nemar-cli 0.8.5-dev.676 → 0.8.5-dev.680
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 +3 -3
- 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
|
${F}
|
|
98
|
-
`)}var Qf=!1;var EW=j(()=>{yD()});var Bf;var Yf=j(()=>{Bf={name:"nemar-cli",version:"0.8.5-dev.676",description:"CLI for NEMAR (Neuroelectromagnetic Data Archive and Tools Resource) dataset management",type:"module",main:"dist/index.js",bin:{nemar:"dist/index.js"},scripts:{dev:"bun run src/index.ts",build:"bun build src/index.ts --outdir dist --target bun --minify && sed '1s|#!/usr/bin/env node|#!/usr/bin/env bun|' dist/index.js > dist/index.js.tmp && mv dist/index.js.tmp dist/index.js",test:"bun test",lint:"biome check src/","lint:fix":"biome check --fix src/",format:"biome format --write src/",typecheck:"tsc --noEmit",prepublishOnly:"bun run build","docs:generate":"bun run scripts/generate-docs.ts","docs:serve":"mkdocs serve","docs:build":"mkdocs build",prepare:"husky",deploy:"wrangler deploy",preview:"wrangler dev"},keywords:["nemar","bids","neuroimaging","eeg","emg","datalad","cli"],author:"NEMAR Team",license:"CC-BY-NC-ND-4.0",repository:{type:"git",url:"git+https://github.com/nemarOrg/nemar-cli.git"},bugs:{url:"https://github.com/nemarOrg/nemar-cli/issues"},homepage:"https://nemar-cli.pages.dev",engines:{bun:">=1.0.0"},files:["dist","README.md","LICENSE"],dependencies:{chalk:"^5.3.0",commander:"^12.1.0",conf:"^13.0.1","fuse.js":"^7.1.0",inquirer:"^9.2.15",ora:"^8.0.1",zod:"^3.23.8"},"lint-staged":{"src/**/*.{ts,tsx}":["biome check --fix"],"backend/src/**/*.{ts,tsx}":["biome check --fix"]},devDependencies:{"@biomejs/biome":"1.9.4","@types/bcryptjs":"^3.0.0","@types/bun":"latest","@types/inquirer":"^9.0.7",bcryptjs:"^3.0.3",husky:"^9.1.7","lint-staged":"^16.3.2",typescript:"^5.5.4",wrangler:"^4.70.0"}}});var x4;var nJ=j(()=>{Yf();x4=Bf.version});function S0(D){if(D instanceof Error)return D.message;return String(D)}function Xf(){if(process.env.TEST_API_URL)return process.env.TEST_API_URL;if(ZW)return VW;return QD().apiUrl||VW}async function l(D,F={},$=!1){let J=`${Xf()}${D}`,Q={"Content-Type":"application/json","X-CLI-Version":x4,...F.headers};if($){let X=QD();if(!X.apiKey&&$===!0)throw new n(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 n(0,`Network error: Could not connect to ${Xf()}`,{originalError:X instanceof Error?X.message:String(X)})}let B;try{B=await Y.json()}catch{throw new n(Y.status,`Invalid response from server (status ${Y.status})`)}if(!Y.ok){if(Y.status===503&&(B.mode==="read-only"||B.mode==="full")){let X=typeof B.message==="string"?B.message:"NEMAR is in maintenance mode. Please retry shortly.",G=typeof B.eta==="string"?B.eta:null,H=new aJ(B.mode,X,G,B.details);throw cJ(H),H}throw new n(Y.status,B.error||B.message||"Request failed",B.details,typeof B.step==="string"?B.step:void 0)}return B}async function Wf(D){return l(`/auth/check-username?username=${encodeURIComponent(D)}`)}async function Hf(D){return l(`/auth/check-github?username=${encodeURIComponent(D)}`)}async function qf(D){return l("/auth/signup",{method:"POST",body:JSON.stringify(D)})}async function Kf(D){return l("/auth/login",{method:"POST",body:JSON.stringify({api_key:D})})}async function zf(D){return l("/auth/resend-verification",{method:"POST",body:JSON.stringify({email:D})})}async function Ef(D,F){return l("/auth/retrieve-key",{method:"POST",body:JSON.stringify({email:D,password:F})})}async function Vf(D){return l("/auth/request-key-regeneration",{method:"POST",body:JSON.stringify({email:D})})}async function oJ(){return l("/users/me",{},!0)}async function Zf(D,F){let $=new URLSearchParams;if(D)$.set("status",D);if(F)$.set("role",F);let J=$.toString()?`?