nemar-cli 0.8.14-dev.828 → 0.8.14-dev.830
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 +5 -5
- 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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`)}var Vf=!1;var RW=I(()=>{xD()});var Uf;var Zf=I(()=>{Uf={name:"nemar-cli",version:"0.8.14-dev.830",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 _4;var sJ=I(()=>{Zf();_4=Uf.version});function w0(D){if(D instanceof Error)return D.message;return String(D)}function Lf(){if(process.env.TEST_API_URL)return process.env.TEST_API_URL;if(OW)return CW;return JD().apiUrl||CW}async function u(D,F={},$=!1){let J=`${Lf()}${D}`,Q={"Content-Type":"application/json","X-CLI-Version":_4,...F.headers};if($){let X=JD();if(!X.apiKey&&$===!0)throw new b(401,"Not authenticated. 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`)}}}var vW=I(()=>{xD()});var Tg={};c4(Tg,{verifyGitHubAuth:()=>x9,toS3Credentials:()=>RD,switchBranch:()=>GE0,setKeyPresent:()=>jg,selectAnnexS3Remote:()=>uW,saveDataset:()=>o8,runCommand:()=>S,resolveUpstreamRef:()=>aW,readRemoteHeadDatasetVersion:()=>iW,readLocalDatasetVersion:()=>nW,pushToGitHub:()=>o1,pushBranch:()=>PF,markInheritedOpenNeuroRemotesIgnored:()=>bW,listDatasetVersions:()=>lW,isWorkingTreeDirty:()=>oW,isGitAnnexDataset:()=>w1,isDataladDataset:()=>zE0,initOrEnableSpecialRemote:()=>Cg,initDataset:()=>n6,gitMergeFastForward:()=>rW,gitFetchOrigin:()=>sW,gitAnnexAdd:()=>i6,getVersionCommit:()=>pW,getRemoteUuid:()=>FH,getLocalDatasetInfo:()=>mW,getKeyHashDirs:()=>qE0,getKeyHashDir:()=>wg,getDatasetStats:()=>YE0,getDatasetIdFromRemote:()=>r8,getDatasetData:()=>HQ,getCurrentBranch:()=>s8,getAnnexWhereisAll:()=>DH,getAnnexS3Remotes:()=>f9,formatBytes:()=>XD,ensureLocalMainBranch:()=>g9,ensureGitAnnexInitialized:()=>gW,enableS3Remote:()=>h4,dropUnusedAnnexObjects:()=>tW,dropFiles:()=>hW,createRevertBranch:()=>dW,createDataladDataset:()=>KE0,countPendingDownload:()=>WQ,copyToAnnexRemote:()=>w8,configureS3Remote:()=>O8,configureLargefiles:()=>g4,configureGitHubRemote:()=>a8,commitRevert:()=>cW,collectFileManifest:()=>eW,cloneDataset:()=>s1,clearAnnexCredentials:()=>kD,checkPrerequisites:()=>y9,checkGitHubSSH:()=>Ag,checkGitAnnexInstalled:()=>fW,checkDownloadPrerequisites:()=>TF,checkAWSCredentials:()=>$E0,batchSetKeysPresent:()=>$H,annexRemoteExists:()=>Rg,acceptGitHubInvitation:()=>_9,NEMAR_S3_REMOTE_NAME:()=>GQ,ANNEX_REMOTE_EXISTS_RE:()=>Ng});import{existsSync as xW,readFileSync as ez0,statSync as DE0}from"fs";import{join as _W}from"path";var{spawn:Lg}=globalThis.Bun;async function S(D,F={}){let $=Lg({cmd:D,cwd:F.cwd,stdout:"pipe",stderr:"pipe",env:{...process.env,GIT_TERMINAL_PROMPT:"0",...F.env}}),J=!1,Q;if(F.timeout)Q=setTimeout(()=>{J=!0,$.kill()},F.timeout);if(kW()){let G=F.cwd?` (cwd=${F.cwd})`:"";v9(W.dim(`$ ${D.join(" ")}${G}`))}let Y=await new Response($.stdout).text(),B=await new Response($.stderr).text(),X=await $.exited;if(Q)clearTimeout(Q);if(kW()){if(Y.trim())v9(W.dim(Y.trimEnd()));if(B.trim())v9(W.yellow(B.trimEnd()));v9(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 Vg(D){return D.split(".").map((F)=>{let $=Number.parseInt(F.replace(/[^0-9]/g,""),10);return Number.isNaN($)?0:$})}function FE0(D,F){let $=Vg(D),J=Vg(F);for(let Q=0;Q<Math.max($.length,J.length);Q++){let Y=$[Q]||0,B=J[Q]||0;if(Y>B)return!0;if(Y<B)return!1}return!0}async function fW(){try{let{stdout:F,exitCode:$,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?FE0(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:$}}}async function