nemar-cli 0.8.50-dev.1362 → 0.8.50-dev.1363

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (2) hide show
  1. package/dist/index.js +1 -1
  2. package/package.json +1 -1
package/dist/index.js CHANGED
@@ -95,7 +95,7 @@ ${W.dim(`eta: ${D.eta}`)}`:"";process.stderr.write(`${F}
95
95
  ${$} ${D.message}
96
96
  ${J}${Q}
97
97
  ${F}
98
- `)}var Pf=!1;var SW=P(()=>{jD()});var Sf;var If=P(()=>{Sf={name:"nemar-cli",version:"0.8.50-dev.1362",description:"CLI for NEMAR (Neuroelectromagnetic Data Archive and Tools Resource) dataset management",type:"module",main:"dist/index.js",bin:{nemar:"dist/index.js"},scripts:{dev:"bun run src/index.ts",build:"bun build src/index.ts --outdir dist --target bun --minify && sed '1s|#!/usr/bin/env node|#!/usr/bin/env bun|' dist/index.js > dist/index.js.tmp && mv dist/index.js.tmp dist/index.js",test:"bun test",lint:"biome check src/","lint:fix":"biome check --fix src/",format:"biome format --write src/",typecheck:"tsc --noEmit",prepublishOnly:"bun run build",prepare:"husky",postinstall:"bun scripts/postinstall-check.mjs",deploy:"wrangler deploy",preview:"wrangler dev"},keywords:["nemar","bids","neuroimaging","eeg","emg","datalad","cli"],author:"NEMAR Team",license:"CC-BY-NC-ND-4.0",repository:{type:"git",url:"git+https://github.com/nemarOrg/nemar-cli.git"},bugs:{url:"https://github.com/nemarOrg/nemar-cli/issues"},homepage:"https://docs.nemar.org",engines:{bun:">=1.0.0"},files:["dist","scripts/postinstall-check.mjs","README.md","LICENSE"],dependencies:{chalk:"^5.3.0",commander:"^12.1.0",conf:"^13.0.1","fuse.js":"^7.1.0",inquirer:"^9.2.15",ora:"^8.0.1",zod:"^3.23.8"},"lint-staged":{"src/**/*.{ts,tsx}":["biome check --fix"],"backend/src/**/*.{ts,tsx}":["biome check --fix"]},devDependencies:{"@biomejs/biome":"1.9.4","@types/bcryptjs":"^3.0.0","@types/bun":"latest","@types/inquirer":"^9.0.7",bcryptjs:"^3.0.3",husky:"^9.1.7","lint-staged":"^16.3.2",typescript:"^5.5.4",wrangler:"^4.70.0",yaml:"^2.8.4"}}});var g4;var DQ=P(()=>{If();g4=Sf.version});function C0(D){if(D instanceof Error)return D.message;return String(D)}function kf(){if(process.env.TEST_API_URL)return process.env.TEST_API_URL;if(vW)return kW;return BD().apiUrl||kW}async function x(D,F={},$=!1){let J=`${kf()}${D}`,Q={"Content-Type":"application/json","X-CLI-Version":g4,...F.headers};if($){let X=BD();if(!X.apiKey&&$===!0)throw new h(401,"Not authenticated. Run 'nemar auth login' first.");if(X.apiKey)Q.Authorization=`Bearer ${X.apiKey}`}let Y;try{Y=await fetch(J,{...F,headers:Q})}catch(X){throw new h(0,`Network error: Could not connect to ${kf()}`,{originalError:X instanceof Error?X.message:String(X)})}let B;try{B=await Y.json()}catch{throw new h(Y.status,`Invalid response from server (status ${Y.status})`)}if(!Y.ok){if(Y.status===503&&(B.mode==="read-only"||B.mode==="full")){let X=typeof B.message==="string"?B.message:"NEMAR is in maintenance mode. Please retry shortly.",G=typeof B.eta==="string"?B.eta:null,H=new $Q(B.mode,X,G,B.details);throw eJ(H),H}throw new h(Y.status,B.error||B.message||"Request failed",B.details,typeof B.step==="string"?B.step:void 0)}return B}async function yf(D){return x(`/auth/check-username?username=${encodeURIComponent(D)}`)}async function xf(D){return x(`/auth/check-github?username=${encodeURIComponent(D)}`)}async function _f(D){return x("/auth/signup",{method:"POST",body:JSON.stringify(D)})}async function ff(D){return x("/auth/login",{method:"POST",body:JSON.stringify({api_key:D})})}async function gf(D){return x("/auth/resend-verification",{method:"POST",body:JSON.stringify({email:D})})}async function hf(D,F){return x("/auth/retrieve-key",{method:"POST",body:JSON.stringify({email:D,password:F})})}async function bf(D){return x("/auth/request-key-regeneration",{method:"POST",body:JSON.stringify({email:D})})}async function JQ(){return x("/users/me",{},!0)}async function uf(D,F){let $=new URLSearchParams;if(D)$.set("status",D);if(F)$.set("role",F);let J=$.toString()?`?${$.toString()}`:"";return x(`/admin/users${J}`,{},!0)}async function mf(D){return x(`/admin/approve/${D}`,{method:"POST"},!0)}async function lf(D){return x(`/admin/revoke/${D}`,{method:"POST"},!0)}async function pf(D,F){return x(`/admin/users/${D}/role`,{method:"POST",body:JSON.stringify({role:F})},!0)}async function yW(D,F){return x(`/admin/datasets/${D}/visibility`,{method:"PATCH",body:JSON.stringify({visibility:F})},!0)}async function df(D){return x(`/datasets/${D}/publish`,{method:"POST"},!0)}async function cf(D){return x(`/admin/datasets/${D}/ci`,{},!0)}async function h4(D){return x(`/admin/datasets/${D}/ci`,{method:"POST"},!0)}async function xW(D){return x(`/admin/datasets/${D}/ci/validate`,{method:"POST"},!0)}async function _W(D){return x(`/admin/datasets/${D}/ci/sync`,{method:"POST"},!0)}async function QQ(D){return x(`/datasets/${D}/ci/status`,{},!0)}async function nf(D){return x(`/datasets/${D}/manifest`,{},!0)}async function YQ(D,F){return x(`/datasets/${D}/manifest/${F}`,{},!0)}function af(D){let F=D;if(!F.status)F.status="active";else if(!