nemar-cli 0.10.10-dev.2983 → 0.10.10-dev.2984

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Files changed (2) hide show
  1. package/dist/index.js +3 -3
  2. package/package.json +1 -1
package/dist/index.js CHANGED
@@ -99,7 +99,7 @@ ${t}`,jSe,qSe,MSe=(e,t,r)=>{let n=r===""?"":`with ${r.trim()}() `,o=NSe.bind(nul
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  `)}var mE=!1;var{spawn:FLe}=globalThis.Bun;async function C(e,t={}){let r={...process.env,GIT_TERMINAL_PROMPT:"0",...t.env};for(let u of t.unsetEnv??[])delete r[u];let n=FLe({cmd:e,cwd:t.cwd,...t.stdin===void 0?{}:{stdin:new TextEncoder().encode(t.stdin)},stdout:"pipe",stderr:"pipe",env:r}),o=!1,i;if(t.timeout)i=setTimeout(()=>{o=!0,n.kill()},t.timeout);if(hE()){let u=t.cwd?` (cwd=${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(`
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  Heads up: some tools NEMAR needs for uploading/validating aren't installed yet:`);for(let r of t)console.warn(` - ${r.name} (${r.purpose})`),console.warn(` Install: ${r.installInstruction}`);return console.warn("Run `nemar doctor` anytime to re-check. You can finish signup without them.\n"),t}async function 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=[`
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  Missing required tools:`];for(let s of o)i.push(` ${s.tool} not installed`),i.push(` Install: ${s.installInstruction}`);throw Error(i.join(`
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- `))}var 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-dev.2983",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}
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+ `))}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-dev.2984",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}
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  `)}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(`
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  `)}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(`
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@@ -196,7 +196,7 @@ Exemplar clone + publish complete: ${i} -> ${o}`)),console.log(l.dim(` GitHub:
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  `)){let n=r.trim().split(/\s+/),o=n[0];if(!o||n.length<2)continue;let i=(a)=>n.find((c)=>c.startsWith(`${a}=`))?.slice(a.length+1),s=i("name");if(!s)continue;t.set(o,{uuid:o,name:s,bucket:i("bucket"),fileprefix:i("fileprefix")})}return t}function AWe(e){if(!e.startsWith("!"))return e;let t=e.slice(1),r=Buffer.from(t,"base64");if(r.toString("base64").replace(/=+$/,"")!==t.replace(/=+$/,""))return e;return r.toString("utf8")}function Dte(e,t){let r=[];for(let o of e.split(`
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  `)){let i=/^(\S+?)s?\s+([0-9a-f-]{36}):V\s+([+-])(\S+)$/.exec(o.trim());if(!i)continue;let s=t.get(i[2]);if(!s?.bucket)continue;let a=AWe(i[4]),c=a.indexOf("#");if(c<=0)continue;let u=Number.parseFloat(i[1])||0;r.push({stamp:u,retracted:i[3]==="-",value:a,pin:{bucket:s.bucket,object:a.slice(c+1),version:a.slice(0,c),remoteName:s.name}})}r.sort((o,i)=>o.stamp-i.stamp);let n=new Map;for(let o of r)if(o.retracted)n.delete(o.value);else n.set(o.value,o.pin);return[...n.values()]}async function Ete(e){let t=["aws","s3api","list-object-versions","--bucket",e.bucket,"--prefix",e.prefix,"--output","json","--query","Versions[].[Key,VersionId,Size,ETag]","--page-size","1000"];if(!e.signed)t.push("--no-sign-request");let{stdout:r,stderr:n,exitCode:o,timedOut:i}=await C(t,{unsetEnv:X2,timeout:J2});if(o!==0||i)throw Error(`listing s3://${e.bucket}/${e.prefix} failed: ${i?"timed out":n.trim()||`exit ${o}`}`);return OWe(r)}function OWe(e){let t=new Map,r=e.trim()?JSON.parse(e):[];for(let[n,o,i,s]of r??[]){let a=t.get(n)??[];a.push({object:n,version:o,size:i,etag:(s??"").replace(/"/g,"")}),t.set(n,a)}return t}function FWe(e){if(e.size!==0)return!1;let t=Ste[e.backend];return t!==void 0&&e.hashHex===t}function $te(e){let t=wte(e.key);if(!t)return{key:e.key,size:0,reason:"not a parseable annex key"};let r={key:e.key,size:t.size};if(FWe(t))return{...r,empty:!0};if(t.size===0&&t.hashHex!==null&&Ste[t.backend])return{...r,reason:"declares zero bytes but not the empty file's hash; no content can satisfy it"};let n=e.pins[e.pins.length-1],o=e.upstream?PWe(t.size,e):null;if(n){let i=o&&o.version!==n.version?