nemar-cli 0.8.9-dev.713 → 0.8.9-dev.715
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.
- package/dist/index.js +1 -1
- 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
|
${F}
|
|
98
|
-
`)}var Wf=!1;var ZW=P(()=>{yD()});var qf;var Hf=P(()=>{qf={name:"nemar-cli",version:"0.8.9-dev.713",description:"CLI for NEMAR (Neuroelectromagnetic Data Archive and Tools Resource) dataset management",type:"module",main:"dist/index.js",bin:{nemar:"dist/index.js"},scripts:{dev:"bun run src/index.ts",build:"bun build src/index.ts --outdir dist --target bun --minify && sed '1s|#!/usr/bin/env node|#!/usr/bin/env bun|' dist/index.js > dist/index.js.tmp && mv dist/index.js.tmp dist/index.js",test:"bun test",lint:"biome check src/","lint:fix":"biome check --fix src/",format:"biome format --write src/",typecheck:"tsc --noEmit",prepublishOnly:"bun run build","docs:generate":"bun run scripts/generate-docs.ts","docs:serve":"mkdocs serve","docs:build":"mkdocs build",prepare:"husky",deploy:"wrangler deploy",preview:"wrangler dev"},keywords:["nemar","bids","neuroimaging","eeg","emg","datalad","cli"],author:"NEMAR Team",license:"CC-BY-NC-ND-4.0",repository:{type:"git",url:"git+https://github.com/nemarOrg/nemar-cli.git"},bugs:{url:"https://github.com/nemarOrg/nemar-cli/issues"},homepage:"https://nemar-cli.pages.dev",engines:{bun:">=1.0.0"},files:["dist","README.md","LICENSE"],dependencies:{chalk:"^5.3.0",commander:"^12.1.0",conf:"^13.0.1","fuse.js":"^7.1.0",inquirer:"^9.2.15",ora:"^8.0.1",zod:"^3.23.8"},"lint-staged":{"src/**/*.{ts,tsx}":["biome check --fix"],"backend/src/**/*.{ts,tsx}":["biome check --fix"]},devDependencies:{"@biomejs/biome":"1.9.4","@types/bcryptjs":"^3.0.0","@types/bun":"latest","@types/inquirer":"^9.0.7",bcryptjs:"^3.0.3",husky:"^9.1.7","lint-staged":"^16.3.2",typescript:"^5.5.4",wrangler:"^4.70.0"}}});var x4;var nJ=P(()=>{Hf();x4=qf.version});function T0(D){if(D instanceof Error)return D.message;return String(D)}function Kf(){if(process.env.TEST_API_URL)return process.env.TEST_API_URL;if(LW)return UW;return QD().apiUrl||UW}async function l(D,F={},$=!1){let J=`${Kf()}${D}`,Q={"Content-Type":"application/json","X-CLI-Version":x4,...F.headers};if($){let X=QD();if(!X.apiKey&&$===!0)throw new c(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 c(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 c(Y.status,`Invalid response from server (status ${Y.status})`)}if(!Y.ok){if(Y.status===503&&(B.mode==="read-only"||B.mode==="full")){let X=typeof B.message==="string"?B.message:"NEMAR is in maintenance mode. Please retry shortly.",G=typeof B.eta==="string"?B.eta:null,H=new aJ(B.mode,X,G,B.details);throw cJ(H),H}throw new c(Y.status,B.error||B.message||"Request failed",B.details,typeof B.step==="string"?B.step:void 0)}return B}async function Ef(D){return l(`/auth/check-username?username=${encodeURIComponent(D)}`)}async function Vf(D){return l(`/auth/check-github?username=${encodeURIComponent(D)}`)}async function Zf(D){return l("/auth/signup",{method:"POST",body:JSON.stringify(D)})}async function Uf(D){return l("/auth/login",{method:"POST",body:JSON.stringify({api_key:D})})}async function Lf(D){return l("/auth/resend-verification",{method:"POST",body:JSON.stringify({email:D})})}async function Af(D,F){return l("/auth/retrieve-key",{method:"POST",body:JSON.stringify({email:D,password:F})})}async function Mf(D){return l("/auth/request-key-regeneration",{method:"POST",body:JSON.stringify({email:D})})}async function oJ(){return l("/users/me",{},!0)}async function Nf(D,F){let $=new URLSearchParams;if(D)$.set("status",D);if(F)$.set("role",F);let J=$.toString()?