nemar-cli 0.8.67-PR823.9a0100a → 0.8.67-PR823.baf2beb
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/dist/index.js +2 -2
- package/package.json +1 -1
package/dist/index.js
CHANGED
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@@ -95,7 +95,7 @@ ${W.dim(`eta: ${D.eta}`)}`:"";process.stderr.write(`${F}
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${$} ${D.message}
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${F}
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Run 'gh auth login' to authenticate.")}return{gitAnnex:D,githubSSH:F,allPassed:$.length===0,errors:$}}async function N1(D){if(!nW(iW(D,".git")))return!1;try{let{exitCode:F}=await T(["git","annex","info"],{cwd:D});return F===0}catch(F){let $=F instanceof Error?F.message:String(F);if(!$.includes("ENOENT")&&!$.includes("not found"))console.error(`Error checking if ${D} is a git-annex dataset:`,$);return!1}}async function n6(D,F={}){if(!F.force&&await N1(D))return{success:!0};try{let $={};if(F.author)$.GIT_AUTHOR_NAME=F.author.name,$.GIT_AUTHOR_EMAIL=F.author.email,$.GIT_COMMITTER_NAME=F.author.name,$.GIT_COMMITTER_EMAIL=F.author.email;let{stderr:J,exitCode:Q}=await T(["git","init","-b","main",D],{...Object.keys($).length>0?{env:$}:{}});if(Q!==0)return{success:!1,error:J.trim()||"Failed to initialize git repository"};let Y=Object.keys($).length>0?{env:$}:{},{stderr:B,exitCode:X}=await T(["git","annex","init"],{cwd:D,...Y});if(X!==0)return{success:!1,error:B.trim()||"Failed to initialize git-annex"};let{stderr:G,exitCode:H}=await T(["git","commit","--allow-empty","-m","Initialize dataset"],{cwd:D,...Y});if(H!==0)return{success:!1,error:G.trim()||"Failed to create initial commit"};let{stderr:q,exitCode:K}=await T(["git","annex","adjust","--unlock"],{cwd:D,...Y});if(K!==0)return{success:!1,error:q.trim()||"Failed to switch to unlocked mode"};return{success:!0}}catch($){return{success:!1,error:$.message}}}async function sW(D){try{let{exitCode:F,stderr:$}=await T(["git","annex","info"],{cwd:D});if(F===0)return{success:!0};if($.includes("First run: git-annex init")){let{stderr:J,exitCode:Q}=await T(["git","annex","init"],{cwd:D});if(Q!==0)return{success:!1,error:J.trim()||"Failed to initialize git-annex"};return{success:!0}}return{success:!1,error:$.trim()||"Failed to check git-annex status"}}catch(F){return{success:!1,error:F.message}}}async function g4(D,F){let $=["*.edf","*.bdf","*.set","*.fif","*.vhdr","*.eeg","*.cnt","*.fdt"],J=["*.tsv","*.json","*.md","*.txt","*.yml","*.yaml","README*","LICENSE*","CHANGES*",".bidsignore",".gitignore"],Q=$.map((G)=>`include=${G}`).join(" or "),Y=J.map((G)=>`exclude=${G}`).join(" and "),B=`(${Q} or largerthan=100kb) and ${Y}`,X=F||B;try{let{stderr:G,exitCode:H}=await T(["git","annex","config","--set","annex.largefiles",X],{cwd:D});if(H!==0)return{success:!1,error:G.trim()||"Failed to configure largefiles"};return{success:!0}}catch(G){return{success:!1,error:G.message}}}async function i6(D,F="."){try{let{stderr:$,exitCode:J}=await T(["git","annex","add",F],{cwd:D});if(J!==0)return{success:!1,error:$.trim()||"Failed to add files to git-annex"};return{success:!0}}catch($){return{success:!1,error:$.message}}}function PD(D){return{accessKeyId:D.access_key_id,secretAccessKey:D.secret_access_key,sessionToken:D.session_token}}function dW(D){let F=[/^\(merging .* into .*\.\.\.\)$/,/^\(recording state in git\.\.\.\)$/,/^\(scanning for /,/^\(checking /];return D.split(`
