@zakodium/nmrium-core 0.6.5 → 0.6.6
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/nmrium-core.d.ts +2 -0
- package/dist/nmrium-core.js +3 -3
- package/package.json +2 -2
package/dist/nmrium-core.d.ts
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@@ -383,6 +383,8 @@ export declare function getOneIfArray<T extends PosibleInput>(data: T | T[], ind
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export declare type IncludeData = 'rawData' | 'dataSource' | 'noData' | 'selfContained' | 'selfContainedExternalDatasource';
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declare interface InfoBlock {
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nameStyle?: TextStyle;
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valueStyle?: TextStyle;
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visible: boolean;
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fields: InfoBlockField[];
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position: {
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package/dist/nmrium-core.js
CHANGED
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@@ -1,6 +1,6 @@
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1
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var ve={NORMAL:"NORMAL",FORMULA:"FORMULA"};var Me={RELATIVE:"relative",ABSOLUTE:"absolute",MIN:"min",MAX:"max"};var Ce=[{name:"pixels",unit:"px"},{name:"inches",unit:"in"},{name:"feet",unit:"ft"},{name:"yards",unit:"yd"},{name:"centimeters",unit:"cm"},{name:"millimeters",unit:"mm"},{name:"meters",unit:"m"},{name:"points",unit:"pt"},{name:"picas",unit:"pc"}];var N=13;var Ae=[{key:"CT",description:"CT from NMR Solutions"}];import{isAnyArray as Fe}from"is-any-array";import{xMultiply as B}from"ml-spectra-processing";var we=crypto.randomUUID.bind(crypto),x=we;function O(e){let{id:t=x(),meta:o,peaks:r={},filters:i=[],info:n={},ranges:c={},integrals:s={},selector:l,sourceId:a,dependentVariables:p=[],...m}=e,u={id:t,meta:o,filters:i},{data:f=Te(p[0]?.components??[])}=e;if(Array.isArray(n.nucleus)&&(n.nucleus=n.nucleus[0]),u.data={x:[],re:[],im:[],...f},"scaleFactor"in 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var De={NORMAL:"NORMAL",FORMULA:"FORMULA"};var Me={RELATIVE:"relative",ABSOLUTE:"absolute",MIN:"min",MAX:"max"};var Ce=[{name:"pixels",unit:"px"},{name:"inches",unit:"in"},{name:"feet",unit:"ft"},{name:"yards",unit:"yd"},{name:"centimeters",unit:"cm"},{name:"millimeters",unit:"mm"},{name:"meters",unit:"m"},{name:"points",unit:"pt"},{name:"picas",unit:"pc"}];var N=13;var Ae=[{key:"CT",description:"CT from NMR Solutions"}];import{isAnyArray as Fe}from"is-any-array";import{xMultiply as B}from"ml-spectra-processing";var we=crypto.randomUUID.bind(crypto),x=we;function O(e){let{id:t=x(),meta:o,peaks:r={},filters:i=[],info:n={},ranges:c={},integrals:s={},selector:l,sourceId:a,dependentVariables:p=[],...m}=e,u={id:t,meta:o,filters:i},{data:f=Te(p[0]?.components??[])}=e;if(Array.isArray(n.nucleus)&&(n.nucleus=n.nucleus[0]),u.data={x:[],re:[],im:[],...f},"scaleFactor"in 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te(e){let{version:t}=e;if(t>=11)return e;let o={...e,version:11};return e?.view?.molecules&&(o.view=et(e.view)),o}function et(e){let{molecules:t,...o}=e,r={};for(let[i,n]of Object.entries(t)){let{showAtomNumber:c,...s}=n;r[i]={...s,atomAnnotation:"none",showLabel:!1}}return{molecules:r,...o}}function re(e){if(e?.version>=12)return e;let t={...e,version:12};if(t.data){let o=e.data.spectra??