nemar-cli 0.8.35-dev.1146 → 0.8.35-dev.1149
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
|
${F}
|
|
98
|
-
`)}var Rf=!1;var wW=P(()=>{vD()});var wf;var Of=P(()=>{wf={name:"nemar-cli",version:"0.8.35-dev.1146",description:"CLI for NEMAR (Neuroelectromagnetic Data Archive and Tools Resource) dataset management",type:"module",main:"dist/index.js",bin:{nemar:"dist/index.js"},scripts:{dev:"bun run src/index.ts",build:"bun build src/index.ts --outdir dist --target bun --minify && sed '1s|#!/usr/bin/env node|#!/usr/bin/env bun|' dist/index.js > dist/index.js.tmp && mv dist/index.js.tmp dist/index.js",test:"bun test",lint:"biome check src/","lint:fix":"biome check --fix src/",format:"biome format --write src/",typecheck:"tsc --noEmit",prepublishOnly:"bun run build","docs:generate":"bun run scripts/generate-docs.ts","docs:serve":"mkdocs serve","docs:build":"mkdocs build",prepare:"husky",deploy:"wrangler deploy",preview:"wrangler dev"},keywords:["nemar","bids","neuroimaging","eeg","emg","datalad","cli"],author:"NEMAR Team",license:"CC-BY-NC-ND-4.0",repository:{type:"git",url:"git+https://github.com/nemarOrg/nemar-cli.git"},bugs:{url:"https://github.com/nemarOrg/nemar-cli/issues"},homepage:"https://nemar-cli.pages.dev",engines:{bun:">=1.0.0"},files:["dist","README.md","LICENSE"],dependencies:{chalk:"^5.3.0",commander:"^12.1.0",conf:"^13.0.1","fuse.js":"^7.1.0",inquirer:"^9.2.15",ora:"^8.0.1",zod:"^3.23.8"},"lint-staged":{"src/**/*.{ts,tsx}":["biome check --fix"],"backend/src/**/*.{ts,tsx}":["biome check --fix"]},devDependencies:{"@biomejs/biome":"1.9.4","@types/bcryptjs":"^3.0.0","@types/bun":"latest","@types/inquirer":"^9.0.7",bcryptjs:"^3.0.3",husky:"^9.1.7","lint-staged":"^16.3.2",typescript:"^5.5.4",wrangler:"^4.70.0",yaml:"^2.8.4"}}});var g4;var eJ=P(()=>{Of();g4=wf.version});function R0(D){if(D instanceof Error)return D.message;return String(D)}function jf(){if(process.env.TEST_API_URL)return process.env.TEST_API_URL;if(TW)return jW;return BD().apiUrl||jW}async function b(D,F={},$=!1){let J=`${jf()}${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 ${jf()}`,{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 ${Y.status})`)}if(!Y.ok){if(Y.status===503&&(B.mode==="read-only"||B.mode==="full")){let X=typeof B.message==="string"?B.message:"NEMAR is in maintenance mode. Please retry shortly.",G=typeof B.eta==="string"?B.eta:null,H=new FQ(B.mode,X,G,B.details);throw tJ(H),H}throw new h(Y.status,B.error||B.message||"Request failed",B.details,typeof B.step==="string"?B.step:void 0)}return B}async function Pf(D){return b(`/auth/check-username?username=${encodeURIComponent(D)}`)}async function If(D){return b(`/auth/check-github?username=${encodeURIComponent(D)}`)}async function Sf(D){return b("/auth/signup",{method:"POST",body:JSON.stringify(D)})}async function kf(D){return b("/auth/login",{method:"POST",body:JSON.stringify({api_key:D})})}async function vf(D){return b("/auth/resend-verification",{method:"POST",body:JSON.stringify({email:D})})}async function yf(D,F){return b("/auth/retrieve-key",{method:"POST",body:JSON.stringify({email:D,password:F})})}async function xf(D){return b("/auth/request-key-regeneration",{method:"POST",body:JSON.stringify({email:D})})}async function $Q(){return b("/users/me",{},!0)}async function _f(D,F){let $=new URLSearchParams;if(D)$.set("status",D);if(F)$.set("role",F);let J=$.toString()?