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`).filter(($)=>{let J=$.trim();if(!J)return!1;if(J.includes("setting annex-ignore"))return!1;if(F.some((Q)=>Q.test(J)))return!1;return!0}).join(`
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@@ -123,7 +123,7 @@ Fix one of these:
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Warning: Your current branch is "${$}", but NEMAR requires "main".`)),console.log(W.yellow(" Without renaming, CI validation, branch protection, and metadata pipelines will not work.")),!F.yes){if(!await NV0($))return!1}let{exitCode:J,stderr:Q}=await T(["git","branch","-m",$,"main"],{cwd:D});if(J!==0){if(console.log(W.red(` Failed to rename branch "${$}" to "main".`)),Q.trim())console.log(W.red(` Git error: ${Q.trim()}`));return!1}return console.log(W.green(` Renamed branch "${$}" to "main".`)),!0}async function NV0(D){let F=(await Promise.resolve().then(() => (k6(),nT))).default;try{let{rename:$}=await F.prompt([{type:"confirm",name:"rename",message:`Rename branch "${D}" to "main"?`,default:!0}]);if(!$)console.log(W.red(" Upload cancelled. Rename your branch to main before uploading:")),console.log(W.dim(` git branch -m '${D}' main`));return $}catch($){return console.log(W.red(` Failed to prompt: ${$ instanceof Error?$.message:String($)}`)),console.log(W.dim(` You can manually rename: git branch -m '${D}' main`)),!1}}async function s8(D){try{let{stdout:F,exitCode:$}=await T(["git","remote","get-url","origin"],{cwd:D});if($!==0||!F.trim())return null;let Q=F.trim().match(/[/:]([^/]+?)(?:\.git)?$/);if(!Q)return null;return Q[1]}catch{return null}}function BH(D){let F=iW(D,"dataset_description.json");if(!nW(F))return{version:null};try{let $=JSON.parse(zV0(F,"utf-8"));return{version:typeof $.DatasetVersion==="string"?$.DatasetVersion:null}}catch($){return{version:null,error:`dataset_description.json is unreadable: ${$.message}`}}}async function XH(D){let F=[];for(let $ of["origin/HEAD","origin/main","origin/master"]){let{stdout:J,stderr:Q,exitCode:Y}=await T(["git","show",`${$}:dataset_description.json`],{cwd:D});if(Y!==0){if(Q&&!/unknown revision|bad revision|does not exist/i.test(Q))F.push(`git show ${$} failed: ${Q.trim()}`);continue}if(!J.trim())continue;try{let B=JSON.parse(J);if(typeof B.DatasetVersion==="string")return{version:B.DatasetVersion,warnings:F}}catch(B){F.push(`${$}:dataset_description.json is malformed: ${B.message}`)}}return{version:null,warnings:F}}async function GH(D){let{stdout:F,exitCode:$}=await T(["git","rev-parse","--abbrev-ref","@{upstream}"],{cwd:D});if($===0&&F.trim())return{ref:F.trim()};for(let J of["origin/HEAD","origin/main","origin/master"]){let{exitCode:Q}=await T(["git","rev-parse","--verify","--quiet",J],{cwd:D});if(Q===0)return{ref:J}}return{ref:null,error:"Could not resolve a remote tracking branch (origin/HEAD, origin/main, origin/master all missing)"}}async function WH(D){let{stdout:F,stderr:$,exitCode:J}=await T(["git","status","--porcelain"],{cwd:D});if(J!==0)return{dirty:!1,error:$.trim()||"git status failed"};return{dirty:F.trim().length>0}}async function HH(D){let{stderr:F,exitCode:$}=await T(["git","fetch","--tags","origin"],{cwd:D});if($!==0)return{success:!1,error:F.trim()||"git fetch failed"};return{success:!0}}async function qH(D,F){let{stderr:$,exitCode:J}=await T(["git","merge","--ff-only",F],{cwd:D});if(J!==0)return{success:!1,error:$.trim()||`Cannot fast-forward to ${F}`};return{success:!0}}async function KH(D){let{stderr:F,exitCode:$}=await T(["git","fetch","--prune","--prune-tags","origin"],{cwd:D});if($!