["active","archived","deleted"].includes(F.status))throw Error(`Invalid dataset status: ${F.status}`);if(!F.visibility)F.visibility="private";else if(!["public","private"].includes(F.visibility))throw Error(`Invalid dataset visibility: ${F.visibility}`);return F}async function y9(D={}){let F=new URLSearchParams;if(D.mine)F.set("mine","true");if(D.search)F.set("search",D.search);if(D.modality)F.set("modality",D.modality);if(D.author)F.set("author",D.author);if(D.task)F.set("task",D.task);if(D.license)F.set("license",D.license);if(D.hasDoi)F.set("has_doi","true");if(D.recent)F.set("recent",String(D.recent));if(D.sort)F.set("sort",D.sort);if(D.limit!=null)F.set("limit",String(D.limit));if(D.offset!=null)F.set("offset",String(D.offset));if(D.owner)F.set("owner",D.owner);let $=F.toString()?`?${F.toString()}`:"",J=await x(`/datasets${$}`,{},D.mine?!0:"optional");return J.datasets=J.datasets.map(af),J}async function of(D){return x(`/datasets/resolve/${D}`,{},"optional")}async function sf(D,F={}){let $=new URLSearchParams({q:D});if(F.modality)$.set("modality",F.modality);if(F.limit)$.set("limit",String(F.limit));return x(`/datasets/search?${$.toString()}`,{},"optional")}async function uD(D){let F=await x(`/datasets/${D}`,{},"optional");return af(F.dataset)}async function rf(D){return x(`/datasets/${D}/versions`,{},!0)}async function BQ(D){return x("/datasets",{method:"POST",body:JSON.stringify(D)},!0)}async function XQ(D){return x(`/datasets/${D}/finalize`,{method:"POST"},!0)}async function o8(D,F){return x(`/datasets/${D}/upload-credentials`,{method:"POST",body:JSON.stringify({duration_seconds:F})},!0)}async function GQ(D,F){return x(`/datasets/${D}/download-credentials`,{method:"POST",body:JSON.stringify({duration_seconds:F})},!0)}async function tf(D,F){return x(`/admin/datasets/${D}/doi/concept`,{method:"POST",body:JSON.stringify(F)},!0)}async function x9(D){return x(`/admin/datasets/${D}/doi`,{},!0)}async function fW(D,F){return x(`/admin/datasets/${D}/doi/update`,{method:"POST",body:JSON.stringify(F)},!0)}async function gW(D){return x(`/datasets/${D}/request-access`,{method:"POST"},!0)}async function ef(D,F){let $=F?`?status=${F}`:"";return x(`/datasets/${D}/access-requests${$}`,{},!0)}async function Dg(D,F){return x(`/datasets/${D}/access-requests/${F}/approve`,{method:"POST"},!0)}async function Fg(D,F){return x(`/datasets/${D}/access-requests/${F}/deny`,{method:"POST"},!0)}async function $g(D,F){return x(`/datasets/${D}/invite`,{method:"POST",body:JSON.stringify({username:F})},!0)}async function Jg(D){return x(`/datasets/${D}/collaborators`,{},!0)}async function Qg(D){return x("/sandbox/complete",{method:"POST",body:JSON.stringify({dataset_id:D})},!0)}async function Yg(){return x("/sandbox/reset",{method:"POST"},!0)}async function Bg(){return x("/sandbox/status",{},!0)}async function WQ(D){return x(`/datasets/${D}/publish/request`,{method:"POST"},!0)}async function Xg(D){return x(`/datasets/${D}/publish/status`,{},!0)}async function Gg(D){return x(`/datasets/${D}/publish/resend`,{method:"POST"},!0)}async function Wg(D){let F=D?`?status=${D}`:"";return x(`/admin/publish/requests${F}`,{},!0)}async function Hg(D,F){return x(`/admin/publish/${D}/deny`,{method:"POST",headers:{"Content-Type":"application/json"},body:JSON.stringify({reason:F})},!0)}function kE0(D,F=[]){if(D){let $=v9.indexOf(D);if($>=0)return $+1}return Math.min(F.length+1,v9.length)}function vE0(D){if(!(D instanceof h))return!1;if(D.statusCode===0)return!0;if(D.statusCode===429)return!0;if(D.statusCode>=500&&D.statusCode<600)return!0;if(D.statusCode===403&&/repository has been locked/i.test(D.message))return!0;return!1}async function HQ(D,F=!1,$=!1,J=!1,Q,Y){let G,H,q=0,K=!1,V,E=F,Z=[],L;function M(A,N,j,S){if(!Y)return;Y({step:A,stepIndex:kE0(A,N),stepTotal:v9.length,s3LockLocked:j,s3LockTotal:S,s3LockResumed:A==="s3_lock"&&K?!0:void 0})}for(let A=1;A<=5;A++)try{let N,j=!0;do{if(N=await x(`/admin/publish/${D}/approve`,{method:"POST",headers:{"Content-Type":"application/json"},body:JSON.stringify({resume:j?E:!0,sandbox:$,s3_lock_continuation_token:G,s3_lock_total:H,skip_ci_check:J})},!0),j=!1,N.step_results)Z.push(...N.step_results);if(N.s3_lock_total!==void 0)H=N.s3_lock_total;if(N.s3_lock_batch_count!==void 0)q+=N.s3_lock_batch_count;let S=N.step??N.step_results?.[N.step_results.length-1]?.step;if(S&&(S!==V||S==="s3_lock"))M(S,N.steps_completed??[],S==="s3_lock"?q:void 0,S==="s3_lock"?H:void 0),V=S;if(N.hasMore&&N.s3_lock_continuation_token!