nemar-cli 0.8.63-dev.1512 → 0.8.63-dev.1519
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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${$} ${D.message}
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${J}${Q}
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${F}
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-
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Run 'gh auth login' to authenticate.")}return{gitAnnex:D,githubSSH:F,allPassed:$.length===0,errors:$}}async function N1(D){if(!cW(nW(D,".git")))return!1;try{let{exitCode:F}=await T(["git","annex","info"],{cwd:D});return F===0}catch(F){let $=F instanceof Error?F.message:String(F);if(!$.includes("ENOENT")&&!$.includes("not found"))console.error(`Error checking if ${D} is a git-annex dataset:`,$);return!1}}async function n6(D,F={}){if(!F.force&&await N1(D))return{success:!0};try{let $={};if(F.author)$.GIT_AUTHOR_NAME=F.author.name,$.GIT_AUTHOR_EMAIL=F.author.email,$.GIT_COMMITTER_NAME=F.author.name,$.GIT_COMMITTER_EMAIL=F.author.email;let{stderr:J,exitCode:Q}=await T(["git","init","-b","main",D],{...Object.keys($).length>0?{env:$}:{}});if(Q!==0)return{success:!1,error:J.trim()||"Failed to initialize git repository"};let Y=Object.keys($).length>0?{env:$}:{},{stderr:B,exitCode:X}=await T(["git","annex","init"],{cwd:D,...Y});if(X!==0)return{success:!1,error:B.trim()||"Failed to initialize git-annex"};let{stderr:G,exitCode:H}=await T(["git","commit","--allow-empty","-m","Initialize dataset"],{cwd:D,...Y});if(H!==0)return{success:!1,error:G.trim()||"Failed to create initial commit"};let{stderr:q,exitCode:K}=await T(["git","annex","adjust","--unlock"],{cwd:D,...Y});if(K!==0)return{success:!1,error:q.trim()||"Failed to switch to unlocked mode"};return{success:!0}}catch($){return{success:!1,error:$.message}}}async function aW(D){try{let{exitCode:F,stderr:$}=await T(["git","annex","info"],{cwd:D});if(F===0)return{success:!0};if($.includes("First run: git-annex init")){let{stderr:J,exitCode:Q}=await T(["git","annex","init"],{cwd:D});if(Q!==0)return{success:!1,error:J.trim()||"Failed to initialize git-annex"};return{success:!0}}return{success:!1,error:$.trim()||"Failed to check git-annex status"}}catch(F){return{success:!1,error:F.message}}}async function g4(D,F){let $=["*.edf","*.bdf","*.set","*.fif","*.vhdr","*.eeg","*.cnt","*.fdt"],J=["*.tsv","*.json","*.md","*.txt","*.yml","*.yaml","README*","LICENSE*","CHANGES*",".bidsignore",".gitignore"],Q=$.map((G)=>`include=${G}`).join(" or "),Y=J.map((G)=>`exclude=${G}`).join(" and "),B=`(${Q} or largerthan=100kb) and ${Y}`,X=F||B;try{let{stderr:G,exitCode:H}=await T(["git","annex","config","--set","annex.largefiles",X],{cwd:D});if(H!==0)return{success:!1,error:G.trim()||"Failed to configure largefiles"};return{success:!0}}catch(G){return{success:!1,error:G.message}}}async function i6(D,F="."){try{let{stderr:$,exitCode:J}=await T(["git","annex","add",F],{cwd:D});if(J!==0)return{success:!1,error:$.trim()||"Failed to add files to git-annex"};return{success:!0}}catch($){return{success:!1,error:$.message}}}function PD(D){return{accessKeyId:D.access_key_id,secretAccessKey:D.secret_access_key,sessionToken:D.session_token}}function dW(D){let F=[/^\(merging .* into .*\.\.\.\)$/,/^\(recording state in git\.\.\.\)$/,/^\(scanning for /,/^\(checking /];return D.split(`
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@@ -384,7 +384,7 @@ nemar.org Sync Status (${F.total} datasets)
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`),F.datasets.length===0){console.log(W.dim(" No published datasets found."));return}console.log(W.dim(` ${"ID".padEnd(12)} ${"Name".padEnd(40)} ${"Status".padEnd(10)} ${"Last Sync".padEnd(20)}`)),console.log(W.dim(` ${"\u2500".repeat(85)}`));for(let $ of F.datasets){let J=$.nemar_sync_status||"pending",Q=J==="synced"?W.green:J==="failed"?W.red:W.yellow,Y=$.nemar_sync_at?new Date($.nemar_sync_at).toLocaleDateString():"-",B=$.name||$.dataset_id,X=B.length>38?`${B.substring(0,35)}...`:B;if(console.log(` ${$.dataset_id.padEnd(12)} ${X.padEnd(40)} ${Q(J.padEnd(10))} ${Y}`),$.nemar_sync_error)console.log(W.red(` Error: ${$.nemar_sync_error}`))}}catch(F){D.fail("Failed to fetch sync status"),console.error(W.red(L0(F)))}});b0.addCommand(yH);var MQ=new I0("import").description("View and recover OpenNeuro import jobs");MQ.command("status").description("Show OpenNeuro import job state (failed/quarantined first)").argument("[dataset-id]","Filter to one dataset id (e.g., on007523)").option("-s, --status <status>","Filter by status (failed, quarantined, copying, ...)").action(async(D,F)=>{if(!w0())return;let $=O("Fetching import status...").start();try{let J=await xg(F.status);$.stop();let Q=J.imports;if(D)Q=Q.filter((B)=>B.dataset_id===D);let Y=J.by_status;if(console.log(W.bold(`
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`)),console.log(` ${W.yellow(`in-flight ${(Y.preparing??0)+(Y.copying??0)+(Y.finalizing??0)}`)} ${W.green(`complete ${Y.complete??0}`)} ${W.red(`failed ${Y.failed??0}`)} ${W.red(`quarantined ${Y.quarantined??0}`)} ${W.dim(`rolled_back ${Y.rolled_back??0}`)}
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`),Q.length===0){console.log(W.dim(" No import jobs match."));return}console.log(W.dim(` ${"ID".padEnd(12)} ${"Source".padEnd(12)} ${"Stage".padEnd(10)} ${"Status".padEnd(12)} ${"Updated".padEnd(20)}`)),console.log(W.dim(` ${"\u2500".repeat(70)}`));for(let B of Q){let X=B.status==="complete"?W.green:B.status==="failed"||B.status==="quarantined"?W.red:B.status==="rolled_back"?W.dim:W.yellow,G=B.updated_at?new Date(B.updated_at).toLocaleString():"-";if(console.log(` ${B.dataset_id.padEnd(12)} ${(B.source_id||"-").padEnd(12)} ${B.stage.padEnd(10)} ${X(B.status.padEnd(12))} ${G}`),B.last_error)console.log(W.red(` ${B.last_error}`));if(B.workflow_run_url)console.log(W.dim(` run: ${B.workflow_run_url}`))}}catch(J){$.fail("Failed to fetch import status"),console.error(W.red(L0(J)))}});MQ.command("rollback").description("Roll back a failed/quarantined import (deletes repo + S3 + D1)").argument("<dataset-id>","NEMAR dataset id (e.g., on007523)").action(async(D)=>{if(!w0())return;let{proceed:F}=await D0.prompt([{type:"confirm",name:"proceed",message:W.red(`Roll back import ${D}? This deletes the GitHub repo, S3 objects, and D1 records. This cannot be undone.`),default:!1}]);if(!F){console.log(W.dim("Cancelled."));return}let $=O(`Rolling back ${D}...`).start();try{let J=await _g(D);if(!J.rolled_back){$.fail(`Rollback incomplete for ${D} (kept quarantined); retry after fixing:`);for(let Q of J.warnings)console.log(W.red(` - ${Q}`))}else if(J.warnings.length>0){$.warn(`Rolled back ${D} with warnings`);for(let Q of J.warnings)console.log(W.yellow(` - ${Q}`))}else $.succeed(`Rolled back ${D}`)}catch(J){$.fail(`Failed to roll back ${D}`),console.error(W.red(L0(J)))}});MQ.command("retry").description("Reset a failed/quarantined import to 'preparing' for re-dispatch").argument("<dataset-id>","NEMAR dataset id (e.g., on007523)").action(async(D)=>{if(!w0())return;let F=O(`Resetting ${D}...