Ag(){if(process.env.GH_TOKEN)return{accessible:!0,username:"token-auth",useHttps:!0};try{let{stdout:D,stderr:F}=await S(["ssh","-T","-o","BatchMode=yes","-o","StrictHostKeyChecking=accept-new","-o","ConnectTimeout=10","git@github.com"]),$=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 $E0(){if(process.env.AWS_ACCESS_KEY_ID&&process.env.AWS_SECRET_ACCESS_KEY)return{configured:!0,source:"environment"};try{let{stdout:D,exitCode:F}=await S(["aws","configure","get","aws_access_key_id"]);if(F===0&&D.trim())return{configured:!0,source:"aws-cli"}}catch(D){let F=D instanceof Error?D.message:String(D);if(F.includes("ENOENT")||F.includes("not found"))console.info("AWS CLI not found in PATH");else console.error("Error checking AWS credentials:",F)}return{configured:!1}}function Mg(){let D=process.platform;if(D==="darwin")return"brew install git-annex";if(D==="linux")return"apt install git-annex (Debian/Ubuntu)";return"See https://git-annex.branchable.com/install/"}async function y9(){let[D,F]=await Promise.all([fW(),Ag()]),$=[];if(!D.installed)$.push(`git-annex is not installed. 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`).filter(($)=>{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(`
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@@ -201,11 +201,11 @@ Making repository public: ${D}
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Making repository private: ${D}
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`)),console.log("This will restrict access to collaborators only."),console.log();let $=await k0(`Make ${D} private?`,F);if($!=="confirmed"){console.log(W.dim($==="declined"?"Skipped":"Cancelled"));return}let J=O(`Setting ${D} to private...`).start();try{await wW(D,"private"),J.succeed(`Repository ${D} is now private`)}catch(Q){QD(Q,J,"Failed to change visibility",{404:"Dataset not found"})}});r0.addCommand(GH);var qQ=new i0("ci").description("CI workflow management");qQ.command("check").description("Check CI workflow status for a dataset").argument("<dataset-id>","Dataset ID (e.g., nm000104)").action(async(D)=>{if(!f0())return;let F=O(`Checking CI status for ${D}...`).start();try{let $=await vf(D);F.stop(),console.log(`
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`);let J=$.bids_validation.present,Q=J?W.green("[x]"):W.red("[ ]");if(console.log(` ${Q} BIDS Validation`),J){let X=$.bids_validation.status==="success"?W.green:$.bids_validation.status==="failure"?W.red:W.yellow;if(console.log(` Status: ${X($.bids_validation.status)}`),$.bids_validation.url)console.log(` URL: ${W.dim($.bids_validation.url)}`)}else console.log(` ${W.dim("Not deployed. Use 'nemar admin ci add' to deploy.")}`);let Y=$.version_check.present,B=Y?W.green("[x]"):W.red("[ ]");if(console.log(` ${B} Version Check`),!Y)console.log(` ${W.dim("Not deployed. Use 'nemar admin ci add' to deploy.")}`);console.log()}catch($){QD($,F,"Failed to check CI status",{404:"Dataset not found"})}});qQ.command("add").description("Deploy CI workflows to a dataset repository (or all with --all)").argument("[dataset-id]","Dataset ID (e.g., nm000104)").option("--all","Deploy to all dataset repositories").option(j0,T0).option(b0,y0).action(async(D,F)=>{if(!f0())return;if(F.all){let
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Deploy CI workflows to ${
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`)),console.log("This will add/update the following workflows on each:"),console.log(" 1. BIDS Validation (runs on PRs)"),console.log(" 2. Version Check (ensures version bump on PRs)"),console.log(" 3. PR Merge Handler (creates releases, publishes DOIs)")
