nemar-cli 0.8.12 → 0.8.13-PR456.7ff9455

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 Ef=!1;var NW=I(()=>{yD()});var Zf;var Vf=I(()=>{Zf={name:"nemar-cli",version:"0.8.12",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","docs:generate":"bun run scripts/generate-docs.ts","docs:serve":"mkdocs serve","docs:build":"mkdocs build",prepare:"husky",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://nemar-cli.pages.dev",engines:{bun:">=1.0.0"},files:["dist","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 x4;var aJ=I(()=>{Vf();x4=Zf.version});function R0(D){if(D instanceof Error)return D.message;return String(D)}function Uf(){if(process.env.TEST_API_URL)return process.env.TEST_API_URL;if(RW)return CW;return $D().apiUrl||CW}async function b(D,F={},$=!1){let J=`${Uf()}${D}`,Q={"Content-Type":"application/json","X-CLI-Version":x4,...F.headers};if($){let X=$D();if(!X.apiKey&&$===!0)throw new p(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 p(0,`Network error: Could not connect to ${Uf()}`,{originalError:X instanceof Error?X.message:String(X)})}let B;try{B=await Y.json()}catch{throw new p(Y.status,`Invalid response from server (status ${Y.status})`)}if(!Y.ok){if(Y.status===503&&(B.mode==="read-only"||B.mode==="full")){let X=typeof B.message==="string"?B.message:"NEMAR is in maintenance mode. Please retry shortly.",G=typeof B.eta==="string"?B.eta:null,H=new sJ(B.mode,X,G,B.details);throw iJ(H),H}throw new p(Y.status,B.error||B.message||"Request failed",B.details,typeof B.step==="string"?B.step:void 0)}return B}async function Af(D){return b(`/auth/check-username?username=${encodeURIComponent(D)}`)}async function Mf(D){return b(`/auth/check-github?username=${encodeURIComponent(D)}`)}async function Nf(D){return b("/auth/signup",{method:"POST",body:JSON.stringify(D)})}async function Cf(D){return b("/auth/login",{method:"POST",body:JSON.stringify({api_key:D})})}async function Rf(D){return b("/auth/resend-verification",{method:"POST",body:JSON.stringify({email:D})})}async function Of(D,F){return b("/auth/retrieve-key",{method:"POST",body:JSON.stringify({email:D,password:F})})}async function Tf(D){return b("/auth/request-key-regeneration",{method:"POST",body:JSON.stringify({email:D})})}async function rJ(){return b("/users/me",{},!0)}async function wf(D,F){let $=new URLSearchParams;if(D)$.set("status",D);if(F)$.set("role",F);let J=$.toString()?`?${$.toString()}`:"";return b(`/admin/users${J}`,{},!0)}async function jf(D){return b(`/admin/approve/${D}`,{method:"POST"},!0)}async function Pf(D){return b(`/admin/revoke/${D}`,{method:"POST"},!0)}async function If(D,F){return b(`/admin/users/${D}/role`,{method:"POST",body:JSON.stringify({role:F})},!0)}async function OW(D,F){return b(`/admin/datasets/${D}/visibility`,{method:"PATCH",body:JSON.stringify({visibility:F})},!0)}async function Sf(D){return b(`/datasets/${D}/publish`,{method:"POST"},!0)}async function kf(D){return b(`/admin/datasets/${D}/ci`,{},!0)}async function _4(D){return b(`/admin/datasets/${D}/ci`,{method:"POST"},!0)}async function TW(D){return b(`/admin/datasets/${D}/ci/sync`,{method:"POST"},!0)}async function tJ(D){return b(`/datasets/${D}/ci/status`,{},!0)}async function vf(D){return b(`/datasets/${D}/manifest`,{},!0)}async function eJ(D,F){return b(`/datasets/${D}/manifest/${F}`,{},!0)}function yf(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 P9(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.