`).start();try{await fg(D),F.succeed(`${D} reset to 'preparing'. Re-run the onboard-openneuro workflow to retry.`)}catch($){F.fail(`Failed to reset ${D}`),console.error(W.red(L0($)))}});b0.addCommand(MQ);function lh(D,F){let $=D.enrichment.status,J=$==="ok"?W.green("enrich:ok"):$==="failed"?W.red("enrich:failed"):W.dim("enrich:skipped"),Q=D.sync.status,Y=Q==="ok"?W.green("sync:ok"):Q==="failed"?W.red("sync:failed"):W.dim("sync:skipped"),B=D.sync.metadata_columns_written===!0?W.green("cols:written"):D.sync.metadata_columns_error?W.red("cols:failed"):"",X=F?.showRef&&D.enrichment.ref?W.dim(`@${D.enrichment.ref}`):"";if(console.log(` ${D.dataset_id.padEnd(12)} ${J}${X} ${Y} ${B}`),D.enrichment.error)console.log(W.red(` enrichment: ${D.enrichment.error}`));if(D.sync.errors?.length)for(let G of D.sync.errors)console.log(W.red(` sync: ${G}`));if(D.sync.metadata_columns_error)console.log(W.red(` metadata columns: ${D.sync.metadata_columns_error}`))}var NQ=new I0("fleet").description("Governance drift reporting and enforcement (epic #713)");NQ.command("drift").description("Report dataset repos that are off the governance spec").option("--prefix <prefix>","Filter datasets by id prefix (e.g. nm, on)").option("--visibility <vis>","Filter by visibility: public or private").option("--limit <n>","Max repos to scan (default 25, max 50)","25").option("--json","Output raw JSON").action(async(D)=>{if(!H0())console.log(W.red("Error: Not authenticated")),process.exit(1);if(D.visibility&&!["public","private"].includes(D.visibility))console.log(W.red("Error: --visibility must be public or private")),process.exit(1);let F=O("Scanning fleet for drift...").start();try{let $=await hg({prefix:D.prefix,visibility:D.visibility,limit:Number.parseInt(D.limit,10)||25});if(F.stop(),D.json){console.log(JSON.stringify($,null,2));return}console.log(),console.log(W.bold(`Fleet drift (scanned ${$.scanned}):`));let J=["PUBLIC_UNPROTECTED","RED_REQUIRED_CHECK","CONTEXT_NAME_MISMATCH","MISSING_REQUIRED_WORKFLOW","PRIVATE_WITH_STRAY_READ","DEFAULT_BRANCH_OUTLIER","DEPRECATED_WORKFLOW_PRESENT","COMPLIANT"];for(let Q of J){let Y=$.buckets[Q];if(!Y||Y.length===0)continue;let B=Q==="COMPLIANT"?W.green:W.yellow;if(console.log(` ${B(Q.padEnd(28))} ${Y.length}`),Q!=="COMPLIANT"){let X=Y.slice(0,20).join(", ");console.log(W.dim(` ${X}${Y.length>20?` ... +${Y.length-20}`:""}`))}}console.log()}catch($){if($ instanceof f)F.fail($.message);else F.fail("Failed to scan fleet"),console.log(W.red(` ${$.message}`));process.exit(1)}});NQ.command("enforce").description("Bring dataset repos to the governance spec (single or --all). Dry-run by default.").argument("[dataset-id]","Dataset to enforce (omit when using --all)").option("--all","Bulk enforce across a filtered set (owner-only)").option("--apply","Actually apply changes (default is a dry run)").option("--prefix <prefix>","Bulk: filter by id prefix").option("--visibility <vis>","Bulk: filter by visibility (public|private)").option("--limit <n>","Bulk: max repos (default 25, max 50)","25").option("--json","Output raw JSON").action(async(D,F)=>{if(!H0())console.log(W.red("Error: Not authenticated")),process.exit(1);if(!D&&!F.all)console.log(W.red("Error: provide a dataset-id or use --all")),process.exit(1);if(D&&F.all)console.log(W.red("Error: provide a dataset-id OR --all, not both")),process.exit(1);let $=!F.apply,J=$?"[dry-run] ":"",Q=O(`${J}Enforcing spec...`).start();try{if(D){let Y=await PF(D,$);if(Q.succeed(`${J}${D} (${Y.result.visibility})`),F.json){console.log(JSON.stringify(Y,null,2));return}for(let[B,X]of Object.entries(Y.result.steps)){let G=X.status==="ok"?W.green:X.status==="skipped"?W.yellow:W.red;console.log(` ${G(X.status.padEnd(8))} ${B}${X.detail?W.dim(` (${X.detail})`):""}`)}}else{let Y=await bg({prefix:F.prefix,visibility:F.visibility,limit:Number.parseInt(F.limit,10)||25,dryRun:$});if(Q.succeed(`${J}processed ${Y.count} repo(s)`),F.json){console.log(JSON.stringify(Y,null,2));return}for(let B of Y.results){if(B.error){console.log(` ${W.red("error")} ${B.dataset_id}: ${B.error}`);continue}let X=Object.entries(B.steps??{}).filter(([,H])=>H.status!=="ok").map(([H,q])=>`${H}=${q.status}`),G=X.length?W.yellow("drift"):W.green("ok");console.log(` ${G} ${B.dataset_id}${X.length?W.dim(` (${X.join(", ")})`):""}`)}}}catch(Y){if(Y instanceof f)Q.fail(Y.message);else Q.fail("Enforcement failed"),console.log(W.red(` ${Y.message}`));process.exit(1)}});var SH=(D)=>new Promise((F)=>setTimeout(F,D));async function DZ0(D,F,$){let J=Date.now()+F,Q="no probe completed";while(Date.now()<J){try{let Y=(await PF(D,!0)).result?.steps?.branch_ruleset;if(Y?.status==="ok")return{status:"green"};if(Y?.detail)Q=Y.detail}catch(Y){Q=Y instanceof f?Y.message:String(Y)}await SH($)}return{status:"timeout",detail:Q}}NQ.command("revalidate").description("Re-run BIDS validation on main HEAD for unprotected datasets, then optionally enforce (epic #713)").argument("[dataset-id]","Dataset to revalidate (omit when using --all/--prefix)").option("--all","Revalidate across unprotected public datasets").option("--prefix <prefix>","Filter by id prefix (with --all), e.g. nm000 / on").option("--enforce","After a dataset goes green, run enforce (dry-run unless --apply)").option("--apply","With --enforce, actually apply the ruleset (default is a dry run)").option("--force","Override the live-dataset guard (nm000103-107)").option("--limit <n>","Max repos for --all/--prefix (default 25)","25").option("--json","Output raw JSON").action(async(D,F)=>{if(!H0())console.log(W.red("Error: Not authenticated")),process.exit(1);let $=Boolean(F.all||!D&&F.prefix);if(!D&&!$)console.log(W.red("Error: provide a dataset-id, or --all/--prefix")),process.exit(1);let J;if(D)J=[D];else{let q=O("Fetching dataset list...").start();try{let K=[];for(let z=0;;z+=200){let Z=await TF({limit:200,offset:z});if(K.push(...Z.datasets),Z.datasets.length<200||K.length>=Z.total_count)break}let V=Number.parseInt(F.limit,10)||25;J=sg(K,{prefix:F.prefix}).slice(0,V),q.succeed(`${J.length} target(s) (from ${K.length} datasets)`)}catch(K){i0(K,q,"Failed to fetch datasets");return}}let Q=Boolean(F.enforce),Y=Boolean(F.apply),B={revalidated:0,green:0,locked:0,stillRed:0,skipped:0,errors:0},X=[],G=[],H=0;for(let q of J){if(H++,uW.has(q)&&!F.force){console.log(` [${H}/${J.length}] ${W.dim(`${q}: skip (live; use --force)`)}`),B.skipped++;continue}try{let K=await ug(q,F.force);if(X.push(K),K.skipped)console.log(` [${H}/${J.length}] ${q}: ${W.dim(`skipped (${K.skipped})`)}`),B.skipped++;else B.revalidated++,G.push(q),console.log(` [${H}/${J.length}] ${q}: ${W.cyan(`revalidating (${K.triggered_by})`)}`)}catch(K){B.errors++,console.log(` [${H}/${J.length}] ${q}: ${W.red(K instanceof f?K.message:String(K))}`)}if(H<J.length)await SH(4000)}if(Q&&G.length>0)if(D){let q=G[0],K=O(`Waiting for ${q} validation to land...`).start(),V=await DZ0(q,300000,15000);if(V.status!