nemar-cli 0.4.0-PR131.f256ebc → 0.4.0-PR131.f8c1d25

package/dist/index.js

@@ -302,7 +302,7 @@ GitHub: ${W.cyan(Q.github_url)}`),console.log(`S3: ${W.cyan(Q.s3_url)}`)}catch(Q
 ${Q.message}`)),Q.details)console.error(W.gray(JSON.stringify(Q.details,null,2)));if(Q.statusCode===403)console.log(W.gray("  You must be the dataset owner or an admin to publish"));else if(Q.statusCode===400&&Q.message.includes("sandbox"))console.log(W.gray("  Sandbox datasets cannot be published"))}else console.error(W.red(`
 ${Q instanceof Error?Q.message:String(Q)}`));process.exit(1)}});A0.command("delete-dataset").description("Delete a dataset and all associated resources (GitHub, S3, D1)").argument("<dataset-id>","Dataset ID (e.g., nm000108)").option("--force","Force deletion of published datasets with DOIs (owner only)").action(async(D,F)=>{if(!jD())console.log(W.red("Not authenticated. Run: nemar auth login")),process.exit(1);let $=R("Looking up dataset...").start();try{let B=await N1(D);if($.stop(),console.log(W.bold(`
 Dataset: ${B.dataset_id}`)),console.log(`  Name: ${B.name||"(unnamed)"}`),console.log(`  Visibility: ${B.visibility}`),B.concept_doi)console.log(`  DOI: ${B.concept_doi}`);if(B.concept_doi){if(console.log(W.yellow(`
-  WARNING: This dataset has a DOI. Only the NEMAR owner can delete it.`)),!F.force)console.log(W.gray("  Use --force to confirm deletion of published datasets.")),process.exit(1)}let{proceed:J}=await ID.prompt([{type:"confirm",name:"proceed",message:W.red(`Delete dataset ${D}? This will remove the GitHub repo, S3 data, and all database records. This cannot be undone.`),default:!1}]);if(!J){console.log(W.gray("Cancelled."));return}$.start("Deleting dataset...");let Q=await tv(D,F.force??!1);if(Q.warnings.length>0)$.warn("Dataset deleted with warnings");else $.succeed("Dataset deleted");if(console.log(W.bold(`
+  WARNING: This dataset has a DOI. Only the NEMAR owner can delete it.`)),!F.force)console.log(W.gray("  Use --force to confirm deletion of published datasets.")),process.exit(1)}let{proceed:J}=await ID.prompt([{type:"confirm",name:"proceed",message:W.red(`Delete dataset ${D}? This will remove the GitHub repo, S3 data, and all database records. This cannot be undone.`),default:!1}]);if(!J){console.log(W.gray("Cancelled."));return}$.start("Deleting dataset...");let Q=await tv(D,F.force??!1);if($.succeed("Dataset deleted"),console.log(W.bold(`
 Deletion summary:`)),console.log(`  GitHub repo: ${Q.steps.github.success?W.green("deleted"):W.red("failed")}`),Q.steps.s3.skipped)console.log(`  S3 objects: ${W.yellow("skipped (published dataset)")}`);else console.log(`  S3 objects: ${W.green(`${Q.steps.s3.deleted} deleted`)}${Q.steps.s3.failed.length>0?W.red(`, ${Q.steps.s3.failed.length} failed`):""}`);if(console.log(`  Database: ${Q.steps.d1.success?W.green("cleaned up"):W.red("failed")}`),Q.steps.d1.versionsDeleted>0)console.log(W.gray(`    ${Q.steps.d1.versionsDeleted} version records removed`));if(Q.steps.d1.pubRequestsDeleted>0)console.log(W.gray(`    ${Q.steps.d1.pubRequestsDeleted} publication requests removed`));if(Q.warnings.length>0){console.log(W.yellow(`