[],r=e.data.molecules??[];for(let i of o){let{sourceId:n,fileCollectionId:c,sourceSelector:s}=i;delete i.sourceId,delete i.fileCollectionId,delete i.sourceSelector,s&&(i.selector={...s,root:c??n})}for(let i of r){let{sourceId:n,fileCollectionId:c,sourceSelector:s}=i;delete i.sourceId,delete i.fileCollectionId,delete i.sourceSelector,s&&(i.selector={...s,root:c??n})}}return t}function oe(e){if(e?.version>=13)return e;let t={...e,version:13};if(t.data){let o=e.data.spectra??[];for(let r of o){let i=r.ranges?.values??[];for(let n of i){let{diaIDs:c,assignment:s,nbAtoms:l,signals:a=[]}=n,p=a.some(m=>m.diaIDs&&m.diaIDs.length>0);for(let m of a)!p&&c&&l&&(m.diaIDs=c,m.nbAtoms=l),!m.assignment&&s&&(m.assignment=s);delete n.diaIDs,delete n.assignment,delete n.nbAtoms}}}return t}function I(e,t){e.plugins||(e.plugins={});let o=e.plugins;for(let r of t.values()){if(!r.shouldSerialize){delete o[r.id];continue}o[r.id]||(o[r.id]={id:r.id,version:r.version}),o[r.id].id=r.id,o[r.id].version=r.version}}var tt=[X,Y,Z,$,G,J,q,H,Q,ee,te,re,oe];function pe(e,t,o){let r=structuredClone(e),i=Object.entries(e?.plugins??{});for(let[s,{version:l}]of i){let a=o.get(s);if(!(a&&a.version>=l)){if(a){console.warn(`Plugin "${a.id}" is loaded with a version older (${a.version}) than the one used to save the state (${l}).
|
|
2
2
|
NMRium may fail to load the state.
|
|
3
3
|
Please update the plugin to the latest version.`);continue}console.warn(`Plugin "${s}@${l}" is not registered. NMRium may fail to load the state.
|
|
4
|
-
Please consider open this file with the plugin installed.`)}}let n=new Set,c=()=>{let s=r.version;for(let l of o.values())for(let a of l.migrations){if(n.has(a)||s<a.minCore||a.maxCore&&s>a.maxCore)continue;if((r.plugins?.[l.id]?.version||0)===l.version)break;r=a.up(r),n.add(a)}};for(let s=e?.version||0;s<t;s++){let l=tt[s];r=l(r),c()}return c(),I(r,o),r}var rt=["topbar.right","topbar.about_us.modal"],ot=[],to=[...rt,...ot],it={},ie={};nt(it,ie);function nt(e,t){for(let[o,r]of Object.entries(e))t[r]||(t[r]=[]),t[r]?.push(o)}function*me(e){let{slot:t,plugins:o,supportedToDeprecatedSlots:r=ie}=e,i=r[t];for(let[n,c]of o.entries()){let s=c.ui;if(!s)continue;let l=s[t];if(l){yield[n,l];continue}if(i)for(let a of i){let p=c.ui?.[a];if(p){yield[n,p],console.warn(`Plugin ${c.id} used deprecated slot "${a}". 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Ne(e){let{subRoots:t,selector:o}=e;if(!o)return;let{root:r}=o;if(r)return t.get(r)}import{FileCollection as bt}from"file-collection";async function be(e){let{source:t,plugins:o,options:r={},sourceId:i=x()}=e,{converter:n,...c}=r,s={...t,id:i},l={spectra:[],molecules:[]},a=await bt.fromSource(s,{unzip:{zipExtensions:["zip","nmredata"]}}),{spectra:p=[],molecules:m=[]}=await L(a,o,{converter:{...n,bruker:{keepFiles:!0,...Reflect.get(n??{},"bruker")}},...c});l.spectra.push(...p),l.molecules.push(...m);for(let g of l.spectra)g.selector??={root:i},g.selector.root=i;for(let g of l.molecules)g.selector??={root:i},g.selector.root=i;l.sources??