`?${$.toString()}`:"";return l(`/admin/users${J}`,{},!0)}async function Cf(D){return l(`/admin/approve/${D}`,{method:"POST"},!0)}async function Rf(D){return l(`/admin/revoke/${D}`,{method:"POST"},!0)}async function Of(D,F){return l(`/admin/users/${D}/role`,{method:"POST",body:JSON.stringify({role:F})},!0)}async function AW(D,F){return l(`/admin/datasets/${D}/visibility`,{method:"PATCH",body:JSON.stringify({visibility:F})},!0)}async function Tf(D){return l(`/datasets/${D}/publish`,{method:"POST"},!0)}async function wf(D){return l(`/admin/datasets/${D}/ci`,{},!0)}async function _4(D){return l(`/admin/datasets/${D}/ci`,{method:"POST"},!0)}async function jf(D){return l(`/datasets/${D}/ci/status`,{},!0)}async function Pf(D){return l(`/datasets/${D}/manifest`,{},!0)}async function sJ(D,F){return l(`/datasets/${D}/manifest/${F}`,{},!0)}function If(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 rJ(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 l(`/datasets${$}`,{},D.mine?!0:"optional");return J.datasets=J.datasets.map(If),J}async function Sf(D){return l(`/datasets/resolve/${D}`,{},"optional")}async function kf(D,F={}){let $=new URLSearchParams({q:D});if(F.modality)$.set("modality",F.modality);if(F.limit)$.set("limit",String(F.limit));return l(`/datasets/search?${$.toString()}`,{},"optional")}async function bD(D){let F=await l(`/datasets/${D}`,{},"optional");return If(F.dataset)}async function vf(D){return l(`/datasets/${D}/versions`,{},!0)}async function tJ(D){return l("/datasets",{method:"POST",body:JSON.stringify(D)},!0)}async function eJ(D){return l(`/datasets/${D}/finalize`,{method:"POST"},!0)}async function C8(D,F){return l(`/datasets/${D}/upload-credentials`,{method:"POST",body:JSON.stringify({duration_seconds:F})},!0)}async function DQ(D,F){return l(`/datasets/${D}/download-credentials`,{method:"POST",body:JSON.stringify({duration_seconds:F})},!0)}async function yf(D,F){return l(`/admin/datasets/${D}/doi/concept`,{method:"POST",body:JSON.stringify(F)},!0)}async function P9(D){return l(`/admin/datasets/${D}/doi`,{},!0)}async function MW(D,F){return l(`/admin/datasets/${D}/doi/update`,{method:"POST",body:JSON.stringify(F)},!0)}async function NW(D){return l(`/datasets/${D}/request-access`,{method:"POST"},!0)}async function xf(D,F){return l(`/datasets/${D}/invite`,{method:"POST",body:JSON.stringify({username:F})},!0)}async function _f(D){return l(`/datasets/${D}/collaborators`,{},!0)}async function ff(D){return l("/sandbox/complete",{method:"POST",body:JSON.stringify({dataset_id:D})},!0)}async function gf(){return l("/sandbox/reset",{method:"POST"},!0)}async function hf(){return l("/sandbox/status",{},!0)}async function FQ(D){return l(`/datasets/${D}/publish/request`,{method:"POST"},!0)}async function bf(D){return l(`/datasets/${D}/publish/status`,{},!0)}async function uf(D){return l(`/datasets/${D}/publish/resend`,{method:"POST"},!0)}async function mf(D){let F=D?