 Warnings:`));for(let X of Q.warnings)console.log(W.yellow(`  - ${X}`))}}catch(B){f0(B,$,"Failed to delete dataset",{403:"Published datasets can only be deleted by the NEMAR owner",404:"Dataset not found",409:"Cannot delete dataset with active publication requests"}),process.exit(1)}});import{appendFileSync as vGD,existsSync as H6,mkdirSync as Ry,readFileSync as h$,writeFileSync as yGD}from"fs";import{homedir as xGD}from"os";import{join as g$}from"path";var{spawn:wy}=globalThis.Bun;function a6(){let D=g$(xGD(),".ssh");return{sshDir:D,privateKey:g$(D,"nemar_ed25519"),publicKey:g$(D,"nemar_ed25519.pub"),configFile:g$(D,"config")}}function Ty(){let D=a6();return H6(D.privateKey)&&H6(D.publicKey)}async function jy(D){let F=a6();if(!H6(F.sshDir))try{Ry(F.sshDir,{mode:448})}catch($){return{success:!1,error:`Cannot create ~/.ssh directory: ${$.message}`}}if(H6(F.privateKey))try{return{success:!0,publicKey:h$(F.publicKey,"utf-8").trim()}}catch($){return{success:!1,error:`NEMAR SSH key exists but cannot read public key: ${$.message}`}}try{let $=wy({cmd:["ssh-keygen","-t","ed25519","-f",F.privateKey,"-N","","-C",`nemar-cli-${D}`],stdout:"pipe",stderr:"pipe"}),B=await new Response($.stderr).text();if(await $.exited!==0)return{success:!1,error:`ssh-keygen failed: ${B}`};return{success:!0,publicKey:h$(F.publicKey,"utf-8").trim()}}catch($){return{success:!1,error:`Failed to generate SSH key: ${$.message}`}}}function Oy(){let D=a6();if(!H6(D.publicKey))return null;try{return h$(D.publicKey,"utf-8").trim()}catch{return null}}function _GD(){let D=a6();if(!H6(D.configFile))return!1;try{let F=h$(D.configFile,"utf-8");return F.includes("IdentityFile ~/.ssh/nemar_ed25519")||F.includes(`IdentityFile ${D.privateKey}`)}catch{return!1}}function Iy(){let D=a6();if(!H6(D.sshDir))try{Ry(D.sshDir,{mode:448})}catch($){return{success:!1,error:`Cannot create ~/.ssh directory: ${$.message}`}}if(_GD())return{success:!0};let F=`
 # NEMAR CLI SSH key (auto-generated)
@@ -649,7 +649,7 @@ Examples:
   $ nemar sandbox           # Run sandbox training
   $ nemar sandbox status    # Check if training is completed
   $ nemar sandbox reset     # Reset for re-training
-`).action(tGD);async function tGD(){if(console.log(),console.log(W.bold("NEMAR Sandbox Training")),console.log(W.gray("Verify your setup and learn the upload workflow")),console.log(),!jD()){console.log(W.red("Not authenticated")),console.log(W.gray("Run 'nemar auth login' first"));return}let D=F0();if(D.sandboxCompleted){console.log(W.green("Sandbox training already completed!")),console.log(W.gray(`Dataset ID: ${D.sandboxDatasetId}`)),console.log(),console.log("You can upload real datasets with:"),console.log(W.cyan("  nemar dataset upload ./your-dataset")),console.log(),console.log(W.gray("To re-run training, use: nemar sandbox reset"));return}console.log(W.bold("Step 1/6: Checking prerequisites..."));let F=R("Checking git-annex and SSH...").start(),$=await I$();if(!$.allPassed){F.fail("Prerequisites check failed"),console.log(),console.log(W.red("Missing requirements:"));for(let P of $.errors)console.log(W.yellow(`  - ${P}`));if(!$.githubSSH.accessible)console.log(W.gray("    Run 'nemar auth setup-ssh' to configure SSH"));return}F.succeed("All prerequisites met");let B=R("Verifying GitHub CLI authentication...").start(),J=await k$(D.githubUsername);if(!J.authenticated){B.fail("GitHub CLI not authenticated"),console.log(W.red(`  ${J.error}`)),console.log(),console.log("GitHub CLI is required for sandbox training. Install and authenticate:"),console.log(W.cyan("  brew install gh       # or visit https://cli.github.com/")),console.log(W.cyan("  gh auth login"));return}if(D.githubUsername&&!J.matches)B.warn("GitHub CLI user mismatch"),console.log(W.yellow(`  ${J.error}`)),console.log(),console.log("Your