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 b(`/datasets${$}`,{},D.mine?!0:"optional");return J.datasets=J.datasets.map(yf),J}async function xf(D){return b(`/datasets/resolve/${D}`,{},"optional")}async function _f(D,F={}){let $=new URLSearchParams({q:D});if(F.modality)$.set("modality",F.modality);if(F.limit)$.set("limit",String(F.limit));return b(`/datasets/search?${$.toString()}`,{},"optional")}async function bD(D){let F=await b(`/datasets/${D}`,{},"optional");return yf(F.dataset)}async function ff(D){return b(`/datasets/${D}/versions`,{},!0)}async function DQ(D){return b("/datasets",{method:"POST",body:JSON.stringify(D)},!0)}async function FQ(D){return b(`/datasets/${D}/finalize`,{method:"POST"},!0)}async function C8(D,F){return b(`/datasets/${D}/upload-credentials`,{method:"POST",body:JSON.stringify({duration_seconds:F})},!0)}async function $Q(D,F){return b(`/datasets/${D}/download-credentials`,{method:"POST",body:JSON.stringify({duration_seconds:F})},!0)}async function gf(D,F){return b(`/admin/datasets/${D}/doi/concept`,{method:"POST",body:JSON.stringify(F)},!0)}async function I9(D){return b(`/admin/datasets/${D}/doi`,{},!0)}async function wW(D,F){return b(`/admin/datasets/${D}/doi/update`,{method:"POST",body:JSON.stringify(F)},!0)}async function jW(D){return b(`/datasets/${D}/request-access`,{method:"POST"},!0)}async function hf(D,F){return b(`/datasets/${D}/invite`,{method:"POST",body:JSON.stringify({username:F})},!0)}async function bf(D){return b(`/datasets/${D}/collaborators`,{},!0)}async function uf(D){return b("/sandbox/complete",{method:"POST",body:JSON.stringify({dataset_id:D})},!0)}async function mf(){return b("/sandbox/reset",{method:"POST"},!0)}async function lf(){return b("/sandbox/status",{},!0)}async function JQ(D){return b(`/datasets/${D}/publish/request`,{method:"POST"},!0)}async function pf(D){return b(`/datasets/${D}/publish/status`,{},!0)}async function df(D){return b(`/datasets/${D}/publish/resend`,{method:"POST"},!0)}async function cf(D){let F=D?`?status=${D}`:"";return b(`/admin/publish/requests${F}`,{},!0)}async function nf(D,F){return b(`/admin/publish/${D}/deny`,{method:"POST",headers:{"Content-Type":"application/json"},body:JSON.stringify({reason:F})},!0)}function cz0(D){if(!(D instanceof p))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 QQ(D,F=!1,$=!1,J=!1,Q){let X,G=F,H=[],q;for(let K=1;K<=5;K++)try{let V,E=!0;do{if(V=await b(`/admin/publish/${D}/approve`,{method:"POST",headers:{"Content-Type":"application/json"},body:JSON.stringify({resume:E?G:!0,sandbox:$,s3_lock_continuation_token:X,skip_ci_check:J})},!0),E=!1,V.step_results)H.push(...V.step_results);if(V.hasMore&&V.s3_lock_continuation_token!==void 0)X=V.s3_lock_continuation_token;else break}while(V.hasMore);if(H.length>0)V.step_results=Lf(H);return V}catch(V){if(q=V,K===5||!cz0(V)){if(V instanceof p&&H.length>0)V.stepResults=Lf(H);throw V}let Z=V;Q?.