=[],l.sources.push(s);let u=T({version:13,data:l},r?.selector?.general),{onLoadProcessing:f}=c,d={filters:f?.filters,autoProcessing:f?.autoProcessing??!1,experimentalFeatures:r.experimentalFeatures};return E({nmriumState:u,plugins:o,options:d}),[u,a,i]}function M(e,t){let o={};for(let r in e)t.includes(r)||(o[r]=e[r]);return o}var Rt=["data","originalData","info","originalInfo","meta","customInfo"],Ot=["data","originalData","info","originalInfo","meta","customInfo"],It=["selector","originalData","originalInfo"];function Re(e,t,o={}){let{version:r,data:i}=e;if(i.actionType)return e;let n={version:r,plugins:e.plugins},{includeData:c,forceRawSpectra:s=[]}=o;c!=="noData"&&(n.data=Dt({...i},c,s));let{includeSettings:l,includeView:a}=o;return l&&(n.settings=e.settings),a&&(n.view=e.view),I(n,t),n}function Dt(e,t="rawData",o){let{spectra:r}=e;switch(t){case"dataSource":return vt(e);case"selfContained":case"selfContainedExternalDatasource":return Mt(e,o);case"rawData":return{...M(e,["sources"]),spectra:r.map(Oe)};default:return e}}function vt(e){let{spectra:t}=e;if(!e.sources)throw new Error("sources property should exists for dataSource serialization");return{...e,spectra:t.map(Ct)}}function Mt(e,t){let{spectra:o,sources:r,...i}=e;return{...i,spectra:o.map(n=>At(n,t))}}function Ct(e){return M(e,Rt)}function At(e,t){return!("selector"in e)||t?.includes(e.id)?Oe(e):M(e,Ot)}function Oe(e){let{data:t,info:o,originalData:r,originalInfo:i}=e,n=M(e,It);return n.data=r||t,n.info=i||o,n}import{FileCollection as wt}from"file-collection";async function Ie(e,t){let{state:o,aggregator:r,externalData:i="embedded",includeData:n=!0,includeSettings:c,includeView:s}=t,{spectra:l,molecules:a}=o.data,p=new wt({filter:{ignoreDotfiles:!1}});return n&&p.appendFileCollection(r),p.toIum({includeData:i==="embedded",mimetype:"chemical/x-nmrium+zip",*getExtraFiles(m){yield{relativePath:"META-INF/NMRIUM_ARCHIVE",data:""},yield{relativePath:"META-INF/VERSION",data:"1"},yield{relativePath:"state.json",data:Ft(e,o,r,{externalData:i,includeData:n,includeView:s,includeSettings:c})},yield{relativePath:"index.txt",data:Tt({aggregator:r,spectra:l,molecules:a,index:m})}}})}function Ft(e,t,o,r){let{includeData:i,includeView:n,includeSettings:c,externalData:s="embedded"}=r,l="noData";i&&(l=s==="embedded"?"selfContained":"selfContainedExternalDatasource");let a=[];if(l!=="noData")for(let u of t.data?.spectra??[]){let f=u.selector?.root;f&&o.subroot(f).files.length>0||a.push(u.id)}let p=e(t,{includeData:l,includeView:n,includeSettings:c,forceRawSpectra:a}),m=JSON.stringify(p,(u,f)=>ArrayBuffer.isView(f)?Array.from(f):f,2);return new Blob([m],{type:"application/json"})}function Tt(e){let{aggregator:t,spectra:o,molecules:r,index:i}=e,n=new Map,c=new Map(i.sources.map(l=>[l.uuid,l]));for(let l of o){let a=l.selector?.root;a&&(n.has(a)||n.set(a,t.subroot(a)))}for(let l of r){let a=l.selector?.root;a&&(n.has(a)||n.set(a,t.subroot(a)))}let s=[];for(let[l,a]of n.entries()){let p=new Map(a.sources.map(u=>[u.uuid,u])),m=`data/${l}/`;s.push(m);for(let u of a.files){let f=c.get(u.sourceUUID),d=p.get(u.sourceUUID),g=f?.baseURL?.startsWith("ium:/")?"embedded":"linked",y=i.paths[u.sourceUUID]?.replace(m,""),P=u.relativePath.replace(d?.relativePath??"",""),h=y?y+P:u.relativePath;s.push(` ${h} (${g})`)}s.push(`
|
|
4
|
+