gh CLI is authenticated as a different GitHub account than your NEMAR account."),console.log("This may cause issues with repository access. To fix:"),console.log(W.cyan(`  gh auth login    # Login as ${D.githubUsername}`)),console.log(),console.log(W.yellow("WARNING: If upload fails with permission errors, this mismatch is the likely cause.")),console.log();else B.succeed(`GitHub CLI authenticated as ${J.username}`);console.log(),console.log(W.bold("Step 2/6: Generating test dataset..."));let Q=R("Creating minimal BIDS structure...").start(),X;try{let P=ly();X=P.root;let QD=dy(P);Q.succeed(`Test dataset created (${PF(QD)})`),console.log(W.gray(`  Location: ${X}`))}catch(P){Q.fail("Failed to generate test dataset"),console.log(W.red(`  ${P instanceof Error?P.message:"Unknown error"}`));return}console.log(),console.log(W.bold("Step 3/6: Registering sandbox dataset..."));let Y=R("Creating dataset on NEMAR...").start(),G,H,E,K,V,A;try{let P=await j$({name:"Sandbox Training Dataset",description:"Placeholder dataset for sandbox training",files:[{path:"sub-01/eeg/sub-01_task-rest_eeg.edf",size:512000,type:"data"},{path:"dataset_description.json",size:200,type:"metadata"},{path:"participants.tsv",size:50,type:"metadata"},{path:"README",size:500,type:"metadata"},{path:"sub-01/eeg/sub-01_task-rest_eeg.json",size:300,type:"metadata"}],sandbox:!0});G=P.dataset.dataset_id,H=P.dataset.ssh_url,E=P.dataset.github_url,K=P.s3_config,V=P.dataset.s3_prefix,A=P.upload_urls||{},Y.succeed(`Sandbox dataset created: ${W.cyan(G)}`),console.log(W.gray(`  GitHub: ${E}`)),await new Promise((QD)=>setTimeout(QD,1e4))}catch(P){if(Y.fail("Failed to create sandbox dataset"),P instanceof c)console.log(W.red(`  ${P.message}`));else console.log(W.red(`  ${P instanceof Error?P.message:"Unknown error"}`));C1(X);return}let Z=R("Accepting GitHub repository invitation...").start(),U=E?.match(/github\.com\/([a-zA-Z0-9_.-]+\/[a-zA-Z0-9_.-]+)/),L=U?U[1].replace(/\.git$/,""):null;if(!L){Z.fail("Invalid GitHub repository URL from backend"),console.log(W.red(`  Received: ${E||"(empty)"}`)),console.log(W.red("  Expected format: https://github.com/owner/repo")),console.log(),console.log("This may indicate a backend issue. Please contact support."),C1(X);return}let M=await v$(L);if(M.accepted)if(M.alreadyCollaborator)Z.succeed("Already a collaborator on this repository");else Z.succeed("GitHub invitation accepted");else Z.warn("Could not auto-accept invitation"),console.log(W.yellow(`  ${M.error}`)),console.log(),console.log("You may need to accept the invitation manually:"),console.log(W.cyan(`  https://github.com/${L}/invitations`)),console.log();console.log(),console.log(W.bold("Step 4/6: Initializing repository..."));let N=R("Setting up git-annex...").start(),O=D.username&&D.email?{name:D.username,email:D.email}:void 0;try{await P$(X,{author:O}),await S$(X),await y$(X,H),N.succeed("Repository initialized")}catch(P){N.fail("Failed to initialize repository"),console.log(W.red(`  ${P instanceof Error?P.message:"Unknown error"}`)),C1(X);return}if(console.log(),console.log(W.bold("Step 5/6: Uploading to S3...")),Object.keys(A).length===0)console.log(W.yellow("  No data files to upload (metadata only)"));else{let P=R("Uploading test data...").start();try{let fD=0,$0=Object.keys(A).length,v=await x$(X,A,{jobs:4,onProgress:(qD)=>{if(qD.status==="completed"||qD.status==="failed")fD++,P.text=`Uploading... ${fD}/${$0} files`}});if(v.failed.length>0){P.fail(`Upload