=="green")K.warn(`${q}: not green within 5m \u2014 last: ${V.detail} (real errors or still running)`),B.stillRed++;else if(B.green++,!Y)K.succeed(`${q}: green (would lock; pass --apply)`);else{let z=await PF(q,!1);if(z.result?.steps?.branch_ruleset?.status==="ok")K.succeed(`${q}: LOCKED`),B.locked++;else K.warn(`${q}: enforce ${z.result?.steps?.branch_ruleset?.status??"?"}`)}}else{let q=O("Waiting ~90s for validations to drain...").start();await SH(90000),q.text="Enforcing green datasets...";for(let K of G)try{if((await PF(K,!0)).result?.steps?.branch_ruleset?.status!=="ok"){B.stillRed++;continue}if(B.green++,Y){if((await PF(K,!1)).result?.steps?.branch_ruleset?.status==="ok")B.locked++}}catch{B.errors++}q.stop()}if(F.json){console.log(JSON.stringify({tally:B,raw:X},null,2));return}console.log(),console.log(W.cyan(`Done: revalidated=${B.revalidated} green=${B.green} locked=${B.locked} still-red=${B.stillRed} skipped=${B.skipped} errors=${B.errors}`))});b0.addCommand(NQ);var ih=new I0("reindex").description("Refresh dataset metadata: enrichment + nemar.org sync + first-class D1 columns");ih.argument("[dataset-id]","Dataset ID to reindex (e.g., nm000103)").option("--all","Reindex every dataset with a GitHub repo").option("--missing-metadata","Reindex only datasets with NULL metadata columns").option("--stale","Reindex only datasets whose metadata is older than --older-than days").option("--older-than <days>","Threshold in days. Default 30 for --stale, 1 (24h) for --missing-metadata recency guard.").option("--skip-enrichment","Skip the LLM enrichment step").option("--skip-sync","Skip the nemar.org sync + D1 column refresh step").option("--ref <ref>","Ref to enrich from (single-dataset only; default: main)").option("--dry-run","List matched datasets without firing the reindex (bulk only)").action(async(D,F)=>{if(!w0())return;let $=[F.all,F.missingMetadata,F.stale].filter(Boolean).length;if(D&&$>0)console.error(W.red("Provide either a dataset-id OR a bulk flag (--all/--missing-metadata/--stale), not both")),process.exit(1);if(!D&&$===0)console.error(W.red("Provide a dataset-id or one of: --all, --missing-metadata, --stale")),process.exit(1);if($>1)console.error(W.red("Use only one of --all, --missing-metadata, --stale")),process.exit(1);if(F.skipEnrichment&&F.skipSync)console.error(W.red("--skip-enrichment and --skip-sync cannot both be set")),process.exit(1);if(D){let K=O(`Reindexing ${D}...`).start();try{let V={skip_enrichment:F.skipEnrichment===!0,skip_sync:F.skipSync===!0,...F.ref&&{ref:F.ref}},z=await WQ(D,V),Z=z.enrichment.status!=="failed"&&z.sync.status!=="failed";if(Z)K.succeed(`${D} reindexed`);else K.warn(`${D} reindexed with errors`);if(console.log(),lh(z,{showRef:!0}),!Z)process.exit(1)}catch(V){K.fail(`Failed to reindex ${D}`),console.error(W.red(L0(V))),process.exit(1)}return}let J=F.all?"all":F.missingMetadata?"missing-metadata":"stale",Q={skip_enrichment:F.skipEnrichment===!0,skip_sync:F.skipSync===!0,dry_run:F.dryRun===!0};if(F.olderThan!==void 0){let K=Number.parseInt(F.olderThan,10);if(!Number.isFinite(K)||K<0)console.error(W.red(`Invalid --older-than: "${F.olderThan}"`)),process.exit(1);Q.older_than_days=K}else if(J==="missing-metadata")Q.older_than_days=1;else if(J==="stale")Q.older_than_days=30;let Y=F.dryRun?`Listing ${J} datasets...`:`Reindexing ${J} datasets...`,B=O(Y).start(),X;try{X=await gg(J,Q)}catch(K){B.fail("Bulk reindex failed"),console.error(W.red(L0(K))),process.exit(1)}if(X.dry_run){if(B.succeed(`${X.total} datasets match filter=${J} (dry run, no changes)`),X.datasets)for(let K of X.datasets)console.log(W.dim(` - ${K}`));return}let G=X.results??[],H=G.filter((K)=>K.enrichment.status!=="failed"&&K.sync.status!=="failed").length,q=G.length-H;if(q===0)B.succeed(`${G.length}/${G.length} datasets reindexed in ${(X.elapsed_ms/1000).toFixed(1)}s`);else B.warn(`${H}/${G.length} ok; ${q} failed in ${(X.elapsed_ms/1000).toFixed(1)}s`);console.log();for(let K of G)lh(K);if(q>0)process.exit(1)});b0.addCommand(ih);var xH=new I0("email-preferences").description("Manage email notification preferences");xH.command("show").description("Show current email notification preferences").action(async()=>{if(!H0())console.error(W.red("Not authenticated. Run: nemar auth login")),process.exit(1);let D=O("Fetching email preferences...").start();try{let F=await mg();D.succeed("Email notification preferences:"),console.log();let $=[{key:"user_approval",label:"User approval notifications"},{key:"publication_request",label:"Publication request notifications"},{key:"announcements",label:"Announcement emails"}];for(let J of $){let Y=F[J.key]?W.green("enabled"):W.dim("disabled");console.log(` ${J.label.padEnd(40)} ${Y}`)}console.log(),console.log(W.dim(" Use 'nemar admin email-preferences update' to change settings."))}catch(F){D.fail("Failed to fetch preferences"),console.error(W.red(L0(F)))}});xH.command("update").description("Update email notification preferences").option("--user-approval <bool>","Enable/disable user approval notifications").option("--publication-request <bool>","Enable/disable publication request notifications").option("--announcements <bool>","Enable/disable announcement emails").option("--all <bool>","Enable/disable all notifications").action(async(D)=>{if(!H0())console.error(W.red("Not authenticated. Run: nemar auth login")),process.exit(1);function F(Q){if(Q===void 0)return;let Y=Q.toLowerCase();if(Y==="true"||Y==="1"||Y==="on"||Y==="yes")return!0;if(Y==="false"||Y==="0"||Y==="off"||Y==="no")return!1;console.error(W.red(`Invalid boolean value: "${Q}". Use true/false, on/off, yes/no.`)),process.exit(1)}let $={};if(D.all!==void 0){let Q=F(D.all);$.user_approval=Q,$.publication_request=Q,$.announcements=Q}else{let Q=F(D.userApproval),Y=F(D.publicationRequest),B=F(D.announcements);if(Q===void 0&&Y===void 0&&B===void 0)console.error(W.red("No preferences specified.")),console.log(" --user-approval <bool> User approval notifications"),console.log(" --publication-request <bool> Publication request notifications"),console.log(" --announcements <bool> Announcement emails"),console.log(" --all <bool> All notifications"),process.exit(1);if(Q!==void 0)$.user_approval=Q;if(Y!==void 0)$.publication_request=Y;if(B!==void 0)$.announcements=B}let J=O("Updating email preferences...").start();try{let Q=await lg($);J.succeed("Email preferences updated:"),console.log(),console.log(` User approval: ${Q.user_approval?W.green("enabled"):W.dim("disabled")}`),console.log(` Publication request: ${Q.publication_request?W.green("enabled"):W.dim("disabled")}`),console.log(` Announcements: ${Q.announcements?W.green("enabled"):W.dim("disabled")}`)}catch(Q){J.fail("Failed to update preferences"),console.error(W.red(L0(Q)))}});b0.addCommand(xH);var RQ=new I0("notice").description("Manage system notices displayed to CLI users");RQ.command("list").description("List all notices (including expired)").action(async()=>{if(!H0())console.error(W.red("Not authenticated. Run: nemar auth login")),process.exit(1);let D=O("Fetching notices...").start();try{let{notices:F}=await dg();if(F.length===0){D.succeed("No notices found.");return}D.succeed(`${F.length} notice(s):`),console.log();for(let $ of F){let Q={critical:W.red.bold,warning:W.yellow,info:W.blue}[$.level]||W.white,Y=$.expires_at&&new Date($.expires_at)<new Date?W.dim(" (expired)"):"";if(console.log(` ${W.dim(`#${$.id}`)} ${Q(`[${$.level.toUpperCase()}]`)} ${W.dim(`scope:${$.scope}`)}${Y}`),console.log(` ${$.message}`),console.log(` ${W.dim(`Created: ${$.created_at}`)}`),$.expires_at)console.log(` ${W.dim(`Expires: ${$.expires_at}`)}`);console.log()}}catch(F){i0(F,D,"Failed to fetch notices")}});RQ.command("set").description("Create a new system notice").requiredOption("-m, --message <text>","Notice message text").option("-l, --level <level>","Notice level: info, warning, critical","info").option("-s, --scope <scope>","Target scope: all, admins, members","all").option("-e, --expires <datetime>","Expiry datetime (ISO 8601)").action(async(D)=>{if(!H0())console.error(W.red("Not authenticated. Run: nemar auth login")),process.exit(1);if(!