npm - nemar-cli - Versions diffs - 0.10.18-dev.3417 → 0.10.18-dev.3427 - Mend

nemar-cli 0.10.18-dev.3417 → 0.10.18-dev.3427

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Files changed (2) hide show

package/dist/index.js +3 -3
package/package.json +1 -1

package/dist/index.js CHANGED Viewed

@@ -99,7 +99,7 @@ ${t}`,eIe,tIe,rIe=(e,t,r)=>{let n=r===""?"":`with ${r.trim()}() `,i=Q6e.bind(nul
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dse(r[2],this.options.loose)}toString(){return this.value}test(e){if(CC("Comparator.test",e,this.options.loose),this.semver===Oh||e===Oh)return!0;if(typeof e==="string")try{e=new dse(e,this.options)}catch(t){return!1}return kC(e,this.operator,this.semver,this.options)}intersects(e,t){if(!(e instanceof Kw))throw TypeError("a Comparator is required");if(this.operator===""){if(this.value==="")return!0;return new fse(e.value,t).test(this.value)}else if(e.operator===""){if(e.value==="")return!0;return new fse(this.value,t).test(e.semver)}if(t=cse(t),t.includePrerelease&&(this.value==="<0.0.0-0"||e.value==="<0.0.0-0"))return!1;if(!t.includePrerelease&&(this.value.startsWith("<0.0.0")||e.value.startsWith("<0.0.0")))return!1;if(this.operator.startsWith(">")&&e.operator.startsWith(">"))return!0;if(this.operator.startsWith("<")&&e.operator.startsWith("<"))return!0;if(this.semver.version===e.semver.version&&this.operator.includes("=")&&e.operator.includes("="))return!0;if(kC(this.semver,"<",e.semver,t)&&this.operator.startsWith(">")&&e.operator.startsWith("<"))return!0;if(kC(this.semver,">",e.semver,t)&&this.operator.startsWith("<")&&e.operator.startsWith(">"))return!0;return!1}}pse.exports=Kw;var cse=Nw(),{safeRe:lse,t:use}=Bf(),kC=$C(),CC=kh(),dse=Jr(),fse=Oi()});var Th=y(function($Ct,mse){var eQe=Oi(),tQe=(e,t,r)=>{try{t=new eQe(t,r)}catch(n){return!1}return t.test(e)};mse.exports=tQe});var gse=y(function(kCt,hse){var rQe=Oi(),nQe=(e,t)=>new rQe(e,t).set.map((r)=>r.map((n)=>n.value).join(" 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Ose=y(function(FCt,Ase){var vQe=Jw(),_Qe=(e,t,r)=>vQe(e,t,">",r);Ase.exports=_Qe});var Fse=y(function(PCt,Tse){var DQe=Jw(),EQe=(e,t,r)=>DQe(e,t,"<",r);Tse.exports=EQe});var Nse=y(function(ICt,Ise){var Pse=Oi(),SQe=(e,t,r)=>(e=new Pse(e,r),t=new Pse(t,r),e.intersects(t,r));Ise.exports=SQe});var Mse=y(function(NCt,jse){var $Qe=Th(),kQe=Ai();jse.exports=(e,t,r)=>{let n=[],i=null,o=null,s=e.sort((d,f)=>kQe(d,f,r));for(let d of s)if($Qe(d,t,r)){if(o=d,!i)i=d}else{if(o)n.push([i,o]);o=null,i=null}if(i)n.push([i,null]);let a=[];for(let[d,f]of n)if(d===f)a.push(d);else if(!f&&d===s[0])a.push("*");else if(!f)a.push(`>=${d}`);else if(d===s[0])a.push(`<=${f}`);else a.push(`${d} - ${f}`);let c=a.join(" || "),u=typeof t.raw==="string"?t.raw:String(t);return c.length<u.length?c:t}});var Vse=y(function(jCt,zse){var qse=Oi(),TC=Ah(),{ANY:AC}=TC,OC=Th(),FC=Ai(),CQe=(e,t,r={})=>{if(e===t)return!0;e=new qse(e,r),t=new qse(t,r);let n=!1;e:for(let i of e.set){for(let o of t.set){let 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a,c,u,d,f=o&&!r.includePrerelease&&o.semver.prerelease.length?o.semver:!1,m=i&&!r.includePrerelease&&i.semver.prerelease.length?i.semver:!1;if(f&&f.prerelease.length===1&&o.operator==="<"&&f.prerelease[0]===0)f=!1;for(let p of t){if(d=d||p.operator===">"||p.operator===">=",u=u||p.operator==="<"||p.operator==="<=",i){if(m){if(p.semver.prerelease&&p.semver.prerelease.length&&p.semver.major===m.major&&p.semver.minor===m.minor&&p.semver.patch===m.patch)m=!1}if(p.operator===">"||p.operator===">="){if(a=Bse(i,p,r),a===p&&a!==i)return!1}else if(i.operator===">="&&!p.test(i.semver))return!1}if(o){if(f){if(p.semver.prerelease&&p.semver.prerelease.length&&p.semver.major===f.major&&p.semver.minor===f.minor&&p.semver.patch===f.patch)f=!1}if(p.operator==="<"||p.operator==="<="){if(c=Use(o,p,r),c===p&&c!