${$.toString()}`:"";return l(`/admin/users${J}`,{},!0)}async function Uf(D){return l(`/admin/approve/${D}`,{method:"POST"},!0)}async function Af(D){return l(`/admin/revoke/${D}`,{method:"POST"},!0)}async function Lf(D,F){return l(`/admin/users/${D}/role`,{method:"POST",body:JSON.stringify({role:F})},!0)}async function UW(D,F){return l(`/admin/datasets/${D}/visibility`,{method:"PATCH",body:JSON.stringify({visibility:F})},!0)}async function Mf(D){return l(`/datasets/${D}/publish`,{method:"POST"},!0)}async function Nf(D){return l(`/admin/datasets/${D}/ci`,{},!0)}async function _4(D){return l(`/admin/datasets/${D}/ci`,{method:"POST"},!0)}async function Cf(D){return l(`/datasets/${D}/ci/status`,{},!0)}async function Rf(D){return l(`/datasets/${D}/manifest`,{},!0)}async function sJ(D,F){return l(`/datasets/${D}/manifest/${F}`,{},!0)}function Of(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(Of),J}async function Tf(D){return l(`/datasets/resolve/${D}`,{},"optional")}async function wf(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 Of(F.dataset)}async function jf(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 Pf(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 AW(D,F){return l(`/admin/datasets/${D}/doi/update`,{method:"POST",body:JSON.stringify(F)},!0)}async function If(D){return l(`/datasets/${D}/request-access`,{method:"POST"},!0)}async function Sf(D,F){return l(`/datasets/${D}/invite`,{method:"POST",body:JSON.stringify({username:F})},!0)}async function kf(D){return l(`/datasets/${D}/collaborators`,{},!0)}async function vf(D){return l("/sandbox/complete",{method:"POST",body:JSON.stringify({dataset_id:D})},!0)}async function yf(){return l("/sandbox/reset",{method:"POST"},!0)}async function xf(){return l("/sandbox/status",{},!0)}async function FQ(D){return l(`/datasets/${D}/publish/request`,{method:"POST"},!0)}async function _f(D){return l(`/datasets/${D}/publish/status`,{},!0)}async function ff(D){return l(`/datasets/${D}/publish/resend`,{method:"POST"},!0)}async function gf(D){let F=D?`?status=${D}`:"";return l(`/admin/publish/requests${F}`,{},!0)}async function hf(D,F){return l(`/admin/publish/${D}/deny`,{method:"POST",headers:{"Content-Type":"application/json"},body:JSON.stringify({reason:F})},!0)}function Iz0(D){if(!(D instanceof n))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 E,V=!0;do{if(E=await l(`/admin/publish/${D}/approve`,{method:"POST",headers:{"Content-Type":"application/json"},body:JSON.stringify({resume:V?G:!0,sandbox:$,s3_lock_offset:X,skip_ci_check:J})},!0),V=!1,E.step_results)H.push(...E.step_results);if(E.hasMore&&E.s3_lock_offset!==void 0)X=E.s3_lock_offset;else break}while(E.hasMore);if(H.length>0)E.step_results=Gf(H);return E}catch(E){if(q=E,K===5||!Iz0(E)){if(E instanceof n&&H.length>0)E.stepResults=Gf(H);throw E}let U=E;Q?.({attempt:K,maxAttempts:5,delayMs:1e4,step:U.step,error:U.message}),await new Promise((A)=>setTimeout(A,1e4)),G=!0}throw q}function Gf(D){let F=new Map;for(let $ of D)F.set($.step,$);return Array.from(F.values())}async function bf(D,F){return l(`/admin/datasets/${D}/enrichment`,{method:"POST",body:JSON.stringify(F)},!0)}async function uf(D){return l(`/admin/datasets/${D}/files`,{},!0)}async function mf(D){let F=0,$=0,J=[],Q=0,Y=!0;while(Y){let B=await l(`/admin/datasets/${D}/s3-lock`,{method:"POST",headers:{"Content-Type":"application/json"},body:JSON.stringify({offset:F})},!0);if($+=B.locked,J.push(...B.failed),Q=B.total,Y=B.hasMore,Y)F+=40}return{locked:$,total:Q,failed:J}}async function lf(D){return l(`/admin/datasets/${D}/reset`,{method:"POST"},!0)}async function pf(D,F=!1){return l(`/admin/datasets/${D}`,{method:"DELETE",headers:{"Content-Type":"application/json"},body:JSON.stringify({force:F})},!0)}async