@zakodium/nmrium-core 0.4.2 → 0.4.4

package/dist/nmrium-core.js

@@ -1,4 +1,4 @@
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o={...e,version:7};for(let r in e.workspaces)o.workspaces[r]=ie(o.workspaces[r]);return o}function ie(e){let{formatting:{nuclei:t,panels:o}={nuclei:null,panels:null},version:r,...i}=e,n={...i};return t&&(n.nuclei=$e(t)),o&&(n.panels=o),n}function $e(e){let t=[],o={name:"nucleus",ppm:"ppmFormat",hz:"hzFormat"};for(let r in e)t.push(x(e[r],o));return t}function Z(e){if(e?.version===7)return e;let t={...e,version:7};return t?.settings&&(t.settings=O(t.settings,"nmrium")),t}function M(e,t="localStorage"){if(e?.version===8)return e;if(t==="nmrium")return ne(e);let o={...e,version:8};for(let r in e.workspaces)o.workspaces[r]=ne(o.workspaces[r]);return o}function ne(e){let{version:t,...o}=e,r={...o};return r.display.panels=Ze(e),r}function Ze(e){let t={},o=e.display.panels;for(let r of Object.keys(o)){let{display:i,open:n}=o[r];t[r]={display:i,visible:i,open:n}}return t}function G(e){if(e?.version===8)return e;let t={...e,version:8};t?.settings&&(t.settings=M(t.settings,"nmrium"));for(let o of t?.data?.spectra||[]){let{filters:r=[]}=o;for(let s=0;s<r.length;s++){let{flag:c,isDeleteAllow:l,label:p,...m}=r[s];r[s]={...m,enabled:c}}let i=r.findIndex(s=>s.name==="apodization");if(i!==-1){let s=r[i],{lineBroadening:c,gaussBroadening:l,lineBroadeningCenter:p}=s.value;s.value={exponential:{apply:!0,options:{lineBroadening:l>0?-c:c}}},l>0&&(s.value.gaussian={apply:!0,options:{lineBroadening:.6*l,lineBroadeningCenter:p}}),r[i]=s}let n=r.findIndex(s=>s.name==="apodizationDimension1"),a=r.findIndex(s=>s.name==="apodizationDimension2");if(n!==-1){let s=r[n],{shapes:c}=s.value.compose;s.value=se(c)}if(a!==-1){let s=r[a],{shapes:c}=s.value.compose;s.value=se(c)}}return t}function se(e){let t={};for(let{shape:o}of e){let{kind:r,options:i}=o;if(r==="sineBell"){let{exponent:n,offset:a}=i,s=n===2?"sineSquare":"sineBell";t[s]={apply:!0,options:{offset:a}}}}return t}function J(e){let{version:t,plugins:o,...r}=e;return t===9?e:{version:9,plugins:{},...r}}function q(e){if(e?.version>=10)return e;let t={...e,version:10};if(e.data){let{source:o,spectra:r,...i}=e.data,n=o?crypto.randomUUID():void 0,a=o?[{...o,id:n}]:[];t.data={...i,sources:a,spectra:o?r.map(s=>({...s,sourceId:n})):r}}return t}var Ge=[B,K,X,W,Y,$,Z,G,J,q];function ae(e,t,o){let r=structuredClone(e),i=Object.entries(e?.plugins??{});for(let[s,{version:c}]of i){let l=o.get(s);if(!(l&&l.version>=c)){if(l){console.warn(`Plugin "${l.id}" is loaded with a version older (${l.version}) than the one used to save the state (${c}).
 NMRium may fail to load the state.
 Please update the plugin to the latest version.`);continue}console.warn(`Plugin "${s}@${c}" is not registered. NMRium may fail to load the state.
