npm - nemar-cli - Versions diffs - 0.9.10-dev.2136 → 0.9.10-dev.2140 - Mend

nemar-cli 0.9.10-dev.2136 → 0.9.10-dev.2140

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Files changed (2) hide show

package/dist/index.js +2 -2
package/package.json +1 -1

package/dist/index.js CHANGED Viewed

@@ -102,7 +102,7 @@ ${u.dim(`eta:  ${e.eta}`)}`:"";process.stderr.write(`${t}
 ${r} ${e.message}
 ${n}${i}
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r=new URLSearchParams({q:e});if(t.modality)r.set("modality",t.modality);if(t.limit)r.set("limit",String(t.limit));if(t.hasHed)r.set("has_hed","1");if(t.author)r.set("author",t.author);if(t.task)r.set("task",t.task);if(t.license)r.set("license",t.license);if(t.hasDoi)r.set("has_doi","true");if(t.dataComplete)r.set("data_complete","1");if(t.recent)r.set("recent",String(t.recent));if(t.facets)for(let[i,s]of Object.entries(t.facets))r.set(i,s);if(t.includeUnknown)r.set("include_unknown","1");return await I(`/datasets/search?${r.toString()}`,{},"optional",gH)}async function gt(e){let t=await I(`/datasets/${e}`,{},"optional");return xH(t.dataset)}async function DH(e){return I(`/datasets/${e}/versions`,{},!0)}async function Nm(e){return I("/datasets",{method:"POST",body:JSON.stringify(e)},!0)}async function qm(e){return I(`/datasets/${e}/finalize`,{method:"POST"},!0)}async function bD(e){return I(`/datasets/${e}/request-access`,{method:"POST"},!0)}async function wH(e,t){let r=t?`?status=${t}`:"";return I(`/datasets/${e}/access-requests${r}`,{},!0)}async function EH(e,t){return I(`/datasets/${e}/access-requests/${t}/approve`,{method:"POST"},!0)}async function SH(e,t){return I(`/datasets/${e}/access-requests/${t}/deny`,{method:"POST"},!0)}async function $H(e,t){return I(`/datasets/${e}/invite`,{method:"POST",body:JSON.stringify({username:t})},!0)}async function CH(e){return I(`/datasets/${e}/collaborators`,{},!0)}async function FH(e,t){return I(`/admin/datasets/${e}/enrichment`,{method:"POST",body:JSON.stringify(t)},!0)}var Pm;var qs=A(()=>{km();Ns();Pm=/^\d{4}-\d{4}-\d{4}-\d{3}[\dX]$/});var Uc;var PH=A(()=>{Uc=["ci_check","enrichment_check","s3_public_read","repo_public","tag_protect","doi_create","update_metadata","update_readme","create_tag","create_release","upload_to_zenodo","publish_doi","version_doi","s3_lock","sync_nemar","notify_user"]});async function Vc(e){return I(`/datasets/${e}/publish/request`,{method:"POST"},!0)}async function TH(e){return I(`/datasets/${e}/publish/status`,{},!0)}async function NH(e){return I(`/datasets/${e}/publish/resend`,{method:"POST"},!0)}async function qH(e){let t=e?`?status=${e}`:"";return I(`/admin/publish/requests${t}`,{},!0)}async function jH(e,t){return I(`/admin/publish/${e}/deny`,{method:"POST",headers:{"Content-Type":"application/json"},body:JSON.stringify({reason:t})},!0)}function eTe(e,t=[]){if(e){let r=Uc.indexOf(e);if(r>=0)return r+1}return Math.min(t.length+1,Uc.length)}function tTe(e){if(!(e instanceof q))return!1;if(e.statusCode===0)return!0;if(e.statusCode===429)return!0;if(e.statusCode>=500&&e.statusCode<600)return!0;if(e.statusCode===403&&/repository has been locked/i.test(e.message))return!0;return!1}async function zc(e,t=!1,r=!1,n=!1,i,s){let c,l,d=0,f=!1,m,p=t,g=[],y;function x(v,_,E,C){if(!s)return;s({step:v,stepIndex:eTe(v,_),stepTotal:Uc.length,s3LockLocked:E,s3LockTotal:C,s3LockResumed:v==="s3_lock"&&f?!0:void 0})}for(let v=1;v<=5;v++)try{let _,E=!0;do{if(_=await 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 gh CLI failed: ${s.error||"could not get token"}
@@ -244,7 +244,7 @@ Deploy CI workflows to: ${e}
 `)),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)"),r)console.log(u.dim("  (post-deploy parseability poll disabled via --no-validate)"));console.log();let n=await Fe(`Deploy CI workflows to ${e}?`,t);if(n!=="confirmed"){console.log(u.dim(n==="declined"?"Skipped":"Cancelled"));return}let i=w(`Deploying CI workflows to ${e}...`).start(),s;try{s=await Ai(e)}catch(o){tt(o,i,"Failed to deploy CI workflows",{404:"Dataset not found"});return}i.succeed("CI workflows deployed"),console.log();for(let o of s.workflows_deployed)console.log(`  ${u.green("[x]")} ${o}`);if(!r){let o=w("Verifying GitHub Actions can parse the workflows...").start(),a=await H5e(e);if(!a)o.warn("Could not verify workflow parseability (deploy succeeded)");else if(a.missing.length===0&&a.errors.length===0)o.succeed("All workflows parseable by GitHub Actions");else{let c=a.missing.length>0?"Some workflows missing from GitHub Actions listing":"Could not fully verify workflow parseability (GitHub API error)";o.warn(c),zG(a)}}console.log()});qd.command("validate").description("Check whether GitHub Actions can parse the deployed CI workflows").argument("<dataset-id>","Dataset ID (e.g., nm000104)").action(async(e)=>{if(!oe())return;let t=w(`Validating CI workflows for ${e}...