nemar-cli 0.8.10-dev.748 → 0.8.10-dev.753
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 +2 -2
- package/package.json +1 -1
package/dist/index.js
CHANGED
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@@ -95,7 +95,7 @@ ${W.dim(`eta: ${D.eta}`)}`:"";process.stderr.write(`${F}
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${$} ${D.message}
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${F}
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`)}var Hf=!1;var UW=P(()=>{yD()});var Kf;var qf=P(()=>{Kf={name:"nemar-cli",version:"0.8.10-dev.748",description:"CLI for NEMAR (Neuroelectromagnetic Data Archive and Tools Resource) dataset management",type:"module",main:"dist/index.js",bin:{nemar:"dist/index.js"},scripts:{dev:"bun run src/index.ts",build:"bun build src/index.ts --outdir dist --target bun --minify && sed '1s|#!/usr/bin/env node|#!/usr/bin/env bun|' dist/index.js > dist/index.js.tmp && mv dist/index.js.tmp dist/index.js",test:"bun test",lint:"biome check src/","lint:fix":"biome check --fix src/",format:"biome format --write src/",typecheck:"tsc --noEmit",prepublishOnly:"bun run build","docs:generate":"bun run scripts/generate-docs.ts","docs:serve":"mkdocs serve","docs:build":"mkdocs build",prepare:"husky",deploy:"wrangler deploy",preview:"wrangler dev"},keywords:["nemar","bids","neuroimaging","eeg","emg","datalad","cli"],author:"NEMAR Team",license:"CC-BY-NC-ND-4.0",repository:{type:"git",url:"git+https://github.com/nemarOrg/nemar-cli.git"},bugs:{url:"https://github.com/nemarOrg/nemar-cli/issues"},homepage:"https://nemar-cli.pages.dev",engines:{bun:">=1.0.0"},files:["dist","README.md","LICENSE"],dependencies:{chalk:"^5.3.0",commander:"^12.1.0",conf:"^13.0.1","fuse.js":"^7.1.0",inquirer:"^9.2.15",ora:"^8.0.1",zod:"^3.23.8"},"lint-staged":{"src/**/*.{ts,tsx}":["biome check --fix"],"backend/src/**/*.{ts,tsx}":["biome check --fix"]},devDependencies:{"@biomejs/biome":"1.9.4","@types/bcryptjs":"^3.0.0","@types/bun":"latest","@types/inquirer":"^9.0.7",bcryptjs:"^3.0.3",husky:"^9.1.7","lint-staged":"^16.3.2",typescript:"^5.5.4",wrangler:"^4.70.0",yaml:"^2.8.4"}}});var x4;var iJ=P(()=>{qf();x4=Kf.version});function T0(D){if(D instanceof Error)return D.message;return String(D)}function zf(){if(process.env.TEST_API_URL)return process.env.TEST_API_URL;if(AW)return LW;return QD().apiUrl||LW}async function h(D,F={},$=!1){let J=`${zf()}${D}`,Q={"Content-Type":"application/json","X-CLI-Version":x4,...F.headers};if($){let X=QD();if(!X.apiKey&&$===!0)throw new p(401,"Not authenticated. 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h(`/datasets/${D}/manifest/${F}`,{},!0)}function Sf(D){let F=D;if(!F.status)F.status="active";else if(!["active","archived","deleted"].includes(F.status))throw Error(`Invalid dataset status: ${F.status}`);if(!F.visibility)F.visibility="private";else if(!