npm - nemar-cli - Versions diffs - 0.8.9-PR414.a8d7554 → 0.8.9-PR414.e0697c4 - Mend

nemar-cli 0.8.9-PR414.a8d7554 → 0.8.9-PR414.e0697c4

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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

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 Sync CI templates across ${Q.length} datasets (writes only diffs)
-`));let Y=await I0(`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=C(`Syncing ${H.dataset_id}...`).start();try{let K=await LW(H.dataset_id),E=K.changed.length+K.added.length;if(K.errors.length>0)q.warn(`${H.dataset_id}: ${E} updated, ${K.errors.length} error(s)`),G++;else if(E===0)q.succeed(`${H.dataset_id}: up to date`),B++;else{let V=[];if(K.added.length>0)V.push(`+${K.added.length} added`);if(K.changed.length>0)V.push(`~${K.changed.length} updated`);q.succeed(`${H.dataset_id}: ${V.join(", ")}`),X++}}catch(K){let E=K instanceof c?K.message:String(K);q.fail(`${H.dataset_id}: ${E}`),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 $=C(`Syncing CI templates for ${D}...`).start();try{let J=await LW(D);if(J.changed.length+J.added.length===0&&J.errors.length===0)$.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.errors.length>0){console.log(`  ${W.red("Errors:")}`);for(let Y of J.errors)console.log(`    - ${Y}`)}console.log()}catch(J){YD(J,$,"Failed to sync CI templates",{404:"Dataset not found"})}});e0.addCommand(BQ);var g9=new r0("doi").description("DOI management");g9.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(T0,w0).option(g0,v0).action(async(D,F)=>{if(!h0())return;let $=C("Fetching dataset info...").start(),J;try{J=await bD(D),$.succeed(`Found dataset: ${J.name}`)}catch(G){if(G instanceof c){if($.fail(G.message),G.statusCode===404)console.log(W.dim("  Dataset not found"))}else $.fail("Failed to fetch dataset");return}try{let G=await I9(D);if(G.concept_doi){if(console.log(W.yellow(`
+`));let Y=await I0(`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=C(`Syncing ${H.dataset_id}...`).start();try{let K=await LW(H.dataset_id),E=K.changed.length+K.added.length;if(K.errors.length>0)q.warn(`${H.dataset_id}: ${E} updated, ${K.errors.length} error(s)`),G++;else if(E===0)q.succeed(`${H.dataset_id}: up to date`),B++;else{let V=[];if(K.added.length>0)V.push(`+${K.added.length} added`);if(K.changed.length>0)V.push(`~${K.changed.length} updated`);q.succeed(`${H.dataset_id}: ${V.join(", ")}`),X++}}catch(K){let E=K instanceof c?K.message:String(K);q.fail(`${H.dataset_id}: ${E}`),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 $=C(`Syncing CI templates for ${D}...`).start();try{let J=await LW(D),Q=J.changed.length+J.added.length;if(J.errors.length>0)$.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(`    - ${Y}`)}console.log()}catch(J){YD(J,$,"Failed to sync CI templates",{404:"Dataset not found"})}});e0.addCommand(BQ);var g9=new r0("doi").description("DOI management");g9.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(T0,w0).option(g0,v0).action(async(D,F)=>{if(!h0())return;let $=C("Fetching dataset info...").start(),J;try{J=await bD(D),$.succeed(`Found dataset: ${J.name}`)}catch(G){if(G instanceof c){if($.fail(G.message),G.statusCode===404)console.log(W.dim("  Dataset not found"))}else $.fail("Failed to fetch dataset");return}try{let G=await I9(D);if(G.concept_doi){if(console.log(W.yellow(`
