nemar-cli 0.8.73-PR876.449f6ec → 0.8.73-PR877.fbd19b5

package/dist/index.js

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Run 'gh auth login' to authenticate.")}return{gitAnnex:D,githubSSH:F,allPassed:$.length===0,errors:$}}async function R1(D){if(!oW(sW(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 R1(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:$.message}}}async function eW(D){try{let{exitCode:F,stderr:$}=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 iW(D){let F=[/^\(merging .* into .*\.\.\.\)$/,/^\(recording state in git\.\.\.\)$/,/^\(scanning for /,/^\(checking /];return D.split(`
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@@ -620,7 +620,7 @@ Description:
 
 Examples:
   $ nemar dataset status nm000104
-  $ nemar dataset status nm000104 --json | jq '.concept_doi'`).action(async(D,F)=>{let $=O(`Fetching dataset info for ${D}...`).start(),J;try{J=await gD(D),$.stop()}catch(Q){if($.fail("Dataset not found"),Q instanceof f)console.log(W.red(`  ${Q.message}`));else console.log(W.red(`  ${Q.message}`));process.exit(1)}if(F.json){console.log(JSON.stringify(J,null,2));return}if(console.log(),console.log(W.bold(`Dataset: ${J.dataset_id}`)),console.log(),console.log(`  Name:        ${J.name}`),console.log(`  Owner:       ${J.owner_username}`),console.log(`  Status:      ${AU0(J.status)}`),console.log(`  Created:     ${new Date(J.created_at).toLocaleDateString()}`),J.description)console.log(`  Description: ${J.description}`);if(J.github_repo)console.log(`  GitHub:      https://github.com/${J.github_repo}`);if(J.concept_doi)console.log(`  DOI:         https://doi.org/${J.concept_doi}`);console.log(),console.log(W.dim("To download this dataset:")),console.log(W.dim(`  nemar dataset download ${D}`))});async function LU0(D){if(!vb(D))return D;let F=null;try{F=await Hg(D)}catch(J){return console.log(W.dim(`Could not check NEMAR availability: ${J.message}`)),null}if(!F?.found||!F.dataset_id)return null;console.log(),console.log(W.green(`This dataset is available on NEMAR as ${W.bold(F.dataset_id)}`)),console.log(W.dim("NEMAR provides git-annex version tracking and selective file download."));let{useNemarBackend:$}=await D0.prompt([{type:"confirm",name:"useNemarBackend",message:`Download from NEMAR (${F.dataset_id}) instead of OpenNeuro?`,default:!0}]);return $?F.dataset_id:null}function AU0(D){switch(D.toLowerCase()){case"published":return W.green(D);case"active":return W.blue(D);case"archived":return W.dim(D);case"pending":return W.yellow(D);default:return D}}function MU0(D,F){let{offset:$,totalCount:J}=F,Q=$+1,Y=$+D.length,B=J>D.length?`${Q}-${Y} of ${J}`:`${J}`;console.log(),console.log(W.bold(`Datasets (${B}):`)),console.log();let X=(Z)=>Z.dataset_id||Z.id||"",G=Math.max(10,...D.map((Z)=>X(Z).length)),H=Math.min(30,Math.max(10,...D.map((Z)=>Z.name.length))),q=10,K=8,V=Math.max(8,...D.map((Z)=>(Z.owner_username||"-").length)),z=["ID".padEnd(G),"Name".padEnd(H),"Modality".padEnd(q),"Subj".padEnd(K),"Owner".padEnd(V),"Status"].join("  ");console.log(W.dim(z)),console.log(W.dim("-".repeat(z.length)));for(let Z of D){let U=X(Z),M=Z.name.length>H?`${Z.name.substring(0,H-3)}...`:Z.name,A=(Z.modalities||"").substring(0,q),C=Z.participants?String(Z.participants):"-",j=Z.owner_username||"-",I=Z.visibility==="public"?W.green("pub"):W.yellow("prv"),R;if(Z.source_type==="catalog")R=W.dim(U.padEnd(G));else R=W.cyan(U.padEnd(G));let w=Z.source_type==="catalog"?W.dim(M):M,v=[R,w.padEnd(H+(Z.source_type==="catalog"?W.dim("").length:0)),A.padEnd(q),C.padEnd(K),j.padEnd(V),I].join("  ");console.log(v)}if(console.log(),J>Y){let Z=Math.floor($/F.limit)+1,U=Math.ceil(J/F.limit);console.log(W.dim(`Page ${Z}/${U}. Next: nemar dataset list --page ${Z+1}`))}console.log(W.dim(`  * = not synced to nemar.org    ${W.dim("dim")} = catalog-only (not on GitHub)`)),console.log(W.dim("For