==void 0)G=N.s3_lock_continuation_token;else break}while(N.hasMore);if(Z.length>0)N.step_results=vf(Z);return N}catch(N){if(L=N,A===5||!vE0(N)){if(N instanceof h&&Z.length>0)N.stepResults=vf(Z);throw N}let S=N;if(Q?.({attempt:A,maxAttempts:5,delayMs:1e4,step:S.step,error:S.message}),await new Promise((O)=>setTimeout(O,1e4)),E=!0,G!==void 0)K=!0}throw L}function vf(D){let F=new Map;for(let $ of D)F.set($.step,$);return Array.from(F.values())}async function qg(D,F){return x(`/admin/datasets/${D}/enrichment`,{method:"POST",body:JSON.stringify(F)},!0)}async function Kg(D){return x(`/admin/datasets/${D}/files`,{},!0)}async function zg(D){let F,$=0,J=[],Q=!0;while(Q){let Y=await x(`/admin/datasets/${D}/s3-lock`,{method:"POST",headers:{"Content-Type":"application/json"},body:JSON.stringify({continuation_token:F})},!0);if($+=Y.locked,Y.failed?.length)J.push(...Y.failed);if(Q=Y.hasMore,F=Y.continuation_token,Q&&!F)throw new h(500,"S3 lock paginated response missing continuation_token; aborting to avoid infinite loop")}return{locked:$,failed:J}}async function Eg(D){return x(`/admin/datasets/${D}/reset`,{method:"POST"},!0)}async function Vg(D,F=!1){return x(`/admin/datasets/${D}`,{method:"DELETE",headers:{"Content-Type":"application/json"},body:JSON.stringify({force:F})},!0)}async function Zg(D){return x("/admin/datasets/bulk-delete",{method:"POST",headers:{"Content-Type":"application/json"},body:JSON.stringify({dataset_ids:D})},!0)}async function Ug(D){return x("/admin/datasets/import",{method:"POST",body:JSON.stringify(D)},!0)}async function Lg(D){return x(`/admin/datasets/${D}/sync`,{method:"POST"},!0)}async function Ag(){return x("/admin/sync/status",{},!0)}async function qQ(D,F){return x(`/admin/datasets/${D}/reindex`,{method:"POST",headers:{"Content-Type":"application/json"},body:JSON.stringify(F??{})},!0)}async function Mg(D,F){return x("/admin/datasets/reindex/bulk",{method:"POST",headers:{"Content-Type":"application/json"},body:JSON.stringify({filter:D,...F??{}})},!0)}async function Ng(D){let F=new URLSearchParams;if(D?.prefix)F.set("prefix",D.prefix);if(D?.visibility)F.set("visibility",D.visibility);if(D?.limit)F.set("limit",String(D.limit));let $=F.toString()?`?${F.toString()}`:"";return x(`/admin/fleet/drift${$}`,{},!0)}async function Rg(D,F){return x(`/admin/datasets/${D}/enforce`,{method:"POST",body:JSON.stringify({dry_run:F})},!0)}async function Cg(D){return x("/admin/datasets/enforce/bulk",{method:"POST",body:JSON.stringify({prefix:D.prefix,visibility:D.visibility,limit:D.limit,dry_run:D.dryRun})},!0)}async function Og(){return x("/admin/email-preferences",{},!0)}async function jg(D){return x("/admin/email-preferences",{method:"PUT",headers:{"Content-Type":"application/json"},body:JSON.stringify(D)},!0)}async function wg(){return x("/notices",{},"optional")}async function Tg(){return x("/admin/notices",{},!0)}async function Pg(D){return x("/admin/notices",{method:"POST",body:JSON.stringify(D)},!0)}async function Ig(D){return x(`/admin/notices/${D}`,{method:"DELETE"},!0)}async function hW(D){return x("/admin/notify",{method:"POST",body:JSON.stringify(D)},!0)}async function Sg(){return x("/admin/summary/coverage",{},!0)}async function kg(D,F,$){return x("/admin/manifest/dispatch",{method:"POST",body:JSON.stringify({dataset_id:D,version:F,skip_canary:$?.skipCanary??!1})},!0)}var kW="https://nemar-api-dev.sccn-org.workers.dev",FQ,h,$Q,vW,v9;var s8=P(()=>{f4();SW();DQ();FQ=/^\d{4}-\d{4}-\d{4}-\d{3}[\dX]$/;h=class h extends Error{statusCode;details;step;constructor(D,F,$,J){super(F);this.statusCode=D;this.details=$;this.step=J;this.name="ApiError"}};$Q=class $Q extends h{mode;eta;constructor(D,F,$,J){super(503,F,J);this.mode=D;this.eta=$;this.name="MaintenanceError"}};vW=kW.includes("workers.dev");v9=["ci_check","enrichment_check","repo_public","s3_public_read","tag_protect","doi_create","update_metadata","update_readme","create_tag","create_release","upload_to_zenodo","publish_doi","version_doi","s3_lock","sync_nemar","notify_user"]});function yg(D){bW=D}function uW(){return bW}function _9(D){if(bW)process.stderr.write(`${D}
98