 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 I0(Y,F);if(B!=="confirmed"){console.log(W.dim(B==="declined"?"Skipped":"Cancelled"));return}let X=C(`Creating concept DOI via ${Q.toUpperCase()}...`).start();try{let G=await If(D,{title:F.title,description:F.description,sandbox:F.sandbox,provider:Q});X.succeed("Concept DOI created successfully");let H=C("Applying branch protection...").start();try{let q=await eJ(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 c){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 c){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(`  ${k0(G)}`))}});g9.command("info").description("Get DOI info for a dataset").argument("<dataset-id>","Dataset ID (e.g., nm000104)").action(async(D)=>{if(!h0())return;let F=C("Fetching DOI info...").start();try{let $=await I9(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 c){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")}});g9.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(T0,w0).option(g0,v0).action(async(D,F)=>{if(!h0())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 I0(`Make DOI for ${D} PUBLIC and permanent?`,F);if(J!=="confirmed"){console.log(W.dim(J==="declined"?"Skipped":"Cancelled"));return}}let $=C("Updating DOI...").start();try{let J=await MW(D,{status:F.makePublic?"public":void 0,refresh_metadata:F.refresh});$.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:     ${J.doi_url}`)}catch(J){if(J instanceof c){if($.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(`  ${k0(J)}`))}});g9.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(T0,w0).option(g0,v0).action(async(D,F)=>{if(!h0())return;let $=C("Fetching dataset and existing enrichment...").start(),J;try{J=await bD(D),$.succeed(`Dataset: ${J.name}`)}catch(V){if(V instanceof c)$.fail(V.message);else $.fail("Failed to fetch dataset");return}let Q,Y=!1;try{Q=await I9(D)}catch(V){if(V instanceof c&&V.statusCode===404);else Y=!0,console.log(W.yellow(`  Warning: Could not fetch DOI info: ${k0(V)}`))}if(Q?.concept_doi)console.log(`  DOI: ${W.cyan(Q.concept_doi)}`);let B={version:"2.0"};if(J.github_repo){let V=C("Reading existing metadata...").start(),U=await Ig(J.github_repo,".nemar/metadata.json");if(U)try{let A=JSON.parse(U);if(A&&typeof A==="object"&&A.version==="2.0")B=A,V.succeed(`Loaded existing metadata (stage: ${A.pipeline_stage||"unknown"})`);else V.warn("Existing metadata has unsupported version, starting fresh")}catch(A){V.warn(`Could not parse existing metadata (${A instanceof Error?A.message:String(A)}), starting fresh`)}else V.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 V=C("Triggering llm-enrichment workflow...").start();try{let{spawn:U}=awaitPromise.resolve(globalThis.Bun),A=J.github_repo,L=U({cmd:["gh","workflow","run","llm-enrichment.yml","--repo",A,"--ref","main"],stdout:"pipe",stderr:"pipe"}),M=await new Response(L.stderr).text();if(await L.exited!==0)throw Error(`Failed to trigger workflow: ${M.trim()}`);V.text="Waiting for workflow to register...",await new Promise((y)=>setTimeout(y,3000)),V.text="Polling workflow status...";let T=60,k="",O=0;for(let y=0;y<T;y++){let p=U({cmd:["gh","run","list","--repo",A,"--workflow","llm-enrichment.yml","-L","1","--json","databaseId,status,conclusion"],stdout:"pipe",stderr:"pipe"}),A0=await new Response(p.stdout).text(),D0=await new Response(p.stderr).text();if(await p.exited!==0){if(O++,O>=3){V.warn(`gh CLI error: ${D0.trim()}`);break}await new Promise((Y0)=>setTimeout(Y0,5000));continue}try{let Y0=JSON.parse(A0.trim());if(O=0,Y0.length>0){let g=Y0[0];if(g.status==="completed"){k=g.conclusion||"unknown";break}V.text=`Workflow ${g.status}... (${y*5}s)`}}catch(Y0){if(O++,O>=3){V.warn(`Unable to parse workflow status: ${Y0 instanceof Error?Y0.message:String(Y0)} (raw: ${A0.trim().slice(0,200)})`);break}}await new Promise((Y0)=>setTimeout(Y0,5000))}let P=!1;if(!k)V.warn("Workflow timed out after 5 minutes (may still be running)");else if(k==="success"){V.succeed("LLM enrichment workflow completed successfully");let y=await Ig(A,".nemar/metadata.json");if(y)try{let p=JSON.parse(y);if(p&&typeof p==="object"&&p.version==="2.0"){Object.assign(B,p),P=!0;let A0=p.pipeline_stage||"unknown";if(console.log(W.dim(`  Pipeline stage: ${A0}`)),B.authors){let D0=Object.keys(B.authors).length;console.log(W.dim(`  Authors: ${D0}`))}}}catch(p){console.log(W.yellow(`  Warning: Could not parse updated metadata: ${p instanceof Error?p.message:String(p)}`)),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 V.fail(`LLM enrichment workflow failed (conclusion: ${k})`);if(!P)console.log(W.yellow("  ORCID discovery did not complete. Authors below may be from previous metadata."))