nemar-cli 0.2.8-PR24.f75e138 → 0.2.8-dev.15
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 +1 -1
- package/package.json +1 -1
package/dist/index.js
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@@ -330,7 +330,7 @@ Examples:
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$ nemar sandbox # Run sandbox training
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$ nemar sandbox status # Check if training is completed
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$ nemar sandbox reset # Reset for re-training
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`).action(iED);async function iED(){if(console.log(),console.log(z.bold("NEMAR Sandbox Training")),console.log(z.gray("Verify your setup and learn the upload workflow")),console.log(),!yD()){console.log(z.red("Not authenticated")),console.log(z.gray("Run 'nemar auth login' first"));return}let D=rD();if(D.sandboxCompleted){console.log(z.green("Sandbox training already completed!")),console.log(z.gray(`Dataset ID: ${D.sandboxDatasetId}`)),console.log(),console.log("You can upload real datasets with:"),console.log(z.cyan(" nemar dataset upload ./your-dataset")),console.log(),console.log(z.gray("To re-run training, use: nemar sandbox reset"));return}console.log(z.bold("Step 1/6: Checking prerequisites..."));let F=_("Checking DataLad, git-annex, and SSH...").start(),$=await G$();if(!$.allPassed){F.fail("Prerequisites check failed"),console.log(),console.log(z.red("Missing requirements:"));for(let U of $.errors)console.log(z.yellow(` - ${U}`));if(!$.githubSSH.accessible)console.log(z.gray(" Run 'nemar auth setup-ssh' to configure SSH"));return}F.succeed("All prerequisites met"),console.log(),console.log(z.bold("Step 2/6: Generating test dataset..."));let B=_("Creating minimal BIDS structure...").start(),J;try{let U=rv();J=U.root;let M=tv(U);B.succeed(`Test dataset created (${V$(M)})`),console.log(z.gray(` Location: ${J}`))}catch(U){B.fail("Failed to generate test dataset"),console.log(z.red(` ${U instanceof Error?U.message:"Unknown error"}`));return}console.log(),console.log(z.bold("Step 3/6: Registering sandbox dataset..."));let Y=_("Creating dataset on NEMAR...").start(),Q,X,E,G,H;try{let U=await X$({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});Q=U.dataset.dataset_id,X=U.dataset.ssh_url,E=U.s3_config,G=U.dataset.s3_prefix,H=U.upload_urls||{},Y.succeed(`Sandbox dataset created: ${z.cyan(Q)}`),console.log(z.gray(` GitHub: ${U.dataset.github_url}`)),await new Promise((M)=>setTimeout(M,3000))}catch(U){if(Y.fail("Failed to create sandbox dataset"),U instanceof QD)console.log(z.red(` ${U.message}`));else console.log(z.red(` ${U instanceof Error?U.message:"Unknown error"}`));k1(J);return}console.log(),console.log(z.bold("Step 4/6: Initializing repository..."));let q=_("Setting up DataLad and git-annex...").start();try{await H$(J),await W$(J),await q$(J,X),q.succeed("Repository initialized")}catch(U){q.fail("Failed to initialize repository"),console.log(z.red(` ${U instanceof Error?U.message:"Unknown error"}`)),k1(J);return}if(console.log(),console.log(z.bold("Step 5/6: Uploading to S3...")),Object.keys(H).length===0)console.log(z.yellow(" No data files to upload (metadata only)"));else{let U=_("Uploading test data...").start();try{let N=0,Z=Object.keys(H).length,C=await A$(J,H,{jobs:4,onProgress:(w)=>{if(w.status==="completed"||w.status==="failed")N++,U.text=`Uploading... ${N}/${Z} files`}});if(C.failed.length>0){U.fail(`Upload failed for ${C.failed.length} file(s)`);for(let w of C.failed)console.log(z.red(` Failed: ${w}`));if(C.error)console.log(z.red(` Error: ${C.error}`));console.log(),console.log(z.yellow("Sandbox training aborted due to upload failures.")),console.log(z.gray("Please check your network connection and try again.")),k1(J);return}U.succeed(`Uploaded ${C.uploaded} file(s)`)}catch(N){U.fail("Upload failed"),console.log(z.red(` ${N instanceof Error?N.message:"Unknown error"}`)),k1(J);return}let