`?${$.toString()}`:"";return b(`/admin/users${J}`,{},!0)}async function ff(D){return b(`/admin/approve/${D}`,{method:"POST"},!0)}async function gf(D){return b(`/admin/revoke/${D}`,{method:"POST"},!0)}async function hf(D,F){return b(`/admin/users/${D}/role`,{method:"POST",body:JSON.stringify({role:F})},!0)}async function PW(D,F){return b(`/admin/datasets/${D}/visibility`,{method:"PATCH",body:JSON.stringify({visibility:F})},!0)}async function bf(D){return b(`/datasets/${D}/publish`,{method:"POST"},!0)}async function uf(D){return b(`/admin/datasets/${D}/ci`,{},!0)}async function h4(D){return b(`/admin/datasets/${D}/ci`,{method:"POST"},!0)}async function IW(D){return b(`/admin/datasets/${D}/ci/validate`,{method:"POST"},!0)}async function SW(D){return b(`/admin/datasets/${D}/ci/sync`,{method:"POST"},!0)}async function JQ(D){return b(`/datasets/${D}/ci/status`,{},!0)}async function mf(D){return b(`/datasets/${D}/manifest`,{},!0)}async function QQ(D,F){return b(`/datasets/${D}/manifest/${F}`,{},!0)}function lf(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 v9(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(lf),J}async function pf(D){return b(`/datasets/resolve/${D}`,{},"optional")}async function df(D,F={}){let $=new URLSearchParams({q:D});if(F.modality)$.set("modality",F.modality);if(F.limit)$.set("limit",String(F.limit));return b(`/datasets/search?${$.toString()}`,{},"optional")}async function hD(D){let F=await b(`/datasets/${D}`,{},"optional");return lf(F.dataset)}async function cf(D){return b(`/datasets/${D}/versions`,{},!0)}async function YQ(D){return b("/datasets",{method:"POST",body:JSON.stringify(D)},!0)}async function BQ(D){return b(`/datasets/${D}/finalize`,{method:"POST"},!0)}async function R8(D,F){return b(`/datasets/${D}/upload-credentials`,{method:"POST",body:JSON.stringify({duration_seconds:F})},!0)}async function XQ(D,F){return b(`/datasets/${D}/download-credentials`,{method:"POST",body:JSON.stringify({duration_seconds:F})},!0)}async function nf(D,F){return b(`/admin/datasets/${D}/doi/concept`,{method:"POST",body:JSON.stringify(F)},!0)}async function y9(D){return b(`/admin/datasets/${D}/doi`,{},!0)}async function kW(D,F){return b(`/admin/datasets/${D}/doi/update`,{method:"POST",body:JSON.stringify(F)},!0)}async function vW(D){return b(`/datasets/${D}/request-access`,{method:"POST"},!0)}async function af(D,F){return b(`/datasets/${D}/invite`,{method:"POST",body:JSON.stringify({username:F})},!0)}async function of(D){return b(`/datasets/${D}/collaborators`,{},!0)}async function sf(D){return b("/sandbox/complete",{method:"POST",body:JSON.stringify({dataset_id:D})},!0)}async function rf(){return b("/sandbox/reset",{method:"POST"},!0)}async function tf(){return b("/sandbox/status",{},!0)}async function GQ(D){return b(`/datasets/${D}/publish/request`,{method:"POST"},!0)}async function ef(D){return b(`/datasets/${D}/publish/status`,{},!0)}async function Dg(D){return b(`/datasets/${D}/publish/resend`,{method:"POST"},!0)}async function Fg(D){let F=D?`?status=${D}`:"";return b(`/admin/publish/requests${F}`,{},!0)}async function $g(D,F){return b(`/admin/publish/${D}/deny`,{method:"POST",headers:{"Content-Type":"application/json"},body:JSON.stringify({reason:F})},!0)}function qE0(D,F=[]){if(D){let $=k9.indexOf(D);if($>=0)return $+1}return Math.min(F.length+1,k9.length)}function KE0(D){if(!