+ `)}var Pf=!1;var SW=P(()=>{jD()});var Sf;var If=P(()=>{Sf={name:"nemar-cli",version:"0.8.50-dev.1363",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/","lint:fix":"biome check --fix src/",format:"biome format --write src/",typecheck:"tsc --noEmit",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","README.md","LICENSE"],dependencies:{chalk:"^5.3.0",commander:"^12.1.0",conf:"^13.0.1","fuse.js":"^7.1.0",inquirer:"^9.2.15",ora:"^8.0.1",zod:"^3.23.8"},"lint-staged":{"src/**/*.{ts,tsx}":["biome check --fix"],"backend/src/**/*.{ts,tsx}":["biome check --fix"]},devDependencies:{"@biomejs/biome":"1.9.4","@types/bcryptjs":"^3.0.0","@types/bun":"latest","@types/inquirer":"^9.0.7",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 g4;var DQ=P(()=>{If();g4=Sf.version});function C0(D){if(D instanceof Error)return D.message;return String(D)}function kf(){if(process.env.TEST_API_URL)return process.env.TEST_API_URL;if(vW)return kW;return BD().apiUrl||kW}async function x(D,F={},$=!1){let J=`${kf()}${D}`,Q={"Content-Type":"application/json","X-CLI-Version":g4,...F.headers};if($){let X=BD();if(!X.apiKey&&$===!0)throw new h(401,"Not authenticated. Run 'nemar auth login' first.");if(X.apiKey)Q.Authorization=`Bearer ${X.apiKey}`}let Y;try{Y=await fetch(J,{...F,headers:Q})}catch(X){throw new h(0,`Network error: Could not connect to ${kf()}`,{originalError:X instanceof Error?X.message:String(X)})}let B;try{B=await Y.json()}catch{throw new h(Y.status,`Invalid response from server (status ${Y.status})`)}if(!Y.ok){if(Y.status===503&&(B.mode==="read-only"||B.mode==="full")){let X=typeof B.message==="string"?B.message:"NEMAR is in maintenance mode. Please retry shortly.",G=typeof B.eta==="string"?B.eta:null,H=new $Q(B.mode,X,G,B.details);throw eJ(H),H}throw new h(Y.status,B.error||B.message||"Request failed",B.details,typeof B.step==="string"?B.step:void 0)}return B}async function yf(D){return x(`/auth/check-username?username=${encodeURIComponent(D)}`)}async function xf(D){return x(`/auth/check-github?username=${encodeURIComponent(D)}`)}async function _f(D){return x("/auth/signup",{method:"POST",body:JSON.stringify(D)})}async function ff(D){return x("/auth/login",{method:"POST",body:JSON.stringify({api_key:D})})}async function gf(D){return x("/auth/resend-verification",{method:"POST",body:JSON.stringify({email:D})})}async function hf(D,F){return x("/auth/retrieve-key",{method:"POST",body:JSON.stringify({email:D,password:F})})}async function bf(D){return x("/auth/request-key-regeneration",{method:"POST",body:JSON.stringify({email:D})})}async function JQ(){return x("/users/me",{},!0)}async function uf(D,F){let $=new URLSearchParams;if(D)$.set("status",D);if(F)$.set("role",F);let J=$.toString()?`?${$.toString()}`:"";return x(`/admin/users${J}`,{},!0)}async function mf(D){return x(`/admin/approve/${D}`,{method:"POST"},!0)}async function lf(D){return x(`/admin/revoke/${D}`,{method:"POST"},!0)}async function pf(D,F){return x(`/admin/users/${D}/role`,{method:"POST",body:JSON.stringify({role:F})},!0)}async function yW(D,F){return x(`/admin/datasets/${D}/visibility`,{method:"PATCH",body:JSON.stringify({visibility:F})},!0)}async function df(D){return x(`/datasets/${D}/publish`,{method:"POST"},!0)}async function cf(D){return x(`/admin/datasets/${D}/ci`,{},!0)}async function h4(D){return x(`/admin/datasets/${D}/ci`,{method:"POST"},!0)}async function xW(D){return x(`/admin/datasets/${D}/ci/validate`,{method:"POST"},!0)}async function _W(D){return x(`/admin/datasets/${D}/ci/sync`,{method:"POST"},!0)}async function QQ(D){return x(`/datasets/${D}/ci/status`,{},!0)}async function nf(D){return x(`/datasets/${D}/manifest`,{},!0)}async function YQ(D,F){return x(`/datasets/${D}/manifest/${F}`,{},!0)}function af(D){let F=D;if(!F.status)F.status="active";else if(!["active","archived","deleted"].includes(F.status))throw Error(`Invalid dataset status: ${F.status}`);if(!F.visibility)F.visibility="private";else if(!["public","private"].includes(F.visibility))throw Error(`Invalid dataset visibility: ${F.visibility}`);return F}async function y9(D={}){let F=new URLSearchParams;if(D.mine)F.set("mine","true");if(D.search)F.set("search",D.search);if(D.modality)F.set("modality",D.modality);if(D.author)F.set("author",D.author);if(D.task)F.set("task",D.task);if(D.license)F.set("license",D.license);if(D.hasDoi)F.set("has_doi","true");if(D.recent)F.set("recent",String(D.recent));if(D.sort)F.set("sort",D.sort);if(D.limit!=null)F.set("limit",String(D.limit));if(D.offset!=null)F.set("offset",String(D.offset));if(D.owner)F.set("owner",D.owner);let $=F.toString()?`?${F.toString()}`:"",J=await x(`/datasets${$}`,{},D.mine?!0:"optional");return J.datasets=J.datasets.map(af),J}async function of(D){return x(`/datasets/resolve/${D}`,{},"optional")}async function sf(D,F={}){let $=new URLSearchParams({q:D});if(F.modality)$.set("modality",F.modality);if(F.limit)$.set("limit",String(F.limit));return x(`/datasets/search?