M=_("Registering file URLs...").start();try{let N={};for(let C of Object.keys(H))N[C]=`${E.public_url}/${G}/${C}`;let Z=await U$(J,N);if(!Z.success){M.fail(`URL registration failed for ${Z.failed.length} file(s)`);for(let C of Z.failed)console.log(z.red(` Failed: ${C}`));console.log(),console.log(z.yellow("Sandbox training aborted due to URL registration failures.")),console.log(z.gray("This may indicate a git-annex configuration issue.")),k1(J);return}M.succeed(`Registered ${Z.registered} file URLs`)}catch(N){M.fail("Failed to register URLs"),console.log(z.red(` ${N instanceof Error?N.message:"Unknown error"}`)),k1(J);return}}console.log(),console.log(z.bold("Step 6/6: Pushing to GitHub..."));let V=_("Saving and pushing...").start();try{await K$(J,"Initial sandbox training upload"),await z$(J),V.succeed("Pushed to GitHub")}catch(U){V.fail("Failed to push to GitHub"),console.log(z.red(` ${U instanceof Error?U.message:"Unknown error"}`)),k1(J);return}let A=_("Finalizing...").start();try{await E$(Q),await Tv(Q),dD("sandboxCompleted",!0),dD("sandboxDatasetId",Q),A.succeed("Sandbox training complete!")}catch(U){A.fail("Failed to finalize"),console.log(z.red(` ${U instanceof Error?U.message:"Unknown error"}`)),k1(J);return}k1(J),console.log(),console.log(z.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(z.cyan(" nemar dataset upload ./your-dataset")),console.log(),console.log(z.gray(`Sandbox dataset: ${Q}`))}O$.command("status").description("Check sandbox training completion status").option("--refresh","Fetch latest status from server").action(async(D)=>{if(!yD()){console.log(z.red("Not authenticated")),console.log(z.gray("Run 'nemar auth login' first"));return}if(D.refresh){let F=_("Checking status...").start();try{let $=await jv();if(dD("sandboxCompleted",$.sandbox_completed),$.sandbox_dataset_id)dD("sandboxDatasetId",$.sandbox_dataset_id);if(F.stop(),$.sandbox_completed){if(console.log(z.green("Sandbox training: Completed")),console.log(z.gray(` Dataset ID: ${$.sandbox_dataset_id}`)),$.sandbox_completed_at)console.log(z.gray(` Completed: ${$.sandbox_completed_at}`))}else console.log(z.yellow("Sandbox training: Not completed")),console.log(),console.log("Run sandbox training with:"),console.log(z.cyan(" nemar sandbox"))}catch($){if(F.fail("Failed to check status"),$ instanceof QD)console.log(z.red(` ${$.message}`))}}else{let F=rD();if(F.sandboxCompleted)console.log(z.green("Sandbox training: Completed")),console.log(z.gray(` Dataset ID: ${F.sandboxDatasetId}`));else console.log(z.yellow("Sandbox training: Not completed")),console.log(),console.log("Run sandbox training with:"),console.log(z.cyan(" nemar sandbox"))}});O$.command("reset").description("Reset sandbox training status for re-training").option("-f, --force","Skip confirmation prompt").action(async(D)=>{if(!yD()){console.log(z.red("Not authenticated")),console.log(z.gray("Run 'nemar auth login' first"));return}if(!rD().sandboxCompleted){console.log(z.yellow("Sandbox training not yet completed")),console.log(z.gray("Nothing to reset"));return}if(!D.force){let B=(await Promise.resolve().then(() => (q3(),FI))).default,{confirm:J}=await B.prompt([{type:"confirm",name:"confirm",message:"Reset sandbox training status? You will need to complete training again.",default:!1}]);if(!J){console.log(z.gray("Cancelled"));return}}let $=_("Resetting sandbox status...").start();try{await wv(),dD("sandboxCompleted",!1),dD("sandboxDatasetId",void 0),$.succeed("Sandbox status reset"),console.log(),console.log("Run sandbox training again with:"),console.log(z.cyan(" nemar sandbox"))}catch(B){if($.fail("Failed to reset"),B instanceof QD)console.log(z.red(` ${B.message}`));else console.log(z.red(` ${B instanceof Error?B.message:"Unknown error"}`))}});var ev={name:"nemar-cli",version:"0.2.8-