(D instanceof h))return!1;if(D.statusCode===0)return!0;if(D.statusCode===429)return!0;if(D.statusCode>=500&&D.statusCode<600)return!0;if(D.statusCode===403&&/repository has been locked/i.test(D.message))return!0;return!1}async function WQ(D,F=!1,$=!1,J=!1,Q,Y){let G,H,q=0,K=!1,V,E=F,Z=[],L;function M(A,N,w,S){if(!Y)return;Y({step:A,stepIndex:qE0(A,N),stepTotal:k9.length,s3LockLocked:w,s3LockTotal:S,s3LockResumed:A==="s3_lock"&&K?!0:void 0})}for(let A=1;A<=5;A++)try{let N,w=!0;do{if(N=await b(`/admin/publish/${D}/approve`,{method:"POST",headers:{"Content-Type":"application/json"},body:JSON.stringify({resume:w?E:!0,sandbox:$,s3_lock_continuation_token:G,s3_lock_total:H,skip_ci_check:J})},!0),w=!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=Tf(Z);return N}catch(N){if(L=N,A===5||!KE0(N)){if(N instanceof h&&Z.length>0)N.stepResults=Tf(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 Tf(D){let F=new Map;for(let $ of D)F.set($.step,$);return Array.from(F.values())}async function Jg(D,F){return b(`/admin/datasets/${D}/enrichment`,{method:"POST",body:JSON.stringify(F)},!0)}async function Qg(D){return b(`/admin/datasets/${D}/files`,{},!0)}async function Yg(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($+=Y.locked,Y.failed?.length)J.push(...Y.failed);if(Q=Y.hasMore,F=Y.continuation_token,Q&&!F)throw new h(500,"S3 lock paginated response missing continuation_token; aborting to avoid infinite loop")}return{locked:$,failed:J}}async function Bg(D){return b(`/admin/datasets/${D}/reset`,{method:"POST"},!0)}async function Xg(D,F=!1){return b(`/admin/datasets/${D}`,{method:"DELETE",headers:{"Content-Type":"application/json"},body:JSON.stringify({force:F})},!0)}async function Gg(D){return b("/admin/datasets/bulk-delete",{method:"POST",headers:{"Content-Type":"application/json"},body:JSON.stringify({dataset_ids:D})},!0)}async function Wg(D){return b("/admin/datasets/import",{method:"POST",body:JSON.stringify(D)},!0)}async function Hg(D){return b(`/admin/datasets/${D}/sync`,{method:"POST"},!0)}async function qg(){return b("/admin/sync/status",{},!0)}async function HQ(D,F){return b(`/admin/datasets/${D}/reindex`,{method:"POST",headers:{"Content-Type":"application/json"},body:JSON.stringify(F??{})},!0)}async function Kg(D,F){return b("/admin/datasets/reindex/bulk",{method:"POST",headers:{"Content-Type":"application/json"},body:JSON.stringify({filter:D,...F??{}})},!0)}async function zg(){return b("/admin/email-preferences",{},!0)}async function Eg(D){return b("/admin/email-preferences",{method:"PUT",headers:{"Content-Type":"application/json"},body:JSON.stringify(D)},!0)}async function Vg(){return b("/notices",{},"optional")}async function Zg(){return b("/admin/notices",{},!0)}async function Ug(D){return b("/admin/notices",{method:"POST",body:JSON.stringify(D)},!0)}async function Lg(D){return b(`/admin/notices/${D}`,{method:"DELETE"},!0)}async function yW(D){return b("/admin/notify",{method:"POST",body:JSON.stringify(D)},!0)}var jW="https://nemar-api-dev.sccn-org.workers.dev",DQ,h,FQ,TW,k9;var i8=P(()=>{f4();wW();eJ();DQ=/^\d{4}-\d{4}-\d{4}-\d{3}[\dX]$/;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"}};FQ=class FQ extends h{mode;eta;constructor(D,F,$,J){super(503,F,J);this.mode=D;this.eta=$;this.name="MaintenanceError"}};TW=jW.includes("workers.dev");k9=["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","generate_archive","sync_nemar","notify_user"]});function Mg(D){xW=D}function _W(){return xW}function x9(D){if(xW)process.stderr.write(`${D}