==o)return!1}else 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Uf=Bf(),Yw=Lf(),OQe=Jr(),Xw=_C(),TQe=zc(),FQe=moe(),PQe=goe(),IQe=xoe(),NQe=_oe(),jQe=Eoe(),MQe=$oe(),qQe=Coe(),LQe=Aoe(),BQe=Ai(),UQe=Poe(),zQe=Noe(),VQe=Bw(),HQe=Loe(),GQe=Uoe(),WQe=Ch(),KQe=Uw(),JQe=EC(),YQe=SC(),XQe=zw(),ZQe=Vw(),QQe=$C(),eet=Xoe(),tet=ese(),ret=Ah(),net=Oi(),iet=Th(),oet=gse(),set=bse(),aet=wse(),cet=Dse(),uet=Sse(),det=Jw(),fet=Ose(),pet=Fse(),met=Nse(),het=Mse(),get=Vse();Hse.exports={parse:TQe,valid:FQe,clean:PQe,inc:IQe,diff:NQe,major:jQe,minor:MQe,patch:qQe,prerelease:LQe,compare:BQe,rcompare:UQe,compareLoose:zQe,compareBuild:VQe,sort:HQe,rsort:GQe,gt:WQe,lt:KQe,eq:JQe,neq:YQe,gte:XQe,lte:ZQe,cmp:QQe,coerce:eet,truncate:tet,Comparator:ret,Range:net,satisfies:iet,toComparators:oet,maxSatisfying:set,minSatisfying:aet,minVersion:cet,validRange:uet,outside:det,gtr:fet,ltr:pet,intersects:met,simplifyRange:het,subset:get,SemVer:OQe,re:Uf.re,src:Uf.src,tokens:Uf.t,SEMVER_SPEC_VERSION:Yw.SEMVER_SPEC_VERSION,RELEASE_TYPES:Yw.RELEASE_TYPES,compareIdentifiers:Xw.compareIdentifiers,rcompareIdentifiers:Xw.rcompareIdentifiers}});function ds(e){let t="";for(let r of e)if(/\p{Lu}/u.test(r))t+="A";else if(/\p{L}/u.test(r))t+="a";else if(/\p{N}/u.test(r))t+="9";else if(/^[ -~]$/.test(r))t+=r;else t+="?";return t.replace(/(.)\1{2,}/g,"$1+")}function tv(e){return IC.has(e.toLowerCase())}function Yse(e){return tv(e)||_et.test(e)||/^\d+$/.test(e)}function Xse(e){let t=e.toLowerCase();return xet.has(t)||IC.has(t)}function $et(e,t){if(e===""||Yse(e))return!1;let r=t?(i)=>wet.has(i.toLowerCase())||vet.has(i.toLowerCase()):Xse;if(/^[\p{L}'._-]+$/u.test(e)){let i=e.split(/['._-]+/).filter((o)=>o!=="");return i.length>0&&!i.every(r)}return(e.match(/\p{L}+/gu)??[]).some((i)=>i.length>=4&&!r(i))}function zf(e,t=!1){if(e===""||Yse(e))return!1;return e.split(Eet).some((r)=>$et(r,t))}function Kse(e,t,r){for(let n=t;n<r;n++)if(e[n]>=128)return!0;return!1}function Zse(e,t,r){let n="";for(let i=t;i<r;i++){let o=e[i];n+=o===0?" 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i=n===""?[]:n.split(/\s+/),o=Ih(n),s=new Set,a=(w,D)=>{if(s.has(w))return;s.add(w),r("edf-patient-birthdate","identifier",w,D)};for(let w of o)if(!Qse(w.candidates))a("patient.birthdate",w.text);let c=["m","f","x","male","female"],u=i.length>=4&&c.includes(i[1].toLowerCase()),d=(w)=>Ph(w,Ih(w)).trim();if(u){let[w,,D,C]=i;if(zf(d(w),!0))r("edf-patient-code","identifier","patient.code",w);if(zf(d(C),!0))r("edf-patient-name","identifier","patient.name",C);if(!(D==="X"||tv(D)||/^(19|20)\d{2}$/.test(D)||/^\d{1,3}y?$/i.test(D)||Ih(D).length>0))a("patient.birthdate",D);let A=i.slice(4).map(d);if(A.some((T)=>zf(T)))r("edf-patient-freetext","identifier","patient.additional",A.join(" "))}else if(Ph(n,o).split(/\s+/).filter((D)=>D!=="").some((D)=>zf(D)))r("edf-patient-freetext","identifier","patient",n);let f=Ph(n,o),p=(()=>{let w=(O,N)=>N>=90&&N<=130?O:void 0,D=u?i[2]:"",C=/^(\d{2,3})y?$/i.exec(D);if(C)return w(D,Number(C[1]));let E=[/\bage[=: 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Set(["timeout","network","deadline","credentials-missing","header-truncated","json-parse","no-body","short-body","unreadable-entry","superseded-absent","blob-missing","blob-closed","internal","error-error","error-rangeerror","error-typeerror","error-syntaxerror","error-referenceerror","error-evalerror","error-urierror","error-aborterror","error-timeouterror"]),Jet=/^http-[1-5]\d\d$/;Yet=/^\d{4}-\d{2}-\d{2}T\d{2}:\d{2}:\d{2}(\.