failed for ${v.failed.length} file(s)`);for(let qD of v.failed)console.log(W.red(`    Failed: ${qD}`));if(v.error)console.log(W.red(`    Error: ${v.error}`));console.log(),console.log(W.yellow("Sandbox training aborted due to upload failures.")),console.log(W.gray("Please check your network connection and try again.")),C1(X);return}P.succeed(`Uploaded ${v.uploaded} file(s)`)}catch(fD){P.fail("Upload failed"),console.log(W.red(`  ${fD instanceof Error?fD.message:"Unknown error"}`)),C1(X);return}let QD=R("Registering file URLs...").start();try{let fD={};for(let v of Object.keys(A))fD[v]=`${K.public_url}/${V}/objects/${v}`;let $0=await _$(X,fD);if(!$0.success){QD.fail(`URL registration failed for ${$0.failed.length} file(s)`);for(let v of $0.failed)console.log(W.red(`    Failed: ${v}`));console.log(),console.log(W.yellow("Sandbox training aborted due to URL registration failures.")),console.log(W.gray("This may indicate a git-annex configuration issue.")),C1(X);return}QD.succeed(`Registered ${$0.registered} file URLs`)}catch(fD){QD.fail("Failed to register URLs"),console.log(W.red(`  ${fD instanceof Error?fD.message:"Unknown error"}`)),C1(X);return}}console.log(),console.log(W.bold("Step 6/6: Pushing to GitHub..."));let b=R("Saving and pushing...").start();try{await M5(X,"Initial sandbox training upload",O),await N5(X),b.succeed("Pushed to GitHub")}catch(P){b.fail("Failed to push to GitHub"),console.log(W.red(`  ${P instanceof Error?P.message:"Unknown error"}`)),C1(X);return}let T=R("Finalizing...").start();try{await O$(G),await uv(G),V0("sandboxCompleted",!0),V0("sandboxDatasetId",G),T.succeed("Sandbox training complete!")}catch(P){T.fail("Failed to finalize"),console.log(W.red(`  ${P instanceof Error?P.message:"Unknown error"}`)),C1(X);return}C1(X),console.log(),console.log(W.green.bold("Congratulations! Sandbox training completed successfully.")),console.log(),console.log("Your setup is verified and you're ready to upload real datasets:"),console.log(W.cyan("  nemar dataset upload ./your-dataset")),console.log(),console.log(W.gray(`Sandbox dataset: ${G}`))}p$.command("status").description("Check sandbox training completion status").option("--refresh","Fetch latest status from server").action(async(D)=>{if(!jD()){console.log(W.red("Not authenticated")),console.log(W.gray("Run 'nemar auth login' first"));return}if(D.refresh){let F=R("Checking status...").start();try{let $=await lv();if(V0("sandboxCompleted",$.sandbox_completed),$.sandbox_dataset_id)V0("sandboxDatasetId",$.sandbox_dataset_id);if(F.stop(),$.sandbox_completed){if(console.log(W.green("Sandbox training: Completed")),console.log(W.gray(`  Dataset ID: ${$.sandbox_dataset_id}`)),$.sandbox_completed_at)console.log(W.gray(`  Completed: ${$.sandbox_completed_at}`))}else console.log(W.yellow("Sandbox training: Not completed")),console.log(),console.log("Run sandbox training with:"),console.log(W.cyan("  nemar sandbox"))}catch($){if(F.fail("Failed to check status"),$ instanceof c)console.log(W.red(`  ${$.message}`))}}else{let F=F0();if(F.sandboxCompleted)console.log(W.green("Sandbox training: Completed")),console.log(W.gray(`  Dataset ID: ${F.sandboxDatasetId}`));else console.log(W.yellow("Sandbox training: Not completed")),console.log(),console.log("Run sandbox training with:"),console.log(W.cyan("  nemar sandbox"))}});p$.command("reset").description("Reset sandbox training status for re-training").option(yD,xD).option(hD,bD).action(async(D)=>{if(!jD()){console.log(W.red("Not authenticated")),console.log(W.gray("Run 'nemar auth login' first"));return}if(!F0().sandboxCompleted){console.log(W.yellow("Sandbox training not yet completed")),console.log(W.gray("Nothing to reset"));return}let $=await gD("Reset sandbox training status? You will need to complete training again.",D);if($!