({attempt:K,maxAttempts:5,delayMs:1e4,step:Z.step,error:Z.message}),await new Promise((L)=>setTimeout(L,1e4)),G=!0}throw q}function Lf(D){let F=new Map;for(let $ of D)F.set($.step,$);return Array.from(F.values())}async function af(D,F){return b(`/admin/datasets/${D}/enrichment`,{method:"POST",body:JSON.stringify(F)},!0)}async function of(D){return b(`/admin/datasets/${D}/files`,{},!0)}async function sf(D){let F,$=0,J=[],Q=!0;while(Q){let Y=await b(`/admin/datasets/${D}/s3-lock`,{method:"POST",headers:{"Content-Type":"application/json"},body:JSON.stringify({continuation_token:F})},!0);if($+=Y.locked,Y.failed?.length)J.push(...Y.failed);if(Q=Y.hasMore,F=Y.continuation_token,Q&&!F)throw new p(500,"S3 lock paginated response missing continuation_token; aborting to avoid infinite loop")}return{locked:$,failed:J}}async function rf(D){return b(`/admin/datasets/${D}/reset`,{method:"POST"},!0)}async function tf(D,F=!1){return b(`/admin/datasets/${D}`,{method:"DELETE",headers:{"Content-Type":"application/json"},body:JSON.stringify({force:F})},!0)}async function ef(D){return b("/admin/datasets/bulk-delete",{method:"POST",headers:{"Content-Type":"application/json"},body:JSON.stringify({dataset_ids:D})},!0)}async function Dg(D){return b("/admin/datasets/import",{method:"POST",body:JSON.stringify(D)},!0)}async function Fg(D){return b(`/admin/datasets/${D}/sync`,{method:"POST"},!0)}async function $g(){return b("/admin/sync/status",{},!0)}async function Jg(D,F){return b(`/admin/datasets/${D}/reindex`,{method:"POST",headers:{"Content-Type":"application/json"},body:JSON.stringify(F??{})},!0)}async function Qg(D,F){return b("/admin/datasets/reindex/bulk",{method:"POST",headers:{"Content-Type":"application/json"},body:JSON.stringify({filter:D,...F??{}})},!0)}async function Yg(){return b("/admin/email-preferences",{},!0)}async function Bg(D){return b("/admin/email-preferences",{method:"PUT",headers:{"Content-Type":"application/json"},body:JSON.stringify(D)},!0)}async function Xg(){return b("/notices",{},"optional")}async function Gg(){return b("/admin/notices",{},!0)}async function Wg(D){return b("/admin/notices",{method:"POST",body:JSON.stringify(D)},!0)}async function Hg(D){return b(`/admin/notices/${D}`,{method:"DELETE"},!0)}async function PW(D){return b("/admin/notify",{method:"POST",body:JSON.stringify(D)},!0)}var CW="https://api.nemar.org",oJ,p,sJ,RW;var i8=I(()=>{y4();NW();aJ();oJ=/^\d{4}-\d{4}-\d{4}-\d{3}[\dX]$/;p=class p extends Error{statusCode;details;step;constructor(D,F,$,J){super(F);this.statusCode=D;this.details=$;this.step=J;this.name="ApiError"}};sJ=class sJ extends p{mode;eta;constructor(D,F,$,J){super(503,F,J);this.mode=D;this.eta=$;this.name="MaintenanceError"}};RW=CW.includes("workers.dev")});function Kg(D){IW=D}function SW(){return IW}function S9(D){if(IW)process.stderr.write(`${D}
98
+ `)}var Ef=!1;var NW=I(()=>{yD()});var Zf;var Vf=I(()=>{Zf={name:"nemar-cli",version:"0.8.13-PR456.7ff9455",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","docs:generate":"bun run scripts/generate-docs.ts","docs:serve":"mkdocs serve","docs:build":"mkdocs build",prepare:"husky",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://nemar-cli.pages.dev",engines:{bun:">=1.0.0"},files:["dist","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 x4;var aJ=I(()=>{Vf();x4=Zf.version});function R0(D){if(D instanceof Error)return D.message;return String(D)}function