`?status=${D}`:"";return l(`/admin/publish/requests${F}`,{},!0)}async function lf(D,F){return l(`/admin/publish/${D}/deny`,{method:"POST",headers:{"Content-Type":"application/json"},body:JSON.stringify({reason:F})},!0)}function fz0(D){if(!(D instanceof c))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 $Q(D,F=!1,$=!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 l(`/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=zf(H);return V}catch(V){if(q=V,K===5||!fz0(V)){if(V instanceof c&&H.length>0)V.stepResults=zf(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 zf(D){let F=new Map;for(let $ of D)F.set($.step,$);return Array.from(F.values())}async function pf(D,F){return l(`/admin/datasets/${D}/enrichment`,{method:"POST",body:JSON.stringify(F)},!0)}async function df(D){return l(`/admin/datasets/${D}/files`,{},!0)}async function cf(D){let F,$=0,J=[],Q=!0;while(Q){let Y=await l(`/admin/datasets/${D}/s3-lock`,{method:"POST",headers:{"Content-Type":"application/json"},body:JSON.stringify({continuation_token:F})},!0);if($+=Y.locked,Y.failed?.length)J.push(...Y.failed);if(Q=Y.hasMore,F=Y.continuation_token,Q&&!F)throw new c(500,"S3 lock paginated response missing continuation_token; aborting to avoid infinite loop")}return{locked:$,failed:J}}async function nf(D){return l(`/admin/datasets/${D}/reset`,{method:"POST"},!0)}async function af(D,F=!1){return l(`/admin/datasets/${D}`,{method:"DELETE",headers:{"Content-Type":"application/json"},body:JSON.stringify({force:F})},!0)}async function of(D){return l("/admin/datasets/bulk-delete",{method:"POST",headers:{"Content-Type":"application/json"},body:JSON.stringify({dataset_ids:D})},!0)}async function sf(D){return l("/admin/datasets/import",{method:"POST",body:JSON.stringify(D)},!0)}async function rf(D){return l(`/admin/datasets/${D}/sync`,{method:"POST"},!0)}async function tf(){return l("/admin/sync/status",{},!0)}async function ef(){return l("/admin/email-preferences",{},!0)}async function Dg(D){return l("/admin/email-preferences",{method:"PUT",headers:{"Content-Type":"application/json"},body:JSON.stringify(D)},!0)}async function Fg(){return l("/notices",{},"optional")}async function $g(){return l("/admin/notices",{},!0)}async function Jg(D){return l("/admin/notices",{method:"POST",body:JSON.stringify(D)},!0)}async function Qg(D){return l(`/admin/notices/${D}`,{method:"DELETE"},!0)}async function CW(D){return l("/admin/notify",{method:"POST",body:JSON.stringify(D)},!0)}var UW="https://nemar-api-dev.sccn-org.workers.dev",iJ,c,aJ,LW;var n8=P(()=>{y4();ZW();nJ();iJ=/^\d{4}-\d{4}-\d{4}-\d{3}[\dX]$/;c=class c extends Error{statusCode;details;step;constructor(D,F,$,J){super(F);this.statusCode=D;this.details=$;this.step=J;this.name="ApiError"}};aJ=class aJ extends c{mode;eta;constructor(D,F,$,J){super(503,F,J);this.mode=D;this.eta=$;this.name="MaintenanceError"}};LW=UW.includes("workers.dev")});function Bg(D){RW=D}function OW(){return RW}function I9(D){if(RW)process.stderr.write(`${D}
|
|
98
|
+