|
|
98
|
+
`)}var Rf=!1;var wW=P(()=>{vD()});var wf;var Of=P(()=>{wf={name:"nemar-cli",version:"0.8.35-dev.1149",description:"CLI for NEMAR (Neuroelectromagnetic Data Archive and Tools Resource) dataset management",type:"module",main:"dist/index.js",bin:{nemar:"dist/index.js"},scripts:{dev:"bun run src/index.ts",build:"bun build src/index.ts --outdir dist --target bun --minify && sed '1s|#!/usr/bin/env node|#!/usr/bin/env bun|' dist/index.js > dist/index.js.tmp && mv dist/index.js.tmp dist/index.js",test:"bun test",lint:"biome check src/","lint:fix":"biome check --fix src/",format:"biome format --write src/",typecheck:"tsc --noEmit",prepublishOnly:"bun run build","docs:generate":"bun run scripts/generate-docs.ts","docs:serve":"mkdocs serve","docs:build":"mkdocs build",prepare:"husky",deploy:"wrangler deploy",preview:"wrangler dev"},keywords:["nemar","bids","neuroimaging","eeg","emg","datalad","cli"],author:"NEMAR Team",license:"CC-BY-NC-ND-4.0",repository:{type:"git",url:"git+https://github.com/nemarOrg/nemar-cli.git"},bugs:{url:"https://github.com/nemarOrg/nemar-cli/issues"},homepage:"https://nemar-cli.pages.dev",engines:{bun:">=1.0.0"},files:["dist","README.md","LICENSE"],dependencies:{chalk:"^5.3.0",commander:"^12.1.0",conf:"^13.0.1","fuse.js":"^7.1.0",inquirer:"^9.2.15",ora:"^8.0.1",zod:"^3.23.8"},"lint-staged":{"src/**/*.{ts,tsx}":["biome check --fix"],"backend/src/**/*.{ts,tsx}":["biome check --fix"]},devDependencies:{"@biomejs/biome":"1.9.4","@types/bcryptjs":"^3.0.0","@types/bun":"latest","@types/inquirer":"^9.0.7",bcryptjs:"^3.0.3",husky:"^9.1.7","lint-staged":"^16.3.2",typescript:"^5.5.4",wrangler:"^4.70.0",yaml:"^2.8.4"}}});var g4;var eJ=P(()=>{Of();g4=wf.version});function R0(D){if(D instanceof Error)return D.message;return String(D)}function jf(){if(process.env.TEST_API_URL)return process.env.TEST_API_URL;if(TW)return jW;return BD().apiUrl||jW}async function b(D,F={},$=!1){let J=`${jf()}${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 ${jf()}`,{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 ${Y.status})`)}if(!Y.ok){if(Y.status===503&&(B.mode==="read-only"||B.mode==="full")){let X=typeof B.message==="string"?B.message:"NEMAR is in maintenance mode. Please retry shortly.",G=typeof B.eta==="string"?B.eta:null,H=new FQ(B.mode,X,G,B.details);throw tJ(H),H}throw new h(Y.status,B.error||B.message||"Request failed",B.details,typeof B.step==="string"?B.step:void 0)}return B}async function Pf(D){return b(`/auth/check-username?username=${encodeURIComponent(D)}`)}async function If(D){return b(`/auth/check-github?username=${encodeURIComponent(D)}`)}async function Sf(D){return b("/auth/signup",{method:"POST",body:JSON.stringify(D)})}async function kf(D){return b("/auth/login",{method:"POST",body:JSON.stringify({api_key:D})})}async function vf(D){return b("/auth/resend-verification",{method:"POST",body:JSON.stringify({email:D})})}async function yf(D,F){return b("/auth/retrieve-key",{method:"POST",body:JSON.stringify({email:D,password:F})})}async function xf(D){return b("/auth/request-key-regeneration",{method:"POST",body:JSON.stringify({email:D})})}async function $Q(){return b("/users/me",{},!0)}async function _f(D,F){let $=new URLSearchParams;if(D)$.set("status",D);if(F)$.set("role",F);let J=$.toString()?