["info","warning","critical"].includes(D.level))console.error(W.red(`Invalid level: ${D.level}. Use info, warning, or critical.`)),process.exit(1);if(!["all","admins","members"].includes(D.scope))console.error(W.red(`Invalid scope: ${D.scope}. Use all, admins, or members.`)),process.exit(1);let F=O("Creating notice...").start();try{let $=await cg({message:D.message,level:D.level,scope:D.scope,expires_at:D.expires});if(F.succeed(`Notice created (ID: ${$.id})`),console.log(` Level: ${$.level}`),console.log(` Scope: ${$.scope}`),console.log(` Message: ${$.message}`),$.expires_at)console.log(` Expires: ${$.expires_at}`)}catch($){i0($,F,"Failed to create notice")}});RQ.command("clear <id>").description("Delete a notice by ID").option(j0,T0).option(g0,v0).action(async(D,F)=>{if(!H0())console.error(W.red("Not authenticated. Run: nemar auth login")),process.exit(1);let $=Number.parseInt(D,10);if(Number.isNaN($))console.error(W.red("Invalid notice ID")),process.exit(1);if(!await P0(`Delete notice #${$}?`,F,!1))return;let Q=O("Deleting notice...").start();try{await ng($),Q.succeed(`Notice #${$} deleted`)}catch(Y){i0(Y,Q,"Failed to delete notice")}});b0.addCommand(RQ);b0.command("notify").description("Send an email to a group or a single user").option("--to <group>","Recipient group: all, admins, members").option("--user <username>","Send to a single user by username").requiredOption("--subject <text>","Email subject line").option("--body <text>","Email body (markdown)").option("--body-file <path>","Read email body from file (markdown)").option("--dry-run","Preview recipients without sending").option(j0,T0).option(g0,v0).action(async(D)=>{if(!H0())console.error(W.red("Not authenticated. Run: nemar auth login")),process.exit(1);if(D.to&&D.user)console.error(W.red("--to and --user are mutually exclusive. Provide exactly one.")),process.exit(1);if(!D.to&&!D.user)console.error(W.red("Provide either --to <group> or --user <username>.")),process.exit(1);if(D.to&&!["all","admins","members"].includes(D.to))console.error(W.red(`Invalid group: ${D.to}. Use all, admins, or members.`)),process.exit(1);let F;if(D.bodyFile){if(!dh(D.bodyFile))console.error(W.red(`File not found: ${D.bodyFile}`)),process.exit(1);F=rV0(D.bodyFile,"utf-8")}else if(D.body)F=D.body;else console.error(W.red("Email body required. Use --body or --body-file.")),process.exit(1);let $=D.user?`user:${D.user}`:D.to,J=D.user?{user:D.user,subject:D.subject,body:F}:{to:D.to,subject:D.subject,body:F};if(D.dryRun){let X=O("Checking recipients...").start();try{let G=await bW({...J,dry_run:!0});if("dry_run"in G){X.succeed(`Dry run: ${G.recipient_count} recipient(s) for "${G.recipient_group}"`),console.log();for(let H of G.recipients)console.log(` ${H}`)}}catch(G){i0(G,X,"Failed to check recipients")}return}console.log(W.bold("Email preview:")),console.log(` To: ${W.cyan($)}`),console.log(` Subject: ${D.subject}`),console.log(` Body: ${F.length>100?`${F.substring(0,100)}...`:F}`),console.log();let Q=D.user?`Send this email to ${D.user}?`:"Send this broadcast email?";if(!await P0(Q,D,!1))return;let B=O(D.user?`Sending to ${D.user}...`:"Sending broadcast...").start();try{let X=await bW(J);if("broadcast_id"in X)if(X.failure_count>0){B.warn(`Email send: ${X.recipient_count} delivered, ${X.failure_count} failed`);for(let G of X.failed_recipients)console.log(W.red(` Failed: ${G}`))}else{let G=D.user?`Email sent to ${D.user}`:`Broadcast sent to ${X.recipient_count} recipient(s)`;B.succeed(`${G} (ID: ${X.broadcast_id})`)}}catch(X){i0(X,B,"Failed to send email")}});var FZ0=1500;function $Z0(D){switch(D.kind){case"ok":return W.green(`ok ${D.schema_version}`);case"stale":return W.yellow(`stale ${D.schema_version}`);case"missing":return W.red("missing");case"error":return W.red(`error ${D.status||"?"}: ${D.message}`)}}function JZ0(D){return D.kind==="stale"||D.kind==="missing"}function QZ0(D){let $=D.replace(/[.+^${}()|[\]\\]/g,"\\$&").replace(/\*/g,".*").replace(/\?/g,".");return new RegExp(`^${$}$`)}var ah=new I0("summary").description("summary.json coverage across published dataset versions");ah.command("check").description("Report which (dataset_id, version) pairs have stale or missing summary.json").option("--fix","Dispatch generate-manifest for every stale/missing version").option("--id <id>","Limit to a single dataset_id (exact match)").option("--match <glob>","Limit to dataset_ids matching a glob pattern: `*` matches any run of chars, `?` matches one char. Examples: `on*`, `nm00010?`, `*99999`. Can be combined with --id (id wins if both passed).").option("--only-stale","Print only rows that are not ok (suppresses ok rows)").option("--json","Emit the full report as JSON instead of a table").option(j0,T0).option(g0,v0).action(async(D)=>{if(!w0())return;let F=O("Building coverage report...").start(),$;try{$=await ig()}catch(V){i0(V,F,"Failed to fetch coverage report");return}F.succeed(`Coverage: target=schema ${$.target_schema}, versions=${$.totals.versions}`);let J=$.versions,Q=null;if(D.id){if(J=J.filter((V)=>V.dataset_id===D.id),Q=`dataset_id=${D.id}`,J.length===0){console.log(W.yellow(`No rows for ${Q}`));return}}else if(D.match){let V=QZ0(D.match);if(J=J.filter((z)=>V.test(z.dataset_id)),Q=`--match ${D.match}`,J.length===0){console.log(W.yellow(`No rows match ${Q}`));return}console.log(W.dim(`Scoped to ${J.length} version(s) matching ${D.match}`))}if(D.json){console.log(JSON.stringify(Q?{...$,versions:J,totals:ph(J)}:$,null,2));return}let Y=D.onlyStale?J.filter((V)=>V.state.kind!=="ok"):J;if(Y.length===0)console.log(W.green("All versions at target schema \u2014 no drift."));else{let V=Math.max(...Y.map((Z)=>Z.dataset_id.length),10),z=Math.max(...Y.map((Z)=>Z.version.length),7);for(let Z of Y)console.log(` ${Z.dataset_id.padEnd(V)} ${Z.version.padEnd(z)} ${$Z0(Z.state)}`)}let B=Q?ph(J):$.totals;if(console.log(),console.log(` Total: ${B.versions} ${W.green(`ok=${B.ok}`)} ${W.yellow(`stale=${B.stale}`)} ${W.red(`missing=${B.missing}`)} ${W.red(`error=${B.error}`)}`),!D.fix){if(B.stale+B.missing>0)console.log(W.dim(`
|
|
387
|
+
