nemar-cli 0.5.1-dev.255 → 0.5.1-dev.256

package/dist/index.js

@@ -400,7 +400,7 @@ Description:
 
 Examples:
   $ nemar auth regenerate-key`).action(async()=>{console.log(W.yellow("API Key Regeneration")),console.log(W.gray(`This will revoke your current key and generate a new one
-`));let{email:D}=await MD.prompt([{type:"input",name:"email",message:"Email address associated with your account:",validate:($)=>{if(!$||!/^[^\s@]+@[^\s@]+\.[^\s@]+$/.test($))return"Please enter a valid email address";return!0}}]),F=C("Sending verification email...").start();try{let $=await uv(D);F.succeed("Verification email sent"),console.log(),console.log("Next steps:"),console.log("  1. Check your email for a verification link"),console.log("  2. Click the link to generate your new API key"),console.log("  3. Copy the new key and run 'nemar auth login'"),console.log(),console.log(W.gray("The link expires in 1 hour"))}catch($){if($ instanceof u)F.fail($.message);else F.fail("Failed to send verification email"),console.log(W.gray("  Check your internet connection"))}});import{existsSync as c0,mkdtempSync as HHD,readFileSync as x5,writeFileSync as FB}from"fs";import{tmpdir as WHD}from"os";import{basename as qHD,join as y5,resolve as Y1}from"path";var{spawn:mD}=globalThis.Bun;import{existsSync as eGD,statSync as DHD}from"fs";import{homedir as s2}from"os";import{join as P5}from"path";var{spawn:k5}=globalThis.Bun;var S5="jsr:@bids/validator",FHD=604800000;async function v5(){try{let D=k5({cmd:["deno","--version"],stdout:"pipe",stderr:"pipe"}),F=await new Response(D.stdout).text();await D.exited;let $=F.match(/deno\s+(\d+\.\d+\.\d+)/);return{installed:!0,version:$?$[1]:void 0}}catch{return{installed:!1}}}function r2(){try{let D=process.platform,F=process.env.DENO_DIR||(D==="darwin"?P5(s2(),"Library","Caches","deno"):D==="win32"?P5(process.env.LOCALAPPDATA||P5(s2(),"AppData","Local"),"deno"):P5(s2(),".cache","deno")),$=P5(F,"deps");if(!eGD($))return!0;let B=DHD($);return Date.now()-B.mtimeMs>FHD}catch{return!0}}async function t2(){try{let D=k5({cmd:["deno","run",`--reload=${S5}`,"-ERWN",S5,"--version"],stdout:"pipe",stderr:"pipe"}),F=await new Response(D.stdout).text();await D.exited;let $=F.match(/(\d+\.\d+\.\d+)/);return $?$[1]:null}catch{return null}}async function e2(){try{let D=k5({cmd:["deno","run","-ERWN",S5,"--version"],stdout:"pipe",stderr:"pipe"}),F=await new Response(D.stdout).text();await D.exited;let $=F.match(/(\d+\.\d+\.\d+)/);return $?$[1]:null}catch{return null}}function iy(D,F={}){let $=["run"];if(F.forceReload)$.push(`--reload=${S5}`);if($.push("-ERWN",S5,D),F.json)$.push("--json");if(F.config)$.push("--config",F.config);if(F.ignoreWarnings)$.push("--ignoreWarnings");if(F.recursive)$.push("--recursive");if(F.prune)$.push("--prune");if(F.verbose)$.push("--verbose");if(F.extraArgs?.length)$.push(...F.extraArgs);return $}async function ay(D,F={}){let $=iy(D,{...F,json:!0}),B=k5({cmd:["deno",...$],stdout:"pipe",stderr:"pipe"}),J=await new Response(B.stdout).text(),Q=await new Response(B.stderr).text(),X=await B.exited;if(X!==0&&!J.trim())throw Error(Q.includes("error:")?Q.split(`