`?${$.toString()}`:"";return b(`/admin/users${J}`,{},!0)}async function ff(D){return b(`/admin/approve/${D}`,{method:"POST"},!0)}async function gf(D){return b(`/admin/revoke/${D}`,{method:"POST"},!0)}async function hf(D,F){return b(`/admin/users/${D}/role`,{method:"POST",body:JSON.stringify({role:F})},!0)}async function PW(D,F){return b(`/admin/datasets/${D}/visibility`,{method:"PATCH",body:JSON.stringify({visibility:F})},!0)}async function bf(D){return b(`/datasets/${D}/publish`,{method:"POST"},!0)}async function uf(D){return b(`/admin/datasets/${D}/ci`,{},!0)}async function h4(D){return b(`/admin/datasets/${D}/ci`,{method:"POST"},!0)}async function IW(D){return b(`/admin/datasets/${D}/ci/validate`,{method:"POST"},!0)}async function SW(D){return b(`/admin/datasets/${D}/ci/sync`,{method:"POST"},!0)}async function JQ(D){return b(`/datasets/${D}/ci/status`,{},!0)}async function mf(D){return b(`/datasets/${D}/manifest`,{},!0)}async function QQ(D,F){return b(`/datasets/${D}/manifest/${F}`,{},!0)}function lf(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 v9(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(lf),J}async function pf(D){return b(`/datasets/resolve/${D}`,{},"optional")}async function df(D,F={}){let $=new URLSearchParams({q:D});if(F.modality)$.set("modality",F.modality);if(F.limit)$.set("limit",String(F.limit));return b(`/datasets/search?${$.toString()}`,{},"optional")}async function hD(D){let F=await b(`/datasets/${D}`,{},"optional");return lf(F.dataset)}async function cf(D){return b(`/datasets/${D}/versions`,{},!0)}async function YQ(D){return b("/datasets",{method:"POST",body:JSON.stringify(D)},!0)}async function BQ(D){return b(`/datasets/${D}/finalize`,{method:"POST"},!0)}async function R8(D,F){return b(`/datasets/${D}/upload-credentials`,{method:"POST",body:JSON.stringify({duration_seconds:F})},!0)}async function XQ(D,F){return b(`/datasets/${D}/download-credentials`,{method:"POST",body:JSON.stringify({duration_seconds:F})},!0)}async function nf(D,F){return b(`/admin/datasets/${D}/doi/concept`,{method:"POST",body:JSON.stringify(F)},!0)}async function y9(D){return b(`/admin/datasets/${D}/doi`,{},!0)}async function kW(D,F){return b(`/admin/datasets/${D}/doi/update`,{method:"POST",body:JSON.stringify(F)},!0)}async function vW(D){return b(`/datasets/${D}/request-access`,{method:"POST"},!0)}async function af(D,F){return b(`/datasets/${D}/invite`,{method:"POST",body:JSON.stringify({username:F})},!0)}async function of(D){return b(`/datasets/${D}/collaborators`,{},!0)}async function sf(D){return b("/sandbox/complete",{method:"POST",body:JSON.stringify({dataset_id:D})},!0)}async function rf(){return b("/sandbox/reset",{method:"POST"},!0)}async function tf(){return b("/sandbox/status",{},!0)}async function GQ(D){return b(`/datasets/${D}/publish/request`,{method:"POST"},!0)}async function ef(D){return b(`/datasets/${D}/publish/status`,{},!0)}async function Dg(D){return b(`/datasets/${D}/publish/resend`,{method:"POST"},!0)}async function Fg(D){let F=D?