`).start();try{let r=await aD(e);if(r.missing.length===0&&r.errors.length===0)t.succeed(`All ${r.valid.length} workflows parseable by GitHub Actions`);else t.warn("Some workflows missing or unreadable"),zG({missing:r.missing,errors:r.errors})}catch(r){tt(r,t,"Failed to validate CI workflows",{404:"Dataset not found"})}});qd.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(Re,Oe).option(je,Te).action(async(e,t)=>{if(!oe())return;if(t.all){let n=w("Fetching dataset list...").start(),i;try{if(i=(await Lc({limit:1000})).datasets,n.succeed(`Found ${i.length} datasets`),i.length>=1000)console.log(u.yellow("Warning: reached 1000 dataset limit; some datasets may be skipped"))}catch(l){tt(l,n,"Failed to fetch datasets");return}console.log(u.cyan(`
 Sync CI templates across ${i.length} datasets (writes only diffs)
 `));let s=await Fe(`Sync templates on all ${i.length} datasets?`,t);if(s!=="confirmed"){console.log(u.dim(s==="declined"?"Skipped":"Cancelled"));return}let o=0,a=0,c=0;for(let l of i){let d=w(`Syncing ${l.dataset_id}...`).start();try{let f=await cD(l.dataset_id),m=f.changed.length+f.added.length;if(f.errors.length>0)d.warn(`${l.dataset_id}: ${m} updated, ${f.errors.length} error(s)`),c++;else if(m===0)d.succeed(`${l.dataset_id}: up to date`),o++;else{let p=[];if(f.added.length>0)p.push(`+${f.added.length} added`);if(f.changed.length>0)p.push(`~${f.changed.length} updated`);d.succeed(`${l.dataset_id}: ${p.join(", ")}`),a++}}catch(f){let m=f instanceof q?f.message:String(f);d.fail(`${l.dataset_id}: ${m}`),c++}}console.log(),console.log(u.cyan(`Done: ${o} up-to-date, ${a} updated, ${c} with errors`));return}if(!e){console.error(u.red("Error: dataset-id is required (or use --all)"));return}let r=w(`Syncing CI templates for ${e}...`).start();try{let n=await cD(e),i=n.changed.length+n.added.length;if(n.errors.length>0)r.warn(`${e}: ${n.errors.length} error(s)`);else if(i===0)r.succeed(`${e}: already up to date`);else r.succeed(`${e}: synced`);if(console.log(),console.log(`  ${u.dim("Checked:")} ${n.checked.join(", ")}`),n.added.length>0)console.log(`  ${u.green("Added:")}   ${n.added.join(", ")}`);if(n.changed.length>0)console.log(`  ${u.yellow("Updated:")} ${n.changed.join(", ")}`);if(!n.committed&&i>0&&n.errors.length===0)console.log(`  ${u.yellow("Note:")}    listed changes were not committed`);if(n.list_failed)console.log(`  ${u.red("Warning:")} workflow directory listing failed; presence is unknown`);if(n.errors.length>0){console.log(`  ${u.red("Errors:")}`);for(let s of n.errors)console.log(`    - ${s}`)}console.log()}catch(n){tt(n,r,"Failed to sync CI templates",{404:"Dataset not found"})}});Ie.addCommand(qd);var jd=new ve("doi").description("DOI management");jd.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(Re,Oe).option(je,Te).action(async(e,t)=>{if(!oe())return;let r=w("Fetching dataset info...").start(),n;try{n=await gt(e),r.succeed(`Found dataset: ${n.name}`)}catch(c){if(c instanceof q){if(r.fail(c.message),c.statusCode===404)console.log(u.dim("  Dataset not found"))}else r.fail("Failed to fetch dataset");return}try{let c=await vd(e);if(c.concept_doi){if(console.log(u.yellow(`
-Dataset already has a concept DOI:`)),console.log(`  Concept DOI: ${u.cyan(c.concept_doi)}`),c.zenodo_concept_url)console.log(`  Zenodo URL:  ${c.zenodo_concept_url}`);return}}catch(c){if(process.env.DEBUG)console.error("[debug] DOI info fetch:",c)}if(console.log(),console.log(u.cyan("Dataset Information:")),console.log(`  ID:          ${n.dataset_id}`),console.log(`  Name:        ${n.name}`),n.github_repo)console.log(`  GitHub:      ${n.github_repo}`);if(t.sandbox)console.log(`  Mode:        ${u.yellow("SANDBOX (test DOI)")}`);console.log();let i=t.provider==="zenodo"?"zenodo":"ezid";if(t.sandbox){if(console.log(u.yellow("\u2501".repeat(60))),console.log(u.yellow.bold("                 SANDBOX MODE ENABLED")),console.log(u.yellow("\u2501".repeat(60))),i==="zenodo")console.log(u.yellow("  \u2022 Using Zenodo sandbox (sandbox.zenodo.org)"));else console.log(u.yellow("  \u2022 Using EZID test shoulder (doi:10.5072/FK2)")),console.log(u.yellow("  \u2022 Test DOIs auto-delete after 2 weeks"));console.log(u.yellow("  \u2022 DOI will NOT be indexed by DataCite")),console.log(u.yellow("  \u2022 DOI will NOT resolve in production")),console.log(u.yellow("  \u2022 Use this for testing workflows only")),console.log(u.yellow("\u2501".repeat(60))),console.log()}console.log(u.red("WARNING: DOIs are PERMANENT and cannot be deleted!")),console.log(u.dim("The DOI will be pre-reserved but not published until the first version release.")),console.log(`  Provider: ${u.cyan(i.toUpperCase())}`),console.log();let s=t.sandbox?