Uf(){if(process.env.TEST_API_URL)return process.env.TEST_API_URL;if(RW)return CW;return $D().apiUrl||CW}async function b(D,F={},$=!1){let J=`${Uf()}${D}`,Q={"Content-Type":"application/json","X-CLI-Version":x4,...F.headers};if($){let X=$D();if(!X.apiKey&&$===!0)throw new p(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 p(0,`Network error: Could not connect to ${Uf()}`,{originalError:X instanceof Error?X.message:String(X)})}let B;try{B=await Y.json()}catch{throw new p(Y.status,`Invalid response from server (status ${Y.status})`)}if(!Y.ok){if(Y.status===503&&(B.mode==="read-only"||B.mode==="full")){let X=typeof B.message==="string"?B.message:"NEMAR is in maintenance mode. Please retry shortly.",G=typeof B.eta==="string"?B.eta:null,H=new sJ(B.mode,X,G,B.details);throw iJ(H),H}throw new p(Y.status,B.error||B.message||"Request failed",B.details,typeof B.step==="string"?B.step:void 0)}return B}async function Af(D){return b(`/auth/check-username?username=${encodeURIComponent(D)}`)}async function Mf(D){return b(`/auth/check-github?username=${encodeURIComponent(D)}`)}async function Nf(D){return b("/auth/signup",{method:"POST",body:JSON.stringify(D)})}async function Cf(D){return b("/auth/login",{method:"POST",body:JSON.stringify({api_key:D})})}async function Rf(D){return b("/auth/resend-verification",{method:"POST",body:JSON.stringify({email:D})})}async function Of(D,F){return b("/auth/retrieve-key",{method:"POST",body:JSON.stringify({email:D,password:F})})}async function Tf(D){return b("/auth/request-key-regeneration",{method:"POST",body:JSON.stringify({email:D})})}async function rJ(){return b("/users/me",{},!0)}async function wf(D,F){let $=new URLSearchParams;if(D)$.set("status",D);if(F)$.set("role",F);let J=$.toString()?`?${$.toString()}`:"";return b(`/admin/users${J}`,{},!0)}async function jf(D){return b(`/admin/approve/${D}`,{method:"POST"},!0)}async function Pf(D){return b(`/admin/revoke/${D}`,{method:"POST"},!0)}async function If(D,F){return b(`/admin/users/${D}/role`,{method:"POST",body:JSON.stringify({role:F})},!0)}async function OW(D,F){return b(`/admin/datasets/${D}/visibility`,{method:"PATCH",body:JSON.stringify({visibility:F})},!0)}async function Sf(D){return b(`/datasets/${D}/publish`,{method:"POST"},!0)}async function kf(D){return b(`/admin/datasets/${D}/ci`,{},!0)}async function _4(D){return b(`/admin/datasets/${D}/ci`,{method:"POST"},!0)}async function TW(D){return b(`/admin/datasets/${D}/ci/sync`,{method:"POST"},!0)}async function tJ(D){return b(`/datasets/${D}/ci/status`,{},!0)}async function vf(D){return b(`/datasets/${D}/manifest`,{},!0)}async function eJ(D,F){return b(`/datasets/${D}/manifest/${F}`,{},!0)}function yf(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 P9(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.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 b(`/datasets${$}`,{},D.mine?!0:"optional");return J.datasets=J.datasets.map(yf),J}async function xf(D){return b(`/datasets/resolve/${D}`,{},"optional")}async function _f(D,F={}){let $=new URLSearchParams({q:D});if(F.modality)$.set("modality",F.modality);if(F.limit)$.set("limit",String(F.limit));return b(`/datasets/search?