`?status=${D}`:"";return b(`/admin/publish/requests${F}`,{},!0)}async function $g(D,F){return b(`/admin/publish/${D}/deny`,{method:"POST",headers:{"Content-Type":"application/json"},body:JSON.stringify({reason:F})},!0)}function qE0(D,F=[]){if(D){let $=k9.indexOf(D);if($>=0)return $+1}return Math.min(F.length+1,k9.length)}function KE0(D){if(!(D instanceof h))return!1;if(D.statusCode===0)return!0;if(D.statusCode===429)return!0;if(D.statusCode>=500&&D.statusCode<600)return!0;if(D.statusCode===403&&/repository has been locked/i.test(D.message))return!0;return!1}async function WQ(D,F=!1,$=!1,J=!1,Q,Y){let G,H,q=0,K=!1,V,E=F,Z=[],L;function M(A,N,w,S){if(!Y)return;Y({step:A,stepIndex:qE0(A,N),stepTotal:k9.length,s3LockLocked:w,s3LockTotal:S,s3LockResumed:A==="s3_lock"&&K?!0:void 0})}for(let A=1;A<=5;A++)try{let N,w=!0;do{if(N=await b(`/admin/publish/${D}/approve`,{method:"POST",headers:{"Content-Type":"application/json"},body:JSON.stringify({resume:w?E:!0,sandbox:$,s3_lock_continuation_token:G,s3_lock_total:H,skip_ci_check:J})},!0),w=!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=Tf(Z);return N}catch(N){if(L=N,A===5||!KE0(N)){if(N instanceof h&&Z.length>0)N.stepResults=Tf(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 Tf(D){let F=new Map;for(let $ of D)F.set($.step,$);return Array.from(F.values())}async function Jg(D,F){return b(`/admin/datasets/${D}/enrichment`,{method:"POST",body:JSON.stringify(F)},!0)}async function Qg(D){return b(`/admin/datasets/${D}/files`,{},!0)}async function Yg(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($+=Y.locked,Y.failed?.length)J.push(...Y.failed);if(Q=Y.hasMore,F=Y.continuation_token,Q&&!F)throw new h(500,"S3 lock paginated response missing continuation_token; aborting to avoid infinite loop")}return{locked:$,failed:J}}async function Bg(D){return b(`/admin/datasets/${D}/reset`,{method:"POST"},!0)}async function Xg(D,F=!1){return b(`/admin/datasets/${D}`,{method:"DELETE",headers:{"Content-Type":"application/json"},body:JSON.stringify({force:F})},!0)}async function Gg(D){return b("/admin/datasets/bulk-delete",{method:"POST",headers:{"Content-Type":"application/json"},body:JSON.stringify({dataset_ids:D})},!0)}async function Wg(D){return b("/admin/datasets/import",{method:"POST",body:JSON.stringify(D)},!0)}async function Hg(D){return b(`/admin/datasets/${D}/sync`,{method:"POST"},!0)}async function qg(){return b("/admin/sync/status",{},!0)}async function HQ(D,F){return b(`/admin/datasets/${D}/reindex`,{method:"POST",headers:{"Content-Type":"application/json"},body:JSON.stringify(F??{})},!0)}async function Kg(D,F){return b("/admin/datasets/reindex/bulk",{method:"POST",headers:{"Content-Type":"application/json"},body:JSON.stringify({filter:D,...F??{}})},!0)}async function zg(){return b("/admin/email-preferences",{},!0)}async function Eg(D){return b("/admin/email-preferences",{method:"PUT",headers:{"Content-Type":"application/json"},body:JSON.stringify(D)},!0)}async function Vg(){return b("/notices",{},"optional")}async function Zg(){return b("/admin/notices",{},!0)}async function Ug(D){return b("/admin/notices",{method:"POST",body:JSON.stringify(D)},!0)}async function Lg(D){return b(`/admin/notices/${D}`,{method:"DELETE"},!0)}async function yW(D){return b("/admin/notify",{method:"POST",body:JSON.stringify(D)},!0)}var