@zakodium/nmrium-core 0.1.7 → 0.2.0
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 +59 -4
- package/dist/nmrium-core.js +2 -2
- package/package.json +10 -9
package/dist/nmrium-core.d.ts
CHANGED
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@@ -16,10 +16,52 @@ import type { NmrData2D } from 'cheminfo-types';
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import type { Peaks } from '@zakodium/nmr-types';
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import type { Ranges } from '@zakodium/nmr-types';
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import type { ReactNode } from 'react';
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import { SerializedNmriumState } from './core_serialize.js';
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import type { Source } from 'file-collection';
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import type { Zones } from '@zakodium/nmr-types';
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declare interface ACSExportOptions {
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/**
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* Filters ranges for generation
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* If signalKind is "all", include all ranges.
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* If signalKind is "signal", only keep ranges that contain at least one signal with kind signal.
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*/
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signalKind: 'all' | 'signal';
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/**
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* If true, sorts the chemical shift values in ascending order (low to high ppm).
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* If false, sorts in descending order (high to low ppm).
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* @default false
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*/
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ascending: boolean;
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/**
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* Specifies which types of information to include for each range or signal in the ACS string output.
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* Each character in the string represents a data type:
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*
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* - 'I': Integral value (e.g., number of protons or integration value)
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* - 'M': Multiplicity (e.g., singlet, doublet, triplet)
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* - 'J': Coupling constants (J values in Hz)
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* - 'A': Assignment (atom or group assignment)
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*
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* The order of characters determines the order of information in the output. Any combination or subset is allowed, e.g.:
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* 'IMJ' (integral, multiplicity, coupling constants)
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* 'MA' (multiplicity, assignment)
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* 'I' (only integral)
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*
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* Example: 'IMJA' includes all available information in the order: Integral, Multiplicity, Assignment, Coupling constants.
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*
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* @default 'IMJA'
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*/
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format: string;
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/**
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* Format string for chemical shift (delta) values, using [numeral.js](https://numeraljs.com/) syntax.
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*/
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deltaFormat: string;
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/**
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* Format string for scalar coupling constants (J values), using [numeral.js](https://numeraljs.com/) syntax.
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* Controls the number of decimals for J values in Hz.
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*/
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couplingFormat: string;
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}
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export declare interface ActiveSpectrum {
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id: string;
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index: number;
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@@ -207,6 +249,13 @@ export declare type DeepPartial<T> = {
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[P in keyof T]?: DeepPartial<T[P]>;
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};
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/**
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* Define a plugin for NMRium.
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* This function is useful for type hinting. It just returns its argument unchanged.
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* @param plugin
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*/
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export declare function defineNMRiumPlugin(plugin: NMRiumPlugin): NMRiumPlugin;
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/**
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* Used by core to mark a slot as deprecated.
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*/
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@@ -435,8 +484,8 @@ export declare interface MultipleSpectraAnalysisPreferences {
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}
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export declare class NMRiumCore {
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#private;
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readonly version = 9;
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private readonly plugins;
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registerPlugin(plugin: NMRiumPlugin): void;
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registerPlugins(plugins: NMRiumPlugin[]): void;
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private migrate;
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@@ -554,7 +603,7 @@ export declare interface NMRiumPluginOnReadProcess {
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* Filter file loader by extension.
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* Extensions should be in lowercase.
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*/
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-
supportedExtensions?: string[];
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supportedExtensions?: readonly string[];
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/**
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* Hooks on processFileCollection, on file iteration.
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* Each file could be processed by all plugins to load and merge to nmrium data.