+`));let{email:D}=await MD.prompt([{type:"input",name:"email",message:"Email address associated with your account:",validate:($)=>{if(!$||!/^[^\s@]+@[^\s@]+\.[^\s@]+$/.test($))return"Please enter a valid email address";return!0}}]),F=C("Sending verification email...").start();try{let $=await uv(D);F.succeed("Verification email sent"),console.log(),console.log("Next steps:"),console.log("  1. Check your email for a verification link"),console.log("  2. Click the link to generate your new API key"),console.log("  3. Copy the new key and run 'nemar auth login'"),console.log(),console.log(W.gray("The link expires in 1 hour"))}catch($){if($ instanceof u)F.fail($.message);else F.fail("Failed to send verification email"),console.log(W.gray("  Check your internet connection"))}});import{existsSync as c0,mkdtempSync as HHD,readFileSync as x5,writeFileSync as FB}from"fs";import{tmpdir as WHD}from"os";import{basename as qHD,join as y5,resolve as Y1}from"path";var{spawn:mD}=globalThis.Bun;import{existsSync as eGD,statSync as DHD}from"fs";import{homedir as s2}from"os";import{join as P5}from"path";var{spawn:k5}=globalThis.Bun;var S5="jsr:@bids/validator@^2",FHD=604800000;async function v5(){try{let D=k5({cmd:["deno","--version"],stdout:"pipe",stderr:"pipe"}),F=await new Response(D.stdout).text();await D.exited;let $=F.match(/deno\s+(\d+\.\d+\.\d+)/);return{installed:!0,version:$?$[1]:void 0}}catch{return{installed:!1}}}function r2(){try{let D=process.platform,F=process.env.DENO_DIR||(D==="darwin"?P5(s2(),"Library","Caches","deno"):D==="win32"?P5(process.env.LOCALAPPDATA||P5(s2(),"AppData","Local"),"deno"):P5(s2(),".cache","deno")),$=P5(F,"deps");if(!eGD($))return!0;let B=DHD($);return Date.now()-B.mtimeMs>FHD}catch{return!0}}async function t2(){try{let D=k5({cmd:["deno","run",`--reload=${S5}`,"-ERWN",S5,"--version"],stdout:"pipe",stderr:"pipe"}),F=await new Response(D.stdout).text();await D.exited;let $=F.match(/(\d+\.\d+\.\d+)/);return $?$[1]:null}catch{return null}}async function e2(){try{let D=k5({cmd:["deno","run","-ERWN",S5,"--version"],stdout:"pipe",stderr:"pipe"}),F=await new Response(D.stdout).text();await D.exited;let $=F.match(/(\d+\.\d+\.\d+)/);return $?$[1]:null}catch{return null}}function iy(D,F={}){let $=["run"];if(F.forceReload)$.push(`--reload=${S5}`);if($.push("-ERWN",S5,D),F.json)$.push("--json");if(F.config)$.push("--config",F.config);if(F.ignoreWarnings)$.push("--ignoreWarnings");if(F.recursive)$.push("--recursive");if(F.prune)$.push("--prune");if(F.verbose)$.push("--verbose");if(F.extraArgs?.length)$.push(...F.extraArgs);return $}async function ay(D,F={}){let $=iy(D,{...F,json:!0}),B=k5({cmd:["deno",...$],stdout:"pipe",stderr:"pipe"}),J=await new Response(B.stdout).text(),Q=await new Response(B.stderr).text(),X=await B.exited;if(X!==0&&!J.trim())throw Error(Q.includes("error:")?Q.split(`
 `).find((K)=>K.includes("error:"))||"Validation failed":`Validation failed with exit code ${X}`);let Y;try{Y=JSON.parse(J)}catch{throw Error(`Failed to parse validator output: ${J.slice(0,200)}`)}let G=Y.issues.issues||[],H=G.filter((K)=>K.severity==="error").length,q=G.filter((K)=>K.severity==="warning").length;return{valid:H===0,issues:G,codeMessages:Y.issues.codeMessages||{},summary:Y.summary,errorCount:H,warningCount:q}}async function oy(D,F={}){let $=iy(D,F),B=k5({cmd:["deno",...$],stdout:"pipe",stderr:"pipe"}),J=await new Response(B.stdout).text(),Q=await new Response(B.stderr).text(),X=await B.exited;return{stdout:J,stderr:Q,exitCode:X}}function sy(D,F=!0){let $=[],B=D.issues.filter((Y)=>Y.severity==="error"),J=D.issues.filter((Y)=>Y.severity==="warning");if(D.valid)$.push(F?"\x1B[32m\u2713 Dataset is valid BIDS\x1B[0m":"\u2713 Dataset is valid BIDS");else $.push(F?"\x1B[31m\u2717 Dataset has validation errors\x1B[0m":"\u2717 Dataset has validation errors");if($.push(""),B.length>0){$.push(F?"\x1B[31mErrors:\x1B[0m":"Errors:");for(let Y of B){let G=F?`\x1B[31m${Y.code}\x1B[0m`:Y.code,H=D.codeMessages[Y.code]?.split(`
 `)[0]||"";if($.push(`  ${G}: ${H}`),$.push(`    ${Y.location}`),Y.issueMessage)$.push(`    ${Y.issueMessage.split(`