["public","private"].includes(F.visibility))throw Error(`Invalid dataset visibility: ${F.visibility}`);return F}async function P9(D={}){let F=new URLSearchParams;if(D.mine)F.set("mine","true");if(D.search)F.set("search",D.search);if(D.modality)F.set("modality",D.modality);if(D.author)F.set("author",D.author);if(D.task)F.set("task",D.task);if(D.hasDoi)F.set("has_doi","true");if(D.recent)F.set("recent",String(D.recent));if(D.sort)F.set("sort",D.sort);if(D.limit!=null)F.set("limit",String(D.limit));if(D.offset!=null)F.set("offset",String(D.offset));if(D.owner)F.set("owner",D.owner);let $=F.toString()?`?${F.toString()}`:"",J=await h(`/datasets${$}`,{},D.mine?!0:"optional");return J.datasets=J.datasets.map(Sf),J}async function kf(D){return h(`/datasets/resolve/${D}`,{},"optional")}async function vf(D,F={}){let $=new URLSearchParams({q:D});if(F.modality)$.set("modality",F.modality);if(F.limit)$.set("limit",String(F.limit));return h(`/datasets/search?${$.toString()}`,{},"optional")}async function bD(D){let F=await h(`/datasets/${D}`,{},"optional");return Sf(F.dataset)}async function yf(D){return h(`/datasets/${D}/versions`,{},!0)}async function tJ(D){return h("/datasets",{method:"POST",body:JSON.stringify(D)},!0)}async function eJ(D){return h(`/datasets/${D}/finalize`,{method:"POST"},!0)}async function C8(D,F){return h(`/datasets/${D}/upload-credentials`,{method:"POST",body:JSON.stringify({duration_seconds:F})},!0)}async function DQ(D,F){return h(`/datasets/${D}/download-credentials`,{method:"POST",body:JSON.stringify({duration_seconds:F})},!0)}async function xf(D,F){return h(`/admin/datasets/${D}/doi/concept`,{method:"POST",body:JSON.stringify(F)},!0)}async function I9(D){return h(`/admin/datasets/${D}/doi`,{},!0)}async 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`)}var Hf=!1;var UW=P(()=>{yD()});var Kf;var qf=P(()=>{Kf={name:"nemar-cli",version:"0.8.10-dev.753",description:"CLI for NEMAR (Neuroelectromagnetic Data Archive and Tools Resource) dataset management",type:"module",main:"dist/index.js",bin:{nemar:"dist/index.js"},scripts:{dev:"bun run src/index.ts",build:"bun build src/index.ts --outdir dist --target bun --minify && sed '1s|#!/usr/bin/env node|#!/usr/bin/env bun|' dist/index.js > dist/index.js.tmp && mv dist/index.js.tmp dist/index.js",test:"bun test",lint:"biome check src/","lint:fix":"biome check --fix src/",format:"biome format --write src/",typecheck:"tsc --noEmit",prepublishOnly:"bun run build","docs:generate":"bun run scripts/generate-docs.ts","docs:serve":"mkdocs serve","docs:build":"mkdocs build",prepare:"husky",deploy:"wrangler deploy",preview:"wrangler dev"},keywords:["nemar","bids","neuroimaging","eeg","emg","datalad","cli"],author:"NEMAR Team",license:"CC-BY-NC-ND-4.0",repository:{type:"git",url:"git+https://github.com/nemarOrg/nemar-cli.git"},bugs:{url:"https://github.com/nemarOrg/nemar-cli/issues"},homepage:"https://nemar-cli.pages.dev",engines:{bun:">=1.0.0"},files:["dist","README.md","LICENSE"],dependencies:{chalk:"^5.3.0",commander:"^12.1.0",conf:"^13.0.1","fuse.js":"^7.1.0",inquirer:"^9.2.15",ora:"^8.0.1",zod:"^3.23.8"},"lint-staged":{"src/**/*.{ts,tsx}":["biome check --fix"],"backend/src/**/*.