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`);let J=$.bids_validation.present,Q=J?W.green("[x]"):W.red("[ ]");if(console.log(` ${Q} BIDS Validation`),J){let X=$.bids_validation.status==="success"?W.green:$.bids_validation.status==="failure"?W.red:W.yellow;if(console.log(` Status: ${X($.bids_validation.status)}`),$.bids_validation.url)console.log(` URL: ${W.dim($.bids_validation.url)}`)}else console.log(` ${W.dim("Not deployed. Use 'nemar admin ci add' to deploy.")}`);let Y=$.version_check.present,B=Y?W.green("[x]"):W.red("[ ]");if(console.log(` ${B} Version Check`),!Y)console.log(` ${W.dim("Not deployed. Use 'nemar admin ci add' to deploy.")}`);console.log()}catch($){QD($,F,"Failed to check CI status",{404:"Dataset not found"})}});qQ.command("add").description("Deploy CI workflows to a dataset repository (or all with --all)").argument("[dataset-id]","Dataset ID (e.g., nm000104)").option("--all","Deploy to all dataset repositories").option("--no-validate","Skip post-deploy parseability check (saves ~2.5 s per dataset; use for fleet deploys with --all)").option(j0,T0).option(b0,y0).action(async(D,F)=>{if(!f0())return;let $=F.validate===!1;if(F.all){let Y=O("Fetching dataset list...").start(),B;try{if(B=(await S9({limit:1000})).datasets,Y.succeed(`Found ${B.length} datasets`),B.length>=1000)console.log(W.yellow("Warning: reached 1000 dataset limit; some datasets may be skipped"))}catch(q){QD(q,Y,"Failed to fetch datasets");return}if(console.log(W.cyan(`
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`)),console.log("This will add/update the following workflows on each:"),console.log(" 1. BIDS Validation (runs on PRs)"),console.log(" 2. Version Check (ensures version bump on PRs)"),console.log(" 3. PR Merge Handler (creates releases, publishes DOIs)"),$)console.log(W.dim(" (post-deploy parseability check disabled via --no-validate)"));console.log();let X=await k0(`Deploy CI workflows to all ${B.length} datasets?`,F);if(X!=="confirmed"){console.log(W.dim(X==="declined"?"Skipped":"Cancelled"));return}let G=0,H=0;for(let q of B){let K=O(`Deploying to ${q.dataset_id}...`).start();try{let V=await f4(q.dataset_id,{validate:!$});if(V.validation_warnings&&V.validation_warnings.length>0){K.warn(`${q.dataset_id}: deployed (with warnings)`);for(let E of V.validation_warnings)console.log(` ${W.yellow("!")} ${E}`)}else K.succeed(`${q.dataset_id}: deployed`);G++}catch(V){let E=V instanceof b?V.message:String(V);K.fail(`${q.dataset_id}: ${E}`),H++}}console.log(),console.log(W.cyan(`Done: ${G} succeeded, ${H} failed out of ${B.length}`));return}if(!D){console.error(W.red("Error: dataset-id is required (or use --all)"));return}if(console.log(W.cyan(`
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`)),console.log("This will add the following workflows:"),console.log(" 1. BIDS Validation (runs on PRs)"),console.log(" 2. Version Check (ensures version bump on PRs)"),console.log(" 3. PR Merge Handler (creates releases, publishes DOIs)")
