return A("/auth/orcid/cli-start",{method:"POST",body:JSON.stringify({mode:e})},!0)}async function DZ(){return A("/auth/orcid/unlink",{method:"POST"},!0)}async function EZ(e){return A("/auth/device/start",{method:"POST",body:JSON.stringify({machine_name:e})},!1,gq)}function sVe(e){return typeof e==="string"&&Wm.options.includes(e)}function aVe(e){if(typeof e!=="object"||e===null)return;let t=e.message;return typeof t==="string"?t:void 0}async function SZ(e,t){try{return{status:"success",data:await A("/auth/device/token",{method:"POST",body:JSON.stringify({device_code:e}),signal:t},!1,xq)}}catch(r){if(r instanceof q&&r.statusCode===400){let n=yq.safeParse(r.rawBody);if(n.success){let o=n.data;if(o.error==="authorization_pending")return{status:"pending"};if(o.error==="slow_down")return{status:"slow_down"};return{status:"terminal",error:o.error,reason:o.reason,message:o.message}}if(sVe(r.code)&&r.code!=="authorization_pending"&&r.code!=="slow_down")return{status:"terminal",error:r.code,reason:void 0,message:aVe(r.rawBody)??mq[r.code]}}throw r}}async function $Z(){return A("/auth/keys",{},!0,Km)}async function CZ(e){return A("/auth/keys",{method:"POST",body:JSON.stringify({name:e})},!0,Ym)}async function Lg(e){return A(`/auth/keys/${e}`,{method:"DELETE"},!0)}async function RZ(e,t){return A(`/auth/keys/${e}`,{method:"DELETE",headers:{Authorization:`Bearer ${t}`}},!1)}async function kZ(){return A("/auth/profile/username-suggestion",{},!0,tq)}Ct();ai();import{spawn as cVe}from"child_process";function lVe(e,t){if(e==="darwin")return{command:"open",args:[t]};if(e==="win32")return{command:"cmd",args:["/c","start","",t]};if(e==="linux")return{command:"xdg-open",args:[t]};return null}function Bg(e){if(process.env.NEMAR_NO_BROWSER==="1")return!1;let t=lVe(process.platform,e);if(!t)return!1;try{let r=cVe(t.command,t.args,{stdio:"ignore",detached:!0});return r.on("error",(n)=>{br(`openInBrowser: ${t.command} failed: ${n instanceof Error?n.message:n}`)}),r.unref(),!0}catch(r){return br(`openInBrowser: could not spawn ${t.command}: ${r instanceof Error?r.message:r}`),!1}}yl();So();ai();We();Jm();import{hostname as uVe}from"os";Ct();ai();function dVe(e){let t=e.replace(/[\x00-\x1f\x7f]/g,"").replace(/\s+/g," ").trim();return t?t.slice(0,pq):xv}function fVe(){try{return dVe(uVe())}catch{return xv}}function pVe(e,t,r=yv){return e+(t+r)*1000}function FZ(e){switch(e.kind){case"cancelled":return{lines:["Sign-in canceled. Run `nemar auth login` to try again."],exitCode:130};case"denied":case"expired":case"invalid":return{lines:[e.message],exitCode:1};case"unreachable":return{lines:[`NEMAR could not be reached: ${e.detail}`,"Run `nemar auth login` again once you're back online."],exitCode:1};case"server_error":return{lines:[`NEMAR keeps answering with an error (${e.detail}). Try again in a few minutes; if it keeps happening, run \`nemar auth login --debug\` and report the log.`],exitCode:1};case"start_failed":return{lines:[`Could not start sign-in: ${e.detail}`],exitCode:1}}}var mVe=15000,AZ=1000,hVe=5000,OZ=3;function gVe(e){if(e instanceof q&&e.statusCode!