function df(D){return l("/admin/datasets/bulk-delete",{method:"POST",headers:{"Content-Type":"application/json"},body:JSON.stringify({dataset_ids:D})},!0)}async function cf(D){return l("/admin/datasets/import",{method:"POST",body:JSON.stringify(D)},!0)}async function nf(D){return l(`/admin/datasets/${D}/sync`,{method:"POST"},!0)}async function af(){return l("/admin/sync/status",{},!0)}async function of(){return l("/admin/email-preferences",{},!0)}async function sf(D){return l("/admin/email-preferences",{method:"PUT",headers:{"Content-Type":"application/json"},body:JSON.stringify(D)},!0)}async function rf(){return l("/notices",{},"optional")}async function tf(){return l("/admin/notices",{},!0)}async function ef(D){return l("/admin/notices",{method:"POST",body:JSON.stringify(D)},!0)}async function Dg(D){return l(`/admin/notices/${D}`,{method:"DELETE"},!0)}async function LW(D){return l("/admin/notify",{method:"POST",body:JSON.stringify(D)},!0)}var VW="https://nemar-api-dev.sccn-org.workers.dev",iJ,n,aJ,ZW;var n8=j(()=>{y4();EW();nJ();iJ=/^\d{4}-\d{4}-\d{4}-\d{3}[\dX]$/;n=class n extends Error{statusCode;details;step;constructor(D,F,$,J){super(F);this.statusCode=D;this.details=$;this.step=J;this.name="ApiError"}};aJ=class aJ extends n{mode;eta;constructor(D,F,$,J){super(503,F,J);this.mode=D;this.eta=$;this.name="MaintenanceError"}};ZW=VW.includes("workers.dev")});function $g(D){MW=D}function NW(){return MW}function I9(D){if(MW)process.stderr.write(`${D}
|
|
98
|
+
`)}var Qf=!1;var EW=j(()=>{yD()});var Bf;var Yf=j(()=>{Bf={name:"nemar-cli",version:"0.8.5-dev.680",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=j(()=>{Yf();x4=Bf.version});function S0(D){if(D instanceof Error)return D.message;return String(D)}function Xf(){if(process.env.TEST_API_URL)return process.env.TEST_API_URL;if(ZW)return VW;return QD().apiUrl||VW}async function l(D,F={},$=!1){let J=`${Xf()}${D}`,Q={"Content-Type":"application/json","X-CLI-Version":x4,...F.headers};if($){let X=QD();if(!X.apiKey&&$===!0)throw new n(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 n(0,`Network error: Could not connect to ${Xf()}`,{originalError:X instanceof Error?X.message:String(X)})}let B;try{B=await Y.json()}catch{throw new n(Y.status,`Invalid response from server (status ${Y.status})`)}if(!Y.ok){if(Y.status===503&&(B.mode==="read-only"||B.mode==="full")){let X=typeof B.message==="string"?B.message:"NEMAR is in maintenance mode. Please retry shortly.",G=typeof B.eta==="string"?B.eta:null,H=new aJ(B.mode,X,G,B.details);throw cJ(H),H}throw new n(Y.status,B.error||B.message||"Request failed",B.details,typeof B.step==="string"?B.step:void 0)}return B}async function Wf(D){return l(`/auth/check-username?username=${encodeURIComponent(D)}`)}async function Hf(D){return l(`/auth/check-github?username=${encodeURIComponent(D)}`)}async function qf(D){return l("/auth/signup",{method:"POST",body:JSON.stringify(D)})}async function Kf(D){return l("/auth/login",{method:"POST",body:JSON.stringify({api_key:D})})}async function zf(D){return l("/auth/resend-verification",{method:"POST",body:JSON.stringify({email:D})})}async function Ef(D,F){return l("/auth/retrieve-key",{method:"POST",body:JSON.stringify({email:D,password:F})})}async function Vf(D){return l("/auth/request-key-regeneration",{method:"POST",body:JSON.stringify({email:D})})}async function oJ(){return l("/users/me",{},!0)}async function Zf(D,F){let $=new URLSearchParams;if(D)$.set("status",D);if(F)$.set("role",F);let J=$.toString()?`?