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`)),console.log("This will add the following workflows:"),console.log(" 1. BIDS Validation (runs on PRs)"),console.log(" 2. Version Check (ensures version bump on PRs)"),console.log(" 3. PR Merge Handler (creates releases, publishes DOIs)"),$)console.log(W.dim(" (post-deploy parseability check disabled via --no-validate)"));console.log();let J=await k0(`Deploy CI workflows to ${D}?`,F);if(J!=="confirmed"){console.log(W.dim(J==="declined"?"Skipped":"Cancelled"));return}let Q=O(`Deploying CI workflows to ${D}...`).start();try{let Y=await f4(D,{validate:!$});Q.succeed("CI workflows deployed"),console.log();for(let B of Y.workflows_deployed)console.log(` ${W.green("[x]")} ${B}`);if(Y.validation_warnings&&Y.validation_warnings.length>0){console.log(),console.log(W.yellow("Validation warnings (best-effort; deploy succeeded):"));for(let B of Y.validation_warnings)console.log(` ${W.yellow("!")} ${B}`)}console.log()}catch(Y){QD(Y,Q,"Failed to deploy CI workflows",{404:"Dataset not found"})}});qQ.command("sync").description("Sync deployed CI workflows to current templates (only writes drifted/missing files)").argument("[dataset-id]","Dataset ID (e.g., nm000104)").option("--all","Sync across all dataset repositories").option(j0,T0).option(b0,y0).action(async(D,F)=>{if(!f0())return;if(F.all){let J=O("Fetching dataset list...").start(),Q;try{if(Q=(await S9({limit:1000})).datasets,J.succeed(`Found ${Q.length} datasets`),Q.length>=1000)console.log(W.yellow("Warning: reached 1000 dataset limit; some datasets may be skipped"))}catch(H){QD(H,J,"Failed to fetch datasets");return}console.log(W.cyan(`
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`));let Y=await k0(`Sync templates on all ${Q.length} datasets?`,F);if(Y!=="confirmed"){console.log(W.dim(Y==="declined"?"Skipped":"Cancelled"));return}let B=0,X=0,G=0;for(let H of Q){let q=O(`Syncing ${H.dataset_id}...`).start();try{let K=await jW(H.dataset_id),V=K.changed.length+K.added.length;if(K.errors.length>0)q.warn(`${H.dataset_id}: ${V} updated, ${K.errors.length} error(s)`),G++;else if(V===0)q.succeed(`${H.dataset_id}: up to date`),B++;else{let E=[];if(K.added.length>0)E.push(`+${K.added.length} added`);if(K.changed.length>0)E.push(`~${K.changed.length} updated`);q.succeed(`${H.dataset_id}: ${E.join(", ")}`),X++}}catch(K){let V=K instanceof b?K.message:String(K);q.fail(`${H.dataset_id}: ${V}`),G++}}console.log(),console.log(W.cyan(`Done: ${B} up-to-date, ${X} updated, ${G} with errors`));return}if(!D){console.error(W.red("Error: dataset-id is required (or use --all)"));return}let $=O(`Syncing CI templates for ${D}...`).start();try{let J=await jW(D),Q=J.changed.length+J.added.length;if(J.errors.length>0)$.warn(`${D}: ${J.errors.length} error(s)`);else if(Q===0)$.succeed(`${D}: already up to date`);else $.succeed(`${D}: synced`);if(console.log(),console.log(` ${W.dim("Checked:")} ${J.checked.join(", ")}`),J.added.length>0)console.log(` ${W.green("Added:")} ${J.added.join(", ")}`);if(J.changed.length>0)console.log(` ${W.yellow("Updated:")} ${J.changed.join(", ")}`);if(!J.committed&&Q>0&&J.errors.length===0)console.log(` ${W.yellow("Note:")} listed changes were not committed`);if(J.list_failed)console.log(` ${W.red("Warning:")} workflow directory listing failed; presence is unknown`);if(J.errors.length>0){console.log(` ${W.red("Errors:")}`);for(let Y of J.errors)console.log(` - ${Y}`)}console.log()}catch(J){QD(J,$,"Failed to sync CI templates",{404:"Dataset not found"})}});r0.addCommand(qQ);var b9=new i0("doi").description("DOI management");b9.command("create").description("Create concept DOI for a dataset").argument("<dataset-id>","Dataset ID (e.g., nm000104)").option("--title <title>","DOI title (defaults to dataset name)").option("--description <desc>","DOI description").option("--provider <provider>","DOI provider: ezid (default) or zenodo","ezid").option("--sandbox","Use sandbox/test DOI").option(j0,T0).option(b0,y0).action(async(D,F)=>{if(!f0())return;let $=O("Fetching dataset info...").start(),J;try{J=await uD(D),$.succeed(`Found dataset: ${J.name}`)}catch(G){if(G instanceof b){if($.fail(G.message),G.statusCode===404)console.log(W.dim(" Dataset not found"))}else $.fail("Failed to fetch dataset");return}try{let G=await k9(D);if(G.concept_doi){if(console.log(W.yellow(`