==0)return{success:!1,error:F.trim()||"git fetch --prune-tags failed"};let{exitCode:J,stderr:Q}=await T(["git","annex","unused"],{cwd:D});if(J!==0)return{success:!1,error:Q.trim()||"git annex unused failed"};let{stdout:Y,stderr:B,exitCode:X}=await T(["git","annex","dropunused","--force","all"],{cwd:D});if(X!==0)return{success:!1,error:B.trim()||"git annex dropunused failed"};let G=Y.match(/^dropunused .+ ok$/gm);return{success:!0,dropped:G?G.length:0}}async function RV0(D,F){try{let{stderr:$,exitCode:J}=await T(["git","checkout",F],{cwd:D});if(J!==0)return{success:!1,error:$.trim()||"Failed to switch branch"};return{success:!0}}catch($){return{success:!1,error:$.message}}}async function zH(D){let F=[],$=0,J=0,Q=0,{stdout:Y,exitCode:B}=await T(["find",".","(","-type","f","-o","-type","l",")","-not","-path","./.git/*","-not","-path","./.nemar/*","-not","-name",".gitattributes"],{cwd:D});if(B!==0)return{files:F,totalSize:$,dataFiles:J,metadataFiles:Q};let X=Y.trim().split(`
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`).filter(Boolean);for(let G of X){let H=G.startsWith("./")?G.slice(2):G,q=iW(D,H);try{let V=EV0(q).size;$+=V;let z=H.toLowerCase().match(/\.[^.]+$/)?.[0]||"",Z=OV0.has(z)||V>CV0,U=Z?"data":"metadata";if(Z)J++;else Q++;F.push({path:H,size:V,type:U})}catch{}}return{files:F,totalSize:$,dataFiles:J,metadataFiles:Q}}function cW(D,F){let $=D.trim();if(!$)return;try{let J=JSON.parse($),Q=J.key;if(!Q)return;let Y=[...J.whereis||[],...J.untrusted||[]];for(let B of Y){if(!Array.isArray(B.urls))continue;for(let X of B.urls)if(typeof X==="string"&&(X.startsWith("http")||X.startsWith("s3://"))){F.set(Q,X);break}if(F.has(Q))break}}catch(J){if(J instanceof SyntaxError)return;console.error(`Warning: failed to process whereis entry: ${J instanceof Error?J.message:String(J)}`)}}async function EH(D){let F=aW({cmd:["git","annex","whereis","--json","--","."],cwd:D,stdout:"pipe",stderr:"pipe",env:{...process.env,GIT_TERMINAL_PROMPT:"0"}}),$=new Response(F.stderr).text(),J=new Map,Q=new TextDecoder,Y="",B=!1;for await(let H of F.stdout){Y+=Q.decode(H,{stream:!0});let q=Y.indexOf(`
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`);while(q!==-1){let K=Y.slice(0,q);if(Y=Y.slice(q+1),K.trim())B=!0,cW(K,J);q=Y.indexOf(`
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`)}}if(Y+=Q.decode(),Y.trim())B=!0,cW(Y,J);let X=(await $).trim(),G=await F.exited;if(G!==0&&!B)throw Error(`git annex whereis failed: ${X}`);if(G!==0){let H=X.match(/whereis:\s*(\d+)\s*failed/);if(H)console.warn(` Warning: ${H[1]} files had no location info (continuing with available files)`);else throw Error(`git annex whereis failed (exit ${G}): ${X}`)}return J}async function zh(D,F){let $=await T(["git","annex","examinekey","--format=${hashdirlower}",F],{cwd:D});if($.exitCode!==0)throw Error(`git annex examinekey failed for ${F}: ${$.stderr.trim()}`);return $.stdout.trim()}async function wV0(D,F){let $=new Map,J=50;for(let Q=0;Q<F.length;Q+=50){let Y=F.slice(Q,Q+50),B=await Promise.allSettled(Y.map(async(X)=>{let G=await zh(D,X);return{key:X,hashDir:G}}));for(let X of B)if(X.status==="fulfilled")$.set(X.value.key,X.value.hashDir);else console.error(`Warning: failed to resolve hash dir: ${X.reason?.message||"unknown"}`)}return $}async function ZQ(D,F){let $=await T(["git","config",`remote.${F}.annex-uuid`],{cwd:D});if($.exitCode!