`)}var Wf=!1;var ZW=P(()=>{yD()});var qf;var Hf=P(()=>{qf={name:"nemar-cli",version:"0.8.9-dev.715",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"}}});var x4;var nJ=P(()=>{Hf();x4=qf.version});function T0(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(LW)return UW;return QD().apiUrl||UW}async function l(D,F={},$=!1){let J=`${Kf()}${D}`,Q={"Content-Type":"application/json","X-CLI-Version":x4,...F.headers};if($){let X=QD();if(!X.apiKey&&$===!0)throw new c(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 c(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 c(Y.status,`Invalid response from server (status ${Y.status})`)}if(!Y.ok){if(Y.status===503&&(B.mode==="read-only"||B.mode==="full")){let X=typeof B.message==="string"?B.message:"NEMAR is in maintenance mode. Please retry shortly.",G=typeof B.eta==="string"?B.eta:null,H=new aJ(B.mode,X,G,B.details);throw cJ(H),H}throw new c(Y.status,B.error||B.message||"Request failed",B.details,typeof B.step==="string"?B.step:void 0)}return B}async function Ef(D){return l(`/auth/check-username?username=${encodeURIComponent(D)}`)}async function Vf(D){return l(`/auth/check-github?username=${encodeURIComponent(D)}`)}async function Zf(D){return l("/auth/signup",{method:"POST",body:JSON.stringify(D)})}async function Uf(D){return l("/auth/login",{method:"POST",body:JSON.stringify({api_key:D})})}async function Lf(D){return l("/auth/resend-verification",{method:"POST",body:JSON.stringify({email:D})})}async function Af(D,F){return l("/auth/retrieve-key",{method:"POST",body:JSON.stringify({email:D,password:F})})}async function Mf(D){return l("/auth/request-key-regeneration",{method:"POST",body:JSON.stringify({email:D})})}async function oJ(){return l("/users/me",{},!0)}async function Nf(D,F){let $=new URLSearchParams;if(D)$.set("status",D);if(F)$.set("role",F);let J=$.toString()?`?${$.toString()}`:"";return l(`/admin/users${J}`,{},!0)}async function Cf(D){return l(`/admin/approve/${D}`,{method:"POST"},!0)}async function Rf(D){return l(`/admin/revoke/${D}`,{method:"POST"},!0)}async function Of(D,F){return l(`/admin/users/${D}/role`,{method:"POST",body:JSON.stringify({role:F})},!0)}async function AW(D,F){return l(`/admin/datasets/${D}/visibility`,{method:"PATCH",body:JSON.stringify({visibility:F})},!0)}async function Tf(D){return l(`/datasets/${D}/publish`,{method:"POST"},!0)}async function wf(D){return l(`/admin/datasets/${D}/ci`,{},!0)}async function _4(D){return l(`/admin/datasets/${D}/ci`,{method:"POST"},!0)}async function jf(D){return l(`/datasets/${D}/ci/status`,{},!0)}async function Pf(D){return l(`/datasets/${D}/manifest`,{},!0)}async function sJ(D,F){return l(`/datasets/${D}/manifest/${F}`,{},!0)}function If(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 rJ(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 l(`/datasets${$}`,{},D.mine?!0:"optional");return J.datasets=J.datasets.map(If),J}async function Sf(D){return l(`/datasets/resolve/${D}`,{},"optional")}async function kf(D,F={}){let $=new URLSearchParams({q:D});if(F.modality)$.set("modality",F.modality);if(F.limit)$.set("limit",String(F.limit));return l(`/datasets/search?${$.toString()}`,{},"optional")}async function bD(D){let F=await l(`/datasets/${D}`,{},"optional");return If(F.dataset)}async function vf(D){return l(`/datasets/${D}/versions`,{},!0)}async function tJ(D){return l("/datasets",{method:"POST",body:JSON.stringify(D)},!0)}async function eJ(D){return l(`/datasets/${D}/finalize`,{method:"POST"},!0)}async function C8(D,F){return l(`/datasets/${D}/upload-credentials`,{method:"POST",body:JSON.stringify({duration_seconds:F})},!0)}async function DQ(D,F){return l(`/datasets/${D}/download-credentials`,{method:"POST",body:JSON.stringify({duration_seconds:F})},!0)}async function yf(D,F){return