Please consider open this file with the plugin installed.`)}}let n=new Set,c=()=>{let s=r.version;for(let l of o.values())for(let a of l.migrations){if(n.has(a)||s<a.minCore||a.maxCore&&s>a.maxCore)continue;if((r.plugins?.[l.id]?.version||0)===l.version)break;r=a.up(r),n.add(a)}};for(let s=e?.version||0;s<t;s++){let l=tt[s];r=l(r),c()}return c(),I(r,o),r}var rt=["topbar.right","topbar.about_us.modal"],ot=[],to=[...rt,...ot],it={},ie={};nt(it,ie);function nt(e,t){for(let[o,r]of Object.entries(e))t[r]||(t[r]=[]),t[r]?.push(o)}function*me(e){let{slot:t,plugins:o,supportedToDeprecatedSlots:r=ie}=e,i=r[t];for(let[n,c]of o.entries()){let s=c.ui;if(!s)continue;let l=s[t];if(l){yield[n,l];continue}if(i)for(let a of i){let p=c.ui?.[a];if(p){yield[n,p],console.warn(`Plugin ${c.id} used deprecated slot "${a}". Please update this plugin to use "${t}" instead.`);break}}}}import{FileCollection as ut}from"file-collection";var ne={SDF:"sdf",MOL:"mol",NMRIUM:"nmrium",NMRIUM_ARCHIVE:"nmrium.zip",JSON:"json",JCAMP:"jcamp",DX:"dx",JDX:"jdx",JDF:"jdf",NMREDATA:"nmredata",SMILES:"smiles",SMI:"smi"};function v(e){return e.includes(".")?e.replace(/^.*\./,"").toLowerCase():""}function T(e,t={},o){let{data:r,...i}=e;if(!r)return e;let{spectra:n=[]}=r,{keep1D:c=!0,keep2D:s=!0,onlyReal:l}=t,a=l?"ft":t.dataSelection||"both",p=[];for(let m of n){if(!m.info){p.push(m);continue}let{isFid:u,dimension:f,name:d}=m.info;if(!F(f===1&&!c,d,o)&&!F(f===2&&!s,d,o)&&!F(u&&a==="ft",d,o)&&!F(!u&&a==="fid",d,o))if(l&&!u)if(m.info.isComplex=!1,st(m)){let{rr:g}=m.data;p.push({...m,data:{rr:g}})}else{let{re:g,x:S}=m.data;p.push({...m,data:{re:g,x:S}})}else p.push(m)}return{data:{...r,spectra:p},...i}}function F(e,t,o){return e?(o?.warn(`Skipping ${t} because it didn't match the import filters.`),!0):!1}function st(e){let{info:t}=e;return t?.dimension===2}function E(e){let{nmriumState:t,plugins:o,options:r}=e;for(let i of o.values()){let n=i.onReadProcess?.onProcessing;n&&n(t,r)}}async function L(e,t,o={}){let{selector:r,converter:i,logger:n}=o,c=[],s=[];for(let u of t.values()){let{onReadProcess:f}=u;f&&(f?.onFiles&&c.push(u),f?.supportedExtensions?.length&&f?.onFile&&s.push(u))}let l=await Promise.allSettled(c.map(u=>u.onReadProcess.onFiles(e,o))),a=[],p=await Promise.allSettled(e.files.flatMap(u=>{let f=v(u.name).toLowerCase();return s.flatMap(d=>{let{supportedExtensions:g,onFile:S}=d.onReadProcess;return g.includes(f)?(a.push({file:u,plugin:d}),S(u,{logger:n,selector:r,converter:i})):[]})})),m={spectra:[],molecules:[]};for(let u=0;u<l.length;u++){let f=l[u];switch(f.status){case"fulfilled":{let{spectra:d=[],molecules:g=[]}=f.value||{};m.spectra.push(...d),m.molecules.push(...g);break}case"rejected":{let d=f.reason,g=c[u];o.logger?.error(`Load file collection with plugin ${g.id}@${g.version} fails with: ${d}`);break}}}for(let u=0;u<p.length;u++){let f=p[u];switch(f.status){case"fulfilled":{let{spectra:d=[],molecules:g=[]}=f.value||{};m.spectra.push(...d),m.molecules.push(...g);break}case"rejected":{let d=f.reason,{file:g,plugin:S}=a[u];o.logger?.error(`Load file ${g.relativePath} with plugin ${S.id}@${S.version} fails with: ${d}`);break}}}return m}import{FileCollection as Se}from"file-collection";import{FileCollection as ge}from"file-collection";import fe from"lodash.merge";import{xIsEquallySpaced as at}from"ml-spectra-processing";async function z(e){let{input:t,spectraResult:o,unserializedSpectrum:r,options:i,plugins:n,migrator:c}=e,l=(await D({input:t,migrator:c,plugins:n,options:{...i,selector:r.selector}}))?.nmriumState?.data?.spectra??