==0)return null;return $.stdout.trim()||null}async function Eh(D,F,$){return(await T(["git","annex","setpresentkey",F,$,"1"],{cwd:D})).exitCode===0}async function VH(D,F,$){let J=0,Q=0,Y=50;for(let B=0;B<F.length;B+=Y){let X=F.slice(B,B+Y),G=await Promise.all(X.map((H)=>Eh(D,H,$)));for(let H of G)if(H)J++;else Q++}return{success:J,failed:Q}}var Xh,Jh=3,Qh,qQ="nemar-s3",CV0=102400,OV0,jV0,TV0;var r8=S(()=>{ND();pW();Xh=/There is already a special remote named "[^"]+"/;Qh=/^[a-zA-Z0-9._-]+$/;OV0=new Set([".edf",".bdf",".eeg",".vhdr",".vmrk",".set",".fdt",".cnt",".mff",".fif",".nii",".nii.gz",".mat",".bin"]);jV0=n6,TV0=N1});var Nh={};r6(Nh,{writeManifestToS3:()=>NH,serverSideS3Copy:()=>Uh,readManifestFromS3:()=>LQ,parseShardArg:()=>yV0,parseS3Url:()=>UH,listExistingObjects:()=>UQ,keyInShard:()=>MH,isAccessDeniedError:()=>Ah,filterAlreadyCopied:()=>AH,curlStreamCopy:()=>Lh,cleanupStaging:()=>RH,batchServerSideCopy:()=>LH});import{mkdtempSync as PV0,rmSync as IV0,writeFileSync as SV0}from"fs";import{tmpdir as kV0}from"os";import{join as Zh}from"path";function ZH(D){try{return decodeURIComponent(D)}catch{return D}}function UH(D){if(!D)return null;if(D.startsWith("s3://")){let H=D.slice(5),q=H.indexOf("/");if(q<0)return null;let K=H.slice(0,q),V=H.slice(q+1);if(!K||!V)return null;return{bucket:K,key:ZH(V)}}let F;try{F=new URL(D)}catch{return null}if(F.protocol!=="http:"&&F.protocol!=="https:")return null;let $=F.hostname;if(!$.endsWith(".amazonaws.com"))return null;let J=$.split("."),Q=J.findIndex((H)=>H==="s3"||H.startsWith("s3-"));if(Q===-1)return null;let Y=F.pathname.replace(/^\//,"");if(Q===0){let H=J.length===4?J[1]:void 0,q=Y.indexOf("/");if(q<0)return null;let K=Y.slice(0,q),V=Y.slice(q+1);if(!K||!V)return null;return{bucket:K,key:ZH(V),region:H}}let B=J.slice(0,Q).join("."),X=J[Q],G;if(X.startsWith("s3-"))G=X.slice(3);else if(J[Q+1]&&J[Q+1]!=="amazonaws")G=J[Q+1];if(!B||!Y)return null;return{bucket:B,key:ZH(Y),region:G}}async function Uh(D,F,$){let J=`s3://${D.bucket}/${D.key}`,Q=await T(["aws","s3","cp",J,F,"--source-region",D.region??"us-east-1","--region",$,"--only-show-errors"],{});if(Q.exitCode!==0)return{success:!1,error:Q.stderr.trim()||`aws exit ${Q.exitCode}`};return{success:!0}}async function Lh(D,F,$){let J=await T(["bash","-c",`set -o pipefail; curl -sfL '${D}' | aws s3 cp - '${F}' --region '${$}'`],{});if(J.exitCode!==0)return{success:!1,error:J.stderr.trim()||`curl/aws exit ${J.exitCode}`};return{success:!0}}function Ah(D){return/Access ?Denied|\bForbidden\b|\b403\b/i.test(D)}async function LH(D,F,$,J,Q=3){let Y=0,B=0,X=[],G=async(H)=>{let q="no S3 source";if(H.source)for(let K=1;K<=Q;K++){let V=await Uh(H.source,H.destUri,F);if(V.success)return"ok";if(q=V.error??"unknown server-side copy error",Ah(q))break;if(K<Q)await new Promise((z)=>setTimeout(z,K*K*1000))}if(H.httpUrl?.startsWith("http")){let K=await Lh(H.httpUrl,H.destUri,F);if(K.success)return H.source?"fallback":"ok";throw Error(`server-side failed (${q}); fallback failed (${K.error})`)}throw Error(q)};for(let H=0;H<D.length;H+=$){let q=D.slice(H,H+$),K=await Promise.allSettled(q.map((V)=>G(V)));for(let V=0;V<K.length;V++){let z=K[V];if(z.status==="fulfilled"){if(Y++,z.value==="fallback")B++}else X.push({key:q[V].key,error:z.reason instanceof Error?z.reason.message:String(z.reason)})}J?.(Y,D.length,q[q.length-1].key)}return{copied:Y,fellBack:B,failed:X}}async function UQ(D,F,$){let J=new Map,Q=await T(["aws","s3api","list-objects-v2","--bucket",D,"--prefix",F,"--region",$,"--output","json"],{});if(Q.exitCode!==0)throw Error(`list-objects-v2 failed for ${F}: ${Q.stderr.trim()}`);let Y=Q.stdout.trim();if(!Y)return J;let B;try{B=JSON.parse(Y)}catch(X){throw Error(`list-objects-v2 returned unparseable JSON for ${F}: ${X instanceof Error?X.message:String(X)}`)}if(B.IsTruncated===!0||B.NextContinuationToken)throw Error(`list-objects-v2 returned a truncated page for ${F} (auto-pagination disabled?). 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|