${$.toString()}`:"";return l(`/admin/users${J}`,{},!0)}async function Uf(D){return l(`/admin/approve/${D}`,{method:"POST"},!0)}async function Af(D){return l(`/admin/revoke/${D}`,{method:"POST"},!0)}async function Lf(D,F){return l(`/admin/users/${D}/role`,{method:"POST",body:JSON.stringify({role:F})},!0)}async function UW(D,F){return l(`/admin/datasets/${D}/visibility`,{method:"PATCH",body:JSON.stringify({visibility:F})},!0)}async function Mf(D){return l(`/datasets/${D}/publish`,{method:"POST"},!0)}async function Nf(D){return l(`/admin/datasets/${D}/ci`,{},!0)}async function _4(D){return l(`/admin/datasets/${D}/ci`,{method:"POST"},!0)}async function Cf(D){return l(`/datasets/${D}/ci/status`,{},!0)}async function Rf(D){return l(`/datasets/${D}/manifest`,{},!0)}async function sJ(D,F){return l(`/datasets/${D}/manifest/${F}`,{},!0)}function Of(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(Of),J}async function Tf(D){return l(`/datasets/resolve/${D}`,{},"optional")}async function wf(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 Of(F.dataset)}async function jf(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 Pf(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 AW(D,F){return l(`/admin/datasets/${D}/doi/update`,{method:"POST",body:JSON.stringify(F)},!0)}async function If(D){return l(`/datasets/${D}/request-access`,{method:"POST"},!0)}async function Sf(D,F){return l(`/datasets/${D}/invite`,{method:"POST",body:JSON.stringify({username:F})},!0)}async function kf(D){return l(`/datasets/${D}/collaborators`,{},!0)}async function vf(D){return l("/sandbox/complete",{method:"POST",body:JSON.stringify({dataset_id:D})},!0)}async function yf(){return l("/sandbox/reset",{method:"POST"},!0)}async function xf(){return l("/sandbox/status",{},!0)}async function FQ(D){return l(`/datasets/${D}/publish/request`,{method:"POST"},!0)}async function _f(D){return l(`/datasets/${D}/publish/status`,{},!0)}async function ff(D){return l(`/datasets/${D}/publish/resend`,{method:"POST"},!0)}async function gf(D){let F=D?`?status=${D}`:"";return l(`/admin/publish/requests${F}`,{},!0)}async function hf(D,F){return l(`/admin/publish/${D}/deny`,{method:"POST",headers:{"Content-Type":"application/json"},body:JSON.stringify({reason:F})},!0)}function Iz0(D){if(!(D instanceof n))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 E,V=!0;do{if(E=await l(`/admin/publish/${D}/approve`,{method:"POST",headers:{"Content-Type":"application/json"},body:JSON.stringify({resume:V?G:!0,sandbox:$,s3_lock_continuation_token:X,skip_ci_check:J})},!0),V=!1,E.step_results)H.push(...E.step_results);if(E.hasMore&&E.s3_lock_continuation_token!==void 0)X=E.s3_lock_continuation_token;else break}while(E.hasMore);if(H.length>0)E.step_results=Gf(H);return E}catch(E){if(q=E,K===5||!Iz0(E)){if(E instanceof n&&H.length>0)E.stepResults=Gf(H);throw E}let U=E;Q?.({attempt:K,maxAttempts:5,delayMs:1e4,step:U.step,error:U.message}),await new Promise((A)=>setTimeout(A,1e4)),G=!0}throw q}function Gf(D){let F=new Map;for(let $ of D)F.set($.step,$);return Array.from(F.values())}async function bf(D,F){return l(`/admin/datasets/${D}/enrichment`,{method:"POST",body:JSON.stringify(F)},!0)}async function uf(D){return l(`/admin/datasets/${D}/files`,{},!0)}async function mf(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($+=Y.locked,Y.failed?.length)J.push(...Y.failed);if(Q=Y.hasMore,F=Y.continuation_token,Q&&!F)throw new n(500,"S3 lock paginated response missing continuation_token; aborting to avoid infinite loop")}return{locked:$,failed:J}}async function lf(D){return l(`/admin/datasets/${D}/reset`,{method:"POST"},!0)}async function pf(D,F=!1){return l(`/admin/datasets/${D}`,{method:"DELETE",headers:{"Content-Type":"application/json"},body:JSON.stringify({force:F})},!0)}async function df(D){return