\d{1,3})?Z$/;Qet={pending:{verdict:"running",tone:"note"},clean:{verdict:"clean",tone:"ok"},"dates-only":{verdict:"clean (acquisition dates only)",tone:"ok"},"no-recordings":{verdict:"clean (no recordings)",tone:"ok"},review:{verdict:"needs review",tone:"warn"},"direct-identifiers":{verdict:"FOUND IDENTIFIERS",tone:"stop"},unchecked:{verdict:"INCOMPLETE",tone:"warn"},"not-screened":{verdict:"recordings NOT screened",tone:"warn"},"clean-edf-only-others-unscreened":{verdict:"EDF/BDF clean, other recordings NOT screened",tone:"warn"},error:{verdict:"DID NOT RUN",tone:"stop"},unreported:{verdict:"DID NOT REPORT",tone:"stop"}};dae=["NEMAR does not change them.","A date can help identify a participant when it is combined with other information.","Remove or coarsen any date that could identify someone before uploading or requesting publication.","Administrators are told of these findings when publication is requested."];yae=new Set([...LC,...rv.map((e)=>`${e}/`),".eeg",".vmrk",".mef",".kdf",".mrk",".elp",".hsp",".raw",".mhd",".tsv.gz","(no extension)",hae]);cae=["scanned_at","status","incomplete","incomplete_reasons","files","findings_by_kind","edf_bdf_files_flagged","unscreened_formats","read_failures"],lv=VC.filter((e)=>Hc(e)==="acknowledge"),ntt=/^nemar-cli@\d{1,4}\.\d{1,4}\.\d{1,6}(-[0-9a-z.]{1,24})?$/});var{spawn:ztt}=globalThis.Bun;async function tu(){try{return await ztt({cmd:["aws","--version"],stdout:"pipe",stderr:"pipe"}).exited===0}catch{return!1}}function uR(e){let t=e.split(`
 `).map((r)=>r.trim()).filter(Boolean);return t[t.length-1]??""}async function Dv(e){let{credentials:t,bucket:r,region:n,prefix:i}=e,o={bucket:r,prefix:i,object:null};if(!await tu())return{...o,outcome:"unavailable",detail:"the aws CLI is not on PATH"};let s={AWS_ACCESS_KEY_ID:t.access_key_id,AWS_SECRET_ACCESS_KEY:t.secret_access_key,AWS_SESSION_TOKEN:t.session_token,AWS_DEFAULT_REGION:n},a=["AWS_PROFILE","AWS_DEFAULT_PROFILE"],c;try{c=await k(["aws","s3api","list-objects-v2","--bucket",r,"--prefix",`${i.replace(/\/$/,"")}/`,"--max-keys","1","--query","Contents[0].Key","--output","text"],{env:s,unsetEnv:a,timeout:60000})}catch(f){return{...o,outcome:"inconclusive",detail:f instanceof Error?f.message:String(f)}}if(c.timedOut)return{...o,outcome:"inconclusive",detail:"the listing timed out"};if(c.exitCode!==0){let f=uR(c.stderr);return/AccessDenied|InvalidAccessKeyId|ExpiredToken|SignatureDoesNotMatch|NoSuchBucket|403|404|An error occurred/i.test(f)?{...o,outcome:"refused",detail:f}:{...o,outcome:"inconclusive",detail:f}}let u=c.stdout.trim();if(!u||u==="None")return{...o,outcome:"empty-prefix"};let d;try{d=await k(["aws","s3api","head-object","--bucket",r,"--key",u],{env:s,unsetEnv:a,timeout:60000})}catch(f){return{...o,object:u,outcome:"inconclusive",detail:f instanceof Error?f.message:String(f)}}if(d.timedOut)return{...o,object:u,outcome:"inconclusive",detail:"the read timed out"};if(d.exitCode!==0){let f=uR(d.stderr);return/AccessDenied|InvalidAccessKeyId|ExpiredToken|SignatureDoesNotMatch|403|404|An error occurred/i.test(f)?{...o,object:u,outcome:"refused",detail:f}:{...o,object:u,outcome:"inconclusive",detail:f}}return{...o,object:u,outcome:"reachable"}}async function nce(e){let{credentials:t,bucket:r,region:n,prefix:i,keys:o}=e;if(o.length===0)return[];if(!await tu())return o.map((m)=>({key:m,outcome:"unknown",detail:"the aws CLI is not on PATH"}));let s=t?{AWS_ACCESS_KEY_ID:t.access_key_id,AWS_SECRET_ACCESS_KEY:t.secret_access_key,AWS_SESSION_TOKEN:t.session_token,AWS_DEFAULT_REGION:n}:{AWS_DEFAULT_REGION:n},a=t?["AWS_PROFILE","AWS_DEFAULT_PROFILE"]:[],c=`${i.replace(/\/$/,"")}/`,u=Array(o.length),d=0;async function f(){while(!0){let m=d++;if(m>=o.length)return;let p=o[m],g;try{g=await k(["aws","s3api","head-object","--bucket",r,"--key",`${c}${p}`],{env:s,unsetEnv:a,timeout:60000})}catch(b){u[m]={key:p,outcome:"unknown",detail:b instanceof Error?b.message:String(b)};continue}if(g.exitCode===0){u[m]={key:p,outcome:"present"};continue}let h=uR(g.stderr);u[m]=/404|Not Found/i.test(h)?