${$.toString()}`,{},"optional")}async function uD(D){let F=await x(`/datasets/${D}`,{},"optional");return af(F.dataset)}async function rf(D){return x(`/datasets/${D}/versions`,{},!0)}async function BQ(D){return x("/datasets",{method:"POST",body:JSON.stringify(D)},!0)}async function XQ(D){return x(`/datasets/${D}/finalize`,{method:"POST"},!0)}async function o8(D,F){return x(`/datasets/${D}/upload-credentials`,{method:"POST",body:JSON.stringify({duration_seconds:F})},!0)}async function GQ(D,F){return x(`/datasets/${D}/download-credentials`,{method:"POST",body:JSON.stringify({duration_seconds:F})},!0)}async function tf(D,F){return x(`/admin/datasets/${D}/doi/concept`,{method:"POST",body:JSON.stringify(F)},!0)}async function x9(D){return x(`/admin/datasets/${D}/doi`,{},!0)}async function fW(D,F){return x(`/admin/datasets/${D}/doi/update`,{method:"POST",body:JSON.stringify(F)},!0)}async function gW(D){return x(`/datasets/${D}/request-access`,{method:"POST"},!0)}async function ef(D,F){let $=F?`?status=${F}`:"";return x(`/datasets/${D}/access-requests${$}`,{},!0)}async function Dg(D,F){return x(`/datasets/${D}/access-requests/${F}/approve`,{method:"POST"},!0)}async function Fg(D,F){return x(`/datasets/${D}/access-requests/${F}/deny`,{method:"POST"},!0)}async function $g(D,F){return x(`/datasets/${D}/invite`,{method:"POST",body:JSON.stringify({username:F})},!0)}async function Jg(D){return x(`/datasets/${D}/collaborators`,{},!0)}async function Qg(D){return x("/sandbox/complete",{method:"POST",body:JSON.stringify({dataset_id:D})},!0)}async function Yg(){return x("/sandbox/reset",{method:"POST"},!0)}async function Bg(){return x("/sandbox/status",{},!0)}async function WQ(D){return x(`/datasets/${D}/publish/request`,{method:"POST"},!0)}async function Xg(D){return x(`/datasets/${D}/publish/status`,{},!0)}async function Gg(D){return x(`/datasets/${D}/publish/resend`,{method:"POST"},!0)}async function Wg(D){let F=D?`?status=${D}`:"";return x(`/admin/publish/requests${F}`,{},!0)}async function Hg(D,F){return x(`/admin/publish/${D}/deny`,{method:"POST",headers:{"Content-Type":"application/json"},body:JSON.stringify({reason:F})},!0)}function kE0(D,F=[]){if(D){let $=v9.indexOf(D);if($>=0)return $+1}return Math.min(F.length+1,v9.length)}function vE0(D){if(!(D instanceof h))return!1;if(D.statusCode===0)return!0;if(D.statusCode===429)return!0;if(D.statusCode>=500&&D.statusCode<600)return!0;if(D.statusCode===403&&/repository has been locked/i.test(D.message))return!0;return!1}async function HQ(D,F=!1,$=!1,J=!1,Q,Y){let G,H,q=0,K=!1,V,E=F,Z=[],L;function M(A,N,j,S){if(!Y)return;Y({step:A,stepIndex:kE0(A,N),stepTotal:v9.length,s3LockLocked:j,s3LockTotal:S,s3LockResumed:A==="s3_lock"&&K?!0:void 0})}for(let A=1;A<=5;A++)try{let N,j=!0;do{if(N=await x(`/admin/publish/${D}/approve`,{method:"POST",headers:{"Content-Type":"application/json"},body:JSON.stringify({resume:j?E:!0,sandbox:$,s3_lock_continuation_token:G,s3_lock_total:H,skip_ci_check:J})},!0),j=!1,N.step_results)Z.push(...N.step_results);if(N.s3_lock_total!==void 0)H=N.s3_lock_total;if(N.s3_lock_batch_count!==void 0)q+=N.s3_lock_batch_count;let S=N.step??N.step_results?.[N.step_results.length-1]?.step;if(S&&(S!==V||S==="s3_lock"))M(S,N.steps_completed??[],S==="s3_lock"?q:void 0,S==="s3_lock"?H:void 0),V=S;if(N.hasMore&&N.s3_lock_continuation_token!==void 0)G=N.s3_lock_continuation_token;else break}while(N.hasMore);if(Z.length>0)N.step_results=vf(Z);return N}catch(N){if(L=N,A===5||!vE0(N)){if(N instanceof h&&Z.length>0)N.stepResults=vf(Z);throw N}let S=N;if(Q?.({attempt:A,maxAttempts:5,delayMs:1e4,step:S.step,error:S.message}),await new Promise((O)=>setTimeout(O,1e4)),E=!0,G!==void 0)K=!0}throw L}function vf(D){let F=new Map;for(let $ of D)F.set($.step,$);return Array.from(F.values())}async function qg(D,F){return x(`/admin/datasets/${D}/enrichment`,{method:"POST",body:JSON.stringify(F)},!0)}async function Kg(D){return x(`/admin/datasets/${D}/files`,{},!0)}async function zg(D){let F,$=0,J=[],Q=!0;while(Q){let Y=await x(`/admin/datasets/${D}/s3-lock`,{method:"POST",headers:{"Content-Type":"application/json"},body:JSON.stringify({continuation_token:F})},!0);if($+=Y.locked,Y.failed?.length)J.push(...Y.failed);if(Q=Y.hasMore,F=Y.continuation_token,Q&&!F)throw new h(500,"S3 lock paginated response missing continuation_token; aborting to avoid infinite loop")}return{locked:$,failed:J}}async function Eg(D){return x(`/admin/datasets/${D}/reset`,{method:"POST"},!0)}async function Vg(D,F=!1){return x(`/admin/datasets/${D}`,{method:"DELETE",headers:{"Content-Type":"application/json"},body:JSON.stringify({force:F})},!0)}async function Zg(D){return x("/admin/datasets/bulk-delete",{method:"POST",headers:{"Content-Type":"application/json"},body:JSON.stringify({dataset_ids:D})},!0)}async function Ug(D){return x("/admin/datasets/import",{method:"POST",body:JSON.stringify(D)},!0)}async function Lg(D){return x(`/admin/datasets/${D}/sync`,{method:"POST"},!0)}async function Ag(){return x("/admin/sync/status",{},!0)}async function qQ(D,F){return x(`/admin/datasets/${D}/reindex`,{method:"POST",headers:{"Content-Type":"application/json"},body:JSON.stringify(F??