{ts,tsx}":["biome check --fix"]},devDependencies:{"@biomejs/biome":"1.9.4","@types/bcryptjs":"^3.0.0","@types/bun":"latest","@types/inquirer":"^9.0.7",bcryptjs:"^3.0.3",husky:"^9.1.7","lint-staged":"^16.3.2",typescript:"^5.5.4",wrangler:"^4.70.0",yaml:"^2.8.4"}}});var x4;var iJ=P(()=>{qf();x4=Kf.version});function T0(D){if(D instanceof Error)return D.message;return String(D)}function zf(){if(process.env.TEST_API_URL)return process.env.TEST_API_URL;if(AW)return LW;return QD().apiUrl||LW}async function h(D,F={},$=!1){let J=`${zf()}${D}`,Q={"Content-Type":"application/json","X-CLI-Version":x4,...F.headers};if($){let X=QD();if(!X.apiKey&&$===!0)throw new p(401,"Not authenticated. 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`)}}}var jW=P(()=>{yD()});var Rg={};d4(Rg,{verifyGitHubAuth:()=>v9,toS3Credentials:()=>CD,switchBranch:()=>ez0,setKeyPresent:()=>Cg,selectAnnexS3Remote:()=>_W,saveDataset:()=>a8,runCommand:()=>I,resolveUpstreamRef:()=>pW,readRemoteHeadDatasetVersion:()=>lW,readLocalDatasetVersion:()=>mW,pushToGitHub:()=>a1,pushBranch:()=>jF,markInheritedOpenNeuroRemotesIgnored:()=>xW,listDatasetVersions:()=>gW,isWorkingTreeDirty:()=>dW,isGitAnnexDataset:()=>O1,isDataladDataset:()=>QE0,initOrEnableSpecialRemote:()=>Ag,initDataset:()=>d6,gitMergeFastForward:()=>nW,gitFetchOrigin:()=>cW,gitAnnexAdd:()=>c6,getVersionCommit:()=>hW,getRemoteUuid:()=>sW,getLocalDatasetInfo:()=>fW,getKeyHashDirs:()=>$E0,getKeyHashDir:()=>Ng,getDatasetStats:()=>sz0,getDatasetIdFromRemote:()=>s8,getDatasetData:()=>BQ,getCurrentBranch:()=>o8,getAnnexWhereisAll:()=>oW,getAnnexS3Remotes:()=>x9,formatBytes:()=>XD,ensureLocalMainBranch:()=>_9,ensureGitAnnexInitialized:()=>vW,enableS3Remote:()=>g4,dropUnusedAnnexObjects:()=>iW,dropFiles:()=>yW,createRevertBranch:()=>bW,createDataladDataset:()=>JE0,countPendingDownload:()=>YQ,copyToAnnexRemote:()=>O8,configureS3Remote:()=>R8,configureLargefiles:()=>f4,configureGitHubRemote:()=>i8,commitRevert:()=>uW,collectFileManifest:()=>aW,cloneDataset:()=>o1,clearAnnexCredentials:()=>kD,checkPrerequisites:()=>k9,checkGitHubSSH:()=>Vg,checkGitAnnexInstalled:()=>kW,checkDownloadPrerequisites:()=>wF,checkAWSCredentials:()=>iz0,batchSetKeysPresent:()=>rW,annexRemoteExists:()=>Lg,acceptGitHubInvitation:()=>y9,NEMAR_S3_REMOTE_NAME:()=>QQ,ANNEX_REMOTE_EXISTS_RE:()=>Ug});import{existsSync as IW,readFileSync as dz0,statSync as cz0}from"fs";import{join as SW}from"path";var{spawn:Eg}=globalThis.Bun;async function I(D,F={}){let $=Eg({cmd:D,cwd:F.cwd,stdout:"pipe",stderr:"pipe",env:{...process.env,GIT_TERMINAL_PROMPT:"0",...F.env}}),J=!1,Q;if(F.timeout)Q=setTimeout(()=>{J=!0,$.kill()},F.timeout);if(wW()){let G=F.cwd?