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+
`)}}if(Y+=Q.decode(),Y.trim())B=!0,cW(Y,J);let X=(await $).trim(),G=await F.exited;if(G!==0&&!B)throw Error(`git annex whereis failed: ${X}`);if(G!==0){let H=X.match(/whereis:\s*(\d+)\s*failed/);if(H)console.warn(` Warning: ${H[1]} files had no location info (continuing with available files)`);else throw Error(`git annex whereis failed (exit ${G}): ${X}`)}return J}async function zh(D,F){let $=await T(["git","annex","examinekey","--format=${hashdirlower}",F],{cwd:D});if($.exitCode!==0)throw Error(`git annex examinekey failed for ${F}: ${$.stderr.trim()}`);return $.stdout.trim()}async function wV0(D,F){let $=new Map,J=50;for(let Q=0;Q<F.length;Q+=50){let Y=F.slice(Q,Q+50),B=await Promise.allSettled(Y.map(async(X)=>{let G=await zh(D,X);return{key:X,hashDir:G}}));for(let X of B)if(X.status==="fulfilled")$.set(X.value.key,X.value.hashDir);else console.error(`Warning: failed to resolve hash dir: ${X.reason?.message||"unknown"}`)}return $}async function ZQ(D,F){let $=await T(["git","config",`remote.${F}.annex-uuid`],{cwd:D});if($.exitCode!==0)return null;return $.stdout.trim()||null}async function Eh(D,F,$){return(await T(["git","annex","setpresentkey",F,$,"1"],{cwd:D})).exitCode===0}async function VH(D,F,$){let J=0,Q=0,Y=50;for(let B=0;B<F.length;B+=Y){let X=F.slice(B,B+Y),G=await Promise.all(X.map((H)=>Eh(D,H,$)));for(let H of G)if(H)J++;else Q++}return{success:J,failed:Q}}var Xh,Jh=3,Qh,qQ="nemar-s3",CV0=102400,OV0,jV0,TV0;var r8=S(()=>{ND();pW();Xh=/There is already a special remote named "[^"]+"/;Qh=/^[a-zA-Z0-9._-]+$/;OV0=new Set([".edf",".bdf",".eeg",".vhdr",".vmrk",".set",".fdt",".cnt",".mff",".fif",".nii",".nii.gz",".mat",".bin"]);jV0=n6,TV0=N1});var Nh={};r6(Nh,{writeManifestToS3:()=>NH,serverSideS3Copy:()=>Uh,readManifestFromS3:()=>LQ,parseShardArg:()=>yV0,parseS3Url:()=>UH,listExistingObjects:()=>UQ,keyInShard:()=>MH,isAccessDeniedError:()=>Ah,filterAlreadyCopied:()=>AH,curlStreamCopy:()=>Lh,cleanupStaging:()=>RH,batchServerSideCopy:()=>LH});import{mkdtempSync as PV0,rmSync as IV0,writeFileSync as SV0}from"fs";import{tmpdir as kV0}from"os";import{join as Zh}from"path";function ZH(D){try{return decodeURIComponent(D)}catch{return D}}function UH(D){if(!D)return null;if(D.startsWith("s3://")){let H=D.slice(5),q=H.indexOf("/");if(q<0)return null;let K=H.slice(0,q),V=H.slice(q+1);if(!K||!V)return null;return{bucket:K,key:ZH(V)}}let F;try{F=new URL(D)}catch{return null}if(F.protocol!=="http:"&&F.protocol!=="https:")return null;let $=F.hostname;if(!$.endsWith(".amazonaws.com"))return null;let J=$.split("."),Q=J.findIndex((H)=>H==="s3"||H.startsWith("s3-"));if(Q===-1)return null;let Y=F.pathname.replace(/^\//,"");if(Q===0){let H=J.length===4?J[1]:void 0,q=Y.indexOf("/");if(q<0)return null;let K=Y.slice(0,q),V=Y.slice(q+1);if(!K||!V)return null;return{bucket:K,key:ZH(V),region:H}}let B=J.slice(0,Q).join("."),X=J[Q],G;if(X.startsWith("s3-"))G=X.slice(3);else if(J[Q+1]&&J[Q+1]!=="amazonaws")G=J[Q+1];if(!B||!Y)return null;return{bucket:B,key:ZH(Y),region:G}}async function Uh(D,F,$){let J=`s3://${D.bucket}/${D.key}`,Q=await T(["aws","s3","cp",J,F,"--source-region",D.region??"us-east-1","--region",$,"--only-show-errors"],{});if(Q.exitCode!