`Create TEST concept DOI via ${i.toUpperCase()} SANDBOX?`:`Create PERMANENT concept DOI via ${i.toUpperCase()} PRODUCTION?`,o=await Fe(s,t);if(o!=="confirmed"){console.log(u.dim(o==="declined"?"Skipped":"Cancelled"));return}let a=w(`Creating concept DOI via ${i.toUpperCase()}...`).start();try{let c=await Nz(e,{title:t.title,description:t.description,sandbox:t.sandbox,provider:i});a.succeed("Concept DOI created successfully");let l=w("Finalizing repository setup...").start();try{let d=await qm(e);if(d.warnings&&d.warnings.length>0){l.warn("Repository setup finalized with warnings");for(let f of d.warnings)console.log(u.yellow(`  Warning: ${f}`))}else l.succeed("Repository setup finalized")}catch(d){if(l.warn("Could not finalize repository setup"),d instanceof q){if(console.log(u.dim(`  ${d.message}`)),d.statusCode===403)console.log(u.dim("  Check admin credentials and permissions"))}else console.log(u.dim(`  ${d instanceof Error?d.message:"Unknown error"}`))}if(console.log(),console.log(u.green("DOI Information:")),console.log(`  Concept DOI: ${u.cyan(c.concept_doi)}`),console.log(`  Provider:    ${c.provider.toUpperCase()}`),c.provider==="ezid")console.log(`  DOI URL:     ${c.doi_url}`),console.log(`  EZID ID:     ${c.ezid_identifier}`);else console.log(`  Zenodo URL:  ${c.zenodo_url}`);if(c.metadata_warning)console.log(u.yellow(`  Warning:     ${c.metadata_warning}`));if(console.log(),console.log(u.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(),t.sandbox)console.log(u.dim("Note: This is a sandbox DOI and will not resolve in production."))}catch(c){if(c instanceof q){if(a.fail(c.message),c.statusCode===403)console.log(u.dim("  This command requires admin privileges"))}else a.fail("Failed to create concept DOI"),console.log(u.dim(`  ${V(c)}`))}});jd.command("info").description("Get DOI info for a dataset").argument("<dataset-id>","Dataset ID (e.g., nm000104)").action(async(e)=>{if(!oe())return;let t=w("Fetching DOI info...").start();try{let r=await vd(e);if(t.stop(),console.log(),console.log(u.cyan(`DOI Information for ${e}:`)),console.log(`  Dataset Name:    ${r.name}`),console.log(),r.concept_doi){if(console.log(u.green("Concept DOI:")),console.log(`  DOI:      ${r.concept_doi}`),console.log(`  URL:      https://doi.org/${r.concept_doi}`),console.log(`  Provider: ${(r.doi_provider||"zenodo").toUpperCase()}`),r.doi_provider==="ezid"){if(r.ezid_identifier)console.log(`  EZID ID:  ${r.ezid_identifier}`);if(r.ezid_status){let n=r.ezid_status==="public"?u.green:u.yellow;console.log(`  Status:   ${n(r.ezid_status)}`)}}if(r.zenodo_concept_url){if(console.log(`  Zenodo:   ${r.zenodo_concept_url}`),r.zenodo_concept_url.includes("sandbox.zenodo.org"))console.log(),console.log(u.yellow("Mode: SANDBOX (test DOI)")),console.log(u.yellow("  This DOI is not indexed by DataCite and will not resolve in production"))}}else console.log(u.yellow("No concept DOI created yet")),console.log(u.dim("  Use 'nemar admin doi create' to create one"));if(console.log(),r.latest_version_doi){if(console.log(u.green("Latest Version DOI:")),console.log(`  DOI:  ${r.latest_version_doi}`),console.log(`  URL:  https://doi.org/${r.latest_version_doi}`),r.zenodo_latest_version_url)console.log(`  Zenodo: ${r.zenodo_latest_version_url}`)}else if(r.concept_doi)console.log(u.yellow("No version DOI published yet")),console.log(u.dim("  Version DOIs are created automatically on PR merge"))}catch(r){if(r instanceof q){if(t.fail(r.message),r.statusCode===404)console.log(u.dim("  Dataset not found"));else if(r.statusCode===403)console.log(u.dim("  This command requires admin privileges"))}else t.fail("Failed to fetch DOI info")}});jd.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("--unavailable","Tombstone the concept DOI (EZID _status=unavailable); concept-only, reversible via --make-public. For a full withdrawal (visibility + every version DOI) use 'nemar admin withdraw' instead.").option("--refresh","Refresh metadata from dataset_description.json and .nemar/metadata.json").option(Re,Oe).option(je,Te).action(async(e,t)=>{if(!oe())return;if(t.makePublic&&t.unavailable){console.log(u.red("Use --make-public or --unavailable, not both."));return}if(!t.makePublic&&!t.unavailable&&!t.refresh){console.log(u.yellow("No action specified. Use --make-public, --unavailable, and/or --refresh."));return}if(t.makePublic){console.log(u.red("WARNING: Making a DOI public is PERMANENT!")),console.log(u.dim("  The DOI will be findable in DataCite and cannot be reverted.")),console.log();let n=await Fe(`Make DOI for ${e} PUBLIC and permanent?