{})},!0)}async function Mg(D,F){return x("/admin/datasets/reindex/bulk",{method:"POST",headers:{"Content-Type":"application/json"},body:JSON.stringify({filter:D,...F??{}})},!0)}async function Ng(D){let F=new URLSearchParams;if(D?.prefix)F.set("prefix",D.prefix);if(D?.visibility)F.set("visibility",D.visibility);if(D?.limit)F.set("limit",String(D.limit));let $=F.toString()?`?${F.toString()}`:"";return x(`/admin/fleet/drift${$}`,{},!0)}async function Rg(D,F){return x(`/admin/datasets/${D}/enforce`,{method:"POST",body:JSON.stringify({dry_run:F})},!0)}async function Cg(D){return x("/admin/datasets/enforce/bulk",{method:"POST",body:JSON.stringify({prefix:D.prefix,visibility:D.visibility,limit:D.limit,dry_run:D.dryRun})},!0)}async function Og(){return x("/admin/email-preferences",{},!0)}async function jg(D){return x("/admin/email-preferences",{method:"PUT",headers:{"Content-Type":"application/json"},body:JSON.stringify(D)},!0)}async function wg(){return x("/notices",{},"optional")}async function Tg(){return x("/admin/notices",{},!0)}async function Pg(D){return x("/admin/notices",{method:"POST",body:JSON.stringify(D)},!0)}async function Ig(D){return x(`/admin/notices/${D}`,{method:"DELETE"},!0)}async function hW(D){return x("/admin/notify",{method:"POST",body:JSON.stringify(D)},!0)}async function Sg(){return x("/admin/summary/coverage",{},!0)}async function kg(D,F,$){return x("/admin/manifest/dispatch",{method:"POST",body:JSON.stringify({dataset_id:D,version:F,skip_canary:$?.skipCanary??!1})},!0)}var kW="https://nemar-api-dev.sccn-org.workers.dev",FQ,h,$Q,vW,v9;var s8=P(()=>{f4();SW();DQ();FQ=/^\d{4}-\d{4}-\d{4}-\d{3}[\dX]$/;h=class h extends Error{statusCode;details;step;constructor(D,F,$,J){super(F);this.statusCode=D;this.details=$;this.step=J;this.name="ApiError"}};$Q=class $Q extends h{mode;eta;constructor(D,F,$,J){super(503,F,J);this.mode=D;this.eta=$;this.name="MaintenanceError"}};vW=kW.includes("workers.dev");v9=["ci_check","enrichment_check","repo_public","s3_public_read","tag_protect","doi_create","update_metadata","update_readme","create_tag","create_release","upload_to_zenodo","publish_doi","version_doi","s3_lock","sync_nemar","notify_user"]});function yg(D){bW=D}function uW(){return bW}function _9(D){if(bW)process.stderr.write(`${D}
99
99
  `)}var bW=!1;function GD(D){if(D===0)return"0 B";let F=["B","KB","MB","GB","TB"],$=Math.min(Math.floor(Math.log(D)/Math.log(1024)),F.length-1);return`${(D/1024**$).toFixed($===0?0:1)} ${F[$]}`}function xg(D){return`${GD(D)}/s`}function yE0(D){if(D<60)return`${Math.round(D)}s`;if(D<3600)return`${Math.floor(D/60)}m ${Math.round(D%60)}s`;return`${Math.floor(D/3600)}h ${Math.floor(D%3600/60)}m`}function xE0(D,F=20){let $=Math.round(D/100*F),J=F-$;return`[${"=".repeat($)}${" ".repeat(J)}]`}class KQ{filesCompleted=0;filesTotal;bytesTotal=0;inFlight=new Map;currentFile="";startTime;lastUpdateTime;lastBytesTransferred=0;totalBytesTransferred=0;speedSamples=[];lastRenderedLine="";constructor(D=0,F=0){this.filesTotal=D,this.bytesTotal=F,this.startTime=Date.now(),this.lastUpdateTime=this.startTime}inFlightBytes(){let D=0;for(let F of this.inFlight.values())D+=F.transferred;return D}processLine(D){let F=D.file??D.action?.file;if(D.ok===!0||D.success===!0){this.filesCompleted++;let $=F??this.currentFile,J=$?this.inFlight.get($):void 0,Q=J?J.total||J.transferred:0;if(this.totalBytesTransferred+=Q,$)this.inFlight.delete($);this.render();return}if(D["byte-progress"]!==void 0){let $=F??this.currentFile;if(!$)return;this.currentFile=$;let J=this.inFlight.get($)??{transferred:0,total:0};if(J.transferred=D["byte-progress"]??J.transferred,D["total-size"]!==void 0)J.total=D["total-size"];this.inFlight.set($,J);let Q=Date.now(),Y=(Q-this.lastUpdateTime)/1000;if(Y>0.5){let B=this.totalBytesTransferred+this.inFlightBytes(),G=(B-this.lastBytesTransferred)/Y;if(G>0){if(this.speedSamples.push(G),this.speedSamples.length>5)this.speedSamples.shift()}this.lastBytesTransferred=B,this.lastUpdateTime=Q}this.render()}}incrementFilesCompleted(){this.filesCompleted++}setFilesTotal(D){this.filesTotal=D}setBytesTotal(D){this.bytesTotal=D}getPercent(){let D=this.totalBytesTransferred+this.inFlightBytes();if(this.bytesTotal>0)return Math.min(100,Math.round(D/this.bytesTotal*100));if(this.filesTotal>0)return Math.min(100,Math.round(this.filesCompleted/this.filesTotal*100));return null}getProgress(){return{filesCompleted:this.filesCompleted,filesTotal:this.filesTotal,bytesTransferred:this.totalBytesTransferred+this.inFlightBytes(),bytesTotal:this.bytesTotal,currentFile:this.currentFile||void 0}}render(){let D=this.speedSamples.length>0?this.speedSamples.reduce((B,X)=>B+X,0)/this.speedSamples.length:0,F=this.totalBytesTransferred+this.inFlightBytes(),$=0,J=!1;if(this.bytesTotal>0)$=Math.min(100,Math.round(F/this.bytesTotal*100)),J=!0;else if(this.filesTotal>0)$=Math.min(100,Math.round(this.filesCompleted/this.filesTotal*100)),J=!0;let Q=this.filesTotal>0?