=="confirmed"){console.log(W.gray($==="declined"?"Skipped":"Cancelled"));return}let B=R("Resetting sandbox status...").start();try{await mv(),T2("sandboxCompleted"),T2("sandboxDatasetId"),B.succeed("Sandbox status reset"),console.log(),console.log("Run sandbox training again with:"),console.log(W.cyan("  nemar sandbox"))}catch(J){if(B.fail("Failed to reset"),J instanceof c)console.log(W.red(`  ${J.message}`));else console.log(W.red(`  ${J instanceof Error?J.message:"Unknown error"}`))}});var py={name:"nemar-cli",version:"0.4.0-PR131.f256ebc",description:"CLI for NEMAR (Neuroelectromagnetic Data Archive and Tools Resource) dataset management",type:"module",main:"dist/index.js",bin:{nemar:"dist/index.js"},scripts:{dev:"bun run src/index.ts",build:"bun build src/index.ts --outdir dist --target bun --minify && sed '1s|#!/usr/bin/env node|#!/usr/bin/env bun|' dist/index.js > dist/index.js.tmp && mv dist/index.js.tmp dist/index.js",test:"bun test",lint:"biome check src/","lint:fix":"biome check --fix src/",format:"biome format --write src/",typecheck:"tsc --noEmit",prepublishOnly:"bun run build","docs:generate":"bun run scripts/generate-docs.ts","docs:serve":"mkdocs serve","docs:build":"mkdocs build"},keywords:["nemar","bids","neuroimaging","eeg","emg","datalad","cli"],author:"NEMAR Team",license:"MIT",repository:{type:"git",url:"git+https://github.com/nemarOrg/nemar-cli.git"},bugs:{url:"https://github.com/nemarOrg/nemar-cli/issues"},homepage:"https://nemar-cli.pages.dev",engines:{bun:">=1.0.0"},files:["dist","README.md","LICENSE"],dependencies:{chalk:"^5.3.0",commander:"^12.1.0",conf:"^13.0.1",inquirer:"^9.2.15",ora:"^8.0.1",zod:"^3.23.8"},devDependencies:{"@biomejs/biome":"1.9.4","@types/bcryptjs":"^3.0.0","@types/bun":"latest","@types/inquirer":"^9.0.7",bcryptjs:"^3.0.3",typescript:"^5.5.4"}};var cy=py.version;var R1=new B0;R1.name("nemar").description(`CLI for NEMAR (Neuroelectromagnetic Data Archive and Tools Resource)
+`).action(tGD);async function tGD(){if(console.log(),console.log(W.bold("NEMAR Sandbox Training")),console.log(W.gray("Verify your setup and learn the upload workflow")),console.log(),!jD()){console.log(W.red("Not authenticated")),console.log(W.gray("Run 'nemar auth login' first"));return}let D=F0();if(D.sandboxCompleted){console.log(W.green("Sandbox training already completed!")),console.log(W.gray(`Dataset ID: ${D.sandboxDatasetId}`)),console.log(),console.log("You can upload real datasets with:"),console.log(W.cyan("  nemar dataset upload ./your-dataset")),console.log(),console.log(W.gray("To re-run training, use: nemar sandbox reset"));return}console.log(W.bold("Step 1/6: Checking prerequisites..."));let F=R("Checking git-annex and SSH...").start(),$=await I$();if(!$.allPassed){F.fail("Prerequisites check failed"),console.log(),console.log(W.red("Missing requirements:"));for(let P of $.errors)console.log(W.yellow(`  - ${P}`));if(!