${$.toString()}`,{},"optional")}async function bD(D){let F=await b(`/datasets/${D}`,{},"optional");return yf(F.dataset)}async function ff(D){return b(`/datasets/${D}/versions`,{},!0)}async function DQ(D){return b("/datasets",{method:"POST",body:JSON.stringify(D)},!0)}async function FQ(D){return b(`/datasets/${D}/finalize`,{method:"POST"},!0)}async function C8(D,F){return b(`/datasets/${D}/upload-credentials`,{method:"POST",body:JSON.stringify({duration_seconds:F})},!0)}async function $Q(D,F){return b(`/datasets/${D}/download-credentials`,{method:"POST",body:JSON.stringify({duration_seconds:F})},!0)}async function gf(D,F){return b(`/admin/datasets/${D}/doi/concept`,{method:"POST",body:JSON.stringify(F)},!0)}async function I9(D){return b(`/admin/datasets/${D}/doi`,{},!0)}async function wW(D,F){return b(`/admin/datasets/${D}/doi/update`,{method:"POST",body:JSON.stringify(F)},!0)}async function jW(D){return b(`/datasets/${D}/request-access`,{method:"POST"},!0)}async function hf(D,F){return b(`/datasets/${D}/invite`,{method:"POST",body:JSON.stringify({username:F})},!0)}async function bf(D){return b(`/datasets/${D}/collaborators`,{},!0)}async function uf(D){return b("/sandbox/complete",{method:"POST",body:JSON.stringify({dataset_id:D})},!0)}async function mf(){return b("/sandbox/reset",{method:"POST"},!0)}async function lf(){return b("/sandbox/status",{},!0)}async function JQ(D){return b(`/datasets/${D}/publish/request`,{method:"POST"},!0)}async function pf(D){return b(`/datasets/${D}/publish/status`,{},!0)}async function df(D){return b(`/datasets/${D}/publish/resend`,{method:"POST"},!0)}async function cf(D){let F=D?`?status=${D}`:"";return b(`/admin/publish/requests${F}`,{},!0)}async function nf(D,F){return b(`/admin/publish/${D}/deny`,{method:"POST",headers:{"Content-Type":"application/json"},body:JSON.stringify({reason:F})},!0)}function cz0(D){if(!(D instanceof p))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 QQ(D,F=!1,$=!1,J=!1,Q){let X,G=F,H=[],q;for(let K=1;K<=5;K++)try{let V,E=!0;do{if(V=await b(`/admin/publish/${D}/approve`,{method:"POST",headers:{"Content-Type":"application/json"},body:JSON.stringify({resume:E?G:!0,sandbox:$,s3_lock_continuation_token:X,skip_ci_check:J})},!0),E=!1,V.step_results)H.push(...V.step_results);if(V.hasMore&&V.s3_lock_continuation_token!==void 0)X=V.s3_lock_continuation_token;else break}while(V.hasMore);if(H.length>0)V.step_results=Lf(H);return V}catch(V){if(q=V,K===5||!cz0(V)){if(V instanceof p&&H.length>0)V.stepResults=Lf(H);throw V}let Z=V;Q?.({attempt:K,maxAttempts:5,delayMs:1e4,step:Z.step,error:Z.message}),await new Promise((L)=>setTimeout(L,1e4)),G=!0}throw q}function Lf(D){let F=new Map;for(let $ of D)F.set($.step,$);return Array.from(F.values())}async function af(D,F){return b(`/admin/datasets/${D}/enrichment`,{method:"POST",body:JSON.stringify(F)},!0)}async function of(D){return b(`/admin/datasets/${D}/files`,{},!0)}async function sf(D){let F,$=0,J=[],Q=!0;while(Q){let Y=await b(`/admin/datasets/${D}/s3-lock`,{method:"POST",headers:{"Content-Type":"application/json"},body:JSON.stringify({continuation_token:F})},!0);if($+=Y.locked,Y.failed?.length)J.push(...Y.failed);if(Q=Y.hasMore,F=Y.continuation_token,Q&&!F)throw new p(500,"S3 lock paginated response missing continuation_token; aborting to avoid infinite