nemar-cli 0.10.6-dev.2852 → 0.10.6

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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
@@ -99,18 +99,18 @@ ${t}`,$Se,CSe,kSe=(e,t,r)=>{let n=r===""?"":`with ${r.trim()}() `,o=SSe.bind(nul
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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 Fa(e){let r=wLe[e].map((s)=>iY[s]).filter(Boolean),n=await Promise.all(r.map(async(s)=>{let a=await aY(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:sY(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 iY,wLe,SLe=4000;var jf=O(()=>{vt();iY={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)"}}},wLe={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 uY;var lY=O(()=>{uY={name:"nemar-cli",version:"0.10.6-dev.2852",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 Ei;var qf=O(()=>{lY();Ei=uY.version});import{mkdirSync as kLe,readdirSync as RLe,unlinkSync as ALe,writeFileSync as OLe}from"fs";import{join as hE}from"path";function gY(){Fl=!0}function Pa(){return Fl}function yY(e,t=process.env){return e.includes("--debug")||t.NEMAR_DEBUG==="1"}function Lf(e){hY=e,$r(`Step: ${e}`)}function Bf(){pY=!0}function bY(){return pY}function yE(){mY=!0}function xY(){return mY}function $r(e){if(Fl)process.stderr.write(`[debug] ${e}
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+ `))}var iY,wLe,SLe=4000;var jf=O(()=>{vt();iY={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)"}}},wLe={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 uY;var lY=O(()=>{uY={name:"nemar-cli",version:"0.10.6",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 Ei;var qf=O(()=>{lY();Ei=uY.version});import{mkdirSync as kLe,readdirSync as RLe,unlinkSync as ALe,writeFileSync as OLe}from"fs";import{join as hE}from"path";function gY(){Fl=!0}function Pa(){return Fl}function yY(e,t=process.env){return e.includes("--debug")||t.NEMAR_DEBUG==="1"}function Lf(e){hY=e,$r(`Step: ${e}`)}function Bf(){pY=!0}function bY(){return pY}function yE(){mY=!0}function xY(){return mY}function $r(e){if(Fl)process.stderr.write(`[debug] ${e}
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  [nemar] You can safely remove the old file.`);return}catch(o){console.error(`[nemar] Failed to migrate config from ${n}:`,o,`
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- [nemar] You can manually copy ${n} to ${t}`)}}function Sn(){let e=_E();if(Uf&&$Y===e)return Uf;if(rBe(e),Uf=new A0({projectName:"nemar",configFileMode:wE,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}),$Y=e,!CY.has(e))CY.add(e),nBe(Uf.path),iBe(),sBe();return Uf}function nBe(e){if(process.platform==="win32")return;if(!vE(e))return;try{if((ZLe(e).mode&511)!==wE)YLe(e,wE)}catch(t){console.error(`[nemar] could not secure config file permissions for ${e}:`,t)}}function iBe(){let e=Sn(),t=e.get("accounts");if(t&&Object.keys(t).length>0)return;let r=e.get("apiKey"),n=e.get("username");if(!r&&!n)return;try{let o=n||"default",i={};for(let s of oBe){let a=e.get(s);if(a!==void 0)i[s]=a}e.store={activeAccount:o,accounts:{[o]:i}}}catch(o){console.error("Config migration failed (legacy config preserved):",o)}}function sBe(){let e=Sn(),t=e.store,r=t.accounts,n=!1;if(r)for(let[i,s]of Object.entries(r)){let a=s?.apiUrl;if(!a)continue;if(QLe.has(eBe(a)))r[i]={...s,apiUrl:Il},console.error(`[nemar] migrated stored apiUrl for account "${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: ${o})`),n=!1}catch(a){console.error("API URL cleanup failed (config file unchanged):",a)}}if(n)try{e.store={...e.store,accounts:r}}catch(i){console.error("API URL migration failed (config file unchanged):",i)}}function zf(){return Sn().get("activeAccount")}function Is(){return Sn().get("accounts")||{}}function