[],a=l.pop();if(a){o.push(de(r,a));for(let p of l)o.push(de(r,lt(p)))}}function de(e,t){let{data:o,...r}=e;if(!t.selector?.root&&e.selector?.root&&(t.selector??=e.selector,t.selector.root=e.selector.root),"ranges"in t){let{data:i,...n}=t;return{...fe(n,r),data:i}}else if("zones"in t){let{data:i,...n}=t;return{...fe(n,r),data:i}}else return t}function lt(e){return{...e,id:x()}}function k(e){let{spectrum:t,spectraResult:o,logger:r}=e,{dimension:i}=t.info;if(i===1){if(!at(t.data)){r?.error('The ".nmrium" file is corrupted; the X-axis values are not equally distant.');return}o.push(O(t))}else i===2&&o.push(C(t))}async function U(e){let{input:t,moleculesResult:o,unserializedMolecule:r,options:i,plugins:n,migrator:c}=e,{selector:s}=r,a=(await D({input:t,migrator:c,plugins:n,options:{...i,selector:s}}))?.nmriumState?.data?.molecules??[];for(let p of a)!p.selector?.root&&s?.root&&(p.selector??=s,p.selector.root=s.root),o.push({...r,...p})}function j(e){let{molecule:t,moleculesResult:o}=e;o.push(t)}async function V(e){let{nmriumObjectInput:t,options:o={},migrator:r,plugins:i,fromSourceOptions:n}=e,c=r(t),{data:s,...l}=c,a=new ge;if(!s)return[{...l},a];let p={data:{...s,spectra:[],molecules:[]},...l},m=p.data,{sources:u=[],spectra:f,molecules:d}=m,g=await Promise.all(u.map(async P=>{let h=await ge.fromSource(P,{unzip:{zipExtensions:["zip","nmredata"]}},n);if(!P.baseURL)for(let R of P.entries)R.baseURL||(R.baseURL=n?.baseURL);return[P.id,h]})),S=new Map(g),y=[];for(let P of s.spectra){let h=P.selector?.root??"",R=S.get(h);if(!R){k({spectrum:P,spectraResult:f,logger:o.logger});continue}y.push(z({input:R,spectraResult:f,unserializedSpectrum:P,migrator:r,plugins:i,options:o}))}for(let P of s.molecules??[]){let h=P.selector?.root??"",R=S.get(h);if(!R){j({molecule:P,moleculesResult:d,logger:o.logger});continue}y.push(U({input:R,unserializedMolecule:P,moleculesResult:d,migrator:r,plugins:i,options:o}))}await Promise.allSettled(y);for(let[P,h]of S.entries())a.appendFileCollection(h,P);return[p,a]}async function _(e){let{file:t,options:o={},migrator:r,plugins:i,fromSourceOptions:n}=e,c="byteLength"in t?t:await t.arrayBuffer(),s=Se.isZip(c)?await ct(c):new TextDecoder("utf-8").decode(c);return V({nmriumObjectInput:JSON.parse(s),plugins:i,migrator:r,options:o,fromSourceOptions:n})}async function ct(e){let t=await Se.fromZip(e);if(t.files.length===0)throw new Error("compressed nmrium file is corrupted");return t.files[0].text()}async function D(e){let{options:t={},input:o,migrator:r,plugins:i,fromSourceOptions:n}=e,{selectorRoot:c=x()}=t,s=ft(await pt(o),t.selector?.files),l=dt(s);if(l){let[d]=await _({file:l,migrator:r,plugins:i,options:t,fromSourceOptions:n});return{nmriumState:d,containsNmrium:!0,fileCollection:gt(s),selectorRoot:c}}let a=await L(s,i,t),p=T({version:13,data:a},t?.selector?.general,t.logger),{onLoadProcessing:m,experimentalFeatures:u}=t,f={...m,autoProcessing:m?.autoProcessing??!1,experimentalFeatures:u};return E({nmriumState:p,plugins:i,options:f}),St(p,c),{nmriumState:p,containsNmrium:!1,fileCollection:s,selectorRoot:c}}function pt(e){return Array.isArray(e)?Promise.reject(new Error("For a set of fileCollectionItems pass a FileCollection instance")):mt(e)?Promise.resolve(e):new ut().appendExtendedSource({...e,uuid:x()})}function mt(e){return typeof e=="object"&&"files"in e}function ft(e,t){if(!t)return e;let o=new Set(t);return e.filter(r=>o.has(r.relativePath))}function dt(e){return e.files.find(t=>v(t.name).toLowerCase()===ne.NMRIUM)}function gt(e){return e.filter(t=>v(t.name).toLowerCase()!