`,t);if(n!=="confirmed"){console.log(u.dim(n==="declined"?"Skipped":"Cancelled"));return}}if(t.unavailable){console.log(u.yellow("This tombstones the concept DOI (EZID _status=unavailable).")),console.log(u.dim("  Reversible with --make-public. Version DOIs are untouched.")),console.log();let n=await Fe(`Mark DOI for ${e} unavailable (tombstone)?`,t);if(n!=="confirmed"){console.log(u.dim(n==="declined"?"Skipped":"Cancelled"));return}}let r=w("Updating DOI...").start();try{let n=await uD(e,{status:t.makePublic?"public":t.unavailable?"unavailable":void 0,refresh_metadata:t.refresh});r.succeed("DOI updated successfully"),console.log(),console.log(`  EZID ID: ${u.cyan(n.ezid_identifier)}`),console.log(`  Status:  ${n.status==="public"?u.green(n.status):u.yellow(n.status)}`),console.log(`  URL:     ${n.doi_url}`)}catch(n){if(n instanceof q){if(r.fail(n.message),n.statusCode===400)console.log(u.dim("  DOI update is only supported for EZID-managed DOIs"))}else r.fail("Failed to update DOI"),console.log(u.dim(`  ${V(n)}`))}});jd.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(Re,Oe).option(je,Te).action(async(e,t)=>{if(!oe())return;let r=w("Fetching dataset and existing enrichment...").start(),n;try{n=await gt(e),r.succeed(`Dataset: ${n.name}`)}catch(p){if(p instanceof q)r.fail(p.message);else r.fail("Failed to fetch dataset");return}let i,s=!1;try{i=await vd(e)}catch(p){if(p instanceof q&&p.statusCode===404);else s=!0,console.log(u.yellow(`  Warning: Could not fetch DOI info: ${V(p)}`))}if(i?.concept_doi)console.log(`  DOI: ${u.cyan(i.concept_doi)}`);let o={version:"2.0"};if(n.github_repo){let p=w("Reading existing metadata...").start(),g=await jG(n.github_repo,".nemar/metadata.json");if(g)try{let y=JSON.parse(g);if(y&&typeof y==="object"&&y.version==="2.0")o=y,p.succeed(`Loaded existing metadata (stage: ${y.pipeline_stage||"unknown"})`);else p.warn("Existing metadata has unsupported version, starting fresh")}catch(y){p.warn(`Could not parse existing metadata (${y instanceof Error?y.message:String(y)}), starting fresh`)}else p.info("No existing .nemar/metadata.json found, starting fresh")}if(t.llm!==!1&&n.github_repo){console.log(),console.log(u.cyan("--- Running LLM enrichment pipeline (CI workflow) ---"));let p=w("Triggering run-enrichment workflow...").start();try{let{spawn:g}=awaitPromise.resolve(globalThis.Bun),y=n.github_repo,x="nemarDatasets/.github",v="run-enrichment.yml",_=g({cmd:["gh","workflow","run","run-enrichment.yml","--repo","nemarDatasets/.github","--ref","main","-f",`dataset_id=${e}`,"-f","ref=main","-f","force=true"],stdout:"pipe",stderr:"pipe"}),E=await new Response(_.stderr).text();if(await _.exited!==0)throw Error(`Failed to trigger workflow: ${E.trim()}`);p.text="Waiting for workflow to register...",await new Promise((k)=>setTimeout(k,3000)),p.text="Polling workflow status...";let D=60,O="",F=0;for(let k=0;k<D;k++){let j=g({cmd:["gh","run","list","--repo","nemarDatasets/.github","--workflow","run-enrichment.yml","-L","10","--json","databaseId,status,conclusion,displayTitle,event"],stdout:"pipe",stderr:"pipe"}),Z=await new Response(j.stdout).text(),_e=await new Response(j.stderr).text();if(await j.exited!==0){if(F++,F>=3){p.warn(`gh CLI error: ${_e.trim()}`);break}await new Promise((Me)=>setTimeout(Me,5000));continue}try{let Me=JSON.parse(Z.trim());F=0;let T=Me.find((B)=>B.event==="workflow_dispatch");if(T){if(T.status==="completed"){O=T.conclusion||"unknown";break}p.text=`Workflow ${T.status}... (${k*5}s)`}}catch(Me){if(F++,F>=3){p.warn(`Unable to parse workflow status: ${Me instanceof Error?Me.message:String(Me)} (raw: ${Z.trim().slice(0,200)})`);break}}await new Promise((Me)=>setTimeout(Me,5000))}let M=!1;if(!O)p.warn("Workflow timed out after 5 minutes (may still be running)");else if(O==="success"){p.succeed("LLM enrichment workflow completed successfully");let k=await jG(y,".nemar/metadata.json");if(k)try{let j=JSON.parse(k);if(j&&typeof j==="object"&&j.version==="2.0"){Object.assign(o,j),M=!0;let Z=j.pipeline_stage||"unknown";if(console.log(u.dim(`  Pipeline stage: ${Z}`)),o.authors){let _e=Object.keys(o.authors).length;console.log(u.dim(`  Authors: ${_e}`))}}}catch(j){console.log(u.yellow(`  Warning: Could not parse updated metadata: ${j instanceof Error?j.message:String(j)}`)),console.log(u.dim("  Using pre-workflow enrichment data"))}else console.log(u.yellow("  Warning: Could not fetch updated metadata after successful workflow.")),console.log(u.dim("  Author data below may be from a previous run."))