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Dataset already has a concept DOI:`)),console.log(` Concept DOI: ${W.cyan(G.concept_doi)}`),G.zenodo_concept_url)console.log(` Zenodo URL: ${G.zenodo_concept_url}`);return}}catch(G){if(process.env.DEBUG)console.error("[debug] DOI info fetch:",G)}if(console.log(),console.log(W.cyan("Dataset Information:")),console.log(` ID: ${J.dataset_id}`),console.log(` Name: ${J.name}`),J.github_repo)console.log(` GitHub: ${J.github_repo}`);if(F.sandbox)console.log(` Mode: ${W.yellow("SANDBOX (test DOI)")}`);console.log();let Q=F.provider==="zenodo"?"zenodo":"ezid";if(F.sandbox){if(console.log(W.yellow("\u2501".repeat(60))),console.log(W.yellow.bold(" SANDBOX MODE ENABLED")),console.log(W.yellow("\u2501".repeat(60))),Q==="zenodo")console.log(W.yellow(" \u2022 Using Zenodo sandbox (sandbox.zenodo.org)"));else console.log(W.yellow(" \u2022 Using EZID test shoulder (doi:10.5072/FK2)")),console.log(W.yellow(" \u2022 Test DOIs auto-delete after 2 weeks"));console.log(W.yellow(" \u2022 DOI will NOT be indexed by DataCite")),console.log(W.yellow(" \u2022 DOI will NOT resolve in production")),console.log(W.yellow(" \u2022 Use this for testing workflows only")),console.log(W.yellow("\u2501".repeat(60))),console.log()}console.log(W.red("WARNING: DOIs are PERMANENT and cannot be deleted!")),console.log(W.dim("The DOI will be pre-reserved but not published until the first version release.")),console.log(` Provider: ${W.cyan(Q.toUpperCase())}`),console.log();let Y=F.sandbox?`Create TEST concept DOI via ${Q.toUpperCase()} SANDBOX?`:`Create PERMANENT concept DOI via ${Q.toUpperCase()} PRODUCTION?`,B=await k0(Y,F);if(B!=="confirmed"){console.log(W.dim(B==="declined"?"Skipped":"Cancelled"));return}let X=O(`Creating concept DOI via ${Q.toUpperCase()}...`).start();try{let G=await hf(D,{title:F.title,description:F.description,sandbox:F.sandbox,provider:Q});X.succeed("Concept DOI created successfully");let H=O("Applying branch protection...").start();try{let q=await JQ(D);if(q.warnings&&q.warnings.length>0){H.warn("Branch protection applied with warnings");for(let K of q.warnings)console.log(W.yellow(` Warning: ${K}`))}else H.succeed("Branch protection applied")}catch(q){if(H.warn("Could not apply branch protection"),q instanceof b){if(console.log(W.dim(` ${q.message}`)),q.statusCode===403)console.log(W.dim(" Check admin credentials and permissions"))}else console.log(W.dim(` ${q instanceof Error?q.message:"Unknown error"}`));console.log(W.dim(" Manual setup: Go to GitHub repo Settings > Branches > Add rule"))}if(console.log(),console.log(W.green("DOI Information:")),console.log(` Concept DOI: ${W.cyan(G.concept_doi)}`),console.log(` Provider: ${G.provider.toUpperCase()}`),G.provider==="ezid")console.log(` DOI URL: ${G.doi_url}`),console.log(` EZID ID: ${G.ezid_identifier}`);else console.log(` Zenodo URL: ${G.zenodo_url}`);if(G.metadata_warning)console.log(W.yellow(` Warning: ${G.metadata_warning}`));if(console.log(),console.log(W.yellow("Next steps:")),console.log(" 1. Update dataset_description.json with DatasetDOI field"),console.log(" 2. Create a PR and merge it to trigger version DOI publication"),console.log(),F.sandbox)console.log(W.dim("Note: This is a sandbox DOI and will not resolve in production."))