ot(){let e={apiUrl:Il},t=zf();if(!t)return e;return Is()[t]||e}function wt(e,t){let r=Sn(),n=r.get("activeAccount")||"default",o=r.get("accounts")||{};if(!o[n])o[n]={apiUrl:Il};o[n][e]=t,r.store={...r.store,accounts:o,activeAccount:n}}function Vf(e){let t=zf();if(!t)return;let r=Is();if(r[t])delete r[t][e],Sn().set("accounts",r)}function kY(){let e=Sn(),t=zf();if(!t){e.clear();return}let r=Is();delete r[t];let n=Object.keys(r);if(n.length>0)e.store={...e.store,accounts:r,activeAccount:n[0]};else e.clear()}function RY(){Sn().clear()}function Ne(){return!!ot().apiKey}function DE(){return Sn().path}function Gf(){let e=Is(),t=zf();return Object.entries(e).map(([r,n])=>({key:r,username:n.username,email:n.email,githubUsername:n.githubUsername,active:r===t,keySource:n.keySource}))}function AY(e){return e.username?.trim()||e.email}function aBe(e){let t=e.trim().toLowerCase();if(!t)return;let r=Object.entries(Is()).filter(([,n])=>n.email&&n.email.toLowerCase()===t).map(([n])=>n);if(r.length>1){$r(`findAccountKeyByEmail: ${r.length} accounts share email ${t}: ${r.join(", ")}`);return}return r[0]}function OY(e,t){let r=Sn(),n=Is(),o;if(n[e])o=e;else if(t.email)o=aBe(t.email);let i=o?n[o]:void 0,s={...i??{apiUrl:Il},...t};if(o&&o!==e)delete n[o];return n[e]=s,r.store={...r.store,accounts:n,activeAccount:e},{key:e,previous:i}}function FY(e){let t=e.trim();if(!t)return"unchanged";let r=Sn(),n=zf();if(!n||n===t)return"unchanged";let o=Is(),i=o[n];if(!i)return"unchanged";if(o[t])return"key_taken";return delete o[n],o[t]={...i,username:t},r.store={...r.store,accounts:o,activeAccount:t},"renamed"}function EE(e){let t=Sn(),r=Is();if(r[e])return t.store={...t.store,activeAccount:e},r[e];for(let[n,o]of Object.entries(r))if(o.githubUsername===e)return t.store={...t.store,activeAccount:n},o;return null}var Il="https://nemar-api-dev.sccn-org.workers.dev",wE=384,QLe,tBe,Jmt,Uf=null,$Y=null,CY,oBe;var qo=O(()=>{nY();en();Cd();jo();QLe=new Set(["https://api.osc.earth/nemar","https://nemar-api.neuromechanist.workers.dev","https://nemar-api-dev.shirazi-10f.workers.dev"]);tBe=U({field:w(),blocks:re(w()).optional(),set_on:re(w()).optional()}).passthrough(),Jmt=U({apiKey:w().optional(),apiUrl:w().url().default(Il),username:w().optional(),email:w().email().optional(),githubUsername:w().optional(),sandboxCompleted:ge().optional(),sandboxDatasetId:w().optional(),dismissedNoticeIds:re(k()).optional(),serviceAccess:ge().optional(),profileGaps:re(tBe).optional(),orcidVerified:ge().optional(),role:w().optional(),accountKind:$d.optional(),pendingEmailChange:w().email().optional()});CY=new Set;oBe=["apiKey","apiUrl","username","email","githubUsername","sandboxCompleted","sandboxDatasetId","dismissedNoticeIds"]});function T0(e){if(PY)return;PY=!0;let t=l.yellow("\u2500".repeat(60)),r=l.yellow.bold("[MAINTENANCE]"),n=l.dim(`mode: ${e.mode}`),o=e.eta?`
108
+ [nemar] You can manually copy ${n} to ${t}`)}}function Sn(){let e=_E();if(Uf&&$Y===e)return Uf;if(rBe(e),Uf=new A0({projectName:"nemar",configFileMode:wE,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}),$Y=e,!CY.has(e))CY.add(e),nBe(Uf.path),iBe(),sBe();return Uf}function nBe(e){if(process.platform==="win32")return;if(!vE(e))return;try{if((ZLe(e).mode&511)!==wE)YLe(e,wE)}catch(t){console.error(`[nemar] could not secure config file permissions for ${e}:`,t)}}function iBe(){let e=Sn(),t=e.get("accounts");if(t&&Object.keys(t).length>0)return;let r=e.get("apiKey"),n=e.get("username");if(!r&&!n)return;try{let o=n||"default",i={};for(let s of oBe){let a=e.get(s);if(a!