$.githubSSH.accessible)console.log(W.gray("    Run 'nemar auth setup-ssh' to configure SSH"));return}F.succeed("All prerequisites met");let B=R("Verifying GitHub CLI authentication...").start(),J=await k$(D.githubUsername);if(!J.authenticated){B.fail("GitHub CLI not authenticated"),console.log(W.red(`  ${J.error}`)),console.log(),console.log("GitHub CLI is required for sandbox training. Install and authenticate:"),console.log(W.cyan("  brew install gh       # or visit https://cli.github.com/")),console.log(W.cyan("  gh auth login"));return}if(D.githubUsername&&!J.matches)B.warn("GitHub CLI user mismatch"),console.log(W.yellow(`  ${J.error}`)),console.log(),console.log("Your gh CLI is authenticated as a different GitHub account than your NEMAR account."),console.log("This may cause issues with repository access. To fix:"),console.log(W.cyan(`  gh auth login    # Login as ${D.githubUsername}`)),console.log(),console.log(W.yellow("WARNING: If upload fails with permission errors, this mismatch is the likely cause.")),console.log();else B.succeed(`GitHub CLI authenticated as ${J.username}`);console.log(),console.log(W.bold("Step 2/6: Generating test dataset..."));let Q=R("Creating minimal BIDS structure...").start(),X;try{let P=ly();X=P.root;let QD=dy(P);Q.succeed(`Test dataset created (${PF(QD)})`),console.log(W.gray(`  Location: ${X}`))}catch(P){Q.fail("Failed to generate test dataset"),console.log(W.red(`  ${P instanceof Error?P.message:"Unknown error"}`));return}console.log(),console.log(W.bold("Step 3/6: Registering sandbox dataset..."));let Y=R("Creating dataset on NEMAR...").start(),G,H,E,K,V,A;try{let P=await j$({name:"Sandbox Training Dataset",description:"Placeholder dataset for sandbox training",files:[{path:"sub-01/eeg/sub-01_task-rest_eeg.edf",size:512000,type:"data"},{path:"dataset_description.json",size:200,type:"metadata"},{path:"participants.tsv",size:50,type:"metadata"},{path:"README",size:500,type:"metadata"},{path:"sub-01/eeg/sub-01_task-rest_eeg.json",size:300,type:"metadata"}],sandbox:!0});G=P.dataset.dataset_id,H=P.dataset.ssh_url,E=P.dataset.github_url,K=P.s3_config,V=P.dataset.s3_prefix,A=P.upload_urls||{},Y.succeed(`Sandbox dataset created: ${W.cyan(G)}`),console.log(W.gray(`  GitHub: ${E}`)),await new Promise((QD)=>setTimeout(QD,1e4))}catch(P){if(Y.fail("Failed to create sandbox dataset"),P instanceof c)console.log(W.red(`  ${P.message}`));else console.log(W.red(`  ${P instanceof Error?P.message:"Unknown error"}`));C1(X);return}let Z=R("Accepting GitHub repository invitation...").start(),U=E?.match(/github\.com\/([a-zA-Z0-9_.-]+\/[a-zA-Z0-9_.-]+)/),L=U?U[1].replace(/\.git$/,""):null;if(!L){Z.fail("Invalid GitHub repository URL from backend"),console.log(W.red(`  Received: ${E||"(empty)"}`)),console.log(W.red("  Expected format: https://github.com/owner/repo")),console.log(),console.log("This may indicate a backend issue. Please contact support."),C1(X);return}let M=await v$(L);if(M.accepted)if(M.alreadyCollaborator)Z.succeed("Already a collaborator on this repository");else Z.succeed("GitHub invitation accepted");else Z.warn("Could not auto-accept invitation"),console.log(W.yellow(`  ${M.error}`)),console.log(),console.log("You may need to accept the invitation manually:"),console.log(W.cyan(`  https://github.com/${L}/invitations`)),console.log();console.log(),console.log(W.bold("Step 4/6: Initializing repository..."));let N=R("Setting up git-annex...").start(),O=D.username&&D.email?