{key:p,outcome:"absent"}:{key:p,outcome:"unknown",detail:h}}}return await Promise.all(Array.from({length:Math.min(Vtt,o.length)},()=>f())),u}async function ice(e){let{credentials:t,bucket:r,region:n,prefix:i}=e;if(!await tu())throw Error("the aws CLI is not on PATH, so the bucket cannot be listed");let o=`${i.replace(/\/$/,"")}/`,{stdout:s,stderr:a,exitCode:c,timedOut:u}=await k(["aws","s3api","list-objects-v2","--bucket",r,"--prefix",o,"--query","Contents[].[Key,Size]","--output","text","--page-size","1000"],{env:{AWS_ACCESS_KEY_ID:t.access_key_id,AWS_SECRET_ACCESS_KEY:t.secret_access_key,AWS_SESSION_TOKEN:t.session_token,AWS_DEFAULT_REGION:n},unsetEnv:["AWS_PROFILE","AWS_DEFAULT_PROFILE","AWS_ENDPOINT_URL","AWS_ENDPOINT_URL_S3"],timeout:600000});if(c!==0||u)throw Error(`listing s3://${r}/${o} failed: ${u?"timed out":a.trim()||`exit ${c}`}`);return Htt(s,o)}function Htt(e,t){let r=t.endsWith("/")?t:`${t}/`,n=new Map;for(let i of e.split(`
 `)){let o=i.trim();if(!o||o==="None")continue;let s=o.lastIndexOf("\t")>=0?o.lastIndexOf("\t"):o.lastIndexOf(" ");if(s<0)continue;let a=o.slice(0,s).trimEnd(),c=Number(o.slice(s+1).trim());if(!a.startsWith(r))continue;let u=a.slice(r.length);if(!Number.isFinite(c))continue;if(u&&!u.includes("/"))n.set(u,c)}return n}var Vtt=8;var Xf=I(()=>{It()});function Er(e){return{accessKeyId:e.access_key_id,secretAccessKey:e.secret_access_key,sessionToken:e.session_token}}function fR(e){let t=[/^\(merging .* into .*\.\.\.\)$/,/^\(recording state in git\.\.\.\)$/,/^\(scanning for /,/^\(checking /];return e.split(`
 `).filter((r)=>{let n=r.trim();if(!n)return!1;if(n.includes("setting annex-ignore"))return!1;if(t.some((i)=>i.test(n)))return!1;return!0}).join(`
@@ -193,7 +193,7 @@ Privacy correction ${e}: ${n}. The checksums in the provenance file describe the
 ${m}`:", ";return`${e.slice(0,c)}${g}${p}${e.slice(c)}`}function sg(e){try{return ag(e).isFile()}catch{return!1}}async function Hit(e,t){for(let r of ln(t))if((await k(["git","-c","annex.largefiles=nothing","add","--",...r],{cwd:e})).exitCode!==0)throw Error(`git add failed for ${r.length} scrubbed file(s)`)}function Git(e){let t=Ii(e,ng);if(!_it(t))return!1;let r;try{r=Lle(t)}catch{return!0}let n=!1;for(let i of r){if(i.action==="history-rewritten")n=!1;if(i.action==="import-scrubbed"&&((i.counts.json_values_blanked??0)>0||(i.counts.git_held_recordings_scrubbed??0)>0))n=!0}return n}async function Wit(e){try{return await Kit(e)}catch(t){if(t instanceof Bt)throw t;throw new Bt("scrub-failed",cg(t))}}async function Kit(e){let{datasetPath:t}=e,r=Bit(),n=[...await iu(t)].sort(),i=await Ti(t),o=n.filter((B)=>gue.test(B));r.recordings=o.length;let s=!e.reimport,a=[],c=[],u=new Set,d=[];for(let B of o){let re=i.get(B);if(re===void 0){a.push(B);continue}if(e.skipData){r.headers_not_read_skip_data++;continue}if(ti(re)===0){r.headers_not_edf++,u.add(re);continue}let Z=e.keyUrlMap.get(re);if(Z===void 0){if(e.reimport)r.headers_not_read_nemar_held++;else r.headers_not_read_no_source++;continue}let J=Cv(Z),rt=J?{kind:"s3",ref:J}:/^https?:\/\//.test(Z)?{kind:"url",url:Z}:null;if(!rt){d.push("source-unsupported");continue}c.push({path:B,key:re,source:rt})}let f=[];for(let B of a){let re=XR(Ii(t,B));if(re===null){d.push("local-unreadable");continue}r.headers_read++;let Z=ZR(re,s);if(Z===null){r.headers_not_edf++;continue}if(Z.change.datesLeft)r.headers_dates_left++;if(Z.change.datesUnproven)r.headers_dates_unproven++;if(Z.change.scrub||Z.change.dates)f.push({path:B,change:Z.change})}let m=await Uit(c,e.concurrency??16,(B)=>e.reader.header(B.source)),p=[...d],g=[],h=[];if(m.forEach((B,re)=>{let Z=c[re];if(!B.ok){p.push(B.failure);return}let J=ti(Z.key);if(J!==null&&B.total===null){p.push("no-length");return}if(J!==null&&B.total!