==0)return{success:!1,error:Q.stderr.trim()||`aws exit ${Q.exitCode}`};return{success:!0}}async function Lh(D,F,$){let J=await T(["bash","-c",`set -o pipefail; curl -sfL '${D}' | aws s3 cp - '${F}' --region '${$}'`],{});if(J.exitCode!==0)return{success:!1,error:J.stderr.trim()||`curl/aws exit ${J.exitCode}`};return{success:!0}}function Ah(D){return/AccessDenied|\bForbidden\b|\b403\b/i.test(D)}async function LH(D,F,$,J,Q=3){let Y=0,B=0,X=[],G=async(H)=>{let q="no S3 source";if(H.source)for(let K=1;K<=Q;K++){let V=await Uh(H.source,H.destUri,F);if(V.success)return"ok";if(q=V.error??"unknown server-side copy error",Ah(q))break;if(K<Q)await new Promise((z)=>setTimeout(z,K*K*1000))}if(H.httpUrl?.startsWith("http")){let K=await Lh(H.httpUrl,H.destUri,F);if(K.success)return H.source?"fallback":"ok";throw Error(`server-side failed (${q}); fallback failed (${K.error})`)}throw Error(q)};for(let H=0;H<D.length;H+=$){let q=D.slice(H,H+$),K=await Promise.allSettled(q.map((V)=>G(V)));for(let V=0;V<K.length;V++){let z=K[V];if(z.status==="fulfilled"){if(Y++,z.value==="fallback")B++}else X.push({key:q[V].key,error:z.reason instanceof Error?z.reason.message:String(z.reason)})}J?.(Y,D.length,q[q.length-1].key)}return{copied:Y,fellBack:B,failed:X}}async function UQ(D,F,$){let J=new Map,Q=await T(["aws","s3api","list-objects-v2","--bucket",D,"--prefix",F,"--region",$,"--output","json"],{});if(Q.exitCode!==0)throw Error(`list-objects-v2 failed for ${F}: ${Q.stderr.trim()}`);let Y=Q.stdout.trim();if(!Y)return J;let B;try{B=JSON.parse(Y)}catch(X){throw Error(`list-objects-v2 returned unparseable JSON for ${F}: ${X instanceof Error?X.message:String(X)}`)}if(B.IsTruncated===!0||B.NextContinuationToken)throw Error(`list-objects-v2 returned a truncated page for ${F} (auto-pagination disabled?). Refusing to proceed on a partial destination view.`);for(let X of B.Contents??[]){if(typeof X.Key!=="string")continue;if(!X.Key.startsWith(F))continue;let G=X.Key.slice(F.length);if(G.length===0)continue;J.set(G,typeof X.Size==="number"?X.Size:0)}return J}function AH(D,F,$){let J=[],Q=[];for(let Y of D){if(!F.has(Y.key)){J.push(Y);continue}let B=$?.get(Y.key);if(B!==void 0&&F.get(Y.key)!==B)J.push(Y);else Q.push(Y.key)}return{toCopy:J,skipped:Q}}function vV0(D){let F=2166136261;for(let $=0;$<D.length;$++)F^=D.charCodeAt($),F=Math.imul(F,16777619);return F>>>0}function yV0(D){let F=D.match(/^(\d+)\/(\d+)$/);if(!F)throw Error(`Invalid --shard "${D}". Expected "i/N" (e.g. "0/8").`);let $=Number(F[1]),J=Number(F[2]);if(J<1)throw Error(`Invalid shard count in "${D}": N must be >= 1.`);if($<0||$>=J)throw Error(`Invalid shard index in "${D}": i must satisfy 0 <= i < N.`);return{index:$,count:J}}function MH(D,F,$){if($<=1)return!0;return vV0(D)%$===F}function Mh(D,F){return`s3://${D}/${F}/staging/import-manifest.json`}async function xV0(D,F,$){let J=PV0(Zh(kV0(),"nemar-staging-")),Q=Zh(J,"payload.json");try{SV0(Q,JSON.stringify(D));let Y=await T(["aws","s3","cp",Q,F,"--region",$,"--content-type","application/json"],{});if(Y.exitCode!==0)throw Error(`Failed to write ${F}: ${Y.stderr.trim()}`)}finally{IV0(J,{recursive:!0,force:!0})}}async function _V0(D,F){let $=await T(["aws","s3","cp",D,"-","--region",F],{});if($.exitCode!==0)throw Error(`Failed to read ${D}: ${$.stderr.trim()}`);try{return JSON.parse($.stdout)}catch(J){throw Error(`Failed to parse JSON from ${D} (corrupt or truncated staging object): ${J instanceof Error?J.message:String(J)}`)}}async function NH(D,F,$){await xV0(D,Mh(F,D.nemarId),$)}async function LQ(D,F,$){return _V0(Mh(F,D),$)}async function RH(D,F,$){let J=await T(["aws","s3","rm",`s3://${F}/${D}/staging/`,"--recursive","--region",$],{});if(J.exitCode!