[o]:void 0;return{...r,source:{...n,origin:"pinned",size:t.size},alternatives:i}}if(!e.upstream)return{...r,reason:"no upstream remote to recover from"};if(o)return{...r,source:o};return{...r,reason:IWe(t.size,e)}}function PWe(e,t){let r=t.upstream;if(!r)return null;let n=t.paths.flatMap((s)=>r.index.get(`${r.prefix}${s}`)?.filter((a)=>a.size===e)??[]),o=new 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r=e.etag?.replace(/"/g,"");if(r&&!r.includes("-")&&t.backend.startsWith("MD5")&&t.hashHex)return r===t.hashHex?{ok:!0,method:"etag"}:{ok:!1,method:"etag",detail:`the object's MD5 is ${r}, the key says ${t.hashHex}`};if(e.size==null)return{ok:!1,method:"unmeasured",detail:"the bucket did not answer for the copy, so nothing about it was checked"};if(e.size!==t.size)return{ok:!1,method:"size",detail:`the object is ${e.size} bytes, the key says ${t.size}`};if(!Cte(e.origin))return{ok:!1,method:"size-and-pin",detail:"only the size could be checked, and nothing pins this source to this key"};if(e.sourceCrc64&&e.crc64)return e.sourceCrc64===e.crc64?{ok:!0,method:"crc64-of-source"}:{ok:!1,method:"crc64-of-source",detail:`the copy's CRC64 is ${e.crc64}, the source reads ${e.sourceCrc64}`};return{ok:!0,method:"size-and-pin"}}function kte(e){let t=`${e.bucket}/${e.object}`;return e.version?`${t}?versionId=${e.version}`:t}function jWe(e){return NWe.test(e)}async function Wo(e,t){let r=await 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Wo(["s3api","create-multipart-upload","--bucket",e.destBucket,"--key",e.destKey,"--checksum-algorithm","CRC64NVME","--checksum-type","FULL_OBJECT","--output","json"],e.env);if(t.exitCode!==0)throw Error(`create-multipart-upload failed: ${t.stderr.trim()||`exit ${t.exitCode}`}`);let r=JSON.parse(t.stdout||"{}").UploadId;if(!r)throw Error("create-multipart-upload returned no UploadId");let n=BWe(e.source.size,CWe);try{let o=await gp(n,kWe,async(a)=>{let c=await Wo(["s3api","upload-part-copy","--bucket",e.destBucket,"--key",e.destKey,"--upload-id",r,"--part-number",String(a.part),"--copy-source",kte(e.source),"--copy-source-range",`bytes=${a.offset}-${a.end}`,"--output","json"],e.env);if(c.exitCode!==0)throw Error(`upload-part-copy ${a.part} failed: ${c.stderr.trim()||`exit ${c.exitCode}`}`);let u=JSON.parse(c.stdout||"{}").CopyPartResult?.ETag;if(!u)throw Error(`upload-part-copy ${a.part} returned no ETag`);return{ETag:u,PartNumber:a.part}}),i=await Wo(["s3api","complete-multipart-upload","--bucket",e.destBucket,"--key",e.destKey,"--upload-id",r,"--multipart-upload",JSON.stringify({Parts:o}),"--output","json"],e.env);if(i.exitCode!==0)throw Error(`complete-multipart-upload failed: ${i.stderr.trim()||`exit ${i.exitCode}`}`);return{checksumSha256:null,etag:JSON.parse(i.stdout||"{}").ETag??null}}catch(o){let i=await Wo(["s3api","abort-multipart-upload","--bucket",e.destBucket,"--key",e.destKey,"--upload-id",r],e.env).catch(()=>({exitCode:1,stderr:"abort-multipart-upload could not be invoked"}));if(i.exitCode!==0)console.warn([`[content-recovery] FAILED to abort multipart upload ${r}`,`for ${e.destBucket}/${e.destKey}: ${i.stderr.trim().slice(0,300)}.`,"It is billable storage invisible to every object listing; clear it with",`aws s3api abort-multipart-upload --bucket ${e.destBucket}`,`--key ${e.destKey} --upload-id ${r}`].join(" "));throw o}}async function bte(e){let{stdout:t,stderr:r,exitCode:n,timedOut:o}=await Wo(["s3api","head-object","--bucket",e.bucket,"--key",e.key,"--checksum-mode","ENABLED","--output","json"],e.env);if(n!==0){let s=o?"timed out":r.trim()||`exit ${n}`;return SWe.test(r)?{object:null,failed:null}:{object:null,failed:s}}let i;try{i=JSON.parse(t||"{}")}catch{return{object:null,failed:"the bucket's answer could not be read as JSON"}}return{object:{size:typeof i.ContentLength==="number"?i.ContentLength:null,etag:i.ETag?.replace(/"/g,"")??null,checksumSha256:i.ChecksumSHA256??null,crc64:i.ChecksumType==="FULL_OBJECT"?i.ChecksumCRC64NVME??null:null},failed:null}}async function Y2(e,t,r=!1){let n=["s3api","head-object","--bucket",e.bucket,"--key",e.object];if(!r)n.push("--no-sign-request");if(e.version)n.push("--version-id",e.version);n.push("--output","json");let{stdout:o,stderr:i,exitCode:s,timedOut:a}=await Wo(n,t);if(s===0)return{readable:!0,refusedByUpstream:!1,size:zWe(o),detail:null};let c=a?"timed out":i.trim()||`exit 