l(`/admin/datasets/${D}/doi/concept`,{method:"POST",body:JSON.stringify(F)},!0)}async function P9(D){return l(`/admin/datasets/${D}/doi`,{},!0)}async function MW(D,F){return l(`/admin/datasets/${D}/doi/update`,{method:"POST",body:JSON.stringify(F)},!0)}async function NW(D){return l(`/datasets/${D}/request-access`,{method:"POST"},!0)}async function xf(D,F){return l(`/datasets/${D}/invite`,{method:"POST",body:JSON.stringify({username:F})},!0)}async function _f(D){return l(`/datasets/${D}/collaborators`,{},!0)}async function ff(D){return l("/sandbox/complete",{method:"POST",body:JSON.stringify({dataset_id:D})},!0)}async function gf(){return l("/sandbox/reset",{method:"POST"},!0)}async function hf(){return l("/sandbox/status",{},!0)}async function FQ(D){return l(`/datasets/${D}/publish/request`,{method:"POST"},!0)}async function bf(D){return l(`/datasets/${D}/publish/status`,{},!0)}async function uf(D){return l(`/datasets/${D}/publish/resend`,{method:"POST"},!0)}async function mf(D){let F=D?`?status=${D}`:"";return l(`/admin/publish/requests${F}`,{},!0)}async function lf(D,F){return l(`/admin/publish/${D}/deny`,{method:"POST",headers:{"Content-Type":"application/json"},body:JSON.stringify({reason:F})},!0)}function fz0(D){if(!(D instanceof c))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 $Q(D,F=!1,$=!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 l(`/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=zf(H);return V}catch(V){if(q=V,K===5||!fz0(V)){if(V instanceof c&&H.length>0)V.stepResults=zf(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 zf(D){let F=new Map;for(let $ of D)F.set($.step,$);return Array.from(F.values())}async function pf(D,F){return l(`/admin/datasets/${D}/enrichment`,{method:"POST",body:JSON.stringify(F)},!0)}async function df(D){return l(`/admin/datasets/${D}/files`,{},!0)}async function cf(D){let F,$=0,J=[],Q=!0;while(Q){let Y=await l(`/admin/datasets/${D}/s3-lock`,{method:"POST",headers:{"Content-Type":"application/json"},body:JSON.stringify({continuation_token:F})},!0);if($+=Y.locked,Y.failed?.length)J.push(...Y.failed);if(Q=Y.hasMore,F=Y.continuation_token,Q&&!F)throw new c(500,"S3 lock paginated response missing continuation_token; aborting to avoid infinite loop")}return{locked:$,failed:J}}async function nf(D){return l(`/admin/datasets/${D}/reset`,{method:"POST"},!0)}async function af(D,F=!1){return l(`/admin/datasets/${D}`,{method:"DELETE",headers:{"Content-Type":"application/json"},body:JSON.stringify({force:F})},!0)}async function of(D){return l("/admin/datasets/bulk-delete",{method:"POST",headers:{"Content-Type":"application/json"},body:JSON.stringify({dataset_ids:D})},!0)}async function sf(D){return l("/admin/datasets/import",{method:"POST",body:JSON.stringify(D)},!0)}async function rf(D){return l(`/admin/datasets/${D}/sync`,{method:"POST"},!0)}async function tf(){return l("/admin/sync/status",{},!0)}async function ef(){return l("/admin/email-preferences",{},!0)}async function Dg(D){return l("/admin/email-preferences",{method:"PUT",headers:{"Content-Type":"application/json"},body:JSON.stringify(D)},!0)}async function Fg(){return l("/notices",{},"optional")}async function $g(){return l("/admin/notices",{},!0)}async function Jg(D){return l("/admin/notices",{method:"POST",body:JSON.stringify(D)},!0)}async function Qg(D){return