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@@ -896,6 +945,11 @@ declare interface ReadReturn {
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containsNmrium: boolean;
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}
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declare type SerializedNmriumState = Omit<Partial<NmriumState>, 'data'> & {
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version: number;
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data?: NmriumData | NmriumDataSource;
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};
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declare interface SerializeNmriumStateOptions {
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includeData?: IncludeData;
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includeSettings?: boolean;
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@@ -1174,6 +1228,7 @@ export declare interface WorkspacePreferences {
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externalAPIs?: ExternalAPI[];
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export?: ExportPreferences;
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peaksLabel?: PeaksLabel;
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acsExportOptions?: ACSExportOptions;
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}
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/**
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@@ -1181,7 +1236,7 @@ export declare interface WorkspacePreferences {
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* predefined : workspace which hardcoded in NMRium
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* user: workspaces which the user create from the general settings
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* component: workspaces which specified at the level of the component `preferences` property
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* nmriumFile: workspaces which is come from the
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* nmriumFile: workspaces which is come from the NMRium file
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*
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* */
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export declare type WorkSpaceSource = 'custom' | 'predefined' | 'user' | 'component' | 'nmriumFile';
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package/dist/nmrium-core.js
CHANGED
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@@ -1,4 +1,4 @@
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1
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-
var ue={NORMAL:"NORMAL",FORMULA:"FORMULA"};var me={RELATIVE:"relative",ABSOLUTE:"absolute",MIN:"min",MAX:"max"};var fe=[{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
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var ue={NORMAL:"NORMAL",FORMULA:"FORMULA"};var me={RELATIVE:"relative",ABSOLUTE:"absolute",MIN:"min",MAX:"max"};var fe=[{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 y=9;var ge=[{key:"CT",description:"CT from NMR Solutions"}];import{isAnyArray as Se}from"is-any-array";import{xMultiply as j}from"ml-spectra-processing";var de=crypto.randomUUID.bind(crypto),b=de;function N(e){let{id:t=b(),meta:o,peaks:r={},filters:n=[],info:i={},ranges:p={},integrals:s={},selector:a,dependentVariables:l=[],...u}=e,c={id:t,meta:o,filters:n},{data:d=Pe(l[0].components)}=e;if(Array.isArray(i.nucleus)&&(i.nucleus=i.nucleus[0]),c.data={x:[],re:[],im:[],...d},"scaleFactor"in i){let{scaleFactor:m}=i,{re:g,im:S}=c.data;j(g,m,{output:g}),S&&j(S,m,{output:S})}a&&(c.selector=a);let f=Se(d.im);if(c.info={phc0:0,phc1:0,nucleus:"1H",isFid:!1,isComplex:f,dimension:1,name:i?.name||t,...i},i.isFid&&i.reverse&&f){let{im:m}=c.data;j(m,-1,{output:m}),c.info.reverse=!1}return