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Wo(["s3api","put-object","--bucket",e.bucket,"--key",e.key,"--content-length","0"],e.env);if(r===0)return{written:!0,detail:null};return{written:!1,detail:n?"timed out":t.trim()||`exit ${r}`}}async function _te(e){let{stderr:t,exitCode:r,timedOut:n}=await Wo(["s3api","delete-object","--bucket",e.bucket,"--key",e.key],e.env);if(r===0)return{deleted:!0,detail:null};return{deleted:!1,detail:n?"timed out":t.trim()||`exit ${r}`}}async function Rte(e){let{entry:t}=e;if(t.empty){if(!e.apply)return{key:t.key,size:0,action:"would-recover",origin:"empty"};let d=await GWe({bucket:e.destBucket,key:e.destKey,env:e.env});if(!d.written)return{key:t.key,size:0,action:"failed",origin:"empty",detail:d.detail??"the bucket refused the write"};let f=await bte({bucket:e.destBucket,key:e.destKey,env:e.env});if(f.object===null||f.object.size!==0){let m=f.object===null?f.failed?`written, but the bucket then answered ${f.failed}`:"written, but the bucket then reported no such 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b=TWe({key:t.key,origin:d.origin,checksumSha256:h,etag:m.etag??p.object?.etag??null,size:p.object?.size??null,crc64:p.object?.crc64??null,sourceCrc64:g?.crc64??null});if(b.ok)return{key:t.key,size:t.size,action:"recovered",origin:d.origin,verification:b.method};let x=await _te({bucket:e.destBucket,key:e.destKey,env:e.env});return{key:t.key,size:t.size,action:"failed",detail:[`refused by ${b.method}: ${b.detail}`,x.deleted?"the object was deleted":`the object was LEFT IN THE BUCKET (delete failed: ${x.detail})`].join("; "),origin:d.origin,leftInBucket:!x.deleted}}if(a.length===i.length)return{key:t.key,size:t.size,action:"unrecoverable",origin:r,detail:a.join("; ")};let c=await Y2(t.source,e.env),u=s[s.length-1]??"no candidate source could be copied";if(c.refusedByUpstream)return{key:t.key,size:t.size,action:"unrecoverable",origin:t.source.origin,detail:`upstream will not serve any recorded source for this key (${c.detail}): 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198
198
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199
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Pb={dataset:["search","download","upload","validate","status","list"],admin:["users","approve","revoke","publish","doi","make-public","delete-dataset","notify","doctor"]};var Ib=process.argv.includes("--help-all");if(process.argv.includes("--no-color"))l.level=0;var A$=process.argv.indexOf("--help-all");if(A$!==-1)process.argv[A$]="--help";var uu=ue.prototype.addHelpText,O$=`
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  Run with --help-all for examples and detailed descriptions.
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  `,Tp=new WeakSet;ue.prototype.addHelpText=function(e,t){if(e==="after"||e==="afterAll"){if(Ib)return uu.call(this,e,t);if(!Tp.has(this))return Tp.add(this),uu.call(this,e,O$);return this}return uu.call(this,e,t)};function Jie(e){let t=[];for(let r=e;r?.parent;r=r.parent)t.unshift(r.name());return t.join(" ")}function Ft(e){let t=[];for(let r=e;r;r=r.parent)t.unshift(r.name());return t.join(" ")}var Xie={formatHelp(e,t){let r=t.helpWidth??80,n=2,o=2,i=40,s=Math.max(8,r-2-2-40),a=(A)=>Math.min(s,A.reduce((q,T)=>Math.max(q,T.length),0));function c(A,q,T,B){if(!T)return q;let Q=B+2;if(A.length>B){let I=t.wrap(T,r-2-4,0);return`${q}
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  ${I.replace(/^/gm," ")}`}let z=" ".repeat(Math.max(0,Q-A.length)),ee=`${A}${z}${T}`,ie=t.wrap(ee,r-2,Q);return q+ie.slice(A.length)}function u(A){return A.join(`
@@ -568,7 +568,7 @@ ${s}/${i.length} data_complete`))});pe.addCommand(nS);var oKe=/^xx0999\d{2}$/,iK
568
568
  ${u} of ${c.length} fleet entries failed`)),process.exit(1);return}if(!e)console.error(l.red("An xx-id argument is required unless --all is passed")),process.exit(1);if(!oKe.test(e))console.error(l.red(`Invalid exemplar id "${e}". Expected xx099900-xx099999.`)),process.exit(1);let s;try{s=pp(o)}catch(c){console.error(l.red(`Failed to load fleet file: ${N(c)}`)),process.exit(1)}let a=t.source??s.find((c)=>c.xx_id===e)?.source_id;if(!a)console.error(l.red(`No source dataset for ${e}. Pass --source <nm/on id> or add it to the fleet file.`)),process.exit(1);if(!iKe.test(a))console.error(l.red(`Invalid source id "${a}". Expected an nm/on dataset id.`)),process.exit(1);try{await z2({xxId:e,sourceId:a,...i})}catch(c){console.error(l.red(`