 Please consider open this file with the plugin installed.`)}}let n=new Set,a=()=>{let s=r.version;for(let c of o.values())for(let l of c.migrations){if(n.has(l)||s<l.minCore||l.maxCore&&s>l.maxCore)continue;if((r.plugins?.[c.id]?.version||0)===c.version)break;r=l.up(r),n.add(l)}};for(let s=e?.version||0;s<t;s++){let c=Ge[s];r=c(r),a()}return a(),b(r,o),r}import{FileCollection as ot}from"file-collection";var le={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 D(e){return e.includes(".")?e.replace(/^.*\./,"").toLowerCase():""}function v(e,t={},o){let{data:r,...i}=e;if(!r)return e;let{spectra:n=[]}=r,{keep1D:a=!0,keep2D:s=!0,onlyReal:c}=t,l=c?"ft":t.dataSelection||"both",p=[];for(let m of n){if(!m.info){p.push(m);continue}let{isFid:u,dimension:d,name:f}=m.info;if(!F(d===1&&!a,f,o)&&!F(d===2&&!s,f,o)&&!F(u&&l==="ft",f,o)&&!F(!u&&l==="fid",f,o))if(c&&!u)if(m.info.isComplex=!1,Je(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 Je(e){let{info:t}=e;return t?.dimension===2}function A(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 w(e,t,o={}){let{sourceSelector:r,converter:i,logger:n}=o,a=[],s=[];for(let u of t.values()){let{onReadProcess:d}=u;d&&(d?.onFiles&&a.push(u),d?.supportedExtensions?.length&&d?.onFile&&s.push(u))}let c=await Promise.allSettled(a.map(u=>u.onReadProcess.onFiles(e,o))),l=[],p=await Promise.allSettled(e.files.flatMap(u=>{let d=D(u.name).toLowerCase();return s.flatMap(f=>{let{supportedExtensions:g,onFile:S}=f.onReadProcess;return g.includes(d)?(l.push({file:u,plugin:f}),S(u,{logger:n,sourceSelector:r,converter:i})):[]})})),m={spectra:[],molecules:[]};for(let u=0;u<c.length;u++){let d=c[u];switch(d.status){case"fulfilled":{let{spectra:f=[],molecules:g=[]}=d.value||{};m.spectra.push(...f),m.molecules.push(...g);break}case"rejected":{let f=d.reason,g=a[u];o.logger?.error(`Load file collection with plugin ${g.id}@${g.version} fails with: ${f}`);break}}}for(let u=0;u<p.length;u++){let d=p[u];switch(d.status){case"fulfilled":{let{spectra:f=[],molecules:g=[]}=d.value||{};m.spectra.push(...f),m.molecules.push(...g);break}case"rejected":{let f=d.reason,{file:g,plugin:S}=l[u];o.logger?.error(`Load file ${g.relativePath} with plugin ${S.id}@${S.version} fails with: ${f}`);break}}}return m}import{FileCollection as et}from"file-collection";import{FileCollection as Qe}from"file-collection";import ce from"lodash.merge";import{xIsEquallySpaced as qe}from"ml-spectra-processing";async function T(e){let{input:t,spectraResult:o,unserializedSpectrum:r,options:i,plugins:n,migrator:a}=e,c=(await R({input:t,migrator:a,plugins:n,options:{...i,sourceSelector:r.sourceSelector}}))?.nmriumState?.data?.spectra??[],l=c.pop();if(l){o.push(ue(r,l));for(let p of c)o.push(ue(r,He(p)))}}function ue(e,t){!e.fileCollectionId&&e.sourceId&&(e.fileCollectionId=e.sourceId),!t.fileCollectionId&&t.sourceId&&(t.fileCollectionId=t.sourceId);let{data:o,...r}=e;if("ranges"in t){let{data:i,...n}=t;return{...ce(n,r),data:i}}else if("zones"in t){let{data:i,...n}=t;return{...ce(n,r),data:i}}else return t}function He(e){return{...e,id:N()}}function E(e){let{spectrum:t,spectraResult:o,logger:r}=e,{dimension:i}=t.info;if(i===1){if(!qe(t.data)){r?.error('The ".nmrium" file is corrupted; the X-axis values are not equally distant.');return}o.push(h(t))}else i===2&&o.push(I(t))}async function j(e){let{input:t,moleculesResult:o,unserializedMolecule:r,options:i,plugins:n,migrator:a}=e,{sourceSelector:s,sourceId:c}=r,p=(await R({input:t,migrator:a,plugins:n,options:{...i,sourceSelector:s}}))?.nmriumState?.data?.molecules??