==void 0)i[s]=a}e.store={activeAccount:o,accounts:{[o]:i}}}catch(o){console.error("Config migration failed (legacy config preserved):",o)}}function sBe(){let e=Sn(),t=e.store,r=t.accounts,n=!1;if(r)for(let[i,s]of Object.entries(r)){let a=s?.apiUrl;if(!a)continue;if(QLe.has(eBe(a)))r[i]={...s,apiUrl:Il},console.error(`[nemar] migrated stored apiUrl for account "${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: ${o})`),n=!1}catch(a){console.error("API URL cleanup failed (config file unchanged):",a)}}if(n)try{e.store={...e.store,accounts:r}}catch(i){console.error("API URL migration failed (config file unchanged):",i)}}function zf(){return Sn().get("activeAccount")}function Is(){return Sn().get("accounts")||{}}function ot(){let e={apiUrl:Il},t=zf();if(!t)return e;return Is()[t]||e}function wt(e,t){let r=Sn(),n=r.get("activeAccount")||"default",o=r.get("accounts")||{};if(!o[n])o[n]={apiUrl:Il};o[n][e]=t,r.store={...r.store,accounts:o,activeAccount:n}}function Vf(e){let t=zf();if(!t)return;let r=Is();if(r[t])delete r[t][e],Sn().set("accounts",r)}function kY(){let e=Sn(),t=zf();if(!t){e.clear();return}let r=Is();delete r[t];let n=Object.keys(r);if(n.length>0)e.store={...e.store,accounts:r,activeAccount:n[0]};else e.clear()}function RY(){Sn().clear()}function Ne(){return!!ot().apiKey}function DE(){return Sn().path}function Gf(){let e=Is(),t=zf();return Object.entries(e).map(([r,n])=>({key:r,username:n.username,email:n.email,githubUsername:n.githubUsername,active:r===t,keySource:n.keySource}))}function AY(e){return e.username?.trim()||e.email}function aBe(e){let t=e.trim().toLowerCase();if(!t)return;let r=Object.entries(Is()).filter(([,n])=>n.email&&n.email.toLowerCase()===t).map(([n])=>n);if(r.length>1){$r(`findAccountKeyByEmail: ${r.length} accounts share email ${t}: ${r.join(", ")}`);return}return r[0]}function OY(e,t){let r=Sn(),n=Is(),o;if(n[e])o=e;else if(t.email)o=aBe(t.email);let i=o?n[o]:void 0,s={...i??{apiUrl:Il},...t};if(o&&o!==e)delete n[o];return n[e]=s,r.store={...r.store,accounts:n,activeAccount:e},{key:e,previous:i}}function FY(e){let t=e.trim();if(!t)return"unchanged";let r=Sn(),n=zf();if(!n||n===t)return"unchanged";let o=Is(),i=o[n];if(!i)return"unchanged";if(o[t])return"key_taken";return delete o[n],o[t]={...i,username:t},r.store={...r.store,accounts:o,activeAccount:t},"renamed"}function EE(e){let t=Sn(),r=Is();if(r[e])return t.store={...t.store,activeAccount:e},r[e];for(let[n,o]of Object.entries(r))if(o.githubUsername===e)return t.store={...t.store,activeAccount:n},o;return null}var Il="https://api.nemar.org",wE=384,QLe,tBe,Jmt,Uf=null,$Y=null,CY,oBe;var qo=O(()=>{nY();en();Cd();jo();QLe=new Set(["https://api.osc.earth/nemar","https://nemar-api.neuromechanist.workers.dev","https://nemar-api-dev.shirazi-10f.workers.dev"]);tBe=U({field:w(),blocks:re(w()).optional(),set_on:re(w()).optional()}).passthrough(),Jmt=U({apiKey:w().optional(),apiUrl:w().url().default(Il),username:w().optional(),email:w().email().optional(),githubUsername:w().optional(),sandboxCompleted:ge().optional(),sandboxDatasetId:w().optional(),dismissedNoticeIds:re(k()).optional(),serviceAccess:ge().optional(),profileGaps:re(tBe).optional(),orcidVerified:ge().optional(),role:w().optional(),accountKind:$d.optional(),pendingEmailChange:w().email().optional()});CY=new Set;oBe=["apiKey","apiUrl","username","email","githubUsername","sandboxCompleted","sandboxDatasetId","dismissedNoticeIds"]});function T0(e){if(PY)return;PY=!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 PY=!1;var SE=O(()=>{Xe()});function N0(){if(process.env.TEST_API_URL)return process.env.TEST_API_URL;if(CE)return $E;return ot().apiUrl||$E}async function F(e,t={},r=!1,n){let o=`${N0()}${e}`,i={"Content-Type":"application/json","X-CLI-Version":Ei,...t.headers};if(r){let m=ot();if(!m.apiKey&&r===!0)throw new q(401,"Not authenticated. 