`),Q.length===0){console.log(W.dim(" No import jobs match."));return}console.log(W.dim(` ${"ID".padEnd(12)} ${"Source".padEnd(12)} ${"Stage".padEnd(10)} ${"Status".padEnd(12)} ${"Updated".padEnd(20)}`)),console.log(W.dim(` ${"\u2500".repeat(70)}`));for(let B of Q){let X=B.status==="complete"?W.green:B.status==="failed"||B.status==="quarantined"?W.red:B.status==="rolled_back"?W.dim:W.yellow,G=B.updated_at?new Date(B.updated_at).toLocaleString():"-";if(console.log(` ${B.dataset_id.padEnd(12)} ${(B.source_id||"-").padEnd(12)} ${B.stage.padEnd(10)} ${X(B.status.padEnd(12))} ${G}`),B.last_error)console.log(W.red(` ${B.last_error}`));if(B.workflow_run_url)console.log(W.dim(` run: ${B.workflow_run_url}`))}}catch(J){$.fail("Failed to fetch import status"),console.error(W.red(L0(J)))}});MQ.command("rollback").description("Roll back a failed/quarantined import (deletes repo + S3 + D1)").argument("<dataset-id>","NEMAR dataset id (e.g., on007523)").action(async(D)=>{if(!w0())return;let{proceed:F}=await D0.prompt([{type:"confirm",name:"proceed",message:W.red(`Roll back import ${D}? This deletes the GitHub repo, S3 objects, and D1 records. This cannot be undone.`),default:!1}]);if(!F){console.log(W.dim("Cancelled."));return}let $=O(`Rolling back ${D}...`).start();try{let J=await _g(D);if(!J.rolled_back){$.fail(`Rollback incomplete for ${D} (kept quarantined); retry after fixing:`);for(let Q of J.warnings)console.log(W.red(` - ${Q}`))}else if(J.warnings.length>0){$.warn(`Rolled back ${D} with warnings`);for(let Q of J.warnings)console.log(W.yellow(` - ${Q}`))}else $.succeed(`Rolled back ${D}`)}catch(J){$.fail(`Failed to roll back ${D}`),console.error(W.red(L0(J)))}});MQ.command("retry").description("Reset a failed/quarantined import to 'preparing' for re-dispatch").argument("<dataset-id>","NEMAR dataset id (e.g., on007523)").action(async(D)=>{if(!w0())return;let F=O(`Resetting ${D}...`).start();try{await fg(D),F.succeed(`${D} reset to 'preparing'. Re-run the onboard-openneuro workflow to retry.`)}catch($){F.fail(`Failed to reset ${D}`),console.error(W.red(L0($)))}});b0.addCommand(MQ);function lh(D,F){let $=D.enrichment.status,J=$==="ok"?W.green("enrich:ok"):$==="failed"?W.red("enrich:failed"):W.dim("enrich:skipped"),Q=D.sync.status,Y=Q==="ok"?W.green("sync:ok"):Q==="failed"?W.red("sync:failed"):W.dim("sync:skipped"),B=D.sync.metadata_columns_written===!0?W.green("cols:written"):D.sync.metadata_columns_error?W.red("cols:failed"):"",X=F?.showRef&&D.enrichment.ref?W.dim(`@${D.enrichment.ref}`):"";if(console.log(` ${D.dataset_id.padEnd(12)} ${J}${X} ${Y} ${B}`),D.enrichment.error)console.log(W.red(` enrichment: ${D.enrichment.error}`));if(D.sync.errors?.length)for(let G of D.sync.errors)console.log(W.red(` sync: ${G}`));if(D.sync.metadata_columns_error)console.log(W.red(` metadata columns: ${D.sync.metadata_columns_error}`))}var NQ=new I0("fleet").description("Governance drift reporting and enforcement (epic #713)");NQ.command("drift").description("Report dataset repos that are off the governance spec").option("--prefix <prefix>","Filter datasets by id prefix (e.g. nm, on)").option("--visibility <vis>","Filter by visibility: public or private").option("--limit <n>","Max repos to scan (default 25, max 50)","25").option("--json","Output raw JSON").action(async(D)=>{if(!H0())console.log(W.red("Error: Not authenticated")),process.exit(1);if(D.visibility&&!["public","private"].includes(D.visibility))console.log(W.red("Error: --visibility must be public or private")),process.exit(1);let F=O("Scanning fleet for drift...").start();try{let $=await hg({prefix:D.prefix,visibility:D.visibility,limit:Number.parseInt(D.limit,10)||25});if(F.stop(),D.json){console.log(JSON.stringify($,null,2));return}console.log(),console.log(W.bold(`Fleet drift (scanned ${$.scanned}):`));let J=["PUBLIC_UNPROTECTED","RED_REQUIRED_CHECK","CONTEXT_NAME_MISMATCH","MISSING_REQUIRED_WORKFLOW","PRIVATE_WITH_STRAY_READ","DEFAULT_BRANCH_OUTLIER","DEPRECATED_WORKFLOW_PRESENT","COMPLIANT"];for(let Q of J){let Y=$.buckets[Q];if(!Y||Y.length===0)continue;let B=Q==="COMPLIANT"?W.green:W.yellow;if(console.log(` ${B(Q.padEnd(28))} ${Y.length}`),Q!=="COMPLIANT"){let X=Y.slice(0,20).join(", ");console.log(W.dim(` ${X}${Y.length>20?` ... +${Y.length-20}`:""}`))}}console.log()}catch($){if($ instanceof f)F.fail($.message);else F.fail("Failed to scan fleet"),console.log(W.red(` ${$.message}`));process.exit(1)}});NQ.command("enforce").description("Bring dataset repos to the governance spec (single or --all). Dry-run by default.").argument("[dataset-id]","Dataset to enforce (omit when using --all)").option("--all","Bulk enforce across a filtered set (owner-only)").option("--apply","Actually apply changes (default is a dry run)").option("--prefix <prefix>","Bulk: filter by id prefix").option("--visibility <vis>","Bulk: filter by visibility (public|private)").option("--limit <n>","Bulk: max repos (default 25, max 50)","25").option("--json","Output raw JSON").action(async(D,F)=>{if(!H0())console.log(W.red("Error: Not authenticated")),process.exit(1);if(!D&&!F.all)console.log(W.red("Error: provide a dataset-id or use --all")),process.exit(1);if(D&&F.all)console.log(W.red("Error: provide a dataset-id OR --all, not both")),process.exit(1);let $=!F.apply,J=$?"[dry-run] ":"",Q=O(`${J}Enforcing spec...`).start();try{if(D){let Y=await PF(D,$);if(Q.succeed(`${J}${D} (${Y.result.visibility})`),F.json){console.log(JSON.stringify(Y,null,2));return}for(let[B,X]of Object.entries(Y.result.steps)){let G=X.status==="ok"?W.green:X.status==="skipped"?W.yellow:W.red;console.log(` ${G(X.status.padEnd(8))} ${B}${X.detail?W.dim(` (${X.detail})`):""}`)}}else{let Y=await bg({prefix:F.prefix,visibility:F.visibility,limit:Number.parseInt(F.limit,10)||25,dryRun:$});if(Q.succeed(`${J}processed ${Y.count} repo(s)`),F.json){console.log(JSON.stringify(Y,null,2));return}for(let B of Y.results){if(B.error){console.log(` ${W.red("error")} ${B.dataset_id}: ${B.error}`);continue}let X=Object.entries(B.steps??{}).filter(([,H])=>H.status!=="ok").map(([H,q])=>`${H}=${q.status}`),G=X.length?W.yellow("drift"):W.green("ok");console.log(` ${G} ${B.dataset_id}${X.length?W.dim(` (${X.join(", ")})`):""}`)}}}catch(Y){if(Y instanceof f)Q.fail(Y.message);else Q.fail("Enforcement failed"),console.log(W.red(` ${Y.message}`));process.exit(1)}});var SH=(D)=>new Promise((F)=>setTimeout(F,D));async function DZ0(D,F,$){let J=Date.now()+F,Q="no probe completed";while(Date.now()<J){try{let Y=(await PF(D,!0)).result?.steps?.branch_ruleset;if(Y?.status==="ok")return{status:"green"};if(Y?.detail)Q=Y.detail}catch(Y){Q=Y instanceof f?Y.message:String(Y)}await SH($)}return{status:"timeout",detail:Q}}NQ.command("revalidate").description("Re-run BIDS validation on main HEAD for unprotected datasets, then optionally enforce (epic #713)").argument("[dataset-id]","Dataset to revalidate (omit when using --all/--prefix)").option("--all","Revalidate across unprotected public datasets").option("--prefix <prefix>","Filter by id prefix (with --all), e.g. nm000 / on").option("--enforce","After a dataset goes green, run enforce (dry-run unless --apply)").option("--apply","With --enforce, actually apply the ruleset (default is a dry run)").option("--force","Override the live-dataset guard (nm000103-107)").option("--limit <n>","Max repos for --all/--prefix (default 25)","25").option("--json","Output raw JSON").action(async(D,F)=>{if(!H0())console.log(W.red("Error: Not authenticated")),process.exit(1);let $=Boolean(F.all||!D&&F.prefix);if(!D&&!