details: nemar dataset status <dataset-id>")),console.log(W.dim("Search: nemar dataset search <query>"))}t0.command("list").description("List datasets on NEMAR (full catalog)").option("--mine","List only your datasets (both private and public)").option("--owner <username>","List datasets owned by a specific user").option("--search <query>","Search by name, description, authors, or tasks").option("--modality <type>","Filter by modality (eeg, emg, meg, etc.)").option("--author <name>","Filter by author name").option("--task <name>","Filter by task name").option("--license <tiers>","Filter by license tier(s), comma-separated: public, attribution, sharealike, noncommercial, noderiv, unknown").option("--doi","Show only datasets with DOIs").option("--recent [days]","Show recently published datasets").option("--sort <order>","Sort: newest, oldest, name, participants, size","newest").option("--json","Output as JSON for scripting").option("-n, --limit <n>","Results per page (default: 20, max: 200)","20").option("--page <n>","Page number (starts at 1)").option("--offset <n>","Skip this many results (alternative to --page)").option("--all","Show all results (up to 200)").addHelpText("after",`
+  $ nemar dataset status nm000104 --json | jq '.concept_doi'`).action(async(D,F)=>{let $=O(`Fetching dataset info for ${D}...`).start(),J;try{J=await gD(D),$.stop()}catch(Q){if($.fail("Dataset not found"),Q instanceof f)console.log(W.red(`  ${Q.message}`));else console.log(W.red(`  ${Q.message}`));process.exit(1)}if(F.json){console.log(JSON.stringify(J,null,2));return}if(console.log(),console.log(W.bold(`Dataset: ${J.dataset_id}`)),console.log(),console.log(`  Name:        ${J.name}`),console.log(`  Owner:       ${J.owner_username}`),console.log(`  Status:      ${AU0(J.status)}`),console.log(`  Created:     ${new Date(J.created_at).toLocaleDateString()}`),J.description)console.log(`  Description: ${J.description}`);if(J.github_repo)console.log(`  GitHub:      https://github.com/${J.github_repo}`);if(J.concept_doi)console.log(`  DOI:         https://doi.org/${J.concept_doi}`);console.log(),console.log(W.dim("To download this dataset:")),console.log(W.dim(`  nemar dataset download ${D}`))});async function LU0(D){if(!vb(D))return D;let F=null;try{F=await Hg(D)}catch(J){return console.log(W.dim(`Could not check NEMAR availability: ${J.message}`)),null}if(!F?.found||!F.dataset_id)return null;console.log(),console.log(W.green(`This dataset is available on NEMAR as ${W.bold(F.dataset_id)}`)),console.log(W.dim("NEMAR provides git-annex version tracking and selective file download."));let{useNemarBackend:$}=await D0.prompt([{type:"confirm",name:"useNemarBackend",message:`Download from NEMAR (${F.dataset_id}) instead of OpenNeuro?`,default:!0}]);return $?F.dataset_id:null}function AU0(D){switch(D.toLowerCase()){case"published":return W.green(D);case"active":return W.blue(D);case"archived":return W.dim(D);case"pending":return W.yellow(D);default:return D}}function MU0(D,F){let{offset:$,totalCount:J}=F,Q=$+1,Y=$+D.length,B=J>D.length?`${Q}-${Y} of ${J}`:`${J}`;console.log(),console.log(W.bold(`Datasets (${B}):`)),console.log();let X=(Z)=>Z.dataset_id||Z.id||"",G=Math.max(10,...D.map((Z)=>X(Z).length)),H=Math.min(30,Math.max(10,...D.map((Z)=>Z.name.length))),q=10,K=8,V=Math.max(8,...D.map((Z)=>(Z.owner_username||"-").length)),z=["ID".padEnd(G),"Name".padEnd(H),"Modality".padEnd(q),"Subj".padEnd(K),"HED".padEnd(3),"Owner".padEnd(V),"Status"].join("  ");console.log(W.dim(z)),console.log(W.dim("-".repeat(z.length)));for(let Z of D){let U=X(Z),M=Z.name.length>H?`${Z.name.substring(0,H-3)}...