==0)console.warn(` Staging cleanup failed (non-fatal): ${J.stderr.trim()}`)}var CH=S(()=>{r8()});var jH={};r6(jH,{seedMetadata:()=>_h,prepareImport:()=>gh,openNeuroCurrentUrl:()=>Sh,isNeverAnnexedMetadata:()=>Th,importOpenNeuro:()=>aV0,findAnnexedRootMetadata:()=>Ph,finalizeImport:()=>bh,ensureRootMetadataUnannexed:()=>kh,ensureReadmeMd:()=>fh,detectModalitiesFromDataset:()=>yh,decideSkipCiCheck:()=>jh,copyShard:()=>hh,coerceFunding:()=>xh,OPENNEURO_UPSTREAM_MARKER:()=>Ih});import{existsSync as Ch,mkdirSync as fV0,mkdtempSync as Oh,readFileSync as gV0,readdirSync as b9,readlinkSync as hV0,renameSync as bV0,rmSync as uV0,writeFileSync as OH}from"fs";import{tmpdir as wh}from"os";import{join as sD}from"path";async function pV0(D,F,$=120000,J=5000){let Q=Date.now()+$,Y,B=!1;while(Date.now()<Q){try{let G=await JQ(D);if(B=!0,G.bids_validation.present&&G.bids_validation.status!=="no_runs")return{kind:"found"}}catch(G){Y=G}let X=Math.max(0,Q-Date.now());F.text=`Waiting for BIDS validation run to register... (${Math.ceil(X/1000)}s left)`,await new Promise((G)=>setTimeout(G,Math.min(J,X)))}if(!B&&Y!==void 0)return{kind:"error",lastError:Y};return{kind:"timeout"}}function jh(D){if(!D.ciDeployed)return{skipCiCheck:!1,abortReason:"CI workflows did not deploy. Aborting before approval: --trust-upstream bypasses validation lookup, not workflow deployment. Re-run after fixing the deploy failure, or run `nemar admin ci add <id>` manually before approving."};let F=D.poll;if(F===null||F.kind==="found")return{skipCiCheck:!1};if(F.kind==="error")return{skipCiCheck:!1,abortReason:`Every BIDS validation poll attempt failed (last error: ${F.lastError instanceof Error?F.lastError.message:String(F.lastError)}). Refusing to bypass under --trust-upstream because validation state was never actually observed. Investigate API/auth health and re-run.`};if(D.trustUpstream)return{skipCiCheck:!0};return{skipCiCheck:!1,abortReason:"BIDS validation run did not register within the bounded poll window. Re-run with --trust-upstream to bypass (OpenNeuro datasets are pre-validated upstream), or investigate why the deployed CI did not trigger."}}function wH(D){let F=D.match(/^ds(\d{6})$/);if(!F)throw Error(`Invalid OpenNeuro ID "${D}". Expected format: ds###### (e.g., ds007262)`);return`on${F[1]}`}function Th(D){let F=D.toLowerCase();if(F.startsWith("readme")||F.startsWith("license")||F.startsWith("changes"))return!0;if(F===".bidsignore"||F===".gitignore")return!0;return/\.(tsv|json|md|txt|yml|yaml)$/.test(F)}function Ph(D){let F;try{F=b9(D,{withFileTypes:!0})}catch(J){let Q=J.code;if(Q==="ENOENT"||Q==="ENOTDIR")return[];throw Error(`Cannot scan ${D} for annexed metadata: ${J instanceof Error?J.message:String(J)}`)}let $=[];for(let J of F){if(!J.isSymbolicLink())continue;if(!Th(J.name))continue;try{if(hV0(sD(D,J.name)).includes("annex/objects"))$.push(J.name)}catch{}}return $.sort()}function Sh(D,F){let $=F.split("/").map(encodeURIComponent).join("/");return`https://s3.amazonaws.com/openneuro.org/${D}/${$}`}async function kh(D,F){let $=Ph(D);if($.length===0)return[];let J=[];for(let Y of $){let B=Sh(F,Y),X;try{let H=await fetch(B);if(!H.ok){J.push(`${Y} (HTTP ${H.status})`);continue}X=Buffer.from(await H.arrayBuffer())}catch(H){J.push(`${Y} (fetch failed: ${H instanceof Error?H.message:String(H)})`);continue}if(X.length===0){J.push(`${Y} (HTTP 200 but empty body)`);continue}let G=sD(D,Y);try{uV0(G,{force:!0}),OH(G,X)}catch(H){throw Error(`Failed to write fetched metadata ${Y} to ${G} (local error, not OpenNeuro): ${H instanceof Error?H.message:String(H)}`)}}if(J.length>0)throw Error(`${Ih} cannot fetch metadata from OpenNeuro: ${J.join(", ")}. These objects are not anonymously readable and NEMAR has no signed OpenNeuro login. This is an OpenNeuro-side access problem, not a NEMAR import bug. (Any files that did fetch are left as regular files on disk, unstaged.)