}catch(G){if(G instanceof b){if(X.fail(G.message),G.statusCode===403)console.log(W.dim(" This command requires admin privileges"))}else X.fail("Failed to create concept DOI"),console.log(W.dim(` ${w0(G)}`))}});b9.command("info").description("Get DOI info for a dataset").argument("<dataset-id>","Dataset ID (e.g., nm000104)").action(async(D)=>{if(!f0())return;let F=O("Fetching DOI info...").start();try{let $=await k9(D);if(F.stop(),console.log(),console.log(W.cyan(`DOI Information for ${D}:`)),console.log(` Dataset Name: ${$.name}`),console.log(),$.concept_doi){if(console.log(W.green("Concept DOI:")),console.log(` DOI: ${$.concept_doi}`),console.log(` URL: https://doi.org/${$.concept_doi}`),console.log(` Provider: ${($.doi_provider||"zenodo").toUpperCase()}`),$.doi_provider==="ezid"){if($.ezid_identifier)console.log(` EZID ID: ${$.ezid_identifier}`);if($.ezid_status){let J=$.ezid_status==="public"?W.green:W.yellow;console.log(` Status: ${J($.ezid_status)}`)}}if($.zenodo_concept_url){if(console.log(` Zenodo: ${$.zenodo_concept_url}`),$.zenodo_concept_url.includes("sandbox.zenodo.org"))console.log(),console.log(W.yellow("Mode: SANDBOX (test DOI)")),console.log(W.yellow(" This DOI is not indexed by DataCite and will not resolve in production"))}}else console.log(W.yellow("No concept DOI created yet")),console.log(W.dim(" Use 'nemar admin doi create' to create one"));if(console.log(),$.latest_version_doi){if(console.log(W.green("Latest Version DOI:")),console.log(` DOI: ${$.latest_version_doi}`),console.log(` URL: https://doi.org/${$.latest_version_doi}`),$.zenodo_latest_version_url)console.log(` Zenodo: ${$.zenodo_latest_version_url}`)}else if($.concept_doi)console.log(W.yellow("No version DOI published yet")),console.log(W.dim(" Version DOIs are created automatically on PR merge"))}catch($){if($ instanceof b){if(F.fail($.message),$.statusCode===404)console.log(W.dim(" Dataset not found"));else if($.statusCode===403)console.log(W.dim(" This command requires admin privileges"))}else F.fail("Failed to fetch DOI info")}});b9.command("update").description("Update EZID DOI metadata or status").argument("<dataset-id>","Dataset ID (e.g., nm000104)").option("--make-public","Transition DOI from reserved to public (permanent)").option("--refresh","Refresh metadata from dataset_description.json and .nemar/metadata.json").option(j0,T0).option(b0,y0).action(async(D,F)=>{if(!f0())return;if(!F.makePublic&&!F.refresh){console.log(W.yellow("No action specified. Use --make-public and/or --refresh."));return}if(F.makePublic){console.log(W.red("WARNING: Making a DOI public is PERMANENT!")),console.log(W.dim(" The DOI will be findable in DataCite and cannot be reverted.")),console.log();let J=await k0(`Make DOI for ${D} PUBLIC and permanent?`,F);if(J!=="confirmed"){console.log(W.dim(J==="declined"?"Skipped":"Cancelled"));return}}let $=O("Updating DOI...").start();try{let J=await TW(D,{status:F.makePublic?"public":void 0,refresh_metadata:F.refresh});$.succeed("DOI updated successfully"),console.log(),console.log(` EZID ID: ${W.cyan(J.ezid_identifier)}`),console.log(` Status: ${J.status==="public"?W.green(J.status):W.yellow(J.status)}`),console.log(` URL: ${J.doi_url}`)}catch(J){if(J instanceof b){if($.fail(J.message),J.statusCode===400)console.log(W.dim(" DOI update is only supported for EZID-managed DOIs"))}else $.fail("Failed to update DOI"),console.log(W.dim(` ${w0(J)}`))}});b9.command("enrich").description("Enrich DOI metadata