loop")}return{locked:$,failed:J}}async function rf(D){return b(`/admin/datasets/${D}/reset`,{method:"POST"},!0)}async function tf(D,F=!1){return b(`/admin/datasets/${D}`,{method:"DELETE",headers:{"Content-Type":"application/json"},body:JSON.stringify({force:F})},!0)}async function ef(D){return b("/admin/datasets/bulk-delete",{method:"POST",headers:{"Content-Type":"application/json"},body:JSON.stringify({dataset_ids:D})},!0)}async function Dg(D){return b("/admin/datasets/import",{method:"POST",body:JSON.stringify(D)},!0)}async function Fg(D){return b(`/admin/datasets/${D}/sync`,{method:"POST"},!0)}async function $g(){return b("/admin/sync/status",{},!0)}async function Jg(D,F){return b(`/admin/datasets/${D}/reindex`,{method:"POST",headers:{"Content-Type":"application/json"},body:JSON.stringify(F??{})},!0)}async function Qg(D,F){return b("/admin/datasets/reindex/bulk",{method:"POST",headers:{"Content-Type":"application/json"},body:JSON.stringify({filter:D,...F??{}})},!0)}async function Yg(){return b("/admin/email-preferences",{},!0)}async function Bg(D){return b("/admin/email-preferences",{method:"PUT",headers:{"Content-Type":"application/json"},body:JSON.stringify(D)},!0)}async function Xg(){return b("/notices",{},"optional")}async function Gg(){return b("/admin/notices",{},!0)}async function Wg(D){return b("/admin/notices",{method:"POST",body:JSON.stringify(D)},!0)}async function Hg(D){return b(`/admin/notices/${D}`,{method:"DELETE"},!0)}async function PW(D){return b("/admin/notify",{method:"POST",body:JSON.stringify(D)},!0)}var CW="https://api.nemar.org",oJ,p,sJ,RW;var i8=I(()=>{y4();NW();aJ();oJ=/^\d{4}-\d{4}-\d{4}-\d{3}[\dX]$/;p=class p extends Error{statusCode;details;step;constructor(D,F,$,J){super(F);this.statusCode=D;this.details=$;this.step=J;this.name="ApiError"}};sJ=class sJ extends p{mode;eta;constructor(D,F,$,J){super(503,F,J);this.mode=D;this.eta=$;this.name="MaintenanceError"}};RW=CW.includes("workers.dev")});function Kg(D){IW=D}function SW(){return IW}function S9(D){if(IW)process.stderr.write(`${D}
99
99
  `)}var IW=!1;function YD(D){if(D===0)return"0 B";let F=["B","KB","MB","GB","TB"],$=Math.min(Math.floor(Math.log(D)/Math.log(1024)),F.length-1);return`${(D/1024**$).toFixed($===0?0:1)} ${F[$]}`}function zg(D){return`${YD(D)}/s`}function nz0(D){if(D<60)return`${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 iz0(D,F=20){let $=Math.round(D/100*F),J=F-$;return`[${"=".repeat($)}${" ".repeat(J)}]`}class YQ{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`:`${this.filesCompleted} files`,Y;if(J)Y=`${iz0($)} ${$}% ${Q}`;else Y=Q;if(F>0){let B=this.bytesTotal>0?`${YD(F)}/${YD(this.bytesTotal)}`:YD(F);Y+=` | ${B}`}if(D>0)Y+=` | ${zg(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 ${nz0(X)}`}}if(Y!==this.lastRenderedLine)process.stderr.write(`\r${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 $=F>0?`${zg(this.totalBytesTransferred/F)}`:"",J=[`${D} file${D!==1?"s":""} downloaded`,this.totalBytesTransferred>0?YD(this.totalBytesTransferred):"",$].filter(Boolean).join(" | ");process.stderr.write(`${W.green(J)}
100
100