[];for(let m of p)o.push({...m,sourceId:c,fileCollectionId:c})}function z(e){let{molecule:t,moleculesResult:o}=e;o.push(t)}async function k(e){let{nmriumObjectInput:t,options:o={},migrator:r,plugins:i}=e,n=r(t),{data:a,...s}=n;if(!a)return[{...s},new Map];let c={data:{...a,spectra:[],molecules:[]},...s},l=c.data,{sources:p=[],spectra:m,molecules:u}=l,d=await Promise.all(p.map(async S=>{let y=await Qe.fromSource(S,{unzip:{zipExtensions:["zip","nmredata"]}});return[S.id,y]})),f=new Map(d),g=[];for(let S of a.spectra){let y=f.get(S.sourceId);if(!y){E({spectrum:S,spectraResult:m,logger:o.logger});continue}g.push(T({input:y,spectraResult:m,unserializedSpectrum:S,migrator:r,plugins:i,options:o}))}for(let S of a.molecules??[]){let y=f.get(S.sourceId);if(!y){z({molecule:S,moleculesResult:u,logger:o.logger});continue}g.push(j({input:y,unserializedMolecule:S,moleculesResult:u,migrator:r,plugins:i,options:o}))}return await Promise.allSettled(g),[c,f]}async function pe(e){let{file:t,options:o={},migrator:r,plugins:i}=e,n=await t.arrayBuffer(),a=await(rt(n)?tt(n):t.text());return k({nmriumObjectInput:JSON.parse(a),plugins:i,migrator:r,options:o})}async function tt(e){let t=await et.fromZip(e);if(t.files.length===0)throw new Error("compressed nmrium file is corrupted");return t.files[0].text()}function rt(e){if(e.byteLength<4)return!1;let t=new Uint8Array(e);return t[0]===80&&t[1]===75&&(t[2]===3||t[2]===5||t[2]===7)&&(t[3]===4||t[3]===6||t[3]===8)}async function R(e){let{options:t={},input:o,migrator:r,plugins:i}=e,n=st(await it(o),t.sourceSelector?.files),a=at(n);if(a){let[u]=await pe({file:a,migrator:r,plugins:i,options:t});return{nmriumState:u,containsNmrium:!0,fileCollection:n}}let s=await w(n,i,t),c=v({version:10,data:s},t?.sourceSelector?.general,t.logger),{onLoadProcessing:l,experimentalFeatures:p}=t,m={...l,autoProcessing:l?.autoProcessing??!1,experimentalFeatures:p};return A({nmriumState:c,plugins:i,options:m}),{nmriumState:c,containsNmrium:!1,fileCollection:n}}function it(e){return Array.isArray(e)?Promise.reject(new Error("For a set of fileCollectionItems pass a FileCollection instance")):nt(e)?Promise.resolve(e):new ot().appendExtendedSource({...e,uuid:crypto.randomUUID()})}function nt(e){return typeof e=="object"&&"files"in e}function st(e,t){if(!t)return e;let o=new Set(t);return e.filter(r=>o.has(r.relativePath))}function at(e){return e.files.find(t=>D(t.name).toLowerCase()===le.NMRIUM)}function C(e,t){let o={};for(let r in e)t.includes(r)||(o[r]=e[r]);return o}var lt=["data","originalData","info","originalInfo","meta","customInfo"],ct=["data","originalData","info","originalInfo","meta","customInfo"],ut=["sourceSelector","sourceId","fileCollectionId","originalData","originalInfo"];function me(e,t,o={}){let{version:r,data:i}=e;if(i.actionType)return e;let n={version:r,plugins:e.plugins},{includeData:a}=o;a!