{name:D.username,email:D.email}:void 0;try{await P$(X,{author:O}),await S$(X),await y$(X,H),N.succeed("Repository initialized")}catch(P){N.fail("Failed to initialize repository"),console.log(W.red(`  ${P instanceof Error?P.message:"Unknown error"}`)),C1(X);return}if(console.log(),console.log(W.bold("Step 5/6: Uploading to S3...")),Object.keys(A).length===0)console.log(W.yellow("  No data files to upload (metadata only)"));else{let P=R("Uploading test data...").start();try{let fD=0,$0=Object.keys(A).length,v=await x$(X,A,{jobs:4,onProgress:(qD)=>{if(qD.status==="completed"||qD.status==="failed")fD++,P.text=`Uploading... ${fD}/${$0} files`}});if(v.failed.length>0){P.fail(`Upload failed for ${v.failed.length} file(s)`);for(let qD of v.failed)console.log(W.red(`    Failed: ${qD}`));if(v.error)console.log(W.red(`    Error: ${v.error}`));console.log(),console.log(W.yellow("Sandbox training aborted due to upload failures.")),console.log(W.gray("Please check your network connection and try again.")),C1(X);return}P.succeed(`Uploaded ${v.uploaded} file(s)`)}catch(fD){P.fail("Upload failed"),console.log(W.red(`  ${fD instanceof Error?fD.message:"Unknown error"}`)),C1(X);return}let QD=R("Registering file URLs...").start();try{let fD={};for(let v of Object.keys(A))fD[v]=`${K.public_url}/${V}/objects/${v}`;let $0=await _$(X,fD);if(!$0.success){QD.fail(`URL registration failed for ${$0.failed.length} file(s)`);for(let v of $0.failed)console.log(W.red(`    Failed: ${v}`));console.log(),console.log(W.yellow("Sandbox training aborted due to URL registration failures.")),console.log(W.gray("This may indicate a git-annex configuration issue.")),C1(X);return}QD.succeed(`Registered ${$0.registered} file URLs`)}catch(fD){QD.fail("Failed to register URLs"),console.log(W.red(`  ${fD instanceof Error?fD.message:"Unknown error"}`)),C1(X);return}}console.log(),console.log(W.bold("Step 6/6: Pushing to GitHub..."));let b=R("Saving and pushing...").start();try{await M5(X,"Initial sandbox training upload",O),await N5(X),b.succeed("Pushed to GitHub")}catch(P){b.fail("Failed to push to GitHub"),console.log(W.red(`  ${P instanceof Error?P.message:"Unknown error"}`)),C1(X);return}let T=R("Finalizing...").start();try{await O$(G),await uv(G),V0("sandboxCompleted",!0),V0("sandboxDatasetId",G),T.succeed("Sandbox training complete!")}catch(P){T.fail("Failed to finalize"),console.log(W.red(`  ${P instanceof Error?P.message:"Unknown error"}`)),C1(X);return}C1(X),console.log(),console.log(W.green.bold("Congratulations! Sandbox training completed successfully.")),console.log(),console.log("Your setup is verified and you're ready to upload real datasets:"),console.log(W.cyan("  nemar dataset upload ./your-dataset")),console.log(),console.log(W.gray(`Sandbox dataset: ${G}`))}p$.command("status").description("Check sandbox training completion status").option("--refresh","Fetch latest status from server").action(async(D)=>{if(!jD()){console.log(W.red("Not authenticated")),console.log(W.gray("Run 'nemar auth login' first"));return}if(D.refresh){let F=R("Checking status...").start();try{let $=await lv();if(V0("sandboxCompleted",$.sandbox_completed),$.sandbox_dataset_id)V0("sandboxDatasetId",$.sandbox_dataset_id);if(F.stop(),$.sandbox_completed){if(console.log(W.green("Sandbox training: Completed")),console.log(W.gray(`  Dataset ID: ${$.sandbox_dataset_id}`)),$.sandbox_completed_at)console.log(W.gray(`  Completed: ${$.sandbox_completed_at}`))}else console.log(W.yellow("Sandbox training: Not completed")),console.log(),console.log("Run sandbox training with:"),console.log(W.cyan("  nemar