 `)[0]}`)}$.push("")}if(J.length>0){$.push(F?"\x1B[33mWarnings:\x1B[0m":"Warnings:");for(let Y of J){let G=F?`\x1B[33m${Y.code}\x1B[0m`:Y.code,H=D.codeMessages[Y.code]?.split(`
@@ -739,7 +739,7 @@ Examples:
   $ nemar sandbox           # Run sandbox training
   $ nemar sandbox status    # Check if training is completed
   $ nemar sandbox reset     # Reset for re-training
-`).action(UHD);async function UHD(){if(console.log(),console.log(W.bold("NEMAR Sandbox Training")),console.log(W.gray("Verify your setup and learn the upload workflow")),console.log(),!vD()){console.log(W.red("Not authenticated")),console.log(W.gray("Run 'nemar auth login' first"));return}let D=Y0();if(D.sandboxCompleted){console.log(W.green("Sandbox training already completed!")),console.log(W.gray(`Dataset ID: ${D.sandboxDatasetId}`)),console.log(),console.log("You can upload real datasets with:"),console.log(W.cyan("  nemar dataset upload ./your-dataset")),console.log(),console.log(W.gray("To re-run training, use: nemar sandbox reset"));return}console.log(W.bold("Step 1/6: Checking prerequisites..."));let F=C("Checking git-annex and SSH...").start(),$=await b$();if(!$.allPassed){F.fail("Prerequisites check failed"),console.log(),console.log(W.red("Missing requirements:"));for(let I of $.errors)console.log(W.yellow(`  - ${I}`));if(!$.githubSSH.accessible)console.log(W.gray("    Run 'nemar auth setup-ssh' to configure SSH"));return}F.succeed("All prerequisites met");let B=C("Verifying GitHub CLI authentication...").start(),J=await l$(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 ${J.username}`);console.log(),console.log(W.bold("Step 2/6: Generating test dataset..."));let Q=C("Creating minimal BIDS structure...").start(),X;try{let I=Bx();X=I.root;let w=Jx(I);Q.succeed(`Test dataset created (${v3(w)})`),console.log(W.gray(`  Location: ${X}`))}catch(I){Q.fail("Failed to generate test dataset"),console.log(W.red(`  ${I instanceof Error?I.message:"Unknown error"}`));return}console.log(),console.log(W.bold("Step 3/6: Registering sandbox dataset..."));let Y=C("Creating dataset on NEMAR...").start(),G,H,q,K,V,Z;try{let I=await g$({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=I.dataset.dataset_id,H=I.dataset.ssh_url,q=I.dataset.github_url,K=I.s3_config,V=I.dataset.s3_prefix,Z=I.upload_urls||{},Y.succeed(`Sandbox dataset created: ${W.cyan(G)}`),console.log(W.gray(`  GitHub: ${q}`)),await new Promise((w)=>setTimeout(w,1e4))}catch(I){if(Y.fail("Failed to create sandbox dataset"),I instanceof u)console.log(W.red(`  ${I.message}`));else console.log(W.red(`  ${I instanceof Error?I.message:"Unknown error"}`));v1(X);return}let A=C("Accepting GitHub repository invitation...").start(),U=q?.match(/github\.com\/([a-zA-Z0-9_.-]+\/[a-zA-Z0-9_.-]+)/),L=U?U[1].replace(/\.git$/,""):null;if(!L){A.fail("Invalid GitHub repository URL from backend"),console.log(W.red(`  Received: ${q||"(empty)"}`)),console.log(W.red("  Expected format: https://github.com/owner/repo")),console.log(),console.log("This may indicate a backend issue. Please contact support."),v1(X);return}let M=await d$(L);if(M.accepted)if(M.alreadyCollaborator)A.succeed("Already a collaborator on this repository");else A.succeed("GitHub invitation accepted");else A.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=C("Setting up git-annex...").start(),O=D.username&&D.email?