569
569
  Exemplar clone failed: ${N(c)}`)),process.exit(1)}});Gy.command("status").description("Show which fleet entries have been cloned and their current state").option("--fleet-file <path>","Path to the fleet JSON (default: scripts/exemplar-fleet.json)").action(async(e)=>{if(!Z())return;await Promise.resolve().then(() => V2());let r=e.fleetFile||Wte(),n;try{n=pp(r)}catch(o){console.error(l.red(`Failed to load fleet file: ${N(o)}`)),process.exit(1)}console.log(l.bold(`
570
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  Exemplar Fleet (${n.length})
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- `));for(let o of n)try{let i=await Tt(o.xx_id);console.log(` ${o.xx_id.padEnd(10)} ${o.modality.padEnd(6)} <- ${o.source_id.padEnd(10)} ${l.green(i.visibility)} doi=${i.concept_doi??"none"}`)}catch(i){if(i instanceof L&&i.statusCode===404)console.log(` ${o.xx_id.padEnd(10)} ${o.modality.padEnd(6)} <- ${o.source_id.padEnd(10)} ${l.dim("not created")}`);else console.log(` ${o.xx_id.padEnd(10)} ${o.modality.padEnd(6)} <- ${o.source_id.padEnd(10)} ${l.red(`status check failed (${N(i)})`)}`)}});Gy.command("remint-dois").description("Re-mint an exemplar's sandbox concept DOI (idempotent)").argument("<xx-id>","Exemplar dataset id (e.g., xx099900)").action(async(e)=>{if(!Z())return;let t=D(`Re-minting DOIs for ${e}...`).start();try{let r=await sJ(e);t.succeed(`Re-minted ${r.concept_doi} (status: ${r.status})`);for(let n of r.warnings??[])console.log(l.yellow(` ${n}`))}catch(r){Qe(r,t,"Failed to re-mint exemplar DOIs",{400:"Not an exemplar dataset",403:"Exemplar DOI re-mint is disabled in production",404:"Dataset not found"}),process.exit(1)}});pe.addCommand(Gy);function sKe(e,t){let r=e.enrichment.status,n=r==="ok"?l.green("enrich:ok"):r==="failed"?l.red("enrich:failed"):l.dim("enrich:skipped"),o=e.sync.status,i=o==="ok"?l.green("sync:ok"):o==="failed"?l.red("sync:failed"):l.dim("sync:skipped"),s=e.sync.metadata_columns_written===!0?l.green("cols:written"):e.sync.metadata_columns_error?l.red("cols:failed"):"",a=t?.showRef&&e.enrichment.ref?l.dim(`@${e.enrichment.ref}`):"",c=[` ${e.dataset_id.padEnd(12)} ${n}${a} ${i} ${s}`];if(e.enrichment.error)c.push(l.red(` enrichment: ${e.enrichment.error}`));for(let d of e.enrichment.warnings??[])c.push(l.yellow(` warning: ${d}`));let u=e.enrichment.doi_resolution;if(u){if(c.push(l.dim(` DOI lookups: ${u.resolved} resolved, ${u.unresolved} unresolved, ${u.failed} failed`)),u.skipped>0)c.push(l.yellow(` ${u.skipped} DOI(s) past the per-run lookup cap were not looked up; their relation labels were chosen without registry metadata`))}if(e.sync.metadata_columns_error)c.push(l.red(` metadata columns: ${e.sync.metadata_columns_error}`));return c}function jte(e,t){for(let r of sKe(e,t))console.log(r)}var Ba=new ue("fleet").description("Governance drift reporting and enforcement (epic #713)");Ba.command("drift").description("Report dataset repos that are off the governance spec").option("--prefix <prefix>","Filter datasets by id prefix (e.g. nm, on)").option("--visibility <vis>","Filter by visibility: public or private").option("--limit <n>","Max repos to scan (default 25, max 50)","25").option("--json","Output raw JSON").action(async(e)=>{if(!je())console.log(l.red("Error: Not authenticated")),process.exit(1);if(e.visibility&&!["public","private"].includes(e.visibility))console.log(l.red("Error: --visibility must be public or private")),process.exit(1);let t=D("Scanning fleet for drift...").start();try{let r=await wJ({prefix:e.prefix,visibility:e.visibility,limit:Number.parseInt(e.limit,10)||25});if(t.stop(),e.json){console.log(JSON.stringify(r,null,2));return}console.log(),console.log(l.bold(`Fleet drift (scanned ${r.scanned}):`));let n=["PUBLIC_UNPROTECTED","RED_REQUIRED_CHECK","CONTEXT_NAME_MISMATCH","MISSING_REQUIRED_WORKFLOW","PRIVATE_WITH_STRAY_READ","DEFAULT_BRANCH_OUTLIER","DEPRECATED_WORKFLOW_PRESENT","COMPLIANT"];for(let o of n){let i=r.buckets[o];if(!i||i.length===0)continue;let s=o==="COMPLIANT"?l.green:l.yellow;if(console.log(` ${s(o.padEnd(28))} ${i.length}`),o!=="COMPLIANT"){let a=i.slice(0,20).join(", ");console.log(l.dim(` ${a}${i.length>20?