==J){g.push(Z.key);return}r.headers_read++,u.add(Z.key);let rt=ZR(B.bytes,s);if(rt===null){r.headers_not_edf++;return}if(rt.change.datesLeft)r.headers_dates_left++;if(rt.change.datesUnproven)r.headers_dates_unproven++;if(rt.change.scrub||rt.change.dates)h.push({...Z,size:J??0,change:rt.change})}),p.length>0){let B=p.every((re)=>re==="http-403"||re==="http-404");throw new Bt("header-unreadable",`${p.length} of ${o.length} recording header(s) could not be read: ${zit(p)}`,B)}if(g.length>0)throw new Bt("upstream-size-mismatch",`${g.length} upstream object(s) are not the size their annex key declares`);let b=h.filter((B)=>B.change.scrub),x=f.filter((B)=>B.change.scrub),w=b.length+x.length;if(e.reimport&&w>0)throw new Bt("already-imported-unscrubbed",`${w} recording(s) in the dataset's own tree need a scrub; correct it with ADR 0085's procedure, not by re-importing`);let D=(B)=>rl.test(B.key)&&B.size>0;if(b.some((B)=>!D(B))){let B=b.filter((re)=>!D(re)).length;throw new Bt("unsupported-key-backend",`${B} recording key(s) to replace are not SHA256E with a declared size`)}let C=e.maxBytes??LR,E=b.reduce((B,re)=>B+re.size,0),A=e.unannexedData.reduce((B,re)=>B+re.size,0);if(E+A>C)throw new Bt("bound-exceeded",`${b.length} recording(s) to scrub, ${(E/1073741824).toFixed(1)} GiB to download and ${(A/1073741824).toFixed(1)} GiB of git-held data to upload, over the ${(C/1073741824).toFixed(1)} GiB bound; run on a host that can move them with --normalize-max-gb`);let T=h.filter((B)=>!B.change.scrub),L=T.filter(D);r.headers_dates_left+=T.length-L.length;let O=L.reduce((B,re)=>B+re.size,0),N=E+A+O<=C;if(!N)r.headers_dates_over_bound=L.length,r.headers_dates_left+=L.length;let W=new Set(N?L:[]),F=h.filter((B)=>B.change.scrub||W.has(B)),H=[];for(let B of F){let re=Ii(t,B.path),Z=`${re}.nemar-scrub-download`,J=await e.reader.download(B.source,Z);if(!B.change.scrub){let si=rl.exec(B.key)?.[2],vs=J.ok&&J.bytes===B.size&&await fue(Z)===si;if(vs)try{YR(Z,s)}catch{vs=!1}if(!vs){nl(Z,{force:!0}),r.headers_dates_failed++,r.headers_dates_left++;continue}r.bytes_downloaded+=B.size,nl(re,{force:!0}),aue(Z,re),H.push(B);continue}if(!J.ok)throw new Bt("header-unreadable",`a recording to scrub could not be downloaded: ${J.failure}`,J.failure==="http-403"||J.failure==="http-404");let rt=rl.exec(B.key)?.[2];if(J.bytes!==B.size||await fue(Z)!==rt)throw nl(Z,{force:!0}),new Bt("content-mismatch","a downloaded recording does not hash to the key it was downloaded for");r.bytes_downloaded+=J.bytes,YR(Z,s),nl(re,{force:!0}),aue(Z,re),H.push(B)}for(let B of f)YR(Ii(t,B.path),s);r.headers_scrubbed=w,r.git_held_recordings_scrubbed=x.length;let te=f.filter((B)=>B.change.dates).length;r.headers_dates_normalized=H.filter((B)=>B.change.dates).length+te,r.git_held_recordings_dates_normalized=te;let P=[],M=new Set,ge=new Set,ce=[],br=f.map((B)=>B.path),Et=[...H.map((B)=>({path:B.path,size:B.size})),...e.skipData?[]:br.map((B)=>({path:B,size:ag(Ii(t,B)).size}))];if(e.skipData)ce.push(...br);if(Et.length>0){if(!e.upload)throw Error("scrubbed recordings need an upload strategy");let B;try{B=await BR({datasetPath:t,files:Et,remoteName:e.remoteName,bucket:e.bucket,nemarId:e.nemarId,maxBytes:C,upload:e.upload,backend:"SHA256E"})}catch(J){throw new Bt("upload-failed",`${Et.length} scrubbed recording(s) could not be annexed or uploaded: ${cg(J)}`)}P.push(...B.items);for(let J of br)ge.add(J);let re=new Map(B.files.map((J)=>[J.path,J.key])),Z={};for(let J of H){let rt=re.get(J.path);if(!rt||!rl.test(rt)||rt===J.key)throw new Bt("scrub-unverified","a scrubbed recording has no new key");Z[J.key]=rt,M.add(J.key)}if(r.upstream_keys_replaced=M.size,M.size>0){let J;try{J=await Kle({repo:t,keymap:Z,remoteUuids:[],execute:!0})}catch(si){throw new Bt("retire-failed",`the git-annex branch could not be updated: ${cg(si)}`)}let rt=new Set(Object.values(Z)).size;if(J.oldStillHeld!==0||J.oldDead!==J.oldKeys||J.deadRefused!==0||J.newPresent!