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TE(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 NE(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 EJ(){return F("/admin/zarr-catalog/publish",{method:"POST"},!0)}async function SJ(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 $J(e){let t=new URLSearchParams;if(e?.limit!=null)t.set("limit",String(e.limit));if(e?.apply)t.set("apply","1");let r=t.toString()?`?${t.toString()}`:"";return F(`/admin/imports/issue-triage${r}`,{method:"POST",headers:{"Content-Type":"application/json"}},!0)}async function CJ(e){let t=e?.apply?"?apply=1":"";return F(`/admin/imports/coverage-sweep${t}`,{method:"POST",headers:{"Content-Type":"application/json"}},!0)}async function kJ(e){let t=e?.apply?"?apply=1":"";return F(`/admin/imports/weekly-summary${t}`,{method:"POST",headers:{"Content-Type":"application/json"}},!0)}async function RJ(e){return F("/admin/users/backfill-names",{method:"POST",headers:{"Content-Type":"application/json"},body:JSON.stringify({apply:e?.apply??!1,...e?.limit!=null?{limit:e.limit}:{}})},!0)}async function AJ(e){return F("/admin/users/backfill-usernames",{method:"POST",headers:{"Content-Type":"application/json"},body:JSON.stringify({apply:e?.apply??!1,...e?.limit!=null?{limit:e.limit}:{}})},!0)}async function OJ(){return F("/admin/users/duplicates",{},!0,jq)}async function FJ(e){return F(`/admin/users/${e}/clear-identity-conflict`,{method:"POST"},!0,qq)}async function PJ(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 IJ(){return F("/admin/datasets/anonymity-sweep?reset=1",{method:"POST",headers:{"Content-Type":"application/json"}},!0)}var jl=O(()=>{sl();Si()});async function dr(e,t){return F(`/datasets/${e}/upload-credentials`,{method:"POST",body:JSON.stringify({duration_seconds:t})},!0)}async function jE(e,t){return F(`/datasets/${e}/download-credentials`,{method:"POST",body:JSON.stringify({duration_seconds:t})},!0)}async function TJ(e){return F(`/admin/datasets/${e}/files`,{},!0)}async function NJ(e){let t,r=0,n=[],o=!0;while(o){let i=await F(`/admin/datasets/${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 q(500,"S3 lock paginated response missing continuation_token; aborting to avoid infinite loop")}return{locked:r,failed:n}}var Ci=O(()=>{Si();Pt()});async function M0(e){return F(`/datasets/${e}/ci/status`,{},!0)}async function jJ(e){return F(`/datasets/${e}/manifest`,{},!0)}async function L0(e,t){return F(`/datasets/${e}/manifest/${t}`,{},!0)}function qJ(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: ${t.visibility}`);return t}async function Ts(e={}){let t=new URLSearchParams;if(e.mine)t.set("mine","true");if(e.search)t.set("search",e.search);if(e.modality)t.set("modality",e.modality);if(e.author)t.set("author",e.author);if(e.task)t.set("task",e.task);if(e.license)t.set("license",e.license);if(e.hasDoi)t.set("has_doi","true");if(e.hasHed)t.set("has_hed","1");if(e.hasZarr)t.set("has_zarr","1");if(e.hasZarrVerified)t.set("has_zarr_verified","1");if(e.dataComplete)t.set("data_complete","1");if(e.recent)t.set("recent",String(e.recent));if(e.sort)t.set("sort",e.sort);if(e.limit!=null)t.set("limit",String(e.limit));if(e.offset!=null)t.set("offset",String(e.offset));if(e.owner)t.set("owner",e.owner);if(e.facets)for(let[o,i]of Object.entries(e.facets))t.set(o,i);if(e.includeUnknown)t.set("include_unknown","1");let r=t.toString()?`?${t.toString()}`:"",n=await F(`/datasets${r}`,{},e.mine?!0:"optional");return n.datasets=n.datasets.map(qJ),n}async function MJ(e){return F(`/datasets/resolve/${e}`,{},"optional")}async function LJ(){return F("/datasets/facets",{signal:AbortSignal.timeout(5000)},"optional",Th)}async function BJ(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?