$)console.log(W.red("Error: provide a dataset-id, or --all/--prefix")),process.exit(1);let J;if(D)J=[D];else{let q=O("Fetching dataset list...").start();try{let K=[];for(let z=0;;z+=200){let Z=await TF({limit:200,offset:z});if(K.push(...Z.datasets),Z.datasets.length<200||K.length>=Z.total_count)break}let V=Number.parseInt(F.limit,10)||25;J=sg(K,{prefix:F.prefix}).slice(0,V),q.succeed(`${J.length} target(s) (from ${K.length} datasets)`)}catch(K){i0(K,q,"Failed to fetch datasets");return}}let Q=Boolean(F.enforce),Y=Boolean(F.apply),B={revalidated:0,green:0,locked:0,stillRed:0,skipped:0,errors:0},X=[],G=[],H=0;for(let q of J){if(H++,uW.has(q)&&!F.force){console.log(` [${H}/${J.length}] ${W.dim(`${q}: skip (live; use --force)`)}`),B.skipped++;continue}try{let K=await ug(q,F.force);if(X.push(K),K.skipped)console.log(` [${H}/${J.length}] ${q}: ${W.dim(`skipped (${K.skipped})`)}`),B.skipped++;else B.revalidated++,G.push(q),console.log(` [${H}/${J.length}] ${q}: ${W.cyan(`revalidating (${K.triggered_by})`)}`)}catch(K){B.errors++,console.log(` [${H}/${J.length}] ${q}: ${W.red(K instanceof f?K.message:String(K))}`)}if(H<J.length)await SH(4000)}if(Q&&G.length>0)if(D){let q=G[0],K=O(`Waiting for ${q} validation to land...`).start(),V=await DZ0(q,300000,15000);if(V.status!=="green")K.warn(`${q}: not green within 5m \u2014 last: ${V.detail} (real errors or still running)`),B.stillRed++;else if(B.green++,!Y)K.succeed(`${q}: green (would lock; pass --apply)`);else{let z=await PF(q,!1);if(z.result?.steps?.branch_ruleset?.status==="ok")K.succeed(`${q}: LOCKED`),B.locked++;else K.warn(`${q}: enforce ${z.result?.steps?.branch_ruleset?.status??"?"}`)}}else{let q=O("Waiting ~90s for validations to drain...").start();await SH(90000),q.text="Enforcing green datasets...";for(let K of G)try{if((await PF(K,!0)).result?.steps?.branch_ruleset?.status!=="ok"){B.stillRed++;continue}if(B.green++,Y){if((await PF(K,!1)).result?.steps?.branch_ruleset?.status==="ok")B.locked++}}catch{B.errors++}q.stop()}if(F.json){console.log(JSON.stringify({tally:B,raw:X},null,2));return}console.log(),console.log(W.cyan(`Done: revalidated=${B.revalidated} green=${B.green} locked=${B.locked} still-red=${B.stillRed} skipped=${B.skipped} errors=${B.errors}`))});b0.addCommand(NQ);var ih=new I0("reindex").description("Refresh dataset metadata: enrichment + nemar.org sync + first-class D1 columns");ih.argument("[dataset-id]","Dataset ID to reindex (e.g., nm000103)").option("--all","Reindex every dataset with a GitHub repo").option("--missing-metadata","Reindex only datasets with NULL metadata columns").option("--stale","Reindex only datasets whose metadata is older than --older-than days").option("--older-than <days>","Threshold in days. Default 30 for --stale, 1 (24h) for --missing-metadata recency guard.").option("--skip-enrichment","Skip the LLM enrichment step").option("--skip-sync","Skip the nemar.org sync + D1 column refresh step").option("--ref <ref>","Ref to enrich from (single-dataset only; default: main)").option("--dry-run","List matched datasets without firing the reindex (bulk only)").action(async(D,F)=>{if(!w0())return;let $=[F.all,F.missingMetadata,F.stale].filter(Boolean).length;if(D&&$>0)console.error(W.red("Provide either a dataset-id OR a bulk flag (--all/--missing-metadata/--stale), not both")),process.exit(1);if(!D&&$===0)console.error(W.red("Provide a dataset-id or one of: --all, --missing-metadata, --stale")),process.exit(1);if($>1)console.error(W.red("Use only one of --all, --missing-metadata, --stale")),process.exit(1);if(F.skipEnrichment&&F.skipSync)console.error(W.red("--skip-enrichment and --skip-sync cannot both be set")),process.exit(1);if(D){let K=O(`Reindexing ${D}...`).start();try{let V={skip_enrichment:F.skipEnrichment===!0,skip_sync:F.skipSync===!0,...F.ref&&{ref:F.ref}},z=await WQ(D,V),Z=z.enrichment.status!=="failed"&&z.sync.status!=="failed";if(Z)K.succeed(`${D} reindexed`);else K.warn(`${D} reindexed with errors`);if(console.log(),lh(z,{showRef:!0}),!Z)process.exit(1)}catch(V){K.fail(`Failed to reindex ${D}`),console.error(W.red(L0(V))),process.exit(1)}return}let J=F.all?"all":F.missingMetadata?"missing-metadata":"stale",Q={skip_enrichment:F.skipEnrichment===!0,skip_sync:F.skipSync===!0,dry_run:F.dryRun===!0};if(F.olderThan!==void 0){let K=Number.parseInt(F.olderThan,10);if(!Number.isFinite(K)||K<0)console.error(W.red(`Invalid --older-than: "${F.olderThan}"`)),process.exit(1);Q.older_than_days=K}else if(J==="missing-metadata")Q.older_than_days=1;else if(J==="stale")Q.older_than_days=30;let Y=F.dryRun?`Listing ${J} datasets...`:`Reindexing ${J} datasets...`,B=O(Y).start(),X;try{X=await gg(J,Q)}catch(K){B.fail("Bulk reindex failed"),console.error(W.red(L0(K))),process.exit(1)}if(X.dry_run){if(B.succeed(`${X.total} datasets match filter=${J} (dry run, no changes)`),X.datasets)for(let K of X.datasets)console.log(W.dim(` - ${K}`));return}let G=X.results??[],H=G.filter((K)=>K.enrichment.status!=="failed"&&K.sync.status!=="failed").length,q=G.length-H;if(q===0)B.succeed(`${G.length}/${G.length} datasets reindexed in ${(X.elapsed_ms/1000).toFixed(1)}s`);else B.warn(`${H}/${G.length} ok; ${q} failed in ${(X.elapsed_ms/1000).toFixed(1)}s`);console.log();for(let K of G)lh(K);if(q>0)process.exit(1)});b0.addCommand(ih);var xH=new I0("email-preferences").description("Manage email notification preferences");xH.command("show").description("Show email notification preferences").option("--user <username>","(owner only) show another user's preferences").action(async(D)=>{if(!H0())console.error(W.red("Not authenticated. Run: nemar auth login")),process.exit(1);let F=O("Fetching email preferences...").start();try{let $=await mg(D.user),J=$.username?`${$.username}'s`:"Your";F.succeed(`${J} email notification preferences:`),console.log();let Q=[{key:"user_approval",label:"User approval notifications"},{key:"publication_request",label:"Publication request notifications"},{key:"announcements",label:"Announcement emails"}];for(let Y of Q){let X=$[Y.key]?W.green("enabled"):W.dim("disabled");console.log(` ${Y.label.padEnd(40)} ${X}`)}console.log(),console.log(W.dim(" Use 'nemar admin email-preferences update' to change settings."))