{name:D.username,email:D.email}:void 0;try{await u$(X,{author:O}),await m$(X),await p$(X,H),N.succeed("Repository initialized")}catch(I){N.fail("Failed to initialize repository"),console.log(W.red(`  ${I instanceof Error?I.message:"Unknown error"}`)),v1(X);return}if(console.log(),console.log(W.bold("Step 5/6: Uploading to S3...")),Object.keys(Z).length===0)console.log(W.yellow("  No data files to upload (metadata only)"));else{let I=C("Uploading test data...").start();try{let c=0,GD=Object.keys(Z).length,S=await c$(X,Z,{jobs:4,onProgress:(JD)=>{if(JD.status==="completed"||JD.status==="failed")c++,I.text=`Uploading... ${c}/${GD} files`}});if(S.failed.length>0){I.fail(`Upload failed for ${S.failed.length} file(s)`);for(let JD of S.failed)console.log(W.red(`    Failed: ${JD}`));if(S.error)console.log(W.red(`    Error: ${S.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.")),v1(X);return}I.succeed(`Uploaded ${S.uploaded} file(s)`)}catch(c){I.fail("Upload failed"),console.log(W.red(`  ${c instanceof Error?c.message:"Unknown error"}`)),v1(X);return}let w=C("Registering file URLs...").start();try{let c={};for(let S of Object.keys(Z))c[S]=`${K.public_url}/${V}/objects/${S}`;let GD=await n$(X,c);if(!GD.success){w.fail(`URL registration failed for ${GD.failed.length} file(s)`);for(let S of GD.failed)console.log(W.red(`    Failed: ${S}`));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.")),v1(X);return}w.succeed(`Registered ${GD.registered} file URLs`)}catch(c){w.fail("Failed to register URLs"),console.log(W.red(`  ${c instanceof Error?c.message:"Unknown error"}`)),v1(X);return}}console.log(),console.log(W.bold("Step 6/6: Pushing to GitHub..."));let g=C("Saving and pushing...").start();try{await j5(X,"Initial sandbox training upload",O),await T5(X),g.succeed("Pushed to GitHub")}catch(I){g.fail("Failed to push to GitHub"),console.log(W.red(`  ${I instanceof Error?I.message:"Unknown error"}`)),v1(X);return}let j=C("Finalizing...").start();try{await h$(G),await Qy(G),R0("sandboxCompleted",!0),R0("sandboxDatasetId",G),j.succeed("Sandbox training complete!")}catch(I){j.fail("Failed to finalize"),console.log(W.red(`  ${I instanceof Error?I.message:"Unknown error"}`)),v1(X);return}v1(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}`))}BB.command("status").description("Check sandbox training completion status").option("--refresh","Fetch latest status from server").action(async(D)=>{if(!vD()){console.log(W.red("Not authenticated")),console.log(W.gray("Run 'nemar auth login' first"));return}if(D.refresh){let F=C("Checking status...").start();try{let $=await Yy();if(R0("sandboxCompleted",$.sandbox_completed),$.sandbox_dataset_id)R0("sandboxDatasetId",$.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 u)console.log(W.red(`  ${$.message}`))}}else{let F=Y0();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"))}});BB.command("reset").description("Reset sandbox training status for re-training").option(yD,xD).option(lD,dD).action(async(D)=>{if(!vD()){console.log(W.red("Not authenticated")),console.log(W.gray("Run 'nemar auth login' first"));return}if(!Y0().sandboxCompleted){console.log(W.yellow("Sandbox training not yet completed")),console.log(W.gray("Nothing to reset"));return}let $=await OD("Reset sandbox training status? You will need to complete training again.",D);if($!=="confirmed"){console.log(W.gray($==="declined"?"Skipped":"Cancelled"));return}let B=C("Resetting sandbox status...").start();try{await Xy(),h2("sandboxCompleted"),h2("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 u)console.log(W.red(`  ${J.message}`));else console.log(W.red(`  ${J instanceof Error?J.message:"Unknown error"}`))}});var Qx={name:"nemar-cli",version:"0.5.1-dev.255",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 Xx=Qx.version;var y1=new H0;y1.name("nemar").description(`CLI for NEMAR (Neuroelectromagnetic Data Archive and Tools Resource)