`:Z.name,A=(Z.modalities||"").substring(0,q),C=Z.participants?String(Z.participants):"-",j=Z.owner_username||"-",I=Z.visibility==="public"?W.green("pub"):W.yellow("prv"),R;if(Z.source_type==="catalog")R=W.dim(U.padEnd(G));else R=W.cyan(U.padEnd(G));let w=Z.source_type==="catalog"?W.dim(M):M,v=[R,w.padEnd(H+(Z.source_type==="catalog"?W.dim("").length:0)),A.padEnd(q),C.padEnd(K),Z.has_hed===1?W.magenta("HED".padEnd(3)):W.dim("-".padEnd(3)),j.padEnd(V),I].join("  ");console.log(v)}if(console.log(),J>Y){let Z=Math.floor($/F.limit)+1,U=Math.ceil(J/F.limit);console.log(W.dim(`Page ${Z}/${U}. Next: nemar dataset list --page ${Z+1}`))}console.log(W.dim(`  * = not synced to nemar.org    ${W.dim("dim")} = catalog-only (not on GitHub)`)),console.log(W.dim("For details: nemar dataset status <dataset-id>")),console.log(W.dim("Search: nemar dataset search <query>"))}t0.command("list").description("List datasets on NEMAR (full catalog)").option("--mine","List only your datasets (both private and public)").option("--owner <username>","List datasets owned by a specific user").option("--search <query>","Search by name, description, authors, or tasks").option("--modality <type>","Filter by modality (eeg, emg, meg, etc.)").option("--author <name>","Filter by author name").option("--task <name>","Filter by task name").option("--license <tiers>","Filter by license tier(s), comma-separated: public, attribution, sharealike, noncommercial, noderiv, unknown").option("--doi","Show only datasets with DOIs").option("--hed","Show only datasets with HED annotations").option("--recent [days]","Show recently published datasets").option("--sort <order>","Sort: newest, oldest, name, participants, size","newest").option("--json","Output as JSON for scripting").option("-n, --limit <n>","Results per page (default: 20, max: 200)","20").option("--page <n>","Page number (starts at 1)").option("--offset <n>","Skip this many results (alternative to --page)").option("--all","Show all results (up to 200)").addHelpText("after",`
 Description:
   Lists the full NEMAR catalog, including legacy datasets from nemar.org
   and datasets managed via nemar-cli. Shows 20 results per page by default.
@@ -651,8 +651,8 @@ Examples:
   $ nemar dataset list --license public,attribution  # Permissive licenses
   $ nemar dataset list --search "motor"        # Search by keyword
   $ nemar dataset list --doi --sort size       # Published, by size
-  $ nemar dataset search "resting state EEG"   # Semantic search`).action(async(D)=>{if(D.mine&&D.owner)console.log(W.red("Error: --mine and --owner cannot be used together")),console.log("Use --mine for your datasets, or --owner <username> for another user's."),process.exit(1);if(D.mine&&!H0())console.log(W.red("Error: Not authenticated")),console.log("Run 'nemar auth login' to see your datasets"),process.exit(1);if(D.license){let X=["public","attribution","sharealike","noncommercial","noderiv","unknown"],G=D.license.split(",").map((H)=>H.trim().toLowerCase()).filter((H)=>H&&!X.includes(H));if(G.length>0)console.log(W.red(`Error: invalid license tier(s): ${G.join(", ")}`)),console.log(`Valid tiers: ${X.join(", ")}`),process.exit(1)}let F=D.all?200:Math.min(Number.parseInt(D.limit,10)||20,200),$=0;if(D.page)$=(Math.max(Number.parseInt(D.page,10)||1,1)-1)*F;else if(D.offset)$=Math.max(Number.parseInt(D.offset,10)||0,0);let J=O("Fetching datasets...").start(),Q;try{Q=await PF({mine:!!D.mine,search:D.search,modality:D.modality,author:D.author,task:D.task,license:D.license,hasDoi:!!D.doi,recent:D.recent?Number.parseInt(D.recent,10)||30:void 0,sort:D.sort,limit:F,offset:$,owner:D.owner}),J.stop()}catch(X){if(J.fail("Failed to fetch datasets"),X instanceof f)console.log(W.red(`  ${X.message}`));else console.log(W.red(`  ${X.message}`));process.exit(1)}let Y=Q.datasets,B=Q.total_count??Q.count;if(D.json){console.log(JSON.stringify({datasets:Y,total_count:B,limit:F,offset:$,fallback:Q.fallback,warning:Q.warning},null,2));return}if(Q.warning)console.log(W.yellow(`