l("/admin/datasets/bulk-delete",{method:"POST",headers:{"Content-Type":"application/json"},body:JSON.stringify({dataset_ids:D})},!0)}async function cf(D){return l("/admin/datasets/import",{method:"POST",body:JSON.stringify(D)},!0)}async function nf(D){return l(`/admin/datasets/${D}/sync`,{method:"POST"},!0)}async function af(){return l("/admin/sync/status",{},!0)}async function of(){return l("/admin/email-preferences",{},!0)}async function sf(D){return l("/admin/email-preferences",{method:"PUT",headers:{"Content-Type":"application/json"},body:JSON.stringify(D)},!0)}async function rf(){return l("/notices",{},"optional")}async function tf(){return l("/admin/notices",{},!0)}async function ef(D){return l("/admin/notices",{method:"POST",body:JSON.stringify(D)},!0)}async function Dg(D){return l(`/admin/notices/${D}`,{method:"DELETE"},!0)}async function LW(D){return l("/admin/notify",{method:"POST",body:JSON.stringify(D)},!0)}var VW="https://nemar-api-dev.sccn-org.workers.dev",iJ,n,aJ,ZW;var n8=j(()=>{y4();EW();nJ();iJ=/^\d{4}-\d{4}-\d{4}-\d{3}[\dX]$/;n=class n extends Error{statusCode;details;step;constructor(D,F,$,J){super(F);this.statusCode=D;this.details=$;this.step=J;this.name="ApiError"}};aJ=class aJ extends n{mode;eta;constructor(D,F,$,J){super(503,F,J);this.mode=D;this.eta=$;this.name="MaintenanceError"}};ZW=VW.includes("workers.dev")});function $g(D){MW=D}function NW(){return MW}function I9(D){if(MW)process.stderr.write(`${D}
|
|
99
99
|
`)}var MW=!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 Jg(D){return`${BD(D)}/s`}function Sz0(D){if(D<60)return`${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 kz0(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`:`${this.filesCompleted} files`,Y;if(J)Y=`${kz0($)} ${$}% ${Q}`;else Y=Q;if(F>0){let B=this.bytesTotal>0?`${BD(F)}/${BD(this.bytesTotal)}`:BD(F);Y+=` | ${B}`}if(D>0)Y+=` | ${Jg(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 ${Sz0(X)}`}}if(Y!==this.lastRenderedLine)process.stderr.write(`\r${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 $=F>0?`${Jg(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 CW=j(()=>{yD()});var zg={};d4(zg,{verifyGitHubAuth:()=>k9,toS3Credentials:()=>CD,switchBranch:()=>mz0,setKeyPresent:()=>Kg,saveDataset:()=>a8,runCommand:()=>S,resolveUpstreamRef:()=>fW,readRemoteHeadDatasetVersion:()=>_W,readLocalDatasetVersion:()=>xW,pushToGitHub:()=>a1,pushBranch:()=>jF,listDatasetVersions:()=>SW,isWorkingTreeDirty:()=>gW,isGitAnnexDataset:()=>O1,isDataladDataset:()=>nz0,initDataset:()=>d6,gitMergeFastForward:()=>bW,gitFetchOrigin:()=>hW,gitAnnexAdd:()=>c6,getVersionCommit:()=>kW,getRemoteUuid:()=>pW,getLocalDatasetInfo:()=>IW,getKeyHashDirs:()=>dz0,getKeyHashDir:()=>qg,getDatasetStats:()=>bz0,getDatasetIdFromRemote:()=>s8,getDatasetData:()=>YQ,getCurrentBranch:()=>o8,getAnnexWhereisAll:()=>lW,getAnnexS3Remotes:()=>y9,formatBytes:()=>BD,ensureLocalMainBranch:()=>x9,ensureGitAnnexInitialized:()=>jW,enableS3Remote:()=>g4,dropUnusedAnnexObjects:()=>uW,dropFiles:()=>PW,createRevertBranch:()=>vW,createDataladDataset:()=>cz0,countPendingDownload:()=>QQ,copyToAnnexRemote:()=>R8,configureS3Remote:()=>C8,configureLargefiles:()=>f4,configureGitHubRemote:()=>i8,commitRevert:()=>yW,collectFileManifest:()=>mW,cloneDataset:()=>o1,clearAnnexCredentials:()=>SD,checkPrerequisites:()=>S9,checkGitHubSSH:()=>Gg,checkGitAnnexInstalled:()=>wW,checkDownloadPrerequisites:()=>wF,checkAWSCredentials:()=>_z0,batchSetKeysPresent:()=>dW,acceptGitHubInvitation:()=>v9});import{existsSync as OW,readFileSync as vz0,statSync as yz0}from"fs";import{join as TW}from"path";var{spawn:Xg}=globalThis.Bun;async function S(D,F={}){let $=Xg({cmd:D,cwd:F.cwd,stdout:"pipe",stderr:"pipe",env:{...process.env,GIT_TERMINAL_PROMPT:"0",...F.env}}),J=!1,Q;if(F.timeout)Q=setTimeout(()=>{J=!0,$.kill()},F.timeout);if(NW()){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(NW()){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 Qg(D){return D.split(".").map((F)=>{let $=Number.parseInt(F.replace(/[^0-9]/g,""),10);return Number.isNaN($)?0:$})}function xz0(D,F){let $=Qg(D),J=Qg(F);for(let Q=0;Q<Math.max($.length,J.length);Q++){let Y=$[Q]||0,B=J[Q]||0;if(Y>B)return!0;if(Y<B)return!1}return!0}async function wW(){try{let{stdout:F,exitCode:$,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?xz0(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:$}}}async function Gg(){if(process.env.GH_TOKEN)return{accessible:!0,username:"token-auth",useHttps:!0};try{let{stdout:D,stderr:F}=await S(["ssh","-T","-o","BatchMode=yes","-o","StrictHostKeyChecking=accept-new","-o","ConnectTimeout=10","git@github.com"]),$=D+F,J=$.match(/Hi ([^!]+)!/);if(J)return{accessible:!0,username:J[1]};if($.includes("Permission denied"))return{accessible:!1};return{accessible:$.includes("successfully authenticated")}}catch(D){let F=D instanceof Error?D.message:String(D);if(F.includes("ENOENT")||F.includes("not found"))console.info("SSH command not found");else console.error("Error checking GitHub SSH access:",F);return{accessible:!1}}}async function _z0(){if(process.env.AWS_ACCESS_KEY_ID&&process.env.AWS_SECRET_ACCESS_KEY)return{configured:!0,source:"environment"};try{let{stdout:D,exitCode:F}=await S(["aws","configure","get","aws_access_key_id"]);if(F===0&&D.trim())return{configured:!0,source:"aws-cli"}}catch(D){let F=D instanceof Error?D.message:String(D);if(F.includes("ENOENT")||F.includes("not found"))console.info("AWS CLI not found in PATH");else console.error("Error checking AWS credentials:",F)}return{configured:!1}}function Wg(){let D=process.platform;if(D==="darwin")return"brew install git-annex";if(D==="linux")return"apt install git-annex (Debian/Ubuntu)";return"See https://git-annex.branchable.com/install/"}async function S9(){let[D,F]=await Promise.all([wW(),Gg()]),$=[];if(!D.installed)$.push(`git-annex is not installed. Install: ${Wg()}`);else if(D.compatible===!1)$.push(`git-annex version ${D.version} is too old. Required: >= ${D.minVersion}`);if(!F.accessible){if(!(await Hg()).token)$.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(!OW(TW(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 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,$.GIT_COMMITTER_EMAIL=F.author.email;let{stderr:J,exitCode:Q}=await S(["git","init","-b","main",D],{...Object.keys($).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:$.message}}}async function jW(D){try{let{exitCode:F,stderr:$}=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 ${Y}`,X=F||B;try{let{stderr:G,exitCode:H}=await S(["git","annex","config","--set","annex.largefiles",X],{cwd:D});if(H!==0)return{success:!1,error:G.trim()||"Failed to configure largefiles"};return{success:!0}}catch(G){return{success:!1,error:G.message}}}async function c6(D,F="."){try{let{stderr:$,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 RW(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(`
|
|
@@ -192,8 +192,8 @@ Examples:
|
|
|
192
192
|
$ nemar admin role john_doe member # Demote to member
|
|
193
193
|