+`).action(UHD);async function UHD(){if(console.log(),console.log(W.bold("NEMAR Sandbox Training")),console.log(W.gray("Verify your setup and learn the upload workflow")),console.log(),!vD()){console.log(W.red("Not authenticated")),console.log(W.gray("Run 'nemar auth login' first"));return}let D=Y0();if(D.sandboxCompleted){console.log(W.green("Sandbox training already completed!")),console.log(W.gray(`Dataset ID: ${D.sandboxDatasetId}`)),console.log(),console.log("You can upload real datasets with:"),console.log(W.cyan("  nemar dataset upload ./your-dataset")),console.log(),console.log(W.gray("To re-run training, use: nemar sandbox reset"));return}console.log(W.bold("Step 1/6: Checking prerequisites..."));let F=C("Checking git-annex and SSH...").start(),$=await b$();if(!$.allPassed){F.fail("Prerequisites check failed"),console.log(),console.log(W.red("Missing requirements:"));for(let I of $.errors)console.log(W.yellow(`  - ${I}`));if(!$.githubSSH.accessible)console.log(W.gray("    Run 'nemar auth setup-ssh' to configure SSH"));return}F.succeed("All prerequisites met");let B=C("Verifying GitHub CLI authentication...").start(),J=await l$(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 ${J.username}`);console.log(),console.log(W.bold("Step 2/6: Generating test dataset..."));let Q=C("Creating minimal BIDS structure...").start(),X;try{let I=Bx();X=I.root;let w=Jx(I);Q.succeed(`Test dataset created (${v3(w)})`),console.log(W.gray(`  Location: ${X}`))}catch(I){Q.fail("Failed to generate test dataset"),console.log(W.red(`  ${I instanceof Error?I.message:"Unknown error"}`));return}console.log(),console.log(W.bold("Step 3/6: Registering sandbox dataset..."));let Y=C("Creating dataset on NEMAR...").start(),G,H,q,K,V,Z;try{let I=await g$({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=I.dataset.dataset_id,H=I.dataset.ssh_url,q=I.dataset.github_url,K=I.s3_config,V=I.dataset.s3_prefix,Z=I.upload_urls||{},Y.succeed(`Sandbox dataset created: ${W.cyan(G)}`),console.log(W.gray(`  GitHub: ${q}`)),await new Promise((w)=>setTimeout(w,1e4))}catch(I){if(Y.fail("Failed to create sandbox dataset"),I instanceof u)console.log(W.red(`  ${I.message}`));else console.log(W.red(`  ${I instanceof Error?I.message:"Unknown error"}`));v1(X);return}let A=C("Accepting GitHub repository invitation...").start(),U=q?.match(/github\.com\/([a-zA-Z0-9_.-]+\/[a-zA-Z0-9_.-]+)/),L=U?U[1].replace(/\.git$/,""):null;if(!L){A.fail("Invalid GitHub repository URL from backend"),console.log(W.red(`  Received: ${q||"(empty)"}`)),console.log(W.red("  Expected format: https://github.com/owner/repo")),console.log(),console.log("This may indicate a backend issue. Please contact support."),v1(X);return}let M=await d$(L);if(M.accepted)if(M.alreadyCollaborator)A.succeed("Already a collaborator on this repository");else A.succeed("GitHub invitation accepted");else A.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=C("Setting up git-annex...").start(),O=D.username&&D.email?{name:D.username,email:D.email}:void 0;try{await u$(X,{author:O}),await m$(X),await p$(X,H),N.succeed("Repository initialized")}catch(I){N.fail("Failed to initialize repository"),console.log(W.red(`  ${I instanceof Error?I.message:"Unknown error"}`)),v1(X);return}if(console.log(),console.log(W.bold("Step 5/6: Uploading to S3...")),Object.keys(Z).length===0)console.log(W.yellow("  No data files to upload (metadata only)"));else{let I=C("Uploading test data...").start();try{let c=0,GD=Object.keys(Z).length,S=await c$(X,Z,{jobs:4,onProgress:(JD)=>{if(JD.status==="completed"||JD.status==="failed")c++,I.text=`Uploading... ${c}/${GD} files`}});if(S.failed.length>0){I.fail(`Upload failed for ${S.failed.length} file(s)`);for(let JD of S.failed)console.log(W.red(`    Failed: ${JD}`));if(S.error)console.log(W.red(`    Error: ${S.