==ne.NMRIUM)}function St(e,t){for(let o of e.data?.spectra??[])o.selector?.root||(o.selector??={root:t},o.selector.root||=t);for(let o of e.data?.molecules??[])o.selector?.root||(o.selector??={root:t},o.selector.root||=t)}import{FileCollection as Pt}from"file-collection";async function ye(e){let t={},o=[];for(let r of e.sources)switch(r.relativePath){case"META-INF/NMRIUM_ARCHIVE":t.archive=r;break;case"META-INF/VERSION":o.push(r.text().then(i=>{t.version=Number.parseInt(i,10)}));break;case"state.json":o.push(r.text().then(i=>{t.state=JSON.parse(i)}));break;default:}return await Promise.all(o),t}function Pe(e){if(!e.archive)throw new Error("Not a valid NMRium archive");if(typeof e.version!="number"||Number.isNaN(e.version))throw new Error("Not a valid NMRium archive, no version specified");if(e.version===0)throw new Error("NMRium Archive generated behind experimental flag are not supported.");if(!e.state)throw new Error("NMRium Archive corrupted, state.json is missing")}function xe(e){return e.filter(t=>!yt(t.relativePath))}function yt(e){return e.startsWith("META-INF/")||e==="state.json"||e==="index.txt"}async function he(e){let{options:t,plugins:o,migrator:r}=e,i=await Pt.fromIum(e.input),n=await ye(i);Pe(n);let c=xe(i),s=r(n.state),l={...s,data:{...s.data,spectra:[],molecules:[]}},a=l.data.spectra,p=l.data.molecules,m=s.data?.spectra??[],u=s.data?.molecules??[],f=xt(i),d=[];for(let g of m)d.push(ht({subRoots:f,unserializedSpectrum:g,spectraResult:a,options:t,plugins:o,migrator:r}));for(let g of u)d.push(Nt({subRoots:f,unserializedMolecule:g,moleculesResult:p,options:t,plugins:o,migrator:r}));return await Promise.allSettled(d),[l,c]}function xt(e){let t=new Map;return{get(o){let r=t.get(o);return r||(r=e.subroot(o),t.set(o,r)),r},[Symbol("debug")]:{ium:e,views:t}}}async function ht(e){let{subRoots:t}=e,{unserializedSpectrum:o,spectraResult:r}=e,{options:i,plugins:n,migrator:c}=e,{selector:s}=o,l=await Ne({subRoots:t,selector:s});if(!l)return k({spectrum:o,spectraResult:r,logger:i?.logger});await z({input:l,unserializedSpectrum:o,spectraResult:r,options:i,plugins:n,migrator:c})}async function Nt(e){let{subRoots:t}=e,{unserializedMolecule:o,moleculesResult:r}=e,{options:i,plugins:n,migrator:c}=e,{selector:s}=o,l=await Ne({subRoots:t,selector:s});if(!l)return j({molecule:o,moleculesResult:r,logger:i?.logger});await U({input:l,unserializedMolecule:o,moleculesResult:r,options:i,plugins:n,migrator:c})}async function Ne(e){let{subRoots:t,selector:o}=e;if(!o)return;let{root:r}=o;if(r)return t.get(r)}import{FileCollection as bt}from"file-collection";async function be(e){let{source:t,plugins:o,options:r={},sourceId:i=x()}=e,{converter:n,...c}=r,s={...t,id:i},l={spectra:[],molecules:[]},a=await bt.fromSource(s,{unzip:{zipExtensions:["zip","nmredata"]}}),{spectra:p=[],molecules:m=[]}=await L(a,o,{converter:{...n,bruker:{keepFiles:!0,...Reflect.get(n??{},"bruker")}},...c});l.spectra.push(...p),l.molecules.push(...m);for(let g of l.spectra)g.selector??={root:i},g.selector.root=i;for(let g of l.molecules)g.selector??={root:i},g.selector.root=i;l.sources??