}else p.fail(`LLM enrichment workflow failed (conclusion: ${O})`);if(!M)console.log(u.yellow("  ORCID discovery did not complete. Authors below may be from previous metadata."))}catch(g){p.fail("LLM enrichment pipeline failed"),console.log(u.dim(`  ${V(g)}`)),console.log(u.yellow("  ORCID discovery did not run. You will need to enter ORCIDs manually."))}}console.log(),console.log(u.cyan("--- Author ORCIDs ---"));let a=o.authors||{},c=Object.keys(a);if(c.length>0){let p=c.filter((y)=>a[y]?.orcid),g=c.filter((y)=>!a[y]?.orcid);console.log(u.dim(`  Discovered ${c.length} authors from pipeline:`));for(let y of p)console.log(u.green(`    [x] ${y}: ${a[y]?.orcid}`));for(let y of g)console.log(u.yellow(`    [ ] ${y}: no ORCID found`));if(g.length>0)console.log(u.dim(`  ${g.length} author(s) missing ORCIDs.`))}let{updateAuthors:l}=await X.prompt([{type:"confirm",name:"updateAuthors",message:c.length>0?"Add or correct author ORCIDs?":"Add author ORCIDs manually?",default:!1}]);if(l){let p={},g=!0;while(g){let{authorName:y}=await X.prompt([{type:"input",name:"authorName",message:'Author name (as in BIDS, e.g., "Shirazi, Yahya"):'}]);if(!y)break;let x=a[y];if(x?.orcid)console.log(u.dim(`  Current ORCID: ${x.orcid}`));let{orcid:v}=await X.prompt([{type:"input",name:"orcid",message:`ORCID for "${y}" (Enter to ${x?.orcid?"keep current":"skip"}):`,validate:(D)=>{if(!D)return!0;return Pm.test(D)||"Invalid ORCID format (XXXX-XXXX-XXXX-XXXX)"}}]),_={};if(v)_.orcid=v;let{affiliation:E}=await X.prompt([{type:"input",name:"affiliation",message:`Affiliation for "${y}" (optional):`}]);if(E)_.affiliations=[{name:E}];if(_.orcid||_.affiliations)p[y]=_;let{more:C}=await X.prompt([{type:"confirm",name:"more",message:"Add another author?",default:!0}]);g=C}if(Object.keys(p).length>0){let y={...o.authors||{}};for(let[x,v]of Object.entries(p)){let _=y[x]||{};y[x]={..._,...v,orcid:v.orcid||_.orcid}}o.authors=y}}console.log(),console.log(u.cyan("--- Dataset stats ---"));let d=w("Computing dataset sizes and formats...").start();try{let p=await uH(e),g=Ze(p.total_size);o.sizes=[`${g} (${p.file_count} files)`],o.formats=p.extensions,d.succeed(`Sizes: ${g} (${p.file_count} files), Formats: ${p.extensions.join(", ")}`)}catch(p){d.warn("Could not compute dataset stats"),console.log(u.dim(`  ${V(p)}`))}console.log(),console.log(u.cyan("--- Review ---")),console.log(JSON.stringify(o,null,2)),console.log();let f=await Fe("Commit to repo and refresh DOI?",t,!0);if(f!=="confirmed"){console.log(u.dim(f==="declined"?"Skipped":"Cancelled"));return}let m=w("Saving enrichment...").start();try{let p=await FH(e,o);if(m.succeed(p.message),p.bidsignore_updated)console.log(u.dim("  .bidsignore updated to include .nemar/"));if(!i&&s)try{i=await vd(e)}catch(g){if(process.env.DEBUG)console.error("[debug] DOI info re-fetch:",g)}if(i?.ezid_identifier){let g=w("Refreshing DOI metadata...").start();try{await uD(e,{refresh_metadata:!0}),g.succeed("DOI metadata refreshed")}catch(y){g.warn("Could not refresh DOI metadata"),console.log(u.dim(`  ${V(y)}`))}}else if(s)console.log(u.yellow("  DOI refresh skipped: could not verify DOI exists. Run 'nemar admin doi update --refresh' manually."))}catch(p){if(p instanceof q)m.fail(p.message);else m.fail("Failed to save enrichment"),console.log(u.dim(`  ${V(p)}`))}});Ie.addCommand(jd);var uh=new ve("publish").description("Publication workflow management");uh.command("list").description("List publication requests").option("-s, --status <status>","Filter by status (requested, approving, published, denied)").addHelpText("after",`
+Dataset already has a concept DOI:`)),console.log(`  Concept DOI: ${u.cyan(c.concept_doi)}`),c.zenodo_concept_url)console.log(`  Zenodo URL:  ${c.zenodo_concept_url}`);return}}catch(c){if(process.env.DEBUG)console.error("[debug] DOI info fetch:",c)}if(console.log(),console.log(u.cyan("Dataset Information:")),console.log(`  ID:          ${n.dataset_id}`),console.log(`  Name:        ${n.name}`),n.github_repo)console.log(`  GitHub:      ${n.github_repo}`);if(t.sandbox)console.log(`  Mode:        ${u.yellow("SANDBOX (test DOI)")}`);console.log();let i=t.provider==="zenodo"?"zenodo":"ezid";if(t.sandbox){if(console.log(u.yellow("\u2501".repeat(60))),console.log(u.yellow.bold("                 SANDBOX MODE ENABLED")),console.log(u.yellow("\u2501".repeat(60))),i==="zenodo")console.log(u.yellow("  \u2022 Using Zenodo sandbox (sandbox.zenodo.org)"));else console.log(u.yellow("  \u2022 Using EZID test shoulder (doi:10.5072/FK2)")),console.log(u.yellow("  \u2022 Test DOIs auto-delete after 2 weeks"));console.log(u.yellow("  \u2022 DOI will NOT be indexed by DataCite")),console.log(u.yellow("  \u2022 DOI will NOT resolve in production")),console.log(u.yellow("  \u2022 Use this for testing workflows only")),console.log(u.yellow("\u2501".repeat(60))),console.log()}console.log(u.red("WARNING: DOIs are PERMANENT and cannot be deleted!")),console.log(u.dim("The DOI will be pre-reserved but not published until the first version release.")),console.log(`  Provider: ${u.cyan(i.toUpperCase())}`),console.log();let s=t.sandbox?`Create TEST concept DOI via ${i.toUpperCase()} SANDBOX?`:`Create PERMANENT concept DOI via ${i.toUpperCase()} PRODUCTION?`,o=await Fe(s,t);if(o!=="confirmed"){console.log(u.dim(o==="declined"?"Skipped":"Cancelled"));return}let a=w(`Creating concept DOI via ${i.toUpperCase()}...`).start();try{let c=await Nz(e,{title:t.title,description:t.description,sandbox:t.sandbox,provider:i});a.succeed("Concept DOI created successfully");let l=w("Finalizing repository setup...").start();try{let d=await qm(e);if(d.warnings&&d.warnings.length>0){l.warn("Repository setup finalized with warnings");for(let f of d.warnings)console.log(u.yellow(`  Warning: ${f}`))}else l.succeed("Repository setup finalized")}catch(d){if(l.warn("Could not finalize repository setup"),d instanceof q){if(console.log(u.dim(`  ${d.message}`)),d.statusCode===403)console.log(u.dim("  Check admin credentials and permissions"))}else console.log(u.dim(`  ${d instanceof Error?d.message:"Unknown error"}`))}if(console.log(),console.log(u.green("DOI Information:")),console.log(`  Concept DOI: ${u.cyan(c.concept_doi)}`),console.log(`  Provider:    ${c.provider.toUpperCase()}`),c.provider==="ezid")console.log(`  DOI URL:     ${c.doi_url}`),console.log(`  EZID ID:     ${c.ezid_identifier}`);else console.log(`  Zenodo URL:  ${c.zenodo_url}`);if(c.metadata_warning)console.log(u.yellow(`  Warning:     ${c.metadata_warning}`));if(console.log(),console.log(u.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(),t.sandbox)console.log(u.dim("Note: This is a sandbox DOI and will not resolve in production."))}catch(c){if(c instanceof q){if(a.fail(c.message),c.statusCode===403)console.log(u.dim("  This command requires admin privileges"))}else a.fail("Failed to create concept DOI"),console.log(u.dim(`  ${V(c)}`))}});jd.command("info").description("Get DOI info for a dataset").argument("<dataset-id>","Dataset ID (e.g., nm000104)").action(async(e)=>{if(!oe())return;let t=w("Fetching DOI info...").start();try{let r=await vd(e);if(t.stop(),console.log(),console.log(u.cyan(`DOI Information for ${e}:`)),console.log(`  Dataset Name:    ${r.name}`),console.log(),r.concept_doi){if(console.log(u.green("Concept DOI:")),console.log(`  DOI:      ${r.concept_doi}`),console.log(`  URL:      https://doi.org/${r.concept_doi}`),console.log(`  Provider: ${(r.doi_provider||"zenodo").toUpperCase()}`),r.doi_provider==="ezid"){if(r.ezid_identifier)console.log(`  EZID ID:  ${r.ezid_identifier}`);if(r.ezid_status){let n=r.ezid_status==="public"?u.green:u.yellow;console.log(`  Status:   ${n(r.ezid_status)}`)}}if(r.zenodo_concept_url){if(console.log(`  Zenodo:   ${r.zenodo_concept_url}`),r.zenodo_concept_url.includes("sandbox.zenodo.org"))console.log(),console.log(u.yellow("Mode: SANDBOX (test DOI)")),console.log(u.yellow("  This DOI is not indexed by DataCite and will not resolve in production"))}}else console.log(u.yellow("No concept DOI created yet")),console.log(u.dim("  Use 'nemar admin doi create' to create one"));if(console.log(),r.latest_version_doi)console.log(u.green("Latest Version DOI:")),console.log(`  DOI:  ${r.latest_version_doi}`),console.log(`  URL:  https://doi.org/${r.latest_version_doi}`);else if(r.concept_doi)console.log(u.yellow("No version DOI published yet")),console.log(u.dim("  Version DOIs are created automatically on PR merge"))}catch(r){if(r instanceof q){if(t.fail(r.message),r.statusCode===404)console.log(u.dim("  Dataset not found"));else if(r.statusCode===403)console.log(u.dim("  This command requires admin privileges"))}else t.fail("Failed to fetch DOI info")}});jd.