with ORCIDs, descriptions, funding, and more").argument("<dataset-id>","Dataset ID (e.g., nm000104)").option("--no-llm","Skip LLM-based enrichment from README").option("--sandbox","Use sandbox DOI").option(j0,T0).option(b0,y0).action(async(D,F)=>{if(!f0())return;let $=O("Fetching dataset and existing enrichment...").start(),J;try{J=await uD(D),$.succeed(`Dataset: ${J.name}`)}catch(E){if(E instanceof b)$.fail(E.message);else $.fail("Failed to fetch dataset");return}let Q,Y=!1;try{Q=await k9(D)}catch(E){if(E instanceof b&&E.statusCode===404);else Y=!0,console.log(W.yellow(` Warning: Could not fetch DOI info: ${w0(E)}`))}if(Q?.concept_doi)console.log(` DOI: ${W.cyan(Q.concept_doi)}`);let B={version:"2.0"};if(J.github_repo){let E=O("Reading existing metadata...").start(),Z=await ug(J.github_repo,".nemar/metadata.json");if(Z)try{let L=JSON.parse(Z);if(L&&typeof L==="object"&&L.version==="2.0")B=L,E.succeed(`Loaded existing metadata (stage: ${L.pipeline_stage||"unknown"})`);else E.warn("Existing metadata has unsupported version, starting fresh")}catch(L){E.warn(`Could not parse existing metadata (${L instanceof Error?L.message:String(L)}), starting fresh`)}else E.info("No existing .nemar/metadata.json found, starting fresh")}if(F.llm!==!1&&J.github_repo){console.log(),console.log(W.cyan("--- Running LLM enrichment pipeline (CI workflow) ---"));let E=O("Triggering llm-enrichment workflow...").start();try{let{spawn:Z}=awaitPromise.resolve(globalThis.Bun),L=J.github_repo,A=Z({cmd:["gh","workflow","run","llm-enrichment.yml","--repo",L,"--ref","main"],stdout:"pipe",stderr:"pipe"}),M=await new Response(A.stderr).text();if(await A.exited!==0)throw Error(`Failed to trigger workflow: ${M.trim()}`);E.text="Waiting for workflow to register...",await new Promise((y)=>setTimeout(y,3000)),E.text="Polling workflow status...";let w=60,P="",C=0;for(let y=0;y<w;y++){let d=Z({cmd:["gh","run","list","--repo",L,"--workflow","llm-enrichment.yml","-L","1","--json","databaseId,status,conclusion"],stdout:"pipe",stderr:"pipe"}),W0=await new Response(d.stdout).text(),F0=await new Response(d.stderr).text();if(await d.exited!==0){if(C++,C>=3){E.warn(`gh CLI error: ${F0.trim()}`);break}await new Promise((e)=>setTimeout(e,5000));continue}try{let e=JSON.parse(W0.trim());if(C=0,e.length>0){let N0=e[0];if(N0.status==="completed"){P=N0.conclusion||"unknown";break}E.text=`Workflow ${N0.status}... (${y*5}s)`}}catch(e){if(C++,C>=3){E.warn(`Unable to parse workflow status: ${e instanceof Error?e.message:String(e)} (raw: ${W0.trim().slice(0,200)})`);break}}await new Promise((e)=>setTimeout(e,5000))}let T=!1;if(!P)E.warn("Workflow timed out after 5 minutes (may still be running)");else if(P==="success"){E.succeed("LLM enrichment workflow completed successfully");let y=await ug(L,".nemar/metadata.json");if(y)try{let d=JSON.parse(y);if(d&&typeof d==="object"&&d.version==="2.0"){Object.assign(B,d),T=!0;let W0=d.pipeline_stage||"unknown";if(console.log(W.dim(` Pipeline stage: ${W0}`)),B.authors){let F0=Object.keys(B.authors).length;console.log(W.dim(` Authors: ${F0}`))}}}catch(d){console.log(W.yellow(` Warning: Could not parse updated metadata: ${d instanceof Error?d.message:String(d)}`)),console.log(W.dim(" Using pre-workflow enrichment data"))}else console.log(W.yellow(" Warning: Could not fetch updated metadata after successful workflow.")),console.log(W.dim(" Author data below may be from a previous run."))}else E.fail(`LLM enrichment workflow failed (conclusion: ${P})`);if(!T)console.log(W.yellow(" ORCID discovery did not complete. Authors below may be from previous metadata."))