  `)}}}var kW=I(()=>{yD()});var wg={};c4(wg,{verifyGitHubAuth:()=>v9,toS3Credentials:()=>CD,switchBranch:()=>JE0,setKeyPresent:()=>Tg,selectAnnexS3Remote:()=>bW,saveDataset:()=>o8,runCommand:()=>S,resolveUpstreamRef:()=>iW,readRemoteHeadDatasetVersion:()=>nW,readLocalDatasetVersion:()=>cW,pushToGitHub:()=>a1,pushBranch:()=>PF,markInheritedOpenNeuroRemotesIgnored:()=>hW,listDatasetVersions:()=>mW,isWorkingTreeDirty:()=>aW,isGitAnnexDataset:()=>O1,isDataladDataset:()=>GE0,initOrEnableSpecialRemote:()=>Cg,initDataset:()=>c6,gitMergeFastForward:()=>sW,gitFetchOrigin:()=>oW,gitAnnexAdd:()=>n6,getVersionCommit:()=>lW,getRemoteUuid:()=>DH,getLocalDatasetInfo:()=>uW,getKeyHashDirs:()=>BE0,getKeyHashDir:()=>Og,getDatasetStats:()=>DE0,getDatasetIdFromRemote:()=>r8,getDatasetData:()=>GQ,getCurrentBranch:()=>s8,getAnnexWhereisAll:()=>eW,getAnnexS3Remotes:()=>x9,formatBytes:()=>YD,ensureLocalMainBranch:()=>_9,ensureGitAnnexInitialized:()=>fW,enableS3Remote:()=>g4,dropUnusedAnnexObjects:()=>rW,dropFiles:()=>gW,createRevertBranch:()=>pW,createDataladDataset:()=>XE0,countPendingDownload:()=>XQ,copyToAnnexRemote:()=>O8,configureS3Remote:()=>R8,configureLargefiles:()=>f4,configureGitHubRemote:()=>a8,commitRevert:()=>dW,collectFileManifest:()=>tW,cloneDataset:()=>o1,clearAnnexCredentials:()=>SD,checkPrerequisites:()=>k9,checkGitHubSSH:()=>Lg,checkGitAnnexInstalled:()=>_W,checkDownloadPrerequisites:()=>jF,checkAWSCredentials:()=>rz0,batchSetKeysPresent:()=>FH,annexRemoteExists:()=>Ng,acceptGitHubInvitation:()=>y9,NEMAR_S3_REMOTE_NAME:()=>BQ,ANNEX_REMOTE_EXISTS_RE:()=>Mg});import{existsSync as yW,readFileSync as az0,statSync as oz0}from"fs";import{join as xW}from"path";var{spawn:Ug}=globalThis.Bun;async function S(D,F={}){let $=Ug({cmd:D,cwd:F.cwd,stdout:"pipe",stderr:"pipe",env:{...process.env,GIT_TERMINAL_PROMPT:"0",...F.env}}),J=!1,Q;if(F.timeout)Q=setTimeout(()=>{J=!0,$.kill()},F.timeout);if(SW()){let G=F.cwd?` (cwd=${F.cwd})`:"";S9(W.dim(`$ ${D.join(" ")}${G}`))}let Y=await new Response($.stdout).text(),B=await new Response($.stderr).text(),X=await $.exited;if(Q)clearTimeout(Q);if(SW()){if(Y.trim())S9(W.dim(Y.trimEnd()));if(B.trim())S9(W.yellow(B.trimEnd()));S9(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 Eg(D){return D.split(".").map((F)=>{let $=Number.parseInt(F.replace(/[^0-9]/g,""),10);return Number.isNaN($)?0:$})}function sz0(D,F){let $=Eg(D),J=Eg(F);for(let Q=0;Q<Math.max($.length,J.length);Q++){let Y=$[Q]||0,B=J[Q]||0;if(Y>B)return!0;if(Y<B)return!1}return!0}async function _W(){try{let{stdout:F,exitCode:$,stderr:J}=await S(["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?sz0(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:$}}}async function Lg(){if(process.env.GH_TOKEN)return{accessible:!0,username:"token-auth",useHttps:!0};try{let{stdout:D,stderr:F}=await S(["ssh","-T","-o","BatchMode=yes","-o","StrictHostKeyChecking=accept-new","-o","ConnectTimeout=10","git@github.com"]),$=D+F,J=$.match(/Hi ([^!]+)!