=[],l.sources.push(s);let u=T({version:13,data:l},r?.selector?.general),{onLoadProcessing:f}=c,d={filters:f?.filters,autoProcessing:f?.autoProcessing??!1,experimentalFeatures:r.experimentalFeatures};return E({nmriumState:u,plugins:o,options:d}),[u,a,i]}function M(e,t){let o={};for(let r in e)t.includes(r)||(o[r]=e[r]);return o}var Rt=["data","originalData","info","originalInfo","meta","customInfo"],Ot=["data","originalData","info","originalInfo","meta","customInfo"],It=["selector","originalData","originalInfo"];function Re(e,t,o={}){let{version:r,data:i}=e;if(i.actionType)return e;let n={version:r,plugins:e.plugins},{includeData:c,forceRawSpectra:s=[]}=o;c!=="noData"&&(n.data=vt({...i},c,s));let{includeSettings:l,includeView:a}=o;return l&&(n.settings=e.settings),a&&(n.view=e.view),I(n,t),n}function vt(e,t="rawData",o){let{spectra:r}=e;switch(t){case"dataSource":return Dt(e);case"selfContained":case"selfContainedExternalDatasource":return Mt(e,o);case"rawData":return{...M(e,["sources"]),spectra:r.map(Oe)};default:return e}}function Dt(e){let{spectra:t}=e;if(!e.sources)throw new Error("sources property should exists for dataSource serialization");return{...e,spectra:t.map(Ct)}}function Mt(e,t){let{spectra:o,sources:r,...i}=e;return{...i,spectra:o.map(n=>At(n,t))}}function Ct(e){return M(e,Rt)}function At(e,t){return!("selector"in e)||t?.includes(e.id)?Oe(e):M(e,Ot)}function Oe(e){let{data:t,info:o,originalData:r,originalInfo:i}=e,n=M(e,It);return n.data=r||t,n.info=i||o,n}import{FileCollection as wt}from"file-collection";async function Ie(e,t){let{state:o,aggregator:r,externalData:i="embedded",includeData:n=!0,includeSettings:c,includeView:s}=t,{spectra:l,molecules:a}=o.data,p=new wt({filter:{ignoreDotfiles:!1}});return n&&p.appendFileCollection(r),p.toIum({includeData:i==="embedded",mimetype:"chemical/x-nmrium+zip",*getExtraFiles(m){yield{relativePath:"META-INF/NMRIUM_ARCHIVE",data:""},yield{relativePath:"META-INF/VERSION",data:"1"},yield{relativePath:"state.json",data:Ft(e,o,r,{externalData:i,includeData:n,includeView:s,includeSettings:c})},yield{relativePath:"index.txt",data:Tt({aggregator:r,spectra:l,molecules:a,index:m})}}})}function Ft(e,t,o,r){let{includeData:i,includeView:n,includeSettings:c,externalData:s="embedded"}=r,l="noData";i&&(l=s==="embedded"?"selfContained":"selfContainedExternalDatasource");let a=[];if(l!=="noData")for(let u of t.data?.spectra??[]){let f=u.selector?.root;f&&o.subroot(f).files.length>0||a.push(u.id)}let p=e(t,{includeData:l,includeView:n,includeSettings:c,forceRawSpectra:a}),m=JSON.stringify(p,(u,f)=>ArrayBuffer.isView(f)?Array.from(f):f,2);return new Blob([m],{type:"application/json"})}function Tt(e){let{aggregator:t,spectra:o,molecules:r,index:i}=e,n=new Map,c=new Map(i.sources.map(l=>[l.uuid,l]));for(let l of o){let a=l.selector?.root;a&&(n.has(a)||n.set(a,t.subroot(a)))}for(let l of r){let a=l.selector?.root;a&&(n.has(a)||n.set(a,t.subroot(a)))}let s=[];for(let[l,a]of n.entries()){let p=new Map(a.sources.map(u=>[u.uuid,u])),m=`data/${l}/`;s.push(m);for(let u of a.files){let f=c.get(u.sourceUUID),d=p.get(u.sourceUUID),g=f?.baseURL?.startsWith("ium:/")?"embedded":"linked",y=i.paths[u.sourceUUID]?.replace(m,""),P=u.relativePath.replace(d?.relativePath??"",""),h=y?y+P:u.relativePath;s.push(` ${h} (${g})`)}s.push(`
|
|
5
5
|
`)}return s.join(`
|
|
6
|
-