}catch(Z){E.fail("LLM enrichment pipeline failed"),console.log(W.dim(` ${w0(Z)}`)),console.log(W.yellow(" ORCID discovery did not run. You will need to enter ORCIDs manually."))}}console.log(),console.log(W.cyan("--- Author ORCIDs ---"));let X=B.authors||{},G=Object.keys(X);if(G.length>0){let E=G.filter((L)=>X[L]?.orcid),Z=G.filter((L)=>!X[L]?.orcid);console.log(W.dim(` Discovered ${G.length} authors from pipeline:`));for(let L of E)console.log(W.green(` [x] ${L}: ${X[L]?.orcid}`));for(let L of Z)console.log(W.yellow(` [ ] ${L}: no ORCID found`));if(Z.length>0)console.log(W.dim(` ${Z.length} author(s) missing ORCIDs.`))}let{updateAuthors:H}=await D0.prompt([{type:"confirm",name:"updateAuthors",message:G.length>0?"Add or correct author ORCIDs?":"Add author ORCIDs manually?",default:!1}]);if(H){let E={},Z=!0;while(Z){let{authorName:L}=await D0.prompt([{type:"input",name:"authorName",message:'Author name (as in BIDS, e.g., "Shirazi, Yahya"):'}]);if(!L)break;let A=X[L];if(A?.orcid)console.log(W.dim(` Current ORCID: ${A.orcid}`));let{orcid:M}=await D0.prompt([{type:"input",name:"orcid",message:`ORCID for "${L}" (Enter to ${A?.orcid?"keep current":"skip"}):`,validate:(C)=>{if(!C)return!0;return rJ.test(C)||"Invalid ORCID format (XXXX-XXXX-XXXX-XXXX)"}}]),N={};if(M)N.orcid=M;let{affiliation:w}=await D0.prompt([{type:"input",name:"affiliation",message:`Affiliation for "${L}" (optional):`}]);if(w)N.affiliations=[{name:w}];if(N.orcid||N.affiliations)E[L]=N;let{more:P}=await D0.prompt([{type:"confirm",name:"more",message:"Add another author?",default:!0}]);Z=P}if(Object.keys(E).length>0){let L={...B.authors||{}};for(let[A,M]of Object.entries(E)){let N=L[A]||{};L[A]={...N,...M,orcid:M.orcid||N.orcid}}B.authors=L}}console.log(),console.log(W.cyan("--- Dataset stats ---"));let q=O("Computing dataset sizes and formats...").start();try{let E=await sf(D),Z=XD(E.total_size);B.sizes=[`${Z} (${E.file_count} files)`],B.formats=E.extensions,q.succeed(`Sizes: ${Z} (${E.file_count} files), Formats: ${E.extensions.join(", ")}`)}catch(E){q.warn("Could not compute dataset stats"),console.log(W.dim(` ${w0(E)}`))}console.log(),console.log(W.cyan("--- Review ---")),console.log(JSON.stringify(B,null,2)),console.log();let K=await k0("Commit to repo and refresh DOI?",F,!0);if(K!=="confirmed"){console.log(W.dim(K==="declined"?"Skipped":"Cancelled"));return}let V=O("Saving enrichment...").start();try{let E=await of(D,B);if(V.succeed(E.message),E.bidsignore_updated)console.log(W.dim(" .bidsignore updated to include .nemar/"));if(!Q&&Y)try{Q=await k9(D)}catch(Z){if(process.env.DEBUG)console.error("[debug] DOI info re-fetch:",Z)}if(Q?.ezid_identifier){let Z=O("Refreshing DOI metadata...").start();try{await TW(D,{refresh_metadata:!0}),Z.succeed("DOI metadata refreshed")}catch(L){Z.warn("Could not refresh DOI metadata"),console.log(W.dim(` ${w0(L)}`))}}else if(Y)console.log(W.yellow(" DOI refresh skipped: could not verify DOI exists. Run 'nemar admin doi update --refresh' manually."))}catch(E){if(E instanceof b)V.fail(E.message);else V.fail("Failed to save enrichment"),console.log(W.dim(` ${w0(E)}`))}});r0.addCommand(b9);var KQ=new i0("publish").description("Publication workflow management");KQ.command("list").description("List publication requests").option("-s, --status <status>","Filter by status (requested, approving, published, denied)").addHelpText("after",`
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package/package.json
CHANGED