/);if(J)return{accessible:!0,username:J[1]};if($.includes("Permission denied"))return{accessible:!1};return{accessible:$.includes("successfully authenticated")}}catch(D){let F=D instanceof Error?D.message:String(D);if(F.includes("ENOENT")||F.includes("not found"))console.info("SSH command not found");else console.error("Error checking GitHub SSH access:",F);return{accessible:!1}}}async function rz0(){if(process.env.AWS_ACCESS_KEY_ID&&process.env.AWS_SECRET_ACCESS_KEY)return{configured:!0,source:"environment"};try{let{stdout:D,exitCode:F}=await S(["aws","configure","get","aws_access_key_id"]);if(F===0&&D.trim())return{configured:!0,source:"aws-cli"}}catch(D){let F=D instanceof Error?D.message:String(D);if(F.includes("ENOENT")||F.includes("not found"))console.info("AWS CLI not found in PATH");else console.error("Error checking AWS credentials:",F)}return{configured:!1}}function Ag(){let D=process.platform;if(D==="darwin")return"brew install git-annex";if(D==="linux")return"apt install git-annex (Debian/Ubuntu)";return"See https://git-annex.branchable.com/install/"}async function k9(){let[D,F]=await Promise.all([_W(),Lg()]),$=[];if(!D.installed)$.push(`git-annex is not installed. Install: ${Ag()}`);else if(D.compatible===!1)$.push(`git-annex version ${D.version} is too old. Required: >= ${D.minVersion}`);if(!F.accessible){if(!(await Rg()).token)$.push("GitHub authentication not configured. Run 'gh auth login' to authenticate.")}return{gitAnnex:D,githubSSH:F,allPassed:$.length===0,errors:$}}async function O1(D){if(!yW(xW(D,".git")))return!1;try{let{exitCode:F}=await S(["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 c6(D,F={}){if(!F.force&&await O1(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,$.GIT_COMMITTER_EMAIL=F.author.email;let{stderr:J,exitCode:Q}=await S(["git","init","-b","main",D],{...Object.keys($).length>0?{env:$}:{}});if(Q!==0)return{success:!1,error:J.trim()||"Failed to initialize git repository"};let Y=Object.keys($).length>0?{env:$}:{},{stderr:B,exitCode:X}=await S(["git","annex","init"],{cwd:D,...Y});if(X!==0)return{success:!1,error:B.trim()||"Failed to initialize git-annex"};let{stderr:G,exitCode:H}=await S(["git","commit","--allow-empty","-m","Initialize dataset"],{cwd:D,...Y});if(H!==0)return{success:!1,error:G.trim()||"Failed to create initial commit"};let{stderr:q,exitCode:K}=await S(["git","annex","adjust","--unlock"],{cwd:D,...Y});if(K!==0)return{success:!1,error:q.trim()||"Failed to switch to unlocked mode"};return{success:!0}}catch($){return{success:!1,error:$.message}}}async function fW(D){try{let{exitCode:F,stderr:$}=await S(["git","annex","info"],{cwd:D});if(F===0)return{success:!0};if($.includes("First run: git-annex init")){let{stderr:J,exitCode:Q}=await S(["git","annex","init"],{cwd:D});if(Q!==0)return{success:!1,error:J.trim()||"Failed to initialize git-annex"};return{success:!0}}return{success:!1,error:$.trim()||"Failed to check git-annex status"}}catch(F){return{success:!1,error:F.message}}}async function f4(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 ${Y}`,X=F||B;try{let{stderr:G,exitCode:H}=await S(["git","annex","config","--set","annex.largefiles",X],{cwd:D});if(H!==0)return{success:!1,error:G.trim()||"Failed to configure largefiles"};return{success:!0}}catch(G){return{success:!1,error:G.message}}}async function n6(D,F="."){try{let{stderr:$,exitCode:J}=await S(["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 vW(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": "0.8.12",
3
+ "version": "0.8.13-PR456.7ff9455",
4
4
  "description": "CLI for NEMAR (Neuroelectromagnetic Data Archive and Tools Resource) dataset management",
5
5
  "type": "module",
6
6
  "main": "dist/index.js",