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`).action(iED);async function iED(){if(console.log(),console.log(z.bold("NEMAR Sandbox Training")),console.log(z.gray("Verify your setup and learn the upload workflow")),console.log(),!yD()){console.log(z.red("Not authenticated")),console.log(z.gray("Run 'nemar auth login' first"));return}let D=rD();if(D.sandboxCompleted){console.log(z.green("Sandbox training already completed!")),console.log(z.gray(`Dataset ID: ${D.sandboxDatasetId}`)),console.log(),console.log("You can upload real datasets with:"),console.log(z.cyan(" nemar dataset upload ./your-dataset")),console.log(),console.log(z.gray("To re-run training, use: nemar sandbox reset"));return}console.log(z.bold("Step 1/6: Checking prerequisites..."));let F=_("Checking DataLad, git-annex, and SSH...").start(),$=await G$();if(!$.allPassed){F.fail("Prerequisites check failed"),console.log(),console.log(z.red("Missing requirements:"));for(let U of $.errors)console.log(z.yellow(` - ${U}`));if(!$.githubSSH.accessible)console.log(z.gray(" Run 'nemar auth setup-ssh' to configure SSH"));return}F.succeed("All prerequisites met"),console.log(),console.log(z.bold("Step 2/6: Generating test dataset..."));let B=_("Creating minimal BIDS structure...").start(),J;try{let U=rv();J=U.root;let M=tv(U);B.succeed(`Test dataset created (${V$(M)})`),console.log(z.gray(` Location: ${J}`))}catch(U){B.fail("Failed to generate test dataset"),console.log(z.red(` ${U instanceof Error?U.message:"Unknown error"}`));return}console.log(),console.log(z.bold("Step 3/6: Registering sandbox dataset..."));let Y=_("Creating dataset on NEMAR...").start(),Q,X,E,G,H;try{let U=await X$({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});Q=U.dataset.dataset_id,X=U.dataset.ssh_url,E=U.s3_config,G=U.dataset.s3_prefix,H=U.upload_urls||{},Y.succeed(`Sandbox dataset created: ${z.cyan(Q)}`),console.log(z.gray(` GitHub: ${U.dataset.github_url}`)),await new Promise((M)=>setTimeout(M,3000))}catch(U){if(Y.fail("Failed to create sandbox dataset"),U instanceof QD)console.log(z.red(` ${U.message}`));else console.log(z.red(` ${U instanceof Error?U.message:"Unknown error"}`));k1(J);return}console.log(),console.log(z.bold("Step 4/6: Initializing repository..."));let q=_("Setting up DataLad and git-annex...").start();try{await H$(J),await W$(J),await q$(J,X),q.succeed("Repository initialized")}catch(U){q.fail("Failed to initialize repository"),console.log(z.red(` ${U instanceof Error?U.message:"Unknown error"}`)),k1(J);return}if(console.log(),console.log(z.bold("Step 5/6: Uploading to S3...")),Object.keys(H).length===0)console.log(z.yellow(" No data files to upload (metadata only)"));else{let U=_("Uploading test data...").start();try{let N=0,Z=Object.keys(H).length,C=await A$(J,H,{jobs:4,onProgress:(w)=>{if(w.status==="completed"||w.status==="failed")N++,U.text=`Uploading... ${N}/${Z} files`}});if(C.failed.length>0){U.fail(`Upload failed for ${C.failed.length} file(s)`);for(let w of C.failed)console.log(z.red(` Failed: ${w}`));if(C.error)console.log(z.red(` Error: ${C.error}`));console.log(),console.log(z.yellow("Sandbox training aborted due to upload failures.")),console.log(z.gray("Please check your network connection and try again.")),k1(J);return}U.succeed(`Uploaded ${C.uploaded} file(s)`)}catch(N){U.fail("Upload failed"),console.log(z.red(` ${N instanceof Error?N.message:"Unknown error"}`)),k1(J);return}let M=_("Registering file URLs...").start();try{let N={};for(let C of Object.keys(H))N[C]=`${E.public_url}/${G}/${C}`;let Z=await U$(J,N);if(!Z.success){M.fail(`URL registration failed for ${Z.failed.length} file(s)`);for(let C of Z.failed)console.log(z.red(` Failed: ${C}`));console.log(),console.log(z.yellow("Sandbox training aborted due to URL registration failures.")),console.log(z.gray("This may indicate a git-annex configuration issue.")),k1(J);return}M.succeed(`Registered ${Z.registered} file URLs`)}catch(N){M.fail("Failed to register URLs"),console.log(z.red(` ${N instanceof Error?N.message:"Unknown error"}`)),k1(J);return}}console.log(),console.log(z.bold("Step 6/6: Pushing to GitHub..."));let V=_("Saving and pushing...").start();try{await K$(J,"Initial sandbox training upload"),await z$(J),V.succeed("Pushed to GitHub")}catch(U){V.fail("Failed to push to GitHub"),console.log(z.red(` ${U instanceof Error?U.message:"Unknown error"}`)),k1(J);return}let A=_("Finalizing...").start();try{await E$(Q),await Tv(Q),dD("sandboxCompleted",!0),dD("sandboxDatasetId",Q),A.succeed("Sandbox training complete!")