==rt)throw new Bt("retire-failed",`${J.oldKeys-J.oldDead} of ${J.oldKeys} replaced key(s) not recorded dead, ${rt-J.newPresent} new key(s) not recorded at the remote`)}}for(let B of n){if(!Iit.test(B))continue;if(i.has(B)){r.json_files_annexed++;continue}let re=Ii(t,B);if(!sg(re)||ag(re).size>Fit){r.json_files_unread++;continue}let Z;try{Z=sue(Xv(re))}catch(J){if(J instanceof ig)throw new Bt("scrub-unverified","a blanked JSON file failed its proof");throw J}if(Z.status==="unreadable"){r.json_files_unread++;continue}if(r.json_files_read++,Z.status==="blanked"&&Z.bytes)og(re,Z.bytes),ce.push(B),r.json_files_blanked++,r.json_values_blanked+=Z.blanked}if(s)for(let B of n){if(!Nit.test(B))continue;if(i.has(B)){r.scans_tables_annexed++;continue}let re=Ii(t,B);if(!sg(re)||ag(re).size>Pit){r.scans_tables_unread++;continue}let Z;try{Z=oue(Xv(re))}catch{Z={status:"unreadable",values:0}}if(Z.status==="unreadable"){r.scans_tables_unread++;continue}if(r.scans_tables_read++,Z.status==="normalized"&&Z.bytes)og(re,Z.bytes),ce.push(B),r.scans_tables_normalized++,r.scans_values_normalized+=Z.values}r.images_or_documents_held=ov(n).filter((B)=>B.kind==="image-or-document-file").length;let gr=r.headers_scrubbed>0||r.headers_dates_normalized>0||r.json_values_blanked>0||r.scans_values_normalized>0,Zr=e.now??new Date,Rr=Zr.toISOString().slice(0,10),qr=r.headers_scrubbed>0?r.headers_dates_normalized>0?"scrubbed-and-dates-set":"scrubbed-in-place":r.headers_dates_normalized>0?"dates-set":null;if(qr!==null){let B=Ii(t,ip);if(n.includes(ip)&&sg(B)){let Z=Xv(B,"utf8"),J=Z.charCodeAt(0)===65279?String.fromCharCode(65279):"",rt=Vit(Z.slice(J.length),VR,Nle(Rr,qr));if(rt!==null)og(B,`${J}${rt}`),ce.push(ip),r.provenance_annotated=1;else r.provenance_not_annotated++}else if(n.includes(ip))r.provenance_not_annotated++;let re=Ii(t,rg);if(n.includes(rg)&&sg(re)){let Z=jle(Rr,qr),J=Xv(re,"utf8");if(!J.endsWith(Z))og(re,`${J}${J===""||J.endsWith(`
 `)?"":`
 `}${Z}`),ce.push(rg);r.provenance_readme_annotated=1}else if(n.includes(rg))r.provenance_not_annotated++}let Q=!1;if(gr){let B=process.env.GITHUB_ACTOR,re=e.actor??(B&&Tit.test(B)?B:Oit);qle(Ii(t,ng),{version:1,at:Zr.toISOString(),dataset:e.nemarId,action:"import-scrubbed",versions:[],counts:{...r},scanner:Ait,verification:"scanner-clean+payload-identical",actor:re}),ce.push(ng),await Hit(t,ce);let Z=[`Recording headers scrubbed: ${r.headers_scrubbed} (identification fields only; signal bytes unchanged).`,`Acquisition dates set to 1 January of their year: ${r.headers_dates_normalized} recording header(s), ${r.scans_values_normalized} scans table value(s) in ${r.scans_tables_normalized} file(s).`,`JSON values blanked: ${r.json_values_blanked} in ${r.json_files_blanked} file(s).`,`Images and documents left for review: ${r.images_or_documents_held}.`,`Recorded in ${ng}.`].join(`
-`),J=[...new Set([...ce,...Et.map((vs)=>vs.path)])],rt=Dit(Ii($it(),"nemar-scrub-pathspec-")),si=Ii(rt,"paths");og(si,`${J.join("\x00")}\x00`,{mode:384});try{if((await k(["git","-c","annex.largefiles=nothing","commit","-m","Privacy correction on import (ADR 0089)","-m",Z,`--pathspec-from-file=${si}`,"--pathspec-file-nul"],{cwd:t})).exitCode!==0)throw Error("could not commit the import scrub")}finally{nl(rt,{recursive:!0,force:!0})}Q=!0}return{counts:r,items:P,replacedKeys:M,handledPaths:ge,historyHoldsOriginals:r.json_values_blanked>0||r.git_held_recordings_scrubbed>0||e.reimport&&Git(t),headerReadKeys:u,committed:Q}}async function Jit(e,t,r){try{return await Yit(e,t,r)}catch(n){if(n instanceof Bt)throw n;throw new Bt("scrub-failed",cg(n))}}async function Yit(e,t,r){let n=new Set((await Ti(e)).values()),i=[...r].filter((d)=>n.has(d)).length;if(i>0)throw new Bt("old-key-still-named",`${i} replaced key(s) are still named by the tree`);let o=new Map;for(let d of t)if(!o.has(d.key))o.set(d.key,d);let s=[...o.values()].filter((d)=>n.has(d.key)),a=o.size-s.length,c=await Gv(e,s.map((d)=>d.key)),u=s.filter((d,f)=>!Wv(c[f]??""));return{items:u,droppedNotInTree:a,droppedDead:s.length-u.length}}async function