sandbox"))}catch($){if(F.fail("Failed to check status"),$ instanceof c)console.log(W.red(`  ${$.message}`))}}else{let F=F0();if(F.sandboxCompleted)console.log(W.green("Sandbox training: Completed")),console.log(W.gray(`  Dataset ID: ${F.sandboxDatasetId}`));else console.log(W.yellow("Sandbox training: Not completed")),console.log(),console.log("Run sandbox training with:"),console.log(W.cyan("  nemar sandbox"))}});p$.command("reset").description("Reset sandbox training status for re-training").option(yD,xD).option(hD,bD).action(async(D)=>{if(!jD()){console.log(W.red("Not authenticated")),console.log(W.gray("Run 'nemar auth login' first"));return}if(!F0().sandboxCompleted){console.log(W.yellow("Sandbox training not yet completed")),console.log(W.gray("Nothing to reset"));return}let $=await gD("Reset sandbox training status? You will need to complete training again.",D);if($!=="confirmed"){console.log(W.gray($==="declined"?"Skipped":"Cancelled"));return}let B=R("Resetting sandbox status...").start();try{await mv(),T2("sandboxCompleted"),T2("sandboxDatasetId"),B.succeed("Sandbox status reset"),console.log(),console.log("Run sandbox training again with:"),console.log(W.cyan("  nemar sandbox"))}catch(J){if(B.fail("Failed to reset"),J instanceof c)console.log(W.red(`  ${J.message}`));else console.log(W.red(`  ${J instanceof Error?J.message:"Unknown error"}`))}});var py={name:"nemar-cli",version:"0.4.0-PR131.f8c1d25",description:"CLI for NEMAR (Neuroelectromagnetic Data Archive and Tools Resource) dataset management",type:"module",main:"dist/index.js",bin:{nemar:"dist/index.js"},scripts:{dev:"bun run src/index.ts",build:"bun build src/index.ts --outdir dist --target bun --minify && sed '1s|#!/usr/bin/env node|#!/usr/bin/env bun|' dist/index.js > dist/index.js.tmp && mv dist/index.js.tmp dist/index.js",test:"bun test",lint:"biome check src/","lint:fix":"biome check --fix src/",format:"biome format --write src/",typecheck:"tsc --noEmit",prepublishOnly:"bun run build","docs:generate":"bun run scripts/generate-docs.ts","docs:serve":"mkdocs serve","docs:build":"mkdocs build"},keywords:["nemar","bids","neuroimaging","eeg","emg","datalad","cli"],author:"NEMAR Team",license:"MIT",repository:{type:"git",url:"git+https://github.com/nemarOrg/nemar-cli.git"},bugs:{url:"https://github.com/nemarOrg/nemar-cli/issues"},homepage:"https://nemar-cli.pages.dev",engines:{bun:">=1.0.0"},files:["dist","README.md","LICENSE"],dependencies:{chalk:"^5.3.0",commander:"^12.1.0",conf:"^13.0.1",inquirer:"^9.2.15",ora:"^8.0.1",zod:"^3.23.8"},devDependencies:{"@biomejs/biome":"1.9.4","@types/bcryptjs":"^3.0.0","@types/bun":"latest","@types/inquirer":"^9.0.7",bcryptjs:"^3.0.3",typescript:"^5.5.4"}};var cy=py.version;var R1=new B0;R1.name("nemar").description(`CLI for NEMAR (Neuroelectromagnetic Data Archive and Tools Resource)
 
 NEMAR is a curated repository for neurophysiology data in BIDS format.
 This CLI provides tools for uploading, downloading, and managing datasets.`).version(cy,"-v, --version","Output the current version").option("--no-color","Disable colored output").option("--verbose","Enable verbose output").addHelpText("after",`

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "nemar-cli",
-  "version": "0.4.0-PR131.f256ebc",
+  "version": "0.4.0-PR131.f8c1d25",
   "description": "CLI for NEMAR (Neuroelectromagnetic Data Archive and Tools Resource) dataset management",
   "type": "module",
   "main": "dist/index.js",