` (cwd=${F.cwd})`:"";S9(W.dim(`$ ${D.join(" ")}${G}`))}let Y=await new Response($.stdout).text(),B=await new Response($.stderr).text(),X=await $.exited;if(Q)clearTimeout(Q);if(wW()){if(Y.trim())S9(W.dim(Y.trimEnd()));if(B.trim())S9(W.yellow(B.trimEnd()));S9(W.dim(`(exit ${X})`))}if(J)return{stdout:Y,stderr:B||`Command timed out after ${Math.round(F.timeout/1000)}s`,exitCode:X??1};return{stdout:Y,stderr:B,exitCode:X}}function qg(D){return D.split(".").map((F)=>{let $=Number.parseInt(F.replace(/[^0-9]/g,""),10);return Number.isNaN($)?0:$})}function nz0(D,F){let $=qg(D),J=qg(F);for(let Q=0;Q<Math.max($.length,J.length);Q++){let Y=$[Q]||0,B=J[Q]||0;if(Y>B)return!0;if(Y<B)return!1}return!0}async function kW(){try{let{stdout:F,exitCode:$,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?nz0(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:$}}}async function Vg(){if(process.env.GH_TOKEN)return{accessible:!0,username:"token-auth",useHttps:!0};try{let{stdout:D,stderr:F}=await I(["ssh","-T","-o","BatchMode=yes","-o","StrictHostKeyChecking=accept-new","-o","ConnectTimeout=10","git@github.com"]),$=D+F,J=$.match(/Hi ([^!]+)!/);if(J)return{accessible:!0,username:J[1]};if($.includes("Permission denied"))return{accessible:!1};return{accessible:$.includes("successfully authenticated")}}catch(D){let F=D instanceof Error?D.message:String(D);if(F.includes("ENOENT")||F.includes("not found"))console.info("SSH command not found");else console.error("Error checking GitHub SSH access:",F);return{accessible:!1}}}async function iz0(){if(process.env.AWS_ACCESS_KEY_ID&&process.env.AWS_SECRET_ACCESS_KEY)return{configured:!0,source:"environment"};try{let{stdout:D,exitCode:F}=await I(["aws","configure","get","aws_access_key_id"]);if(F===0&&D.trim())return{configured:!0,source:"aws-cli"}}catch(D){let F=D instanceof Error?D.message:String(D);if(F.includes("ENOENT")||F.includes("not found"))console.info("AWS CLI not found in PATH");else console.error("Error checking AWS credentials:",F)}return{configured:!1}}function Zg(){let D=process.platform;if(D==="darwin")return"brew install git-annex";if(D==="linux")return"apt install git-annex (Debian/Ubuntu)";return"See https://git-annex.branchable.com/install/"}async function k9(){let[D,F]=await Promise.all([kW(),Vg()]),$=[];if(!D.installed)$.push(`git-annex is not installed. 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@@ -126,7 +126,7 @@ Fix one of these:
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`)}async function ZE0(D,F,$){let J=await I(["bash","-c",`curl -sfL '${D}' | aws s3 cp - '${F}' --region '${$}'`],{});if(J.exitCode!==0)return{success:!1,error:J.stderr.trim()};return{success:!0}}async function UE0(D,F,$,J){let Q=0,Y=[];for(let B=0;B<D.length;B+=$){let X=D.slice(B,B+$),G=await Promise.allSettled(X.map(async(H)=>{let q=await ZE0(H.sourceUrl,H.destUri,F);if(!q.success)throw Error(q.error||"Unknown S3 copy error");return H.key}));for(let H=0;H<G.length;H++){let q=G[H];if(q.status==="fulfilled")Q++;else Y.push({key:X[H].key,error:q.reason?.message||"Unknown error"})}J?.(Q,D.length,X[X.length-1].key)}return{copied:Q,failed:Y}}async function LE0(D,F={}){let $=qE0(D),J=F.workDir||BE0(f9(WE0(),`nemar-import-${$}-`)),Q=f9(J,$);console.log(W.cyan(`