l(`/admin/notices/${D}`,{method:"DELETE"},!0)}async function CW(D){return l("/admin/notify",{method:"POST",body:JSON.stringify(D)},!0)}var UW="https://nemar-api-dev.sccn-org.workers.dev",iJ,c,aJ,LW;var n8=P(()=>{y4();ZW();nJ();iJ=/^\d{4}-\d{4}-\d{4}-\d{3}[\dX]$/;c=class c extends Error{statusCode;details;step;constructor(D,F,$,J){super(F);this.statusCode=D;this.details=$;this.step=J;this.name="ApiError"}};aJ=class aJ extends c{mode;eta;constructor(D,F,$,J){super(503,F,J);this.mode=D;this.eta=$;this.name="MaintenanceError"}};LW=UW.includes("workers.dev")});function Bg(D){RW=D}function OW(){return RW}function I9(D){if(RW)process.stderr.write(`${D}
|
|
99
99
|
`)}var RW=!1;function BD(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`${BD(D)}/s`}function gz0(D){if(D<60)return`${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 hz0(D,F=20){let $=Math.round(D/100*F),J=F-$;return`[${"=".repeat($)}${" ".repeat(J)}]`}class JQ{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`:`${this.filesCompleted} files`,Y;if(J)Y=`${hz0($)} ${$}% ${Q}`;else Y=Q;if(F>0){let B=this.bytesTotal>0?`${BD(F)}/${BD(this.bytesTotal)}`:BD(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 ${gz0(X)}`}}if(Y!==this.lastRenderedLine)process.stderr.write(`\r${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?BD(this.totalBytesTransferred):"",$].filter(Boolean).join(" | ");process.stderr.write(`${W.green(J)}
|
|
100
100
|
`)}}}var TW=P(()=>{yD()});var Mg={};d4(Mg,{verifyGitHubAuth:()=>k9,toS3Credentials:()=>CD,switchBranch:()=>az0,setKeyPresent:()=>Ag,selectAnnexS3Remote:()=>yW,saveDataset:()=>a8,runCommand:()=>I,resolveUpstreamRef:()=>mW,readRemoteHeadDatasetVersion:()=>uW,readLocalDatasetVersion:()=>bW,pushToGitHub:()=>a1,pushBranch:()=>jF,markInheritedOpenNeuroRemotesIgnored:()=>vW,listDatasetVersions:()=>_W,isWorkingTreeDirty:()=>lW,isGitAnnexDataset:()=>O1,isDataladDataset:()=>ez0,initOrEnableSpecialRemote:()=>Zg,initDataset:()=>d6,gitMergeFastForward:()=>dW,gitFetchOrigin:()=>pW,gitAnnexAdd:()=>c6,getVersionCommit:()=>fW,getRemoteUuid:()=>aW,getLocalDatasetInfo:()=>xW,getKeyHashDirs:()=>rz0,getKeyHashDir:()=>Lg,getDatasetStats:()=>cz0,getDatasetIdFromRemote:()=>s8,getDatasetData:()=>BQ,getCurrentBranch:()=>o8,getAnnexWhereisAll:()=>iW,getAnnexS3Remotes:()=>y9,formatBytes:()=>BD,ensureLocalMainBranch:()=>x9,ensureGitAnnexInitialized:()=>SW,enableS3Remote:()=>g4,dropUnusedAnnexObjects:()=>cW,dropFiles:()=>kW,createRevertBranch:()=>gW,createDataladDataset:()=>tz0,countPendingDownload:()=>YQ,copyToAnnexRemote:()=>O8,configureS3Remote:()=>R8,configureLargefiles:()=>f4,configureGitHubRemote:()=>i8,commitRevert:()=>hW,collectFileManifest:()=>nW,cloneDataset:()=>o1,clearAnnexCredentials:()=>kD,checkPrerequisites:()=>S9,checkGitHubSSH:()=>Kg,checkGitAnnexInstalled:()=>IW,checkDownloadPrerequisites:()=>wF,checkAWSCredentials:()=>lz0,batchSetKeysPresent:()=>oW,annexRemoteExists:()=>Vg,acceptGitHubInvitation:()=>v9,NEMAR_S3_REMOTE_NAME:()=>QQ,ANNEX_REMOTE_EXISTS_RE:()=>Eg});import{existsSync as jW,readFileSync as bz0,statSync as uz0}from"fs";import{join as PW}from"path";var{spawn:qg}=globalThis.Bun;async function I(D,F={}){let $=qg({cmd:D,cwd:F.cwd,stdout:"pipe",stderr:"pipe",env:{...process.env,GIT_TERMINAL_PROMPT:"0",...F.env}}),J=!1,Q;if(F.timeout)Q=setTimeout(()=>{J=!0,$.kill()},F.timeout);if(OW()){let G=F.cwd?