` ... +${i.length-20}`:""}`))}}console.log()}catch(r){if(r instanceof L)t.fail(r.message);else t.fail("Failed to scan fleet"),console.log(l.red(` ${r.message}`));process.exit(1)}});Ba.command("enforce").description("Bring dataset repos to the governance spec (single or --all). Dry-run by default.").argument("[dataset-id]","Dataset to enforce (omit when using --all)").option("--all","Bulk enforce across a filtered set (owner-only)").option("--apply","Actually apply changes (default is a dry run)").option("--prefix <prefix>","Bulk: filter by id prefix").option("--visibility <vis>","Bulk: filter by visibility (public|private)").option("--limit <n>","Bulk: max repos (default 25, max 50)","25").option("--json","Output raw JSON").action(async(e,t)=>{if(!je())console.log(l.red("Error: Not authenticated")),process.exit(1);if(!e&&!t.all)console.log(l.red("Error: provide a dataset-id or use --all")),process.exit(1);if(e&&t.all)console.log(l.red("Error: provide a dataset-id OR --all, not both")),process.exit(1);let r=!t.apply,n=r?"[dry-run] ":"",o=D(`${n}Enforcing spec...`).start();try{if(e){let i=await Nl(e,r);if(o.succeed(`${n}${e} (${i.result.visibility})`),t.json){console.log(JSON.stringify(i,null,2));return}for(let[s,a]of Object.entries(i.result.steps)){let c=a.status==="ok"?l.green:a.status==="skipped"?l.yellow:l.red;console.log(` ${c(a.status.padEnd(8))} ${s}${a.detail?l.dim(` (${a.detail})`):""}`)}}else{let i=await DJ({prefix:t.prefix,visibility:t.visibility,limit:Number.parseInt(t.limit,10)||25,dryRun:r});if(o.succeed(`${n}processed ${i.count} repo(s)`),t.json){console.log(JSON.stringify(i,null,2));return}for(let s of i.results){if(s.error){console.log(` ${l.red("error")} ${s.dataset_id}: ${s.error}`);continue}let a=Object.entries(s.steps??{}).filter(([,u])=>u.status!=="ok").map(([u,d])=>`${u}=${d.status}`),c=a.length?l.yellow("drift"):l.green("ok");console.log(` ${c} ${s.dataset_id}${a.length?l.dim(` (${a.join(", ")})`):""}`)}}}catch(i){if(i instanceof L)o.fail(i.message);else o.fail("Enforcement failed"),console.log(l.red(` ${i.message}`));process.exit(1)}});var eu=(e)=>new Promise((t)=>setTimeout(t,e));async function aKe(e,t,r){let n=Date.now()+t,o="no probe completed";while(Date.now()<n){try{let i=(await Nl(e,!0)).result?.steps?.branch_ruleset;if(i?.status==="ok")return{status:"green"};if(i?.detail)o=i.detail}catch(i){o=i instanceof L?i.message:String(i)}await eu(r)}return{status:"timeout",detail:o}}Ba.command("revalidate").description("Re-run BIDS validation on main HEAD for unprotected datasets, then optionally enforce (epic #713)").argument("[dataset-id]","Dataset to revalidate (omit when using --all/--prefix)").option("--all","Revalidate across unprotected public datasets").option("--prefix <prefix>","Filter by id prefix (with --all), e.g. nm000 / on").option("--enforce","After a dataset goes green, run enforce (dry-run unless --apply)").option("--apply","With --enforce, actually apply the ruleset (default is a dry run)").option("--force","Override the live-dataset guard (nm000103-107)").option("--limit <n>","Max repos for --all/--prefix (default 25)","25").option("--json","Output raw JSON").action(async(e,t)=>{if(!je())console.log(l.red("Error: Not authenticated")),process.exit(1);let r=Boolean(t.all||!e&&t.prefix);if(!e&&!r)console.log(l.red("Error: provide a dataset-id, or --all/--prefix")),process.exit(1);let n;if(e)n=[e];else{let d=D("Fetching dataset list...").start();try{let f=[];for(let p=0;;p+=200){let h=await Ns({limit:200,offset:p});if(f.push(...h.datasets),h.datasets.length<200||f.length>=h.total_count)break}let m=Number.parseInt(t.limit,10)||25;n=RX(f,{prefix:t.prefix}).slice(0,m),d.succeed(`${n.length} target(s) (from ${f.length} datasets)`)}catch(f){Qe(f,d,"Failed to fetch datasets");return}}let o=Boolean(t.enforce),i=Boolean(t.apply),s={revalidated:0,green:0,locked:0,stillRed:0,skipped:0,errors:0},a=[],c=[],u=0;for(let d of n){if(u++,Ri.has(d)&&!t.force){console.log(` [${u}/${n.length}] ${l.dim(`${d}: skip (live; use --force)`)}`),s.skipped++;continue}try{let f=await EJ(d,t.force);if(a.push(f),f.skipped)console.log(` [${u}/${n.length}] ${d}: ${l.dim(`skipped (${f.skipped})`)}`),s.skipped++;else s.revalidated++,c.push(d),console.log(` [${u}/${n.length}] ${d}: ${l.cyan(`revalidating (${f.triggered_by})`)}`)}catch(f){s.errors++,console.log(` [${u}/${n.length}] ${d}: ${l.red(f instanceof L?f.message:String(f))}`)}if(u<n.length)await eu(4000)}if(o&&c.length>0)if(e){let d=c[0],f=D(`Waiting for ${d} validation to land...