bue(e){let t=await Wit({datasetPath:e.datasetPath,nemarId:e.nemarId,keyUrlMap:e.keyUrlMap,unannexedData:e.unannexedData,reimport:e.reimport,skipData:e.skipData,maxBytes:e.maxBytes,reader:e.reader,upload:e.upload,remoteName:e.remoteName,bucket:e.bucket,now:e.now,actor:e.actor}),r=await Uv({datasetPath:e.datasetPath,nemarId:e.nemarId,bucket:e.bucket,remoteName:e.remoteName,unannexedData:e.unannexedData.filter((a)=>!t.handledPaths.has(a.path)),upstreamKeys:new Set(e.keyUrlMap.keys()),carryOverUnaccountedKeys:e.reimport&&!e.skipData,upload:e.upload,maxBytes:e.maxBytes}),n=e.skipData?{items:[],droppedNotInTree:0,droppedDead:0}:await Jit(e.datasetPath,[...e.upstreamItems,...t.items,...r.items],t.replacedKeys),i;try{i=await Ti(e.datasetPath)}catch(a){throw new Bt("scrub-failed",cg(a))}let o=new Set([...i].filter(([a])=>gue.test(a)).map(([,a])=>a)),s=n.items.filter((a)=>!ep(a)&&o.has(a.key)&&!t.headerReadKeys.has(a.key)).length;if(s>0)throw new Bt("header-unreadable",`${s} recording(s) in the copy manifest whose header this run did not read`);return{scrub:t,normalized:r,manifest:n,privacy:{version:1,historyHoldsOriginals:t.historyHoldsOriginals}}}var Bt,Cit,Rit,Ait,Oit="nemar-importer",Tit,Fit=1048576,Pit=8388608,gue,Iit,Nit,cue="nemar-cli-import-scrub",Mit;var xue=I(()=>{Vv();Jle();GR();Ql();JR();cs();It();ri();eg();io();tl();Bt=class Bt extends Error{code;constructor(e,t,r=!1){super(`${r?`${zv} `:""}${kle} refused: ${e} (${t}). Nothing was pushed, and the copy phase did not run.`);this.code=e;this.name="ImportScrubRefused"}};Cit=new Set(["GitScrubError","ContractError","LedgerRefused"]),Rit=/^[A-Z][A-Z0-9_]{1,20}$/;Ait=`identifier-scan@${"0dc24ef08c95fa1f"}`,Tit=/^[a-z0-9][a-z0-9-]{0,38}$/i,gue=/\.(edf|bdf)$/i,Iit=/\.json$/i,Nit=/_scans\.tsv$/;Mit=new Set(["ENOSPC","EACCES","EPERM","EROFS","EIO","EMFILE","ENFILE"])});import{existsSync as vue,mkdirSync as Xit,mkdtempSync as _ue,readFileSync as Zit,readdirSync as lg,readlinkSync as Qit,renameSync as eot,rmSync as tot,statSync as rot,writeFileSync as QR}from"fs";import{tmpdir as Due}from"os";import{join as En}from"path";async function eA(e,t,r=120000,n=5000){let i=Date.now()+r,o,s=!1;while(Date.now()<i){try{let c=await pw(e);if(s=!0,c.bids_validation.present&&c.bids_validation.status!=="no_runs")return{kind:"found"}}catch(c){o=c}let a=Math.max(0,i-Date.now());t.text=`Waiting for BIDS validation run to register... (${Math.ceil(a/1000)}s left)`,await new Promise((c)=>setTimeout(c,Math.min(n,a)))}if(!s&&o!==void 0)return{kind:"error",lastError:o};return{kind:"timeout"}}function oot(e){if(!e.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 t=e.poll;if(t===null||t.kind==="found")return{skipCiCheck:!1};if(t.kind==="error")return{skipCiCheck:!1,abortReason:`Every BIDS validation poll attempt failed (last error: ${t.lastError instanceof Error?t.lastError.message:String(t.lastError)}). Refusing to bypass under --trust-upstream because validation state was never actually observed. Investigate API/auth health and re-run.`};if(e.trustUpstream)return{skipCiCheck:!0};return{skipCiCheck:!1,abortReason:"BIDS validation run did not register within the bounded poll window. Re-run with --trust-upstream to bypass (OpenNeuro datasets are pre-validated upstream), or investigate why the deployed CI did not trigger."}}function sot(e){return e.includes("already exists")||e.includes("409")}function aot(e){return e==="public"?"skip-already-published":"request"}function cot(e){return e.originMainSha!==null&&e.originMainSha!==""&&e.currentBranch==="main"}function tA(e){let t=e.match(/^ds(\d{6})$/);if(!t)throw Error(`Invalid OpenNeuro ID "${e}". 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+`),J=[...new Set([...ce,...Et.map((vs)=>vs.path)])],rt=Dit(Ii($it(),"nemar-scrub-pathspec-")),si=Ii(rt,"paths");og(si,`${J.join("\x00")}\x00`,{mode:384});try{if((await k(["git","-c","annex.largefiles=nothing","commit","-m","Privacy correction on import (ADR 0089)","-m",Z,`--pathspec-from-file=${si}`,"--pathspec-file-nul"],{cwd:t})).exitCode!