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`)),console.log(W.dim(`Working directory: ${J}`));let Y=C("Cloning OpenNeuro dataset...").start(),B=`https://github.com/${HE0}/${D}.git`,X=await o1(B,Q);if(!X.success)Y.fail(`Failed to clone: ${X.error}`),process.exit(1);if(Y.succeed(`Cloned ${D}`),!await _9(Q,{yes:!0}))console.error(W.red("Cannot proceed with import: branch must be named 'main'.")),process.exit(1);let H=KE0(Q),q=H.Name||D,K=EE0(H);if(console.log(W.dim(` Dataset: ${q}`)),K)console.log(W.dim(` OpenNeuro DOI: ${K}`));let V=C("Creating NEMAR dataset record...").start();try{let g=await rf({dataset_id:$,name:q,description:`Imported from OpenNeuro ${D}`,source:"openneuro",source_id:D});V.succeed(`Created ${g.dataset_id} (${g.github_repo})`)}catch(g){let N0=g instanceof Error?g.message:String(g);if(N0.includes("already exists")||N0.includes("409"))V.warn(`Dataset ${$} already exists, continuing...`);else V.fail(`Failed to create dataset: ${N0}`),process.exit(1)}let E=C("Deploying CI workflows...").start();try{await _4($),E.succeed("CI workflows deployed (BIDS validation, LLM enrichment, archive generation)")}catch(g){let N0=g instanceof Error?g.message:String(g);E.warn(`CI deployment failed (non-fatal): ${N0}`),console.log(W.dim(` Workflows can be deployed later with: nemar admin ci add ${$}`))}let Z=new Map;if(!F.skipData){let g=C("Mapping annexed files from OpenNeuro S3...").start(),N0=await I(["git","annex","enableremote","s3-PUBLIC"],{cwd:Q});if(N0.exitCode!==0)g.fail(`Failed to enable s3-PUBLIC remote: ${N0.stderr.trim()}`),process.exit(1);if(Z=await oW(Q),Z.size===0)g.warn("No annexed files found, skipping data copy");else g.succeed(`Found ${Z.size} annexed files`)}await xW(Q,(g,N0)=>{console.log(W.yellow(` Warning: could not mark ${g} as annex-ignore (${N0}). Future pushes may try to upload to ${g}; run 'git config remote.${g}.annex-ignore true' manually.`))});let L=C("Configuring NEMAR remote...").start(),A=await I(["git","remote","remove","origin"],{cwd:Q});if(A.exitCode!==0&&!A.stderr.includes("No such remote"))L.fail(`Failed to remove OpenNeuro remote: ${A.stderr.trim()}`),process.exit(1);let M=`git@github.com:nemarDatasets/${$}.git`,R=await i8(Q,M,"origin");if(!R.success)L.fail(`Failed to configure remote: ${R.error}`),process.exit(1);if(L.succeed("Configured NEMAR remote"),!F.skipData&&Z.size>0){let g=C("Setting up NEMAR S3 remote...").start(),N0=zE0(),N=await R8(Q,{name:"nemar-s3",bucket:Og,prefix:`${$}/objects`,region:Tg},N0);if(!N.success)g.fail(`Failed to configure S3 remote: ${N.error}`),process.exit(1);let n=await sW(Q,"nemar-s3");if(!n)g.fail("Failed to get NEMAR S3 remote UUID"),process.exit(1);g.succeed("Configured NEMAR S3 remote");let l=C("Preparing S3-to-S3 copy...").start(),C0=[],m0=[];for(let[GD,G1]of Z){if(!G1.startsWith("http")){m0.push(GD);continue}let Jb=`s3://${Og}/${$}/objects/${GD}`;C0.push({key:GD,sourceUrl:G1,destUri:Jb})}if(m0.length>0)console.log(W.yellow(` Skipped ${m0.length} keys (no source URL)`));l.succeed(`Prepared ${C0.length} files for S3-to-S3 copy`);let $D=C(`Copying ${C0.length} files to NEMAR S3...`).start(),z0=await UE0(C0,Tg,8,(GD,G1)=>{$D.text=`Copying files to NEMAR S3... ${GD}/${G1}`});if(z0.failed.length>0){console.error(W.red(`
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