`).start(),m=await aKe(d,300000,15000);if(m.status!=="green")f.warn(`${d}: not green within 5m \u2014 last: ${m.detail} (real errors or still running)`),s.stillRed++;else if(s.green++,!i)f.succeed(`${d}: green (would lock; pass --apply)`);else{let p=await Nl(d,!1);if(p.result?.steps?.branch_ruleset?.status==="ok")f.succeed(`${d}: LOCKED`),s.locked++;else f.warn(`${d}: enforce ${p.result?.steps?.branch_ruleset?.status??"?"}`)}}else{let d=D("Waiting ~90s for validations to drain...").start();await eu(90000),d.text="Enforcing green datasets...";for(let f of c)try{if((await Nl(f,!0)).result?.steps?.branch_ruleset?.status!=="ok"){s.stillRed++;continue}if(s.green++,i){if((await Nl(f,!1)).result?.steps?.branch_ruleset?.status==="ok")s.locked++}}catch{s.errors++}d.stop()}if(t.json){console.log(JSON.stringify({tally:s,raw:a},null,2));return}console.log(),console.log(l.cyan(`Done: revalidated=${s.revalidated} green=${s.green} locked=${s.locked} still-red=${s.stillRed} skipped=${s.skipped} errors=${s.errors}`))});Ba.command("annex-policy").description("Report, and optionally fix, dataset repos that NEMAR's annex policy does not actually govern (#1374, ADR 0060)").argument("[dataset-id...]","Specific datasets to act on (omit to sweep by prefix)").option("--prefix <prefix>","Dataset id prefix to sweep (default on: the imported fleet)","on").option("--limit <n>","Act on at most this many datasets, in id order").option("--apply","Make the change (default is a read-only report)").option("--include-data","Also move data a repo keeps in git, which uploads to S3").option("--via-aws-cli","With --include-data, move the bytes with this machine's aws CLI").option("--no-push","With --apply, commit locally and push nothing (a rehearsal)").option("--dir <path>","Where clones go while they are being fixed (default: a temp dir)").option("--keep-clones","Do not delete each clone after its dataset is done").option("--concurrency <n>","Parallel GitHub reads during the scan (default 4)","4").option("--json <path>","Write the full report as JSON").option("--force","Include the live datasets (nm000103-107)").option(Pe,Ie).option(He,qe).addHelpText("after",`
571
+ `));for(let o of n)try{let i=await Tt(o.xx_id);console.log(` ${o.xx_id.padEnd(10)} ${o.modality.padEnd(6)} <- ${o.source_id.padEnd(10)} ${l.green(i.visibility)} doi=${i.concept_doi??"none"}`)}catch(i){if(i instanceof L&&i.statusCode===404)console.log(` ${o.xx_id.padEnd(10)} ${o.modality.padEnd(6)} <- ${o.source_id.padEnd(10)} ${l.dim("not created")}`);else console.log(` ${o.xx_id.padEnd(10)} ${o.modality.padEnd(6)} <- ${o.source_id.padEnd(10)} ${l.red(`status check failed (${N(i)})`)}`)}});Gy.command("remint-dois").description("Re-mint an exemplar's sandbox concept DOI (idempotent)").argument("<xx-id>","Exemplar dataset id (e.g., xx099900)").action(async(e)=>{if(!Z())return;let t=D(`Re-minting DOIs for ${e}...`).start();try{let r=await sJ(e);t.succeed(`Re-minted ${r.concept_doi} (status: ${r.status})`);for(let n of r.warnings??[])console.log(l.yellow(` ${n}`))}catch(r){Qe(r,t,"Failed to re-mint exemplar DOIs",{400:"Not an exemplar dataset",403:"Exemplar DOI re-mint is disabled in production",404:"Dataset not found"}),process.exit(1)}});pe.addCommand(Gy);function sKe(e,t){let r=e.enrichment.status,n=r==="ok"?l.green("enrich:ok"):r==="failed"?l.red("enrich:failed"):l.dim("enrich:skipped"),o=e.sync.status,i=o==="ok"?l.green("sync:ok"):o==="failed"?l.red("sync:failed"):l.dim("sync:skipped"),s=e.sync.metadata_columns_written===!0?l.green("cols:written"):e.sync.metadata_columns_error?l.red("cols:failed"):"",a=t?.showRef&&e.enrichment.ref?l.dim(`@${e.enrichment.ref}`):"",c=[` ${e.dataset_id.padEnd(12)} ${n}${a} ${i} ${s}`];if(e.enrichment.error)c.push(l.red(` enrichment: ${e.enrichment.error}`));for(let d of e.enrichment.warnings??[])c.push(l.yellow(` warning: ${d}`));let u=e.enrichment.doi_resolution;if(u){let d=` DOI lookups: ${u.resolved} resolved, ${u.unresolved} unresolved, ${u.failed} failed`;if(u.failed>0){let f=(e.enrichment.warnings??