}catch(U){A.fail("Failed to finalize"),console.log(z.red(` ${U instanceof Error?U.message:"Unknown error"}`)),k1(J);return}k1(J),console.log(),console.log(z.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(z.cyan(" nemar dataset upload ./your-dataset")),console.log(),console.log(z.gray(`Sandbox dataset: ${Q}`))}O$.command("status").description("Check sandbox training completion status").option("--refresh","Fetch latest status from server").action(async(D)=>{if(!yD()){console.log(z.red("Not authenticated")),console.log(z.gray("Run 'nemar auth login' first"));return}if(D.refresh){let F=_("Checking status...").start();try{let $=await jv();if(dD("sandboxCompleted",$.sandbox_completed),$.sandbox_dataset_id)dD("sandboxDatasetId",$.sandbox_dataset_id);if(F.stop(),$.sandbox_completed){if(console.log(z.green("Sandbox training: Completed")),console.log(z.gray(` Dataset ID: ${$.sandbox_dataset_id}`)),$.sandbox_completed_at)console.log(z.gray(` Completed: ${$.sandbox_completed_at}`))}else console.log(z.yellow("Sandbox training: Not completed")),console.log(),console.log("Run sandbox training with:"),console.log(z.cyan(" nemar sandbox"))}catch($){if(F.fail("Failed to check status"),$ instanceof QD)console.log(z.red(` ${$.message}`))}}else{let F=rD();if(F.sandboxCompleted)console.log(z.green("Sandbox training: Completed")),console.log(z.gray(` Dataset ID: ${F.sandboxDatasetId}`));else console.log(z.yellow("Sandbox training: Not completed")),console.log(),console.log("Run sandbox training with:"),console.log(z.cyan(" nemar sandbox"))}});O$.command("reset").description("Reset sandbox training status for re-training").option("-f, --force","Skip confirmation prompt").action(async(D)=>{if(!yD()){console.log(z.red("Not authenticated")),console.log(z.gray("Run 'nemar auth login' first"));return}if(!rD().sandboxCompleted){console.log(z.yellow("Sandbox training not yet completed")),console.log(z.gray("Nothing to reset"));return}if(!D.force){let B=(await Promise.resolve().then(() => (q3(),FI))).default,{confirm:J}=await B.prompt([{type:"confirm",name:"confirm",message:"Reset sandbox training status? You will need to complete training again.",default:!1}]);if(!J){console.log(z.gray("Cancelled"));return}}let $=_("Resetting sandbox status...").start();try{await wv(),dD("sandboxCompleted",!1),dD("sandboxDatasetId",void 0),$.succeed("Sandbox status reset"),console.log(),console.log("Run sandbox training again with:"),console.log(z.cyan(" nemar sandbox"))}catch(B){if($.fail("Failed to reset"),B instanceof QD)console.log(z.red(` ${B.message}`));else console.log(z.red(` ${B instanceof Error?B.message:"Unknown error"}`))}});var ev={name:"nemar-cli",version:"0.2.8-dev.15",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/nemarDatasets/nemar-cli.git"},bugs:{url:"https://github.com/nemarDatasets/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 Dy=ev.version;var Q1=new f0;Q1.name("nemar").description(`CLI for NEMAR (Neuroelectromagnetic Data Archive and Tools Resource)
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NEMAR is a curated repository for neurophysiology data in BIDS format.
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This CLI provides tools for uploading, downloading, and managing datasets.`).version(Dy,"-v, --version","Output the current version").option("--no-color","Disable colored output").option("--verbose","Enable verbose output").addHelpText("after",`
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package/package.json
CHANGED