=="noData"&&(n.data=pt({...i},a));let{includeSettings:s,includeView:c}=o;return s&&(n.settings=e.settings),c&&(n.view=e.view),b(n,t),n}function pt(e,t="rawData"){let{spectra:o}=e;switch(t){case"dataSource":return mt(e);case"selfContained":case"selfContainedExternalDatasource":return ft(e);case"rawData":return{...C(e,["sources"]),spectra:o.map(St)};default:return e}}function mt(e){let{spectra:t}=e;if(!e.sources)throw new Error("sources property should exists for dataSource serialization");return{...e,spectra:t.map(dt)}}function ft(e){let{spectra:t}=e;return{...e,spectra:t.map(gt)}}function dt(e){return C(e,lt)}function gt(e){return C(e,ct)}function St(e){let{data:t,info:o,originalData:r,originalInfo:i}=e,n=C(e,ut);return n.data=r||t,n.info=i||o,n}import{FileCollection as yt}from"file-collection";async function de(e){let{spectra:t,molecules:o,fileCollections:r,serializedState:i,includeData:n=!0}=e,a=new yt({filter:{ignoreDotfiles:!1}}),s=new Set,c=[];for(let l of t)fe({builder:a,fileCollections:r,fileCollectionId:l.fileCollectionId,includeData:n,alreadyAdded:s,asyncTasks:c});for(let l of o)fe({builder:a,fileCollections:r,fileCollectionId:l.fileCollectionId,includeData:n,alreadyAdded:s,asyncTasks:c});return await Promise.all(c),a.toIum({*getExtraFiles(){yield{relativePath:"state.json",data:i},yield{relativePath:".META-NMRIUM/NMRIUM_ARCHIVE.json",data:JSON.stringify(Pt({fileCollections:r,toSerialize:s}),null,2)},n?yield{relativePath:".META-NMRIUM/EMBED_ALL_DATA",data:""}:yield{relativePath:".META-NMRIUM/USE_EXTERNAL_SOURCES",data:""},yield{relativePath:"index.txt",data:xt({fileCollections:r,toIndex:s})}}})}function fe(e){let{builder:t,fileCollections:o,fileCollectionId:r,includeData:i,alreadyAdded:n,asyncTasks:a}=e;if(!r||n.has(r))return;let s=o[r];s&&(n.add(r),a.push(s.toIum({includeData:i}).then(c=>{let l=new Blob([c],{type:"application/zip"});return t.appendExtendedSource({uuid:r,name:r,relativePath:`${r}.ium.zip`,size:l.size,text:()=>l.text(),stream:()=>l.stream(),arrayBuffer:()=>l.arrayBuffer()},{unzip:{zipExtensions:[]}})})))}function Pt(e){let{fileCollections:t,toSerialize:o}=e,r={};for(let i of o){let n=t[i];if(!n)continue;let{logger:a,...s}=n.options;r[i]={sourceUUID:i,filePath:`${i}.ium.zip`,options:s}}return r}function xt(e){let{fileCollections:t,toIndex:o}=e,r=[];for(let i of o){let n=t[i];if(n){r.push(`data/${i}.ium.zip`);for(let a of n.sources)r.push(`	data/${a.relativePath}`);r.push(`

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@zakodium/nmrium-core",
-  "version": "0.4.2",
+  "version": "0.4.4",
   "description": "The core of NMRium: types, state, state migration and plugin system.",
   "author": "Zakodium Sàrl",
   "license": "CC-BY-NC-SA-4.0",
@@ -26,7 +26,7 @@
     "@types/lodash.merge": "^4.6.9",
     "@types/node": "^24.9.1",
     "@types/react": "^18.3.13",
-    "@zakodium/nmr-types": "^0.3.2",
+    "@zakodium/nmr-types": "^0.4.0",
     "esbuild": "^0.25.11",
     "jest-matcher-deep-close-to": "^3.0.2",
     "rimraf": "^6.0.1",
@@ -36,7 +36,7 @@
   "dependencies": {
     "cheminfo-types": "^1.8.1",
     "fifo-logger": "^2.0.1",
-    "file-collection": "^5.4.0",
+    "file-collection": "^6.0.0",
     "is-any-array": "^2.0.1",
     "lodash.merge": "^4.6.2",
     "ml-spectra-processing": "^14.18.0",
@@ -45,5 +45,5 @@
   "volta": {
     "extends": "../../../package.json"
   },
-  "gitHead": "7e754ead7fd27266a86c6a1a1a57f24b76c38a77"
+  "gitHead": "1310603aac371c50b102bf75a893da385d2a4ee4"
 }