==0)throw Error("could not commit the import scrub")}finally{nl(rt,{recursive:!0,force:!0})}Q=!0}return{counts:r,items:P,replacedKeys:M,handledPaths:ge,historyHoldsOriginals:r.json_values_blanked>0||r.git_held_recordings_scrubbed>0||e.reimport&&Git(t),headerReadKeys:u,committed:Q}}async function Jit(e,t,r){try{return await Yit(e,t,r)}catch(n){if(n instanceof Bt)throw n;throw new Bt("scrub-failed",cg(n))}}async function Yit(e,t,r){let n=new Set((await Ti(e)).values()),i=[...r].filter((d)=>n.has(d)).length;if(i>0)throw new Bt("old-key-still-named",`${i} replaced key(s) are still named by the tree`);let o=new Map;for(let d of t)if(!o.has(d.key))o.set(d.key,d);let s=[...o.values()].filter((d)=>n.has(d.key)),a=o.size-s.length,c=await Gv(e,s.map((d)=>d.key)),u=s.filter((d,f)=>!Wv(c[f]??""));return{items:u,droppedNotInTree:a,droppedDead:s.length-u.length}}async function bue(e){let t=await Wit({datasetPath:e.datasetPath,nemarId:e.nemarId,keyUrlMap:e.keyUrlMap,unannexedData:e.unannexedData,reimport:e.reimport,skipData:e.skipData,maxBytes:e.maxBytes,reader:e.reader,upload:e.upload,remoteName:e.remoteName,bucket:e.bucket,now:e.now,actor:e.actor}),r=await Uv({datasetPath:e.datasetPath,nemarId:e.nemarId,bucket:e.bucket,remoteName:e.remoteName,unannexedData:e.unannexedData.filter((a)=>!t.handledPaths.has(a.path)),upstreamKeys:new Set(e.keyUrlMap.keys()),carryOverUnaccountedKeys:e.reimport&&!e.skipData,upload:e.upload,maxBytes:e.maxBytes}),n=e.skipData?{items:[],droppedNotInTree:0,droppedDead:0}:await Jit(e.datasetPath,[...e.upstreamItems,...t.items,...r.items],t.replacedKeys),i;try{i=await Ti(e.datasetPath)}catch(a){throw new Bt("scrub-failed",cg(a))}let o=new Set([...i].filter(([a])=>gue.test(a)).map(([,a])=>a)),s=n.items.filter((a)=>!ep(a)&&o.has(a.key)&&!t.headerReadKeys.has(a.key)).length;if(s>0)throw new Bt("header-unreadable",`${s} recording(s) in the copy manifest whose header this run did not read`);return{scrub:t,normalized:r,manifest:n,privacy:{version:1,historyHoldsOriginals:t.historyHoldsOriginals}}}var Bt,Cit,Rit,Ait,Oit="nemar-importer",Tit,Fit=1048576,Pit=8388608,gue,Iit,Nit,cue="nemar-cli-import-scrub",Mit;var xue=I(()=>{Vv();Jle();GR();Ql();JR();cs();It();ri();eg();io();tl();Bt=class Bt extends Error{code;constructor(e,t,r=!1){super(`${r?`${zv} `:""}${kle} refused: ${e} (${t}). 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Re-run with --trust-upstream to bypass (OpenNeuro datasets are pre-validated upstream), or investigate why the deployed CI did not trigger."}}function sot(e){return e.includes("already exists")||e.includes("409")}function aot(e){return e==="public"?"skip-already-published":"request"}function cot(e){return e.originMainSha!==null&&e.originMainSha!==""&&e.currentBranch==="main"}function tA(e){let t=e.match(/^ds(\d{6})$/);if(!t)throw Error(`Invalid OpenNeuro ID "${e}". 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 `)}function xot(e,t,r){let i=lg(e,{withFileTypes:!0}).filter((f)=>f.isFile()&&bot.test(f.name)),o=i.find((f)=>f.name.includes("."));if(o)return{kind:"kept",path:o.name};let s=i.find((f)=>!f.name.includes("."));if(s)return eot(En(e,s.name),En(e,"README.md")),{kind:"renamed",from:"README",to:"README.md"};let a="<!-- nemar:provenance -->",c=`https://openneuro.org/datasets/${t}`,u=r?`
 - DOI: [${r}](https://doi.org/${r})`:"",d=`${a}
 ## Provenance

package/package.json CHANGED Viewed

@@ -1,7 +1,7 @@
 {
   "name": "nemar-cli",
   "packageManager": "bun@1.4.3",
-  "version": "0.10.18-dev.3417",
+  "version": "0.10.18-dev.3427",
   "description": "CLI for NEMAR (Neuroelectromagnetic Data Archive and Tools Resource) dataset management",
   "type": "module",
   "main": "dist/index.js",