${r.toString()}`,{},"optional",Iq)}async function It(e){let t=await F(`/datasets/${e}`,{},"optional");return qJ(t.dataset)}async function UJ(e){return F(`/datasets/${e}/versions`,{},!0)}async function B0(e){return F("/datasets",{method:"POST",body:JSON.stringify(e)},!0)}async function U0(e){return F(`/datasets/${e}/finalize`,{method:"POST"},!0)}async function qE(e){return F(`/datasets/${e}/request-access`,{method:"POST"},!0)}async function zJ(e,t){let r=t?`?status=${t}`:"";return F(`/datasets/${e}/access-requests${r}`,{},!0)}async function VJ(e,t){return F(`/datasets/${e}/access-requests/${t}/approve`,{method:"POST"},!0)}async function GJ(e,t){return F(`/datasets/${e}/access-requests/${t}/deny`,{method:"POST"},!0)}async function HJ(e,t){return F(`/datasets/${e}/invite`,{method:"POST",body:JSON.stringify({username:t})},!0)}async function WJ(e){return F(`/datasets/${e}/collaborators`,{},!0)}async function KJ(e,t){return F(`/admin/datasets/${e}/enrichment`,{method:"POST",body:JSON.stringify(t)},!0)}var q0;var Ns=O(()=>{sl();Si();q0=/^\d{4}-\d{4}-\d{4}-\d{3}[\dX]$/});async function ql(e,t={}){return F(`/datasets/${e}/publish/request`,t.anonymous?{method:"POST",headers:{"Content-Type":"application/json"},body:JSON.stringify({anonymous:!0})}:{method:"POST"},!0)}async function z0(e){return F(`/datasets/${e}/publish/status`,{},!0)}async function eX(e){return F(`/datasets/${e}/publish/resend`,{method:"POST"},!0)}async function tX(e){let t=e?`?status=${e}`:"";return F(`/admin/publish/requests${t}`,{},!0)}async function rX(e,t){return F(`/admin/publish/${e}/deny`,{method:"POST",headers:{"Content-Type":"application/json"},body:JSON.stringify({reason:t})},!0)}function cBe(e,t=[]){if(e){let r=bs.indexOf(e);if(r>=0)return r+1}return Math.min(t.length+1,bs.length)}function lBe(e){if(!(e instanceof q))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=[],y;function x(b,v,S,A){if(!i)return;i({step:b,stepIndex:cBe(b,v),stepTotal:bs.length,s3LockLocked:S,s3LockTotal:A,s3LockResumed:b==="s3_lock"&&f?!0:void 0})}for(let b=1;b<=5;b++)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 A=v.step??v.step_results?.[v.step_results.length-1]?.step;if(A&&(A!==m||A==="s3_lock"))x(A,v.steps_completed??[],A==="s3_lock"?d:void 0,A==="s3_lock"?u:void 0),m=A;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=QJ(h);return v}catch(v){if(y=v,b===5||!lBe(v)){if(v instanceof q&&h.length>0)v.stepResults=QJ(h);throw v}let A=v;if(o?.({attempt:b,maxAttempts:5,delayMs:1e4,step:A.step,error:A.message}),await new Promise((E)=>setTimeout(E,1e4)),p=!0,c!==void 0)f=!0}throw y}function QJ(e){let t=new Map;for(let r of e)t.set(r.step,r);return Array.from(t.values())}var Wf=O(()=>{Yh();Si();Pt()});function EX(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"&&!ki.has(r)).filter((r)=>t.prefix?r.startsWith(t.prefix):!0).sort()}var ki;var W0=O(()=>{ki=new Set(["nm000103","nm000104","nm000105","nm000106","nm000107"])});async function hBe(){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 Ia(){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 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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=${o}'`],{cwd:e})}else if(t.startsWith("git@github.com:")){let o=t.replace("git@github.com:",""),i=await Ia();if(i.token)n=`https://github.com/${o}`,await C(["git","config","credential.https://github.com.helper",`!printf 'username=x-access-token\\npassword=${i.token}'`],{cwd:e});else{let s=await hBe();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"}
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "nemar-cli",
3
- "version": "0.10.6-dev.2852",
3
+ "version": "0.10.6",
4
4
  "description": "CLI for NEMAR (Neuroelectromagnetic Data Archive and Tools Resource) dataset management",
5
5
  "type": "module",
6
6
  "main": "dist/index.js",