}catch($){F.fail("Failed to fetch preferences"),console.error(W.red(L0($)))}});xH.command("update").description("Update email notification preferences").option("--user-approval <bool>","Enable/disable user approval notifications").option("--publication-request <bool>","Enable/disable publication request notifications").option("--announcements <bool>","Enable/disable announcement emails").option("--all <bool>","Enable/disable all notifications").option("--user <username>","(owner only) update another user's preferences").action(async(D)=>{if(!H0())console.error(W.red("Not authenticated. Run: nemar auth login")),process.exit(1);function F(Q){if(Q===void 0)return;let Y=Q.toLowerCase();if(Y==="true"||Y==="1"||Y==="on"||Y==="yes")return!0;if(Y==="false"||Y==="0"||Y==="off"||Y==="no")return!1;console.error(W.red(`Invalid boolean value: "${Q}". Use true/false, on/off, yes/no.`)),process.exit(1)}let $={};if(D.all!==void 0){let Q=F(D.all);$.user_approval=Q,$.publication_request=Q,$.announcements=Q}else{let Q=F(D.userApproval),Y=F(D.publicationRequest),B=F(D.announcements);if(Q===void 0&&Y===void 0&&B===void 0)console.error(W.red("No preferences specified.")),console.log(" --user-approval <bool> User approval notifications"),console.log(" --publication-request <bool> Publication request notifications"),console.log(" --announcements <bool> Announcement emails"),console.log(" --all <bool> All notifications"),process.exit(1);if(Q!==void 0)$.user_approval=Q;if(Y!==void 0)$.publication_request=Y;if(B!==void 0)$.announcements=B}let J=O("Updating email preferences...").start();try{let Q=await lg($,D.user),Y=Q.username?`${Q.username}'s`:"Your";J.succeed(`${Y} email preferences updated:`),console.log(),console.log(` User approval: ${Q.user_approval?W.green("enabled"):W.dim("disabled")}`),console.log(` Publication request: ${Q.publication_request?W.green("enabled"):W.dim("disabled")}`),console.log(` Announcements: ${Q.announcements?W.green("enabled"):W.dim("disabled")}`)}catch(Q){J.fail("Failed to update preferences"),console.error(W.red(L0(Q)))}});b0.addCommand(xH);var RQ=new I0("notice").description("Manage system notices displayed to CLI users");RQ.command("list").description("List all notices (including expired)").action(async()=>{if(!H0())console.error(W.red("Not authenticated. Run: nemar auth login")),process.exit(1);let D=O("Fetching notices...").start();try{let{notices:F}=await dg();if(F.length===0){D.succeed("No notices found.");return}D.succeed(`${F.length} notice(s):`),console.log();for(let $ of F){let Q={critical:W.red.bold,warning:W.yellow,info:W.blue}[$.level]||W.white,Y=$.expires_at&&new Date($.expires_at)<new Date?W.dim(" (expired)"):"";if(console.log(` ${W.dim(`#${$.id}`)} ${Q(`[${$.level.toUpperCase()}]`)} ${W.dim(`scope:${$.scope}`)}${Y}`),console.log(` ${$.message}`),console.log(` ${W.dim(`Created: ${$.created_at}`)}`),$.expires_at)console.log(` ${W.dim(`Expires: ${$.expires_at}`)}`);console.log()}}catch(F){i0(F,D,"Failed to fetch notices")}});RQ.command("set").description("Create a new system notice").requiredOption("-m, --message <text>","Notice message text").option("-l, --level <level>","Notice level: info, warning, critical","info").option("-s, --scope <scope>","Target scope: all, admins, members","all").option("-e, --expires <datetime>","Expiry datetime (ISO 8601)").action(async(D)=>{if(!H0())console.error(W.red("Not authenticated. Run: nemar auth login")),process.exit(1);if(!["info","warning","critical"].includes(D.level))console.error(W.red(`Invalid level: ${D.level}. Use info, warning, or critical.`)),process.exit(1);if(!["all","admins","members"].includes(D.scope))console.error(W.red(`Invalid scope: ${D.scope}. Use all, admins, or members.`)),process.exit(1);let F=O("Creating notice...").start();try{let $=await cg({message:D.message,level:D.level,scope:D.scope,expires_at:D.expires});if(F.succeed(`Notice created (ID: ${$.id})`),console.log(` Level: ${$.level}`),console.log(` Scope: ${$.scope}`),console.log(` Message: ${$.message}`),$.expires_at)console.log(` Expires: ${$.expires_at}`)}catch($){i0($,F,"Failed to create notice")}});RQ.command("clear <id>").description("Delete a notice by ID").option(j0,T0).option(g0,v0).action(async(D,F)=>{if(!H0())console.error(W.red("Not authenticated. Run: nemar auth login")),process.exit(1);let $=Number.parseInt(D,10);if(Number.isNaN($))console.error(W.red("Invalid notice ID")),process.exit(1);if(!await P0(`Delete notice #${$}?`,F,!1))return;let Q=O("Deleting notice...").start();try{await ng($),Q.succeed(`Notice #${$} deleted`)}catch(Y){i0(Y,Q,"Failed to delete notice")}});b0.addCommand(RQ);b0.command("notify").description("Send an email to a group or a single user").option("--to <group>","Recipient group: all, admins, members").option("--user <username>","Send to a single user by username").requiredOption("--subject <text>","Email subject line").option("--body <text>","Email body (markdown)").option("--body-file <path>","Read email body from file (markdown)").option("--dry-run","Preview recipients without sending").option(j0,T0).option(g0,v0).action(async(D)=>{if(!H0())console.error(W.red("Not authenticated. Run: nemar auth login")),process.exit(1);if(D.to&&D.user)console.error(W.red("--to and --user are mutually exclusive. Provide exactly one.")),process.exit(1);if(!D.to&&!D.user)console.error(W.red("Provide either --to <group> or --user <username>.")),process.exit(1);if(D.to&&!["all","admins","members"].includes(D.to))console.error(W.red(`Invalid group: ${D.to}. Use all, admins, or members.`)),process.exit(1);let F;if(D.bodyFile){if(!dh(D.bodyFile))console.error(W.red(`File not found: ${D.bodyFile}`)),process.exit(1);F=rV0(D.bodyFile,"utf-8")}else if(D.body)F=D.body;else console.error(W.red("Email body required. Use --body or --body-file.")),process.exit(1);let $=D.user?`user:${D.user}`:D.to,J=D.user?{user:D.user,subject:D.subject,body:F}:{to:D.to,subject:D.subject,body:F};if(D.dryRun){let X=O("Checking recipients...").start();try{let G=await bW({...J,dry_run:!0});if("dry_run"in G){X.succeed(`Dry run: ${G.recipient_count} recipient(s) for "${G.recipient_group}"`),console.log();for(let H of G.recipients)console.log(` ${H}`)}}catch(G){i0(G,X,"Failed to check recipients")}return}console.log(W.bold("Email preview:")),console.log(` To: ${W.cyan($)}`),console.log(` Subject: ${D.subject}`),console.log(` Body: ${F.length>100?`${F.substring(0,100)}...`:F}`),console.log();let Q=D.user?`Send this email to ${D.user}?`:"Send this broadcast email?";if(!await P0(Q,D,!1))return;let B=O(D.user?`Sending to ${D.user}...`:"Sending broadcast...").start();try{let X=await bW(J);if("broadcast_id"in X)if(X.failure_count>0){B.warn(`Email send: ${X.recipient_count} delivered, ${X.failure_count} failed`);for(let G of X.failed_recipients)console.log(W.red(` Failed: ${G}`))}else{let G=D.user?`Email sent to ${D.user}`:`Broadcast sent to ${X.recipient_count} recipient(s)`;B.succeed(`${G} (ID: ${X.broadcast_id})`)}}catch(X){i0(X,B,"Failed to send email")}});var FZ0=1500;function $Z0(D){switch(D.kind){case"ok":return W.green(`ok ${D.schema_version}`);case"stale":return W.yellow(`stale ${D.schema_version}`);case"missing":return W.red("missing");case"error":return W.red(`error ${D.status||"?"}: ${D.message}`)}}function JZ0(D){return D.kind==="stale"||D.kind==="missing"}function QZ0(D){let $=D.replace(/[.+^${}()|[\]\\]/g,"\\$&").replace(/\*/g,".*").replace(/\?