jW="https://nemar-api-dev.sccn-org.workers.dev",DQ,h,FQ,TW,k9;var i8=P(()=>{f4();wW();eJ();DQ=/^\d{4}-\d{4}-\d{4}-\d{3}[\dX]$/;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"}};FQ=class FQ extends h{mode;eta;constructor(D,F,$,J){super(503,F,J);this.mode=D;this.eta=$;this.name="MaintenanceError"}};TW=jW.includes("workers.dev");k9=["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","generate_archive","sync_nemar","notify_user"]});function Mg(D){xW=D}function _W(){return xW}function x9(D){if(xW)process.stderr.write(`${D}
|
|
99
99
|
`)}var xW=!1;function GD(D){if(D===0)return"0 B";let F=["B","KB","MB","GB","TB"],$=Math.min(Math.floor(Math.log(D)/Math.log(1024)),F.length-1);return`${(D/1024**$).toFixed($===0?0:1)} ${F[$]}`}function Ng(D){return`${GD(D)}/s`}function zE0(D){if(D<60)return`${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 EE0(D,F=20){let $=Math.round(D/100*F),J=F-$;return`[${"=".repeat($)}${" ".repeat(J)}]`}class qQ{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`:`${this.filesCompleted} files`,Y;if(J)Y=`${EE0($)} ${$}% ${Q}`;else Y=Q;if(F>0){let B=this.bytesTotal>0?`${GD(F)}/${GD(this.bytesTotal)}`:GD(F);Y+=` | ${B}`}if(D>0)Y+=` | ${Ng(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 ${zE0(X)}`}}if(Y!==this.lastRenderedLine)process.stderr.write(`\r${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 $=F>0?`${Ng(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 fW=P(()=>{vD()});var xg={};i4(xg,{verifyGitHubAuth:()=>f9,toS3Credentials:()=>CD,switchBranch:()=>OE0,setKeyPresent:()=>yg,selectAnnexS3Remote:()=>dW,saveDataset:()=>o8,runCommand:()=>I,resolveUpstreamRef:()=>tW,readRemoteHeadDatasetVersion:()=>rW,readLocalDatasetVersion:()=>sW,pushToGitHub:()=>a1,pushBranch:()=>kF,markInheritedOpenNeuroRemotesIgnored:()=>pW,listDatasetVersions:()=>nW,isWorkingTreeDirty:()=>eW,isGitAnnexDataset:()=>C1,isDataladDataset:()=>IE0,initOrEnableSpecialRemote:()=>Sg,initDataset:()=>a6,gitMergeFastForward:()=>FH,gitFetchOrigin:()=>DH,gitAnnexAdd:()=>o6,getVersionCommit:()=>iW,getRemoteUuid:()=>YH,getLocalDatasetInfo:()=>cW,getKeyHashDirs:()=>TE0,getKeyHashDir:()=>vg,getDatasetStats:()=>NE0,getDatasetIdFromRemote:()=>r8,getDatasetData:()=>VQ,getCurrentBranch:()=>s8,getAnnexWhereisAll:()=>QH,getAnnexS3Remotes:()=>h9,formatBytes:()=>GD,ensureLocalMainBranch:()=>b9,ensureGitAnnexInitialized:()=>mW,enableS3Remote:()=>u4,dropUnusedAnnexObjects:()=>$H,dropFiles:()=>lW,detectImportMarker:()=>EQ,createRevertBranch:()=>aW,createDataladDataset:()=>PE0,countPendingDownload:()=>zQ,copyToAnnexRemote:()=>w8,configureS3Remote:()=>O8,configureLargefiles:()=>b4,configureGitHubRemote:()=>a8,commitRevert:()=>oW,collectFileManifest:()=>JH,cloneDataset:()=>o1,clearAnnexCredentials:()=>SD,checkPrerequisites:()=>_9,checkGitHubSSH:()=>jg,checkGitAnnexInstalled:()=>uW,checkDownloadPrerequisites:()=>SF,checkAWSCredentials:()=>LE0,batchSetKeysPresent:()=>BH,annexRemoteExists:()=>Ig,acceptGitHubInvitation:()=>g9,NEMAR_S3_REMOTE_NAME:()=>KQ,ANNEX_REMOTE_EXISTS_RE:()=>Pg});import{existsSync as hW,readFileSync as VE0,statSync as ZE0}from"fs";import{join as bW}from"path";var{spawn:wg}=globalThis.Bun;async function I(D,F={}){let $=wg({cmd:D,cwd:F.cwd,stdout:"pipe",stderr:"pipe",env:{...process.env,GIT_TERMINAL_PROMPT:"0",...F.env}}),J=!1,Q;if(F.timeout)Q=setTimeout(()=>{J=!0,$.kill()},F.timeout);if(_W()){let G=F.cwd?