[]).some((m)=>m.startsWith("doi_resolution:"));c.push(l.yellow(f?d:`${d} (reindex this dataset again)`))}else c.push(l.dim(d));if(u.skipped>0)c.push(l.yellow(` ${u.skipped} DOI(s) past the per-run lookup cap were not looked up; their relation labels were chosen without registry metadata`))}if(e.sync.metadata_columns_error)c.push(l.red(` metadata columns: ${e.sync.metadata_columns_error}`));return c}function jte(e,t){for(let r of sKe(e,t))console.log(r)}var Ba=new ue("fleet").description("Governance drift reporting and enforcement (epic #713)");Ba.command("drift").description("Report dataset repos that are off the governance spec").option("--prefix <prefix>","Filter datasets by id prefix (e.g. nm, on)").option("--visibility <vis>","Filter by visibility: public or private").option("--limit <n>","Max repos to scan (default 25, max 50)","25").option("--json","Output raw JSON").action(async(e)=>{if(!je())console.log(l.red("Error: Not authenticated")),process.exit(1);if(e.visibility&&!["public","private"].includes(e.visibility))console.log(l.red("Error: --visibility must be public or private")),process.exit(1);let t=D("Scanning fleet for drift...").start();try{let r=await wJ({prefix:e.prefix,visibility:e.visibility,limit:Number.parseInt(e.limit,10)||25});if(t.stop(),e.json){console.log(JSON.stringify(r,null,2));return}console.log(),console.log(l.bold(`Fleet drift (scanned ${r.scanned}):`));let n=["PUBLIC_UNPROTECTED","RED_REQUIRED_CHECK","CONTEXT_NAME_MISMATCH","MISSING_REQUIRED_WORKFLOW","PRIVATE_WITH_STRAY_READ","DEFAULT_BRANCH_OUTLIER","DEPRECATED_WORKFLOW_PRESENT","COMPLIANT"];for(let o of n){let i=r.buckets[o];if(!i||i.length===0)continue;let s=o==="COMPLIANT"?l.green:l.yellow;if(console.log(` ${s(o.padEnd(28))} ${i.length}`),o!=="COMPLIANT"){let a=i.slice(0,20).join(", ");console.log(l.dim(` ${a}${i.length>20?` ... +${i.length-20}`:""}`))}}console.log()}catch(r){if(r instanceof L)t.fail(r.message);else t.fail("Failed to scan fleet"),console.log(l.red(` ${r.message}`));process.exit(1)}});Ba.command("enforce").description("Bring dataset repos to the governance spec (single or --all). Dry-run by default.").argument("[dataset-id]","Dataset to enforce (omit when using --all)").option("--all","Bulk enforce across a filtered set (owner-only)").option("--apply","Actually apply changes (default is a dry run)").option("--prefix <prefix>","Bulk: filter by id prefix").option("--visibility <vis>","Bulk: filter by visibility (public|private)").option("--limit <n>","Bulk: max repos (default 25, max 50)","25").option("--json","Output raw JSON").action(async(e,t)=>{if(!je())console.log(l.red("Error: Not authenticated")),process.exit(1);if(!e&&!t.all)console.log(l.red("Error: provide a dataset-id or use --all")),process.exit(1);if(e&&t.all)console.log(l.red("Error: provide a dataset-id OR --all, not both")),process.exit(1);let r=!t.apply,n=r?"[dry-run] ":"",o=D(`${n}Enforcing spec...`).start();try{if(e){let i=await Nl(e,r);if(o.succeed(`${n}${e} (${i.result.visibility})`),t.json){console.log(JSON.stringify(i,null,2));return}for(let[s,a]of Object.entries(i.result.steps)){let c=a.status==="ok"?l.green:a.status==="skipped"?l.yellow:l.red;console.log(` ${c(a.status.padEnd(8))} ${s}${a.detail?l.dim(` (${a.detail})`):""}`)}}else{let i=await DJ({prefix:t.prefix,visibility:t.visibility,limit:Number.parseInt(t.limit,10)||25,dryRun:r});if(o.succeed(`${n}processed ${i.count} repo(s)`),t.json){console.log(JSON.stringify(i,null,2));return}for(let s of i.results){if(s.error){console.log(` ${l.red("error")} ${s.dataset_id}: ${s.error}`);continue}let a=Object.entries(s.steps??{}).filter(([,u])=>u.status!=="ok").map(([u,d])=>`${u}=${d.status}`),c=a.length?l.yellow("drift"):l.green("ok");console.log(` ${c} ${s.dataset_id}${a.length?l.dim(` (${a.join(", ")})`):""}`)}}}catch(i){if(i instanceof L)o.fail(i.message);else o.fail("Enforcement failed"),console.log(l.red(` ${i.message}`));process.exit(1)}});var eu=(e)=>new Promise((t)=>setTimeout(t,e));async function aKe(e,t,r){let n=Date.now()+t,o="no probe completed";while(Date.now()<n){try{let i=(await Nl(e,!0)).result?.steps?.branch_ruleset;if(i?.status==="ok")return{status:"green"};if(i?.detail)o=i.detail}catch(i){o=i instanceof L?i.message:String(i)}await eu(r)}return{status:"timeout",detail:o}}Ba.command("revalidate").description("Re-run BIDS validation on main HEAD for unprotected datasets, then optionally enforce (epic #713)").argument("[dataset-id]","Dataset to revalidate (omit when using --all/--prefix)").option("--all","Revalidate across unprotected public datasets").option("--prefix <prefix>","Filter by id prefix (with --all), e.g. nm000 / on").option("--enforce","After a dataset goes green, run enforce (dry-run unless --apply)").option("--apply","With --enforce, actually apply the ruleset (default is a dry run)").option("--force","Override the live-dataset guard (nm000103-107)").option("--limit <n>","Max repos for --all/--prefix (default 25)","25").option("--json","Output raw JSON").action(async(e,t)=>{if(!je())console.log(l.red("Error: Not authenticated")),process.exit(1);let r=Boolean(t.all||!e&&t.prefix);if(!e&&!r)console.log(l.red("Error: provide a dataset-id, or --all/--prefix")),process.exit(1);let n;if(e)n=[e];else{let d=D("Fetching dataset list...").start();try{let f=[];for(let p=0;;p+=200){let h=await Ns({limit:200,offset:p});if(f.push(...h.datasets),h.datasets.length<200||f.length>=h.total_count)break}let m=Number.parseInt(t.limit,10)||25;n=RX(f,{prefix:t.prefix}).slice(0,m),d.succeed(`${n.length} target(s) (from ${f.length} datasets)`)}catch(f){Qe(f,d,"Failed to fetch datasets");return}}let o=Boolean(t.enforce),i=Boolean(t.apply),s={revalidated:0,green:0,locked:0,stillRed:0,skipped:0,errors:0},a=[],c=[],u=0;for(let d of n){if(u++,Ri.has(d)&&!t.force){console.log(` [${u}/${n.length}] ${l.dim(`${d}: skip (live; use --force)`)}`),s.skipped++;continue}try{let f=await EJ(d,t.force);if(a.push(f),f.skipped)console.log(` [${u}/${n.length}] ${d}: ${l.dim(`skipped (${f.skipped})`)}`),s.skipped++;else s.revalidated++,c.push(d),console.log(` [${u}/${n.length}] ${d}: ${l.cyan(`revalidating (${f.triggered_by})`)}`)}catch(f){s.errors++,console.log(` [${u}/${n.length}] ${d}: ${l.red(f instanceof L?f.message:String(f))}`)}if(u<n.length)await eu(4000)}if(o&&c.length>0)if(e){let d=c[0],f=D(`Waiting for ${d} validation to land...`).start(),m=await aKe(d,300000,15000);if(m.status!=="green")f.warn(`${d}: not green within 5m \u2014 last: ${m.detail} (real errors or still running)`),s.stillRed++;else if(s.green++,!i)f.succeed(`${d}: green (would lock; pass --apply)`);else{let p=await Nl(d,!1);if(p.result?.steps?.branch_ruleset?.status==="ok")f.succeed(`${d}: LOCKED`),s.locked++;else f.warn(`${d}: enforce ${p.result?.steps?.branch_ruleset?.status??"?"}`)}}else{let d=D("Waiting ~90s for validations to drain...").start();await eu(90000),d.text="Enforcing green datasets...";for(let f of c)try{if((await Nl(f,!0)).result?.steps?.branch_ruleset?.status!=="ok"){s.stillRed++;continue}if(s.green++,i){if((await Nl(f,!1)).result?.steps?.branch_ruleset?.status==="ok")s.locked++}}catch{s.errors++}d.stop()}if(t.json){console.log(JSON.stringify({tally:s,raw:a},null,2));return}console.log(),console.log(l.cyan(`Done: revalidated=${s.revalidated} green=${s.green} locked=${s.locked} still-red=${s.stillRed} skipped=${s.skipped} errors=${s.errors}`))});Ba.command("annex-policy").description("Report, and optionally fix, dataset repos that NEMAR's annex policy does not actually govern (#1374, ADR 0060)").argument("[dataset-id...]","Specific datasets to act on (omit to sweep by prefix)").option("--prefix <prefix>","Dataset id prefix to sweep (default on: the imported fleet)","on").option("--limit <n>","Act on at most this many datasets, in id order").option("--apply","Make the change (default is a read-only report)").option("--include-data","Also move data a repo keeps in git, which uploads to S3").option("--via-aws-cli","With --include-data, move the bytes with this machine's aws CLI").option("--no-push","With --apply, commit locally and push nothing (a rehearsal)").option("--dir <path>","Where clones go while they are being fixed (default: a temp dir)").option("--keep-clones","Do not delete each clone after its dataset is done").option("--concurrency <n>","Parallel GitHub reads during the scan (default 4)","4").option("--json <path>","Write the full report as JSON").option("--force","Include the live datasets (nm000103-107)").option(Pe,Ie).option(He,qe).addHelpText("after",`
572
572
  Two things govern what git-annex takes, and an imported dataset has neither (#1374):
573
573
  upstream's .gitattributes outranks NEMAR's configured expression, and the expression
574
574
  was never written to the git-annex branch at all. The scan reads both from GitHub
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "nemar-cli",
3
- "version": "0.10.10-dev.2983",
3
+ "version": "0.10.10-dev.2984",
4
4
  "description": "CLI for NEMAR (Neuroelectromagnetic Data Archive and Tools Resource) dataset management",
5
5
  "type": "module",
6
6
  "main": "dist/index.js",