-\u26A0 ${Q.warning}`));if(Y.length===0){if(console.log(),D.mine)console.log(W.yellow("You don't have any datasets yet.")),console.log(W.dim("Create one with: nemar dataset upload <path>"));else if(D.owner)console.log(W.yellow(`No datasets found for user '${D.owner}'.`));else if(D.search||D.modality||D.author)console.log(W.yellow("No datasets match your filters.")),console.log(W.dim("Try broader search terms or remove filters."));else console.log(W.yellow("No datasets found."));return}MU0(Y,{limit:F,offset:$,totalCount:B})});t0.command("search <query>").description("Search datasets using semantic matching").option("--modality <type>","Filter by modality (eeg, emg, meg, etc.)").option("--json","Output as JSON for scripting").option("--limit <n>","Limit results (default: 20)","20").addHelpText("after",`
+  $ nemar dataset search "resting state EEG"   # Semantic search`).action(async(D)=>{if(D.mine&&D.owner)console.log(W.red("Error: --mine and --owner cannot be used together")),console.log("Use --mine for your datasets, or --owner <username> for another user's."),process.exit(1);if(D.mine&&!H0())console.log(W.red("Error: Not authenticated")),console.log("Run 'nemar auth login' to see your datasets"),process.exit(1);if(D.license){let X=["public","attribution","sharealike","noncommercial","noderiv","unknown"],G=D.license.split(",").map((H)=>H.trim().toLowerCase()).filter((H)=>H&&!X.includes(H));if(G.length>0)console.log(W.red(`Error: invalid license tier(s): ${G.join(", ")}`)),console.log(`Valid tiers: ${X.join(", ")}`),process.exit(1)}let F=D.all?200:Math.min(Number.parseInt(D.limit,10)||20,200),$=0;if(D.page)$=(Math.max(Number.parseInt(D.page,10)||1,1)-1)*F;else if(D.offset)$=Math.max(Number.parseInt(D.offset,10)||0,0);let J=O("Fetching datasets...").start(),Q;try{Q=await PF({mine:!!D.mine,search:D.search,modality:D.modality,author:D.author,task:D.task,license:D.license,hasDoi:!!D.doi,hasHed:!!D.hed,recent:D.recent?Number.parseInt(D.recent,10)||30:void 0,sort:D.sort,limit:F,offset:$,owner:D.owner}),J.stop()}catch(X){if(J.fail("Failed to fetch datasets"),X instanceof f)console.log(W.red(`  ${X.message}`));else console.log(W.red(`  ${X.message}`));process.exit(1)}let Y=Q.datasets,B=Q.total_count??Q.count;if(D.json){console.log(JSON.stringify({datasets:Y,total_count:B,limit:F,offset:$,fallback:Q.fallback,warning:Q.warning},null,2));return}if(Q.warning)console.log(W.yellow(`
+\u26A0 ${Q.warning}`));if(Y.length===0){if(console.log(),D.mine)console.log(W.yellow("You don't have any datasets yet.")),console.log(W.dim("Create one with: nemar dataset upload <path>"));else if(D.owner)console.log(W.yellow(`No datasets found for user '${D.owner}'.`));else if(D.search||D.modality||D.author||D.hed||D.license||D.task)console.log(W.yellow("No datasets match your filters.")),console.log(W.dim("Try broader search terms or remove filters."));else console.log(W.yellow("No datasets found."));return}MU0(Y,{limit:F,offset:$,totalCount:B})});t0.command("search <query>").description("Search datasets using semantic matching").option("--modality <type>","Filter by modality (eeg, emg, meg, etc.)").option("--hed","Show only datasets with HED annotations").option("--json","Output as JSON for scripting").option("--limit <n>","Limit results (default: 20)","20").addHelpText("after",`
 Description:
   Performs semantic search across the NEMAR dataset catalog. Unlike
   --search on the list command (which uses exact text matching), this
@@ -664,7 +664,7 @@ Description:
 Examples:
   $ nemar dataset search "motor imagery EEG"
   $ nemar dataset search "resting state" --modality eeg