`${this.filesCompleted}/${this.filesTotal} files`:`${this.filesCompleted} files`,Y;if(J)Y=`${xE0($)} ${$}% ${Q}`;else Y=Q;if(F>0){let B=this.bytesTotal>0?`${GD(F)}/${GD(this.bytesTotal)}`:GD(F);Y+=` | ${B}`}if(D>0)Y+=` | ${xg(D)}`;if(D>0){let B=0;if(this.bytesTotal>0)B=Math.max(0,this.bytesTotal-F);else for(let X of this.inFlight.values())if(X.total>X.transferred)B+=X.total-X.transferred;if(B>0){let X=B/D;if(X>0)Y+=` | ETA ${yE0(X)}`}}if(Y!==this.lastRenderedLine)process.stderr.write(`\r${W.cyan(Y)}${" ".repeat(10)}`),this.lastRenderedLine=Y}finish(D){let F=(Date.now()-this.startTime)/1000;if(process.stderr.write(`\r${" ".repeat(this.lastRenderedLine.length+15)}\r`),D>0){let $=F>0?`${xg(this.totalBytesTransferred/F)}`:"",J=[`${D} file${D!==1?"s":""} downloaded`,this.totalBytesTransferred>0?GD(this.totalBytesTransferred):"",$].filter(Boolean).join(" | ");process.stderr.write(`${W.green(J)}
100
100
  `)}}}var mW=P(()=>{jD()});var ig={};a4(ig,{verifyGitHubAuth:()=>g9,toS3Credentials:()=>CD,switchBranch:()=>dE0,setKeyPresent:()=>ng,selectAnnexS3Remote:()=>oW,saveDataset:()=>t8,runCommand:()=>I,resolveUpstreamRef:()=>JH,readRemoteHeadDatasetVersion:()=>$H,readLocalDatasetVersion:()=>FH,pushToGitHub:()=>r1,pushBranch:()=>vF,markInheritedOpenNeuroRemotesIgnored:()=>aW,listDatasetVersions:()=>rW,isWorkingTreeDirty:()=>QH,isGitAnnexDataset:()=>j1,isDataladDataset:()=>oE0,initOrEnableSpecialRemote:()=>pg,initDataset:()=>o6,gitMergeFastForward:()=>BH,gitFetchOrigin:()=>YH,gitAnnexAdd:()=>s6,getVersionCommit:()=>tW,getRemoteUuid:()=>HH,getLocalDatasetInfo:()=>sW,getKeyHashDirs:()=>iE0,getKeyHashDir:()=>cg,getDatasetStats:()=>mE0,getDatasetIdFromRemote:()=>D6,getDatasetData:()=>ZQ,getCurrentBranch:()=>e8,getAnnexWhereisAll:()=>WH,getAnnexS3Remotes:()=>b9,formatBytes:()=>GD,ensureLocalMainBranch:()=>u9,ensureGitAnnexInitialized:()=>nW,enableS3Remote:()=>u4,dropUnusedAnnexObjects:()=>XH,dropFiles:()=>iW,detectImportMarker:()=>VQ,createRevertBranch:()=>eW,createDataladDataset:()=>aE0,countPendingDownload:()=>EQ,copyToAnnexRemote:()=>T8,configureS3Remote:()=>w8,configureLargefiles:()=>b4,configureGitHubRemote:()=>r8,commitRevert:()=>DH,collectFileManifest:()=>GH,cloneDataset:()=>t1,clearAnnexCredentials:()=>vD,checkPrerequisites:()=>f9,checkGitHubSSH:()=>bg,checkGitAnnexInstalled:()=>cW,checkDownloadPrerequisites:()=>kF,checkAWSCredentials:()=>hE0,batchSetKeysPresent:()=>qH,annexRemoteExists:()=>lg,acceptGitHubInvitation:()=>h9,NEMAR_S3_REMOTE_NAME:()=>zQ,ANNEX_REMOTE_EXISTS_RE:()=>mg});import{existsSync as pW,readFileSync as _E0,statSync as fE0}from"fs";import{join as dW}from"path";var{spawn:hg}=globalThis.Bun;async function I(D,F={}){let $=hg({cmd:D,cwd:F.cwd,stdout:"pipe",stderr:"pipe",env:{...process.env,GIT_TERMINAL_PROMPT:"0",...F.env}}),J=!1,Q;if(F.timeout)Q=setTimeout(()=>{J=!0,$.kill()},F.timeout);if(uW()){let G=F.cwd?` (cwd=${F.cwd})`:"";_9(W.dim(`$ ${D.join(" ")}${G}`))}let Y=await new Response($.stdout).text(),B=await new Response($.stderr).text(),X=await $.exited;if(Q)clearTimeout(Q);if(uW()){if(Y.trim())_9(W.dim(Y.trimEnd()));if(B.trim())_9(W.yellow(B.trimEnd()));_9(W.dim(`(exit ${X})`))}if(J)return{stdout:Y,stderr:B||`Command timed out after ${Math.round(F.timeout/1000)}s`,exitCode:X??1};return{stdout:Y,stderr:B,exitCode:X}}function _g(D){return D.split(".").map((F)=>{let $=Number.parseInt(F.replace(/[^0-9]/g,""),10);return Number.isNaN($)?0:$})}function gE0(D,F){let $=_g(D),J=_g(F);for(let Q=0;Q<Math.max($.length,J.length);Q++){let Y=$[Q]||0,B=J[Q]||0;if(Y>B)return!0;if(Y<B)return!1}return!0}async function cW(){try{let{stdout:F,exitCode:$,stderr:J}=await I(["git-annex","version"]);if($!==0)return console.warn("git-annex version returned non-zero exit code:",$),console.warn("stderr:",J),{installed:!1,minVersion:"10.0",error:`Version check failed: ${J.trim()}`};let Q=F.match(/version:\s*(\d+\.\d+)/),Y=Q?Q[1]:void 0;if(!Y)console.warn("Could not parse git-annex version from output:",F);return{installed:!0,version:Y,minVersion:"10.0",compatible:Y?gE0(Y,"10.0"):void 0}}catch(F){let $=F instanceof Error?F.message:String(F);if($.includes("ENOENT")||$.includes("not found"))return console.info("git-annex not found in PATH"),{installed:!1,minVersion:"10.0"};return console.error("Error checking git-annex installation:",$),{installed:!1,minVersion:"10.0",error:$}}}async function bg(){if(process.env.GH_TOKEN)return{accessible:!0,username:"token-auth",useHttps:!0};try{let{stdout:D,stderr:F}=await I(["ssh","-T","-o","BatchMode=yes","-o","StrictHostKeyChecking=accept-new","-o","ConnectTimeout=10","git@github.com"]),$=D+F,J=$.match(/Hi ([^!]+)!