`);let Q=await T(["git","-c","annex.largefiles=nothing","add",...$],{cwd:D});if(Q.exitCode!==0)throw Error(`Failed to stage un-annexed metadata (${$.join(", ")}): ${Q.stderr.trim()}. The files are already regular files on disk; recover with: git -C ${D} -c annex.largefiles=nothing add ${$.join(" ")}`);return $}function dV0(D){let F=sD(D,"dataset_description.json");if(!Ch(F))throw Error(`dataset_description.json not found at ${F}`);try{return JSON.parse(gV0(F,"utf-8"))}catch($){throw Error(`Failed to parse dataset_description.json at ${F}: ${$ instanceof Error?$.message:String($)}`)}}function vh(){let D=process.env.AWS_ACCESS_KEY_ID,F=process.env.AWS_SECRET_ACCESS_KEY;if(!D||!F)throw Error("AWS_ACCESS_KEY_ID and AWS_SECRET_ACCESS_KEY must be set in environment for S3 operations");return{accessKeyId:D,secretAccessKey:F,sessionToken:process.env.AWS_SESSION_TOKEN}}function cV0(D){return typeof D.DatasetDOI==="string"?D.DatasetDOI.replace(/^doi:/,""):null}function yh(D){let F=new Set,$=[];try{$=b9(D,{withFileTypes:!0}).filter((J)=>J.isDirectory()&&J.name.startsWith("sub-")).map((J)=>J.name)}catch{return[]}for(let J of $){let Q=sD(D,J),Y=[];try{Y=b9(Q,{withFileTypes:!0})}catch{continue}for(let B of Y){if(!B.isDirectory())continue;if(B.name.startsWith("ses-")){let X=[];try{X=b9(sD(Q,B.name),{withFileTypes:!0})}catch{continue}for(let G of X)if(G.isDirectory()&&Rh.includes(G.name))F.add(G.name)}else if(Rh.includes(B.name))F.add(B.name)}}return[...F].sort()}function xh(D){let F=D.Funding;if(!Array.isArray(F))return[];return F.filter(($)=>typeof $==="string"&&$.trim().length>0).map(($)=>({funder_name:$.trim()}))}function _h(D,F,$,J,Q){let Y=sD(D,".nemar");if(!Ch(Y))fV0(Y,{recursive:!0});let B=Q?[{identifier:Q,identifier_type:"DOI",relation_type:"IsIdenticalTo"}]:[],X=yh(D),G=xh(J),H={version:"2.0",dataset_id:F,source:"openneuro",source_id:$,title:J.Name||F,authors:Array.isArray(J.Authors)?Object.fromEntries(J.Authors.map((q)=>[q,{}])):{},license:J.License||"CC0",dataset_type:J.DatasetType||"raw",related_identifiers:B,pipeline_stage:"seeded"};if(typeof J.BIDSVersion==="string")H.bids_version=J.BIDSVersion;if(X.length>0)H.recording_modality=X;if(X.length>0)H.datatypes=X;if(G.length>0)H.funding_references=G;if(typeof J.Acknowledgements==="string"&&J.Acknowledgements.trim().length>0)H.acknowledgements=J.Acknowledgements.trim();OH(sD(Y,"metadata.json"),`${JSON.stringify(H,null,2)}
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`)}function fh(D,F,$){let Q=b9(D,{withFileTypes:!0}).filter((K)=>K.isFile()&&nV0.test(K.name)),Y=Q.find((K)=>K.name.includes("."));if(Y)return{kind:"kept",path:Y.name};let B=Q.find((K)=>!K.name.includes("."));if(B)return bV0(sD(D,B.name),sD(D,"README.md")),{kind:"renamed",from:"README",to:"README.md"};let X="<!-- nemar:provenance -->",G=`https://openneuro.org/datasets/${F}`,H=$?`
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- DOI: [${$}](https://doi.org/${$})`:"",q=`${X}
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## Provenance
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package/package.json
CHANGED