-  $ nemar dataset search "sleep spindles" --json`).action(async(D,F)=>{let $=O("Searching datasets...").start();try{let J=await qg(D,{modality:F.modality,limit:Number.parseInt(F.limit,10)});if($.stop(),F.json){console.log(JSON.stringify(J,null,2));return}if(J.results.length===0){console.log(),console.log(W.yellow("No datasets match your search.")),console.log(W.dim("Try different search terms or use 'nemar dataset list' for browsing."));return}console.log(),console.log(W.bold(`Search results for "${D}" (${J.results.length} found, ${J.method}):`)),console.log();let Q=Math.max(10,...J.results.map((H)=>H.id.length)),Y=Math.min(35,Math.max(10,...J.results.map((H)=>H.name.length))),B=10,X=6,G=["Score".padEnd(5),"ID".padEnd(Q),"Name".padEnd(Y),"Modality".padEnd(B),"Subj".padEnd(X)].join("  ");console.log(W.dim(G)),console.log(W.dim("-".repeat(G.length)));for(let H of J.results){let q=H.name.length>Y?`${H.name.substring(0,Y-3)}...`:H.name,V=[(H.score>=0.8?W.green:H.score>=0.5?W.yellow:W.dim)(String(H.score).padEnd(5)),W.cyan(H.id.padEnd(Q)),q.padEnd(Y),(H.modalities||"-").substring(0,B).padEnd(B),(H.participants?String(H.participants):"-").padEnd(X)].join("  ");console.log(V)}console.log(),console.log(W.dim("For details: nemar dataset status <dataset-id>"))}catch(J){if($.fail("Search failed"),J instanceof f)console.log(W.red(`  ${J.message}`));else console.log(W.red(`  ${J.message}`));process.exit(1)}});t0.command("release").description("Create a version bump PR for a dataset").argument("<dataset-id>","Dataset ID (e.g., nm000104)").option("--type <type>","Bump type: patch, minor, or major").option("--version <version>","Explicit version (e.g., 2.0.0)").option("--dir <path>","Use existing local clone instead of cloning").option("--monitor","Watch CI checks and offer to merge").option(j0,w0).addHelpText("after",`
+  $ nemar dataset search "sleep spindles" --json`).action(async(D,F)=>{let $=O("Searching datasets...").start();try{let J=await qg(D,{modality:F.modality,hasHed:!!F.hed,limit:Number.parseInt(F.limit,10)});if($.stop(),F.json){console.log(JSON.stringify(J,null,2));return}if(J.results.length===0){console.log(),console.log(W.yellow("No datasets match your search.")),console.log(W.dim("Try different search terms or use 'nemar dataset list' for browsing."));return}console.log(),console.log(W.bold(`Search results for "${D}" (${J.results.length} found, ${J.method}):`)),console.log();let Q=Math.max(10,...J.results.map((H)=>H.id.length)),Y=Math.min(35,Math.max(10,...J.results.map((H)=>H.name.length))),B=10,X=6,G=["Score".padEnd(5),"ID".padEnd(Q),"Name".padEnd(Y),"Modality".padEnd(B),"Subj".padEnd(X),"HED".padEnd(3)].join("  ");console.log(W.dim(G)),console.log(W.dim("-".repeat(G.length)));for(let H of J.results){let q=H.name.length>Y?`${H.name.substring(0,Y-3)}...`:H.name,V=[(H.score>=0.8?W.green:H.score>=0.5?W.yellow:W.dim)(String(H.score).padEnd(5)),W.cyan(H.id.padEnd(Q)),q.padEnd(Y),(H.modalities||"-").substring(0,B).padEnd(B),(H.participants?String(H.participants):"-").padEnd(X),H.has_hed===1?W.magenta("HED"):W.dim("-")].join("  ");console.log(V)}console.log(),console.log(W.dim("For details: nemar dataset status <dataset-id>"))}catch(J){if($.fail("Search failed"),J instanceof f)console.log(W.red(`  ${J.message}`));else console.log(W.red(`  ${J.message}`));process.exit(1)}});t0.command("release").description("Create a version bump PR for a dataset").argument("<dataset-id>","Dataset ID (e.g., nm000104)").option("--type <type>","Bump type: patch, minor, or major").option("--version <version>","Explicit version (e.g., 2.0.0)").option("--dir <path>","Use existing local clone instead of cloning").option("--monitor","Watch CI checks and offer to merge").option(j0,w0).addHelpText("after",`
 Description:
   Create a pull request that bumps the dataset version in
   dataset_description.json. The PR triggers CI checks (BIDS validation,

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "nemar-cli",
-  "version": "0.8.73-PR876.449f6ec",
+  "version": "0.8.73-PR877.fbd19b5",
   "description": "CLI for NEMAR (Neuroelectromagnetic Data Archive and Tools Resource) dataset management",
   "type": "module",
   "main": "dist/index.js",