}catch(U){V.fail("LLM enrichment pipeline failed"),console.log(W.dim(`  ${k0(U)}`)),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 V=G.filter((A)=>X[A]?.orcid),U=G.filter((A)=>!X[A]?.orcid);console.log(W.dim(`  Discovered ${G.length} authors from pipeline:`));for(let A of V)console.log(W.green(`    [x] ${A}: ${X[A]?.orcid}`));for(let A of U)console.log(W.yellow(`    [ ] ${A}: no ORCID found`));if(U.length>0)console.log(W.dim(`  ${U.length} author(s) missing ORCIDs.`))}let{updateAuthors:H}=await e.prompt([{type:"confirm",name:"updateAuthors",message:G.length>0?"Add or correct author ORCIDs?":"Add author ORCIDs manually?",default:!1}]);if(H){let V={},U=!0;while(U){let{authorName:A}=await e.prompt([{type:"input",name:"authorName",message:'Author name (as in BIDS, e.g., "Shirazi, Yahya"):'}]);if(!A)break;let L=X[A];if(L?.orcid)console.log(W.dim(`  Current ORCID: ${L.orcid}`));let{orcid:M}=await e.prompt([{type:"input",name:"orcid",message:`ORCID for "${A}" (Enter to ${L?.orcid?"keep current":"skip"}):`,validate:(O)=>{if(!O)return!0;return aJ.test(O)||"Invalid ORCID format (XXXX-XXXX-XXXX-XXXX)"}}]),R={};if(M)R.orcid=M;let{affiliation:T}=await e.prompt([{type:"input",name:"affiliation",message:`Affiliation for "${A}" (optional):`}]);if(T)R.affiliations=[{name:T}];if(R.orcid||R.affiliations)V[A]=R;let{more:k}=await e.prompt([{type:"confirm",name:"more",message:"Add another author?",default:!0}]);U=k}if(Object.keys(V).length>0){let A={...B.authors||{}};for(let[L,M]of Object.entries(V)){let R=A[L]||{};A[L]={...R,...M,orcid:M.orcid||R.orcid}}B.authors=A}}console.log(),console.log(W.cyan("--- Dataset stats ---"));let q=C("Computing dataset sizes and formats...").start();try{let V=await mf(D),U=XD(V.total_size);B.sizes=[`${U} (${V.file_count} files)`],B.formats=V.extensions,q.succeed(`Sizes: ${U} (${V.file_count} files), Formats: ${V.extensions.join(", ")}`)}catch(V){q.warn("Could not compute dataset stats"),console.log(W.dim(`  ${k0(V)}`))}console.log(),console.log(W.cyan("--- Review ---")),console.log(JSON.stringify(B,null,2)),console.log();let K=await I0("Commit to repo and refresh DOI?",F,!0);if(K!=="confirmed"){console.log(W.dim(K==="declined"?"Skipped":"Cancelled"));return}let E=C("Saving enrichment...").start();try{let V=await uf(D,B);if(E.succeed(V.message),V.bidsignore_updated)console.log(W.dim("  .bidsignore updated to include .nemar/"));if(!Q&&Y)try{Q=await I9(D)}catch(U){if(process.env.DEBUG)console.error("[debug] DOI info re-fetch:",U)}if(Q?.ezid_identifier){let U=C("Refreshing DOI metadata...").start();try{await MW(D,{refresh_metadata:!0}),U.succeed("DOI metadata refreshed")}catch(A){U.warn("Could not refresh DOI metadata"),console.log(W.dim(`  ${k0(A)}`))}}else if(Y)console.log(W.yellow("  DOI refresh skipped: could not verify DOI exists. Run 'nemar admin doi update --refresh' manually."))}catch(V){if(V instanceof c)E.fail(V.message);else E.fail("Failed to save enrichment"),console.log(W.dim(`  ${k0(V)}`))}});e0.addCommand(g9);var XQ=new r0("publish").description("Publication workflow management");XQ.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.

package/package.json CHANGED Viewed

@@ -1,6 +1,6 @@
 {
   "name": "nemar-cli",
-  "version": "0.8.9-PR414.a8d7554",
+  "version": "0.8.9-PR414.e0697c4",
   "description": "CLI for NEMAR (Neuroelectromagnetic Data Archive and Tools Resource) dataset management",
   "type": "module",
   "main": "dist/index.js",