` (cwd=${F.cwd})`:"";x9(W.dim(`$ ${D.join(" ")}${G}`))}let Y=await new Response($.stdout).text(),B=await new Response($.stderr).text(),X=await $.exited;if(Q)clearTimeout(Q);if(_W()){if(Y.trim())x9(W.dim(Y.trimEnd()));if(B.trim())x9(W.yellow(B.trimEnd()));x9(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 Cg(D){return D.split(".").map((F)=>{let $=Number.parseInt(F.replace(/[^0-9]/g,""),10);return Number.isNaN($)?0:$})}function UE0(D,F){let $=Cg(D),J=Cg(F);for(let Q=0;Q<Math.max($.length,J.length);Q++){let Y=$[Q]||0,B=J[Q]||0;if(Y>B)return!0;if(Y<B)return!1}return!0}async function uW(){try{let{stdout:F,exitCode:$,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?UE0(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:$}}}async function jg(){if(process.env.GH_TOKEN)return{accessible:!0,username:"token-auth",useHttps:!0};try{let{stdout:D,stderr:F}=await I(["ssh","-T","-o","BatchMode=yes","-o","StrictHostKeyChecking=accept-new","-o","ConnectTimeout=10","git@github.com"]),$=D+F,J=$.match(/Hi ([^!]+)!/);if(J)return{accessible:!0,username:J[1]};if($.includes("Permission denied"))return{accessible:!1};return{accessible:$.includes("successfully authenticated")}}catch(D){let F=D instanceof Error?D.message:String(D);if(F.includes("ENOENT")||F.includes("not found"))console.info("SSH command not found");else console.error("Error checking GitHub SSH access:",F);return{accessible:!1}}}async function LE0(){if(process.env.AWS_ACCESS_KEY_ID&&process.env.AWS_SECRET_ACCESS_KEY)return{configured:!0,source:"environment"};try{let{stdout:D,exitCode:F}=await I(["aws","configure","get","aws_access_key_id"]);if(F===0&&D.trim())return{configured:!0,source:"aws-cli"}}catch(D){let F=D instanceof Error?D.message:String(D);if(F.includes("ENOENT")||F.includes("not found"))console.info("AWS CLI not found in PATH");else console.error("Error checking AWS credentials:",F)}return{configured:!1}}function Tg(){let D=process.platform;if(D==="darwin")return"brew install git-annex";if(D==="linux")return"apt install git-annex (Debian/Ubuntu)";return"See https://git-annex.branchable.com/install/"}async function _9(){let[D,F]=await Promise.all([uW(),jg()]),$=[];if(!D.installed)$.push(`git-annex is not installed. Install: ${Tg()}`);else if(D.compatible===!1)$.push(`git-annex version ${D.version} is too old. Required: >= ${D.minVersion}`);if(!F.accessible){if(!(await kg()).token)$.push("GitHub authentication not configured. Run 'gh auth login' to authenticate.")}return{gitAnnex:D,githubSSH:F,allPassed:$.length===0,errors:$}}async function C1(D){if(!hW(bW(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 a6(D,F={}){if(!F.force&&await C1(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:$.message}}}async function mW(D){try{let{exitCode:F,stderr:$}=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 ${Y}`,X=F||B;try{let{stderr:G,exitCode:H}=await I(["git","annex","config","--set","annex.largefiles",X],{cwd:D});if(H!==0)return{success:!1,error:G.trim()||"Failed to configure largefiles"};return{success:!0}}catch(G){return{success:!1,error:G.message}}}async function o6(D,F="."){try{let{stderr:$,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 gW(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