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.")),v1(X);return}I.succeed(`Uploaded ${S.uploaded} file(s)`)}catch(c){I.fail("Upload failed"),console.log(W.red(`  ${c instanceof Error?c.message:"Unknown error"}`)),v1(X);return}let w=C("Registering file URLs...").start();try{let c={};for(let S of Object.keys(Z))c[S]=`${K.public_url}/${V}/objects/${S}`;let GD=await n$(X,c);if(!GD.success){w.fail(`URL registration failed for ${GD.failed.length} file(s)`);for(let S of GD.failed)console.log(W.red(`    Failed: ${S}`));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.")),v1(X);return}w.succeed(`Registered ${GD.registered} file URLs`)}catch(c){w.fail("Failed to register URLs"),console.log(W.red(`  ${c instanceof Error?c.message:"Unknown error"}`)),v1(X);return}}console.log(),console.log(W.bold("Step 6/6: Pushing to GitHub..."));let g=C("Saving and pushing...").start();try{await j5(X,"Initial sandbox training upload",O),await T5(X),g.succeed("Pushed to GitHub")}catch(I){g.fail("Failed to push to GitHub"),console.log(W.red(`  ${I instanceof Error?I.message:"Unknown error"}`)),v1(X);return}let j=C("Finalizing...").start();try{await h$(G),await Qy(G),R0("sandboxCompleted",!0),R0("sandboxDatasetId",G),j.succeed("Sandbox training complete!")}catch(I){j.fail("Failed to finalize"),console.log(W.red(`  ${I instanceof Error?I.message:"Unknown error"}`)),v1(X);return}v1(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}`))}BB.command("status").description("Check sandbox training completion status").option("--refresh","Fetch latest status from server").action(async(D)=>{if(!vD()){console.log(W.red("Not authenticated")),console.log(W.gray("Run 'nemar auth login' first"));return}if(D.refresh){let F=C("Checking status...").start();try{let $=await Yy();if(R0("sandboxCompleted",$.sandbox_completed),$.sandbox_dataset_id)R0("sandboxDatasetId",$.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 u)console.log(W.red(`  ${$.message}`))}}else{let F=Y0();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"))}});BB.command("reset").description("Reset sandbox training status for re-training").option(yD,xD).option(lD,dD).action(async(D)=>{if(!vD()){console.log(W.red("Not authenticated")),console.log(W.gray("Run 'nemar auth login' first"));return}if(!Y0().sandboxCompleted){console.log(W.yellow("Sandbox training not yet completed")),console.log(W.gray("Nothing to reset"));return}let $=await OD("Reset sandbox training status? You will need to complete training again.",D);if($!=="confirmed"){console.log(W.gray($==="declined"?"Skipped":"Cancelled"));return}let B=C("Resetting sandbox status...").start();try{await Xy(),h2("sandboxCompleted"),h2("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 u)console.log(W.red(`  ${J.message}`));else console.log(W.red(`  ${J instanceof Error?J.message:"Unknown error"}`))}});var Qx={name:"nemar-cli",version:"0.5.1-dev.256",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 Xx=Qx.version;var y1=new H0;y1.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(Xx,"-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": "0.5.1-dev.255",
+  "version": "0.5.1-dev.256",
   "description": "CLI for NEMAR (Neuroelectromagnetic Data Archive and Tools Resource) dataset management",
   "type": "module",
   "main": "dist/index.js",