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("--unavailable","Tombstone the concept DOI (EZID _status=unavailable); concept-only, reversible via --make-public. For a full withdrawal (visibility + every version DOI) use 'nemar admin withdraw' instead.").option("--refresh","Refresh metadata from dataset_description.json and .nemar/metadata.json").option(Re,Oe).option(je,Te).action(async(e,t)=>{if(!oe())return;if(t.makePublic&&t.unavailable){console.log(u.red("Use --make-public or --unavailable, not both."));return}if(!t.makePublic&&!t.unavailable&&!t.refresh){console.log(u.yellow("No action specified. Use --make-public, --unavailable, and/or --refresh."));return}if(t.makePublic){console.log(u.red("WARNING: Making a DOI public is PERMANENT!")),console.log(u.dim("  The DOI will be findable in DataCite and cannot be reverted.")),console.log();let n=await Fe(`Make DOI for ${e} PUBLIC and permanent?`,t);if(n!=="confirmed"){console.log(u.dim(n==="declined"?"Skipped":"Cancelled"));return}}if(t.unavailable){console.log(u.yellow("This tombstones the concept DOI (EZID _status=unavailable).")),console.log(u.dim("  Reversible with --make-public. Version DOIs are untouched.")),console.log();let n=await Fe(`Mark DOI for ${e} unavailable (tombstone)?`,t);if(n!=="confirmed"){console.log(u.dim(n==="declined"?"Skipped":"Cancelled"));return}}let r=w("Updating DOI...").start();try{let n=await uD(e,{status:t.makePublic?"public":t.unavailable?"unavailable":void 0,refresh_metadata:t.refresh});r.succeed("DOI updated successfully"),console.log(),console.log(`  EZID ID: ${u.cyan(n.ezid_identifier)}`),console.log(`  Status:  ${n.status==="public"?u.green(n.status):u.yellow(n.status)}`),console.log(`  URL:     ${n.doi_url}`)}catch(n){if(n instanceof q){if(r.fail(n.message),n.statusCode===400)console.log(u.dim("  DOI update is only supported for EZID-managed DOIs"))}else r.fail("Failed to update DOI"),console.log(u.dim(`  ${V(n)}`))}});jd.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(Re,Oe).option(je,Te).action(async(e,t)=>{if(!oe())return;let r=w("Fetching dataset and existing enrichment...").start(),n;try{n=await gt(e),r.succeed(`Dataset: ${n.name}`)}catch(p){if(p instanceof q)r.fail(p.message);else r.fail("Failed to fetch dataset");return}let i,s=!1;try{i=await vd(e)}catch(p){if(p instanceof q&&p.statusCode===404);else s=!0,console.log(u.yellow(`  Warning: Could not fetch DOI info: ${V(p)}`))}if(i?.concept_doi)console.log(`  DOI: ${u.cyan(i.concept_doi)}`);let o={version:"2.0"};if(n.github_repo){let p=w("Reading existing metadata...").start(),g=await jG(n.github_repo,".nemar/metadata.json");if(g)try{let y=JSON.parse(g);if(y&&typeof y==="object"&&y.version==="2.0")o=y,p.succeed(`Loaded existing metadata (stage: ${y.pipeline_stage||"unknown"})`);else p.warn("Existing metadata has unsupported version, starting fresh")}catch(y){p.warn(`Could not parse existing metadata (${y instanceof Error?y.message:String(y)}), starting fresh`)}else p.info("No existing .nemar/metadata.json found, starting fresh")}if(t.llm!==!1&&n.github_repo){console.log(),console.log(u.cyan("--- Running LLM enrichment pipeline (CI workflow) ---"));let p=w("Triggering run-enrichment workflow...").start();try{let{spawn:g}=awaitPromise.resolve(globalThis.Bun),y=n.github_repo,x="nemarDatasets/.github",v="run-enrichment.yml",_=g({cmd:["gh","workflow","run","run-enrichment.yml","--repo","nemarDatasets/.github","--ref","main","-f",`dataset_id=${e}`,"-f","ref=main","-f","force=true"],stdout:"pipe",stderr:"pipe"}),E=await new Response(_.stderr).text();if(await _.exited!==0)throw Error(`Failed to trigger workflow: ${E.trim()}`);p.text="Waiting for workflow to register...",await new Promise((k)=>setTimeout(k,3000)),p.text="Polling workflow status...";let D=60,O="",F=0;for(let k=0;k<D;k++){let j=g({cmd:["gh","run","list","--repo","nemarDatasets/.github","--workflow","run-enrichment.yml","-L","10","--json","databaseId,status,conclusion,displayTitle,event"],stdout:"pipe",stderr:"pipe"}),Z=await new Response(j.stdout).text(),_e=await new Response(j.stderr).text();if(await j.exited!==0){if(F++,F>=3){p.warn(`gh CLI error: ${_e.trim()}`);break}await new Promise((Me)=>setTimeout(Me,5000));continue}try{let Me=JSON.parse(Z.trim());F=0;let T=Me.find((B)=>B.event==="workflow_dispatch");if(T){if(T.status==="completed"){O=T.conclusion||"unknown";break}p.text=`Workflow ${T.status}... (${k*5}s)`}}catch(Me){if(F++,F>=3){p.warn(`Unable to parse workflow status: ${Me instanceof Error?Me.message:String(Me)} (raw: ${Z.trim().slice(0,200)})`);break}}await new Promise((Me)=>setTimeout(Me,5000))}let M=!1;if(!O)p.warn("Workflow timed out after 5 minutes (may still be running)");else if(O==="success"){p.succeed("LLM enrichment workflow completed successfully");let k=await jG(y,".nemar/metadata.json");if(k)try{let j=JSON.parse(k);if(j&&typeof j==="object"&&j.version==="2.0"){Object.assign(o,j),M=!0;let Z=j.pipeline_stage||"unknown";if(console.log(u.dim(`  Pipeline stage: ${Z}`)),o.authors){let _e=Object.keys(o.authors).length;console.log(u.dim(`  Authors: ${_e}`))}}}catch(j){console.log(u.yellow(`  Warning: Could not parse updated metadata: ${j instanceof Error?j.message:String(j)}`)),console.log(u.dim("  Using pre-workflow enrichment data"))}else console.log(u.yellow("  Warning: Could not fetch updated metadata after successful workflow.")),console.log(u.dim("  Author data below may be from a previous run."))