$ nemar admin role jane_doe owner -y # Promote to owner (skip confirm)`).action(async(D,F,$)=>{if(!u0())return;if(!["owner","admin","member"].includes(F))console.error(W.red(`Invalid role '${F}'. Must be: owner, admin, or member`)),process.exit(1);if(!$.yes){let{confirmed:Q}=await e.prompt([{type:"confirm",name:"confirmed",message:`Change ${D}'s role to '${F}'?`,default:!1}]);if(!Q){console.log(W.dim("Cancelled"));return}}let J=C(`Changing ${D}'s role to '${F}'...`).start();try{let Q=await Lf(D,F);if(J.succeed(Q.message),Q.tokens_revoked!==void 0&&Q.tokens_revoked>0)console.log(W.yellow(` ${Q.tokens_revoked} token(s) revoked (user must re-login)`))}catch(Q){WD(Q,J,"Failed to change role",{400:"Invalid request (check if you are an owner)",403:"Owner access required",404:"User not found",409:"User already has that role"})}});var oW=new r0("s3").description("S3 and IAM credential management");oW.command("regenerate-iam").description("Regenerate AWS IAM credentials for a user").argument("<username>","Username to regenerate credentials for").option(j0,P0).option(b0,x0).action(jg);oW.command("lock").description("Apply S3 Object Lock (Governance mode) to a dataset").argument("<dataset-id>","Dataset ID to lock").option(j0,P0).option(b0,x0).action(async(D,F)=>{if(!u0())return;console.log(W.cyan(`
|
|
194
194
|
Apply S3 Object Lock to ${D}
|
|
195
|
-
`)),console.log("This will:"),console.log(" \u2022 Set GOVERNANCE mode Object Lock on all objects"),console.log(" \u2022 Retention period: 100 years"),console.log(" \u2022 Objects cannot be deleted or modified without bypass"),console.log();let $=await k0(`Apply S3 Object Lock to ${D}?`,F);if($!=="confirmed"){console.log(W.dim($==="declined"?"Skipped":"Cancelled"));return}let J=C("Applying S3 Object Lock...").start();try{let Q=await mf(D);if(Q.failed.length>0){J.fail(`Partial lock: ${Q.locked}
|
|
196
|
-
Failed objects:`));for(let Y of Q.failed.slice(0,10))console.log(` \u2022 ${Y}`);if(Q.failed.length>10)console.log(` ... and ${Q.failed.length-10} more`)}else J.succeed(`All ${Q.locked} objects locked successfully`)}catch(Q){J.fail("S3 lock failed"),console.log(W.dim(` ${S0(Q)}`))}});e0.addCommand(oW);e0.command("regenerate-iam",{hidden:!0}).argument("<username>").option(j0,P0).option(b0,x0).action(jg);async function jg(D,F){if(!u0())return;console.log(W.yellow(`
|
|
195
|
+
`)),console.log("This will:"),console.log(" \u2022 Set GOVERNANCE mode Object Lock on all objects"),console.log(" \u2022 Retention period: 100 years"),console.log(" \u2022 Objects cannot be deleted or modified without bypass"),console.log();let $=await k0(`Apply S3 Object Lock to ${D}?`,F);if($!=="confirmed"){console.log(W.dim($==="declined"?"Skipped":"Cancelled"));return}let J=C("Applying S3 Object Lock...").start();try{let Q=await mf(D);if(Q.failed.length>0){J.fail(`Partial lock: ${Q.locked} locked, ${Q.failed.length} failed`),console.log(W.yellow(`
|
|
196
|
+
Failed objects:`));for(let Y of Q.failed.slice(0,10))console.log(` \u2022 ${Y.key}: ${W.dim(Y.error)}`);if(Q.failed.length>10)console.log(` ... and ${Q.failed.length-10} more`)}else J.succeed(`All ${Q.locked} objects locked successfully`)}catch(Q){J.fail("S3 lock failed"),console.log(W.dim(` ${S0(Q)}`))}});e0.addCommand(oW);e0.command("regenerate-iam",{hidden:!0}).argument("<username>").option(j0,P0).option(b0,x0).action(jg);async function jg(D,F){if(!u0())return;console.log(W.yellow(`
|
|
197
197
|
This command is deprecated.
|
|
198
198
|
`)),console.log("S3 access is now managed through backend-scoped credentials."),console.log("Per-user IAM credentials are no longer needed."),console.log(),console.log(W.dim("Users can upload datasets without any IAM setup."))}var sW=new r0("repo").description("Repository visibility management");sW.command("public").description("Make a dataset repository public").argument("<dataset-id>","Dataset ID (e.g., nm000104)").option(j0,P0).option(b0,x0).action(async(D,F)=>{if(!u0())return;console.log(W.cyan(`
|
|
199
199
|
Making repository public: ${D}
|
package/package.json
CHANGED