`)}var se=class{version=13;#e=new Map;registerPlugin(t){if(this.#e.has(t.id)){console.warn(`Plugin ${t.id} is already registered. skip.`),console.debug("Plugin already registered:",this.#e.get(t.id)),console.debug("Plugin to register:",t);return}this.#e.set(t.id,t)}registerPlugins(t){for(let o of t)this.registerPlugin(o)}getPlugin(t){return this.#e.get(t)}migrate(t){return pe(t,this.version,this.#e)}read(t,o={},r){return
|
|
6
|
+
`)}var se=class{version=13;#e=new Map;registerPlugin(t){if(this.#e.has(t.id)){console.warn(`Plugin ${t.id} is already registered. skip.`),console.debug("Plugin already registered:",this.#e.get(t.id)),console.debug("Plugin to register:",t);return}this.#e.set(t.id,t)}registerPlugins(t){for(let o of t)this.registerPlugin(o)}getPlugin(t){return this.#e.get(t)}migrate(t){return pe(t,this.version,this.#e)}read(t,o={},r){return D({input:t,options:o,fromSourceOptions:r,migrator:this.migrate.bind(this),plugins:this.#e})}readNMRiumArchive(t,o={}){return he({input:t,options:o,plugins:this.#e,migrator:this.migrate.bind(this)})}readNMRiumObject(t,o,r){return V({nmriumObjectInput:t,options:o,fromSourceOptions:r,plugins:this.#e,migrator:this.migrate.bind(this)})}readNMRiumFile(t,o={},r){return _({file:t,options:o,fromSourceOptions:r,plugins:this.#e,migrator:this.migrate.bind(this)})}readFromWebSource(t,o){return be({source:t,options:o,plugins:this.#e})}serializeNmriumState(t,o){return Re(t,this.#e,o)}serializeNmriumArchive(t){let o=this.serializeNmriumState.bind(this);return Ie(o,t)}serializePlugins(){let t={plugins:{}};return I(t,this.#e),t.plugins}slot(t){return me({slot:t,plugins:this.#e})}};function Et(e,t){if(t>13)return 0;let o=-1;for(let r=0;r<e.length;r++)if(e[r].version>t){o=r;break}return o}var ve=[{version:6,fun:A},{version:7,fun:w}];function Lt(e){let{version:t}=e||{},o=Et(ve,t);if(o===-1)return{...e,version:13};let r=ve.slice(o);for(let i of r)e=i.fun(e);return e}export{De as ANALYSIS_COLUMN_TYPES,Me as ANALYSIS_COLUMN_VALUES_KEYS,N as CURRENT_EXPORT_VERSION,Ae as EXTERNAL_API_KEYS,se as NMRiumCore,Ze as defineNMRiumPlugin,Ye as formatSpectra,x as generateID,W as getOneIfArray,Lt as migrateSettings,Ce as units};
|
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
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{
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"name": "@zakodium/nmrium-core",
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3
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-
"version": "0.6.
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3
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+
"version": "0.6.6",
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"description": "The core of NMRium: types, state, state migration and plugin system.",
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"author": "Zakodium Sàrl",
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"license": "CC-BY-NC-SA-4.0",
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@@ -47,5 +47,5 @@
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"volta": {
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"extends": "../../../package.json"
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},
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-
"gitHead": "
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50
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+
"gitHead": "4d3c8596b3915192be8b0825c4d8f5819a8fd9f1"
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}
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