}else p.fail(`LLM enrichment workflow failed (conclusion: ${O})`);if(!M)console.log(u.yellow("  ORCID discovery did not complete. Authors below may be from previous metadata."))}catch(g){p.fail("LLM enrichment pipeline failed"),console.log(u.dim(`  ${V(g)}`)),console.log(u.yellow("  ORCID discovery did not run. You will need to enter ORCIDs manually."))}}console.log(),console.log(u.cyan("--- Author ORCIDs ---"));let a=o.authors||{},c=Object.keys(a);if(c.length>0){let p=c.filter((y)=>a[y]?.orcid),g=c.filter((y)=>!a[y]?.orcid);console.log(u.dim(`  Discovered ${c.length} authors from pipeline:`));for(let y of p)console.log(u.green(`    [x] ${y}: ${a[y]?.orcid}`));for(let y of g)console.log(u.yellow(`    [ ] ${y}: no ORCID found`));if(g.length>0)console.log(u.dim(`  ${g.length} author(s) missing ORCIDs.`))}let{updateAuthors:l}=await X.prompt([{type:"confirm",name:"updateAuthors",message:c.length>0?"Add or correct author ORCIDs?":"Add author ORCIDs manually?",default:!1}]);if(l){let p={},g=!0;while(g){let{authorName:y}=await X.prompt([{type:"input",name:"authorName",message:'Author name (as in BIDS, e.g., "Shirazi, Yahya"):'}]);if(!y)break;let x=a[y];if(x?.orcid)console.log(u.dim(`  Current ORCID: ${x.orcid}`));let{orcid:v}=await X.prompt([{type:"input",name:"orcid",message:`ORCID for "${y}" (Enter to ${x?.orcid?"keep current":"skip"}):`,validate:(D)=>{if(!D)return!0;return Pm.test(D)||"Invalid ORCID format (XXXX-XXXX-XXXX-XXXX)"}}]),_={};if(v)_.orcid=v;let{affiliation:E}=await X.prompt([{type:"input",name:"affiliation",message:`Affiliation for "${y}" (optional):`}]);if(E)_.affiliations=[{name:E}];if(_.orcid||_.affiliations)p[y]=_;let{more:C}=await X.prompt([{type:"confirm",name:"more",message:"Add another author?",default:!0}]);g=C}if(Object.keys(p).length>0){let y={...o.authors||{}};for(let[x,v]of Object.entries(p)){let _=y[x]||{};y[x]={..._,...v,orcid:v.orcid||_.orcid}}o.authors=y}}console.log(),console.log(u.cyan("--- Dataset stats ---"));let d=w("Computing dataset sizes and formats...").start();try{let p=await uH(e),g=Ze(p.total_size);o.sizes=[`${g} (${p.file_count} files)`],o.formats=p.extensions,d.succeed(`Sizes: ${g} (${p.file_count} files), Formats: ${p.extensions.join(", ")}`)}catch(p){d.warn("Could not compute dataset stats"),console.log(u.dim(`  ${V(p)}`))}console.log(),console.log(u.cyan("--- Review ---")),console.log(JSON.stringify(o,null,2)),console.log();let f=await Fe("Commit to repo and refresh DOI?",t,!0);if(f!=="confirmed"){console.log(u.dim(f==="declined"?"Skipped":"Cancelled"));return}let m=w("Saving enrichment...").start();try{let p=await FH(e,o);if(m.succeed(p.message),p.bidsignore_updated)console.log(u.dim("  .bidsignore updated to include .nemar/"));if(!i&&s)try{i=await vd(e)}catch(g){if(process.env.DEBUG)console.error("[debug] DOI info re-fetch:",g)}if(i?.ezid_identifier){let g=w("Refreshing DOI metadata...").start();try{await uD(e,{refresh_metadata:!0}),g.succeed("DOI metadata refreshed")}catch(y){g.warn("Could not refresh DOI metadata"),console.log(u.dim(`  ${V(y)}`))}}else if(s)console.log(u.yellow("  DOI refresh skipped: could not verify DOI exists. Run 'nemar admin doi update --refresh' manually."))}catch(p){if(p instanceof q)m.fail(p.message);else m.fail("Failed to save enrichment"),console.log(u.dim(`  ${V(p)}`))}});Ie.addCommand(jd);var uh=new ve("publish").description("Publication workflow management");uh.command("list").description("List publication requests").option("-s, --status <status>","Filter by status (requested, approving, published, denied)").addHelpText("after",`
 Description:
   List all publication requests from users, with optional filtering by status.
   Shows dataset ID, status, requesting user, and current progress.

package/package.json CHANGED Viewed

@@ -1,6 +1,6 @@
 {
   "name": "nemar-cli",
-  "version": "0.9.10-dev.2136",
+  "version": "0.9.10-dev.2140",
   "description": "CLI for NEMAR (Neuroelectromagnetic Data Archive and Tools Resource) dataset management",
   "type": "module",
   "main": "dist/index.js",