/g,".");return new RegExp(`^${$}$`)}var ah=new I0("summary").description("summary.json coverage across published dataset versions");ah.command("check").description("Report which (dataset_id, version) pairs have stale or missing summary.json").option("--fix","Dispatch generate-manifest for every stale/missing version").option("--id <id>","Limit to a single dataset_id (exact match)").option("--match <glob>","Limit to dataset_ids matching a glob pattern: `*` matches any run of chars, `?` matches one char. Examples: `on*`, `nm00010?`, `*99999`. Can be combined with --id (id wins if both passed).").option("--only-stale","Print only rows that are not ok (suppresses ok rows)").option("--json","Emit the full report as JSON instead of a table").option(j0,T0).option(g0,v0).action(async(D)=>{if(!w0())return;let F=O("Building coverage report...").start(),$;try{$=await ig()}catch(V){i0(V,F,"Failed to fetch coverage report");return}F.succeed(`Coverage: target=schema ${$.target_schema}, versions=${$.totals.versions}`);let J=$.versions,Q=null;if(D.id){if(J=J.filter((V)=>V.dataset_id===D.id),Q=`dataset_id=${D.id}`,J.length===0){console.log(W.yellow(`No rows for ${Q}`));return}}else if(D.match){let V=QZ0(D.match);if(J=J.filter((z)=>V.test(z.dataset_id)),Q=`--match ${D.match}`,J.length===0){console.log(W.yellow(`No rows match ${Q}`));return}console.log(W.dim(`Scoped to ${J.length} version(s) matching ${D.match}`))}if(D.json){console.log(JSON.stringify(Q?{...$,versions:J,totals:ph(J)}:$,null,2));return}let Y=D.onlyStale?J.filter((V)=>V.state.kind!=="ok"):J;if(Y.length===0)console.log(W.green("All versions at target schema \u2014 no drift."));else{let V=Math.max(...Y.map((Z)=>Z.dataset_id.length),10),z=Math.max(...Y.map((Z)=>Z.version.length),7);for(let Z of Y)console.log(` ${Z.dataset_id.padEnd(V)} ${Z.version.padEnd(z)} ${$Z0(Z.state)}`)}let B=Q?ph(J):$.totals;if(console.log(),console.log(` Total: ${B.versions} ${W.green(`ok=${B.ok}`)} ${W.yellow(`stale=${B.stale}`)} ${W.red(`missing=${B.missing}`)} ${W.red(`error=${B.error}`)}`),!D.fix){if(B.stale+B.missing>0)console.log(W.dim(`
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388
388
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Run with --fix to dispatch generate-manifest for the ${B.stale+B.missing} drifted version(s).`));return}let X=J.filter((V)=>JZ0(V.state));if(X.length===0){console.log(W.green(`
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Nothing to dispatch.`));return}let G=Q?` (scoped to ${Q})`:"",H=await P0(`Dispatch generate-manifest for ${X.length} version(s)${G}? Each dispatch queues a runner job on nemarDatasets/.github.`,D);if(H!=="confirmed"){console.log(W.dim(H==="declined"?"Skipped":"Cancelled"));return}let q=0,K=0;console.log();for(let[V,z]of X.entries()){let Z=`${z.dataset_id}@${z.version}`,U=O(`[${V+1}/${X.length}] dispatching ${Z}...`).start();try{await ag(z.dataset_id,z.version),U.succeed(`[${V+1}/${X.length}] dispatched ${Z}`),q++}catch(M){U.fail(`[${V+1}/${X.length}] ${Z}: ${L0(M)}`),K++}if(V<X.length-1)await new Promise((M)=>setTimeout(M,FZ0))}if(console.log(),console.log(K===0?W.green(`All ${q} dispatches succeeded.`):W.yellow(`${q} succeeded, ${K} failed.`)),console.log(W.dim("Workflow runs will appear on https://github.com/nemarDatasets/.github/actions. Re-run `nemar admin summary check` once they complete to verify drift cleared.")),K>0)process.exitCode=1});function ph(D){return{versions:D.length,ok:D.filter((F)=>F.state.kind==="ok").length,stale:D.filter((F)=>F.state.kind==="stale").length,missing:D.filter((F)=>F.state.kind==="missing").length,error:D.filter((F)=>F.state.kind==="error").length}}b0.addCommand(ah);ND();k6();c3();n8();x4();r8();var oh={git:{name:"git",purpose:"version control for dataset metadata",cmd:["git","--version"],required:!0,installInstructions:{macos:"brew install git (or install Xcode Command Line Tools)",linux:"sudo apt-get install git OR sudo dnf install git",windows:"winget install Git.Git (or https://git-scm.com/download/win)"}},"git-annex":{name:"git-annex",purpose:"large-file data transfer (upload/download)",cmd:["git-annex","version"],required:!0,installInstructions:{macos:"brew install git-annex",linux:"sudo apt-get install git-annex OR sudo dnf install git-annex",windows:"Download the installer from https://git-annex.branchable.com/install/Windows/"}},gh:{name:"GitHub CLI (gh)",purpose:"GitHub authentication + repository operations",cmd:["gh","--version"],required:!0,installInstructions:{macos:"brew install gh",linux:"See https://cli.github.com/manual/installation",windows:"winget install GitHub.cli (or: scoop install gh)"}},aws:{name:"AWS CLI",purpose:"S3 data upload/download",cmd:["aws","--version"],required:!0,installInstructions:{macos:"brew install awscli",linux:"pip install awscli OR sudo snap install aws-cli --classic",windows:"winget install Amazon.AWSCLI (or the MSI from https://aws.amazon.com/cli/)"}},deno:{name:"Deno",purpose:"BIDS validation",cmd:["deno","--version"],required:!0,installInstructions:{macos:"brew install deno (or: curl -fsSL https://deno.land/install.sh | sh)",linux:"curl -fsSL https://deno.land/install.sh | sh",windows:"winget install DenoLand.Deno (or: irm https://deno.land/install.ps1 | iex)"}}},YZ0={upload:["git-annex","gh","aws","deno"],download:["gh"],clone:["git","gh"],push:["git-annex","gh"],publish:["gh","aws"],update:["git","gh"],release:["git","gh"]};function BZ0(){if(process.platform==="darwin")return"macos";if(process.platform==="win32")return"windows";return"linux"}function sh(D,F=BZ0()){return D.installInstructions[F]}function XZ0(D){let F=D.match(/(\d+\.\d+(?:\.\d+)?)/);return F?F[1]:void 0}async function rh(D){try{let{exitCode:F,stdout:$}=await T(D.cmd);if(F!==0)return{available:!1};return{available:!0,version:XZ0($)}}catch(F){let $=F instanceof Error?F.message:String(F);if(!$.includes("ENOENT")&&!$.includes("not found"))console.error(` Warning: ${D.name} check failed unexpectedly: ${$}`);return{available:!1}}}async function _H(){let D=Object.entries(oh);return Promise.all(D.map(async([F,$])=>{let{available:J,version:Q}=await rh($);return{key:F,name:$.name,purpose:$.purpose,required:$.required,available:J,version:Q,installInstruction:sh($)}}))}async function th(){let F=(await _H()).filter(($)=>$.required&&!$.available);if(F.length===0)return[];console.warn(`
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Heads up: some tools NEMAR needs for uploading/validating aren't installed yet:`);for(let $ of F)console.warn(` - ${$.name} (${$.purpose})`),console.warn(` Install: ${$.installInstruction}`);return console.warn("Run `nemar doctor` anytime to re-check. You can finish signup without them.\n"),F}async function u4(D){let $=YZ0[D].map((B)=>oh[B]).filter(Boolean),Q=(await Promise.all($.map(async(B)=>({check:B,available:(await rh(B)).available})))).filter((B)=>!B.available&&B.check.required).map((B)=>({tool:B.check.name,installInstruction:sh(B.check)}));if(Q.length===0)return;let Y=[`
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package/package.json
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