/);if(J)return{accessible:!0,username:J[1]};if($.includes("Permission denied"))return{accessible:!1};return{accessible:$.includes("successfully authenticated")}}catch(D){let F=D instanceof Error?D.message:String(D);if(F.includes("ENOENT")||F.includes("not found"))console.info("SSH command not found");else console.error("Error checking GitHub SSH access:",F);return{accessible:!1}}}async function hE0(){if(process.env.AWS_ACCESS_KEY_ID&&process.env.AWS_SECRET_ACCESS_KEY)return{configured:!0,source:"environment"};try{let{stdout:D,exitCode:F}=await I(["aws","configure","get","aws_access_key_id"]);if(F===0&&D.trim())return{configured:!0,source:"aws-cli"}}catch(D){let F=D instanceof Error?D.message:String(D);if(F.includes("ENOENT")||F.includes("not found"))console.info("AWS CLI not found in PATH");else console.error("Error checking AWS credentials:",F)}return{configured:!1}}function ug(){let D=process.platform;if(D==="darwin")return"brew install git-annex";if(D==="linux")return"apt install git-annex (Debian/Ubuntu)";return"See https://git-annex.branchable.com/install/"}async function f9(){let[D,F]=await Promise.all([cW(),bg()]),$=[];if(!D.installed)$.push(`git-annex is not installed. Install: ${ug()}`);else if(D.compatible===!1)$.push(`git-annex version ${D.version} is too old. Required: >= ${D.minVersion}`);if(!F.accessible){if(!(await dg()).token)$.push("GitHub authentication not configured. Run 'gh auth login' to authenticate.")}return{gitAnnex:D,githubSSH:F,allPassed:$.length===0,errors:$}}async function j1(D){if(!pW(dW(D,".git")))return!1;try{let{exitCode:F}=await I(["git","annex","info"],{cwd:D});return F===0}catch(F){let $=F instanceof Error?F.message:String(F);if(!$.includes("ENOENT")&&!$.includes("not found"))console.error(`Error checking if ${D} is a git-annex dataset:`,$);return!1}}async function o6(D,F={}){if(!F.force&&await j1(D))return{success:!0};try{let $={};if(F.author)$.GIT_AUTHOR_NAME=F.author.name,$.GIT_AUTHOR_EMAIL=F.author.email,$.GIT_COMMITTER_NAME=F.author.name,$.GIT_COMMITTER_EMAIL=F.author.email;let{stderr:J,exitCode:Q}=await I(["git","init","-b","main",D],{...Object.keys($).length>0?{env:$}:{}});if(Q!==0)return{success:!1,error:J.trim()||"Failed to initialize git repository"};let Y=Object.keys($).length>0?{env:$}:{},{stderr:B,exitCode:X}=await I(["git","annex","init"],{cwd:D,...Y});if(X!==0)return{success:!1,error:B.trim()||"Failed to initialize git-annex"};let{stderr:G,exitCode:H}=await I(["git","commit","--allow-empty","-m","Initialize dataset"],{cwd:D,...Y});if(H!==0)return{success:!1,error:G.trim()||"Failed to create initial commit"};let{stderr:q,exitCode:K}=await I(["git","annex","adjust","--unlock"],{cwd:D,...Y});if(K!==0)return{success:!1,error:q.trim()||"Failed to switch to unlocked mode"};return{success:!0}}catch($){return{success:!1,error:$.message}}}async function nW(D){try{let{exitCode:F,stderr:$}=await I(["git","annex","info"],{cwd:D});if(F===0)return{success:!0};if($.includes("First run: git-annex init")){let{stderr:J,exitCode:Q}=await I(["git","annex","init"],{cwd:D});if(Q!==0)return{success:!1,error:J.trim()||"Failed to initialize git-annex"};return{success:!0}}return{success:!1,error:$.trim()||"Failed to check git-annex status"}}catch(F){return{success:!1,error:F.message}}}async function b4(D,F){let $=["*.edf","*.bdf","*.set","*.fif","*.vhdr","*.eeg","*.cnt","*.fdt"],J=["*.tsv","*.json","*.md","*.txt","*.yml","*.yaml","README*","LICENSE*","CHANGES*",".bidsignore",".gitignore"],Q=$.map((G)=>`include=${G}`).join(" or "),Y=J.map((G)=>`exclude=${G}`).join(" and "),B=`(${Q} or largerthan=100kb) and ${Y}`,X=F||B;try{let{stderr:G,exitCode:H}=await I(["git","annex","config","--set","annex.largefiles",X],{cwd:D});if(H!==0)return{success:!1,error:G.trim()||"Failed to configure largefiles"};return{success:!0}}catch(G){return{success:!1,error:G.message}}}async function s6(D,F="."){try{let{stderr:$,exitCode:J}=await I(["git","annex","add",F],{cwd:D});if(J!==0)return{success:!1,error:$.trim()||"Failed to add files to git-annex"};return{success:!0}}catch($){return{success:!1,error:$.message}}}function CD(D){return{accessKeyId:D.access_key_id,secretAccessKey:D.secret_access_key,sessionToken:D.session_token}}function lW(D){let F=[/^\(merging .* into .*\.\.\.\)$/,/^\(recording state in git\.\.\.\)$/,/^\(scanning for /,/^\(checking /];return D.split(`
101
101
  `).filter(($)=>{let J=$.trim();if(!J)return!1;if(J.includes("setting annex-ignore"))return!1;if(F.some((Q)=>Q.test(J)))return!1;return!0}).join(`
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "nemar-cli",
3
- "version": "0.8.50-dev.1362",
3
+ "version": "0.8.50-dev.1363",
4
4
  "description": "CLI for NEMAR (Neuroelectromagnetic Data Archive and Tools Resource) dataset management",
5
5
  "type": "module",
6
6
  "main": "dist/index.js",