` (cwd=${F.cwd})`:"";I9(W.dim(`$ ${D.join(" ")}${G}`))}let Y=await new Response($.stdout).text(),B=await new Response($.stderr).text(),X=await $.exited;if(Q)clearTimeout(Q);if(OW()){if(Y.trim())I9(W.dim(Y.trimEnd()));if(B.trim())I9(W.yellow(B.trimEnd()));I9(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 Gg(D){return D.split(".").map((F)=>{let $=Number.parseInt(F.replace(/[^0-9]/g,""),10);return Number.isNaN($)?0:$})}function mz0(D,F){let $=Gg(D),J=Gg(F);for(let Q=0;Q<Math.max($.length,J.length);Q++){let Y=$[Q]||0,B=J[Q]||0;if(Y>B)return!0;if(Y<B)return!1}return!0}async function IW(){try{let{stdout:F,exitCode:$,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?mz0(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:$}}}async function Kg(){if(process.env.GH_TOKEN)return{accessible:!0,username:"token-auth",useHttps:!0};try{let{stdout:D,stderr:F}=await I(["ssh","-T","-o","BatchMode=yes","-o","StrictHostKeyChecking=accept-new","-o","ConnectTimeout=10","git@github.com"]),$=D+F,J=$.match(/Hi ([^!]+)!/);if(J)return{accessible:!0,username:J[1]};if($.includes("Permission denied"))return{accessible:!1};return{accessible:$.includes("successfully authenticated")}}catch(D){let F=D instanceof Error?D.message:String(D);if(F.includes("ENOENT")||F.includes("not found"))console.info("SSH command not found");else console.error("Error checking GitHub SSH access:",F);return{accessible:!1}}}async function lz0(){if(process.env.AWS_ACCESS_KEY_ID&&process.env.AWS_SECRET_ACCESS_KEY)return{configured:!0,source:"environment"};try{let{stdout:D,exitCode:F}=await I(["aws","configure","get","aws_access_key_id"]);if(F===0&&D.trim())return{configured:!0,source:"aws-cli"}}catch(D){let F=D instanceof Error?D.message:String(D);if(F.includes("ENOENT")||F.includes("not found"))console.info("AWS CLI not found in PATH");else console.error("Error checking AWS credentials:",F)}return{configured:!1}}function zg(){let D=process.platform;if(D==="darwin")return"brew install git-annex";if(D==="linux")return"apt install git-annex (Debian/Ubuntu)";return"See https://git-annex.branchable.com/install/"}async function S9(){let[D,F]=await Promise.all([IW(),Kg()]),$=[];if(!D.installed)$.push(`git-annex is not installed. Install: ${zg()}`);else if(D.compatible===!1)$.push(`git-annex version ${D.version} is too old. Required: >= ${D.minVersion}`);if(!F.accessible){if(!(await Ug()).token)$.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(!jW(PW(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 d6(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,$.GIT_COMMITTER_EMAIL=F.author.email;let{stderr:J,exitCode:Q}=await I(["git","init","-b","main",D],{...Object.keys($).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:$.message}}}async function SW(D){try{let{exitCode:F,stderr:$}=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 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 ${Y}`,X=F||B;try{let{stderr:G,exitCode:H}=await I(["git","annex","config","--set","annex.largefiles",X],{cwd:D});if(H!==0)return{success:!1,error:G.trim()||"Failed to configure largefiles"};return{success:!0}}catch(G){return{success:!1,error:G.message}}}async function c6(D,F="."){try{let{stderr:$,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 wW(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