==0)return`HTTP ${e.statusCode}`;return P(e)}function yVe(e){if(typeof AbortSignal.any==="function")return AbortSignal.any(e);let t=new AbortController;for(let r of e){if(r.aborted){t.abort();break}r.addEventListener("abort",()=>t.abort(),{once:!0})}return t.signal}function xVe(e,t){return new Promise((r)=>{if(t.aborted){r();return}let n=setTimeout(()=>{t.removeEventListener("abort",o),r()},e);function o(){clearTimeout(n),r()}t.addEventListener("abort",o,{once:!0})})}async function bVe(e,t={}){let r=Date.now(),n=pVe(r,e.expires_in,t.graceSeconds??yv),o=Math.max(e.interval*1000,AZ),i=new AbortController,s=()=>i.abort();process.on("SIGINT",s);let a=0;try{while(!0){if(i.signal.aborted)return{kind:"cancelled"};if(Date.now()>=n)return{kind:"unreachable",detail:"gave up waiting to reach NEMAR"};if(await xVe(o,i.signal),i.signal.aborted)return{kind:"cancelled"};let c=yVe([i.signal,AbortSignal.timeout(mVe)]),u;try{u=await SZ(e.device_code,c),a=0}catch(d){if(i.signal.aborted)return{kind:"cancelled"};if(d instanceof q&&d.statusCode===0){console.log(l.dim("  NEMAR is unreachable; retrying...")),a=0;continue}let f=gVe(d);if(a+=1,br(`poll error ${a}/${OZ}: ${f} -- ${P(d)}`),console.log(l.dim(`  NEMAR answered with an error (${f}); retrying...`)),a>=OZ)return{kind:"server_error",detail:f};continue}if(u.status==="pending")continue;if(u.status==="slow_down"){o=Math.max(o+hVe,e.interval*1000,AZ);continue}if(u.status==="success")return{...u.data,kind:"success"};if(u.error==="expired_token")return{kind:"expired",message:u.message};if(u.error==="access_denied")return{kind:"denied",message:u.message};return{kind:"invalid",message:u.message}}}finally{process.off("SIGINT",s)}}async function R2(e={}){let t;try{t=await EZ(fVe())}catch(r){return{kind:"start_failed",detail:P(r)}}if(console.log(`  ${t.verification_uri_complete}`),console.log(`  Code: ${l.cyan(t.user_code)}`),console.log(l.dim("  (if the page asks for it)")),console.log(),e.open!==!1&&Bg(t.verification_uri_complete))console.log(l.dim("  (trying to open your browser; use the link above if it doesn't)")),console.log();return bVe(t)}rf();import{appendFileSync as _Ve,existsSync as bs,mkdirSync as PZ,readFileSync as Vg,writeFileSync as vVe}from"fs";import{homedir as wVe}from"os";import{join as Ug}from"path";var{spawn:IZ}=globalThis.Bun;function fa(){let e=Ug(wVe(),".ssh");return{sshDir:e,privateKey:Ug(e,"nemar_ed25519"),publicKey:Ug(e,"nemar_ed25519.pub"),configFile:Ug(e,"config")}}function TZ(){let e=fa();return bs(e.privateKey)&&bs(e.publicKey)}async function NZ(e){let t=fa();if(!bs(t.sshDir))try{PZ(t.sshDir,{mode:448})}catch(r){return{success:!1,error:`Cannot create ~/.ssh directory: ${r.message}`}}if(bs(t.privateKey))try{return{success:!0,publicKey:Vg(t.publicKey,"utf-8").trim()}}catch(r){return{success:!1,error:`NEMAR SSH key exists but cannot read public key: ${r.message}`}}try{let r=IZ({cmd:["ssh-keygen","-t","ed25519","-f",t.privateKey,"-N","","-C",`nemar-cli-${e}`],stdout:"pipe",stderr:"pipe"}),n=await new Response(r.stderr).text();if(await r.exited!==0)return{success:!1,error:`ssh-keygen failed: ${n}`};return{success:!0,publicKey:Vg(t.publicKey,"utf-8").trim()}}catch(r){return{success:!1,error:`Failed to generate SSH key: ${r.message}`}}}function qZ(){let e=fa();if(!bs(e.publicKey))return null;try{return Vg(e.publicKey,"utf-8").trim()}catch{return null}}function DVe(){let e=fa();if(!bs(e.configFile))return!1;try{let t=Vg(e.configFile,"utf-8");return t.includes("IdentityFile ~/.ssh/nemar_ed25519")||t.includes(`IdentityFile ${e.privateKey}`)}catch{return!1}}function jZ(){let e=fa();if(!bs(e.sshDir))try{PZ(e.sshDir,{mode:448})}catch(r){return{success:!1,error:`Cannot create ~/.ssh directory: ${r.message}`}}if(DVe())return{success:!0};let t=`
 # NEMAR CLI SSH key (auto-generated)
 Host github.com
   AddKeysToAgent yes

package/package.json CHANGED Viewed

@@ -1,6 +1,6 @@
 {
   "name": "nemar-cli",
-  "version": "0.10.1-PR1333.6f5d7fe",
+  "version": "0.10.1-PR1333.9a5fdee",
   "description": "CLI for NEMAR (Neuroelectromagnetic Data Archive and Tools Resource) dataset management",
   "type": "module",
   "main": "dist/index.js",