c.display={isVisible:!0,isPeaksMarkersVisible:!0,isRealSpectrumVisible:!0,isVisibleInDomain:!0,...e.display},c.peaks={values:[],options:{},...r},c.ranges={values:[],options:{sum:null,isSumConstant:!0,sumAuto:!0},...p},c.integrals={values:[],options:{},...s},{...u,...c}}function Pe(e){let t=e[0]?.data?.x||[],o=e[0]?.data?.re||e[0]?.data?.y||[],r=e[0]?.data?.im||e[1]?.data?.y||null;return t.length>0&&t[0]>t[1]&&(t.reverse(),o.reverse(),r&&r.reverse()),{x:t,re:o,im:r}}import{matrixToArray as ye,xMinMaxValues as xe,xNoiseSanPlot as be}from"ml-spectra-processing";var L={z:[[]],minX:0,minY:0,maxX:0,maxY:0},Ne={re:L,im:L},he={rr:L};function O(e){let{id:t=b(),meta:o={},dependentVariables:r=[],info:n={},filters:i=[],zones:p=[],...s}=e,a={id:t,meta:o,filters:i};a.info={nucleus:["1H","1H"],isFid:!1,isComplex:!1,name:n?.name||b(),...n},a.originalInfo=structuredClone(a.info),a.display={isPositiveVisible:!0,isNegativeVisible:!0,isVisible:!0,dimension:2,...e.display,...e.display};let{data:l=r[0].components}=e;if(a.data={...a.info.isFid?Ne:he,...l},a.originalData=structuredClone(a.data),!("spectrumSize"in n)){let u=n.isFid?"re":"rr",c=a.data[u].z.length,d=c>0?a.data[u].z[0].length:0;a.info.spectrumSize=[d,c]}if(!n.isFid){let u=a.data.rr,c=ye(u.z),{positive:d,negative:f}=be(c),{min:m,max:g}=xe(c);a.data.rr={...u,minZ:m,maxZ:g},a.info.noise={positive:d,negative:f}}return a.zones={values:[],options:{},...p},{...s,...a}}import{xSequentialFillFromTo as Oe}from"ml-spectra-processing";import{isAnyArray as De}from"is-any-array";function U(e,t=0){if(De(e)){let o=e.at(t);if(o!==void 0)return o;throw new RangeError("An array with a index out of boundaries")}return e}var Re=new Set(["t1ir","T1"]);function J(e){let t=[];for(let o of e){let{info:{pulseSequence:r,isFid:n}}=o,{data:i,info:p,meta:{vdlistValues:s=[]}}=o;if(!(r&&Re.has(r))||s.length===0){t.push(o);continue}let l=n?"re":"rr",u={};for(let P in p)u[P]=U(p[P]);let{z:c,maxX:d,minX:f}=i[l],m=Oe({from:f,to:d,size:c[0].length}),[g,S]=Ce(o);for(let P=0;P<s.length;P++){let h={re:m,x:m};for(let D in i)h[Ie(D)]=i[D].z.at(g*(P+S));t.push(N({data:h,info:{...u,name:`${u.name}_${s[P]}`,dimension:1,vd:s[P]}}))}}return t}function Ie(e){return["rr","re"].includes(e)?"re":["im","ri","ir","ii"].includes(e)?"im":"x"}function Ce(e){let{meta:{PAGE:t}}=e,o=!0;if(t){let r=n=>Number.parseFloat(n.replace(/[F|T]1=/,""));o=r(t[0])>r(t[2])}return o?[-1,1]:[1,0]}var ve=2,Te=1;function we(e){let{spectra:t=[],molecules:o}=e,r=[];for(let n of t){let{info:i}=n;switch(i.dimension){case Te:r.push(N(n));break;case ve:r.push(O(n));break;default:throw new Error("dimension does not supported")}}return{molecules:o,spectra:J(r)}}function Ae(e){return e}function R(e,t){e.plugins||(e.plugins={});let o=e.plugins;for(let r of t.values())o[r.id]||(o[r.id]={id:r.id,version:r.version}),o[r.id].id=r.id,o[r.id].version=r.version}function x(e,t){return JSON.parse(JSON.stringify(e),function(r,n){if(r in t){this[t[r]]=n;return}return n})}function V(e){if(e?.version===1)return e;let t={...e,version:1},o={j:"js",signal:"signals",integral:"integration",peak:"peaks",diaID:"diaIDs"};for(let r of t.spectra){if(r.ranges){let n=x(r.ranges,o);r.ranges=Array.isArray(n)?{values:n}:n}else if(r.zones){let n=x(r.zones,o);r.zones=Array.isArray(n)?{values:n}:n}r.peaks&&(r.peaks=Array.isArray(r.peaks)?{values:r.peaks}:r.peaks),r.integrals&&(r.integrals=Array.isArray(r.integrals)?{values:r.integrals}:r.integrals)}return t}function _(e){if(e?.version===2)return e;let t={...e,version:2},o={peaks:{delta:"x",originDelta:"originalX",intensity:"y"},ranges:{atomIDs:"atoms",intensity:"y"}};for(let r of t.spectra)r.peaks?r.peaks=x(r.peaks,o.peaks):r.ranges?r.ranges=x(r.ranges,o.ranges):r.zones&&(r.zones.values=Me(r.zones.values));return t}function Me(e){return e.map(t=>(t.signals&&(t.signals=t.signals.map(o=>{if(o.x&&o.y){let{x:{fromTo:r,...n},y:{fromTo:i,...p}}=o;o={...o,x:{...n,...r},y:{...p,...i}}}else{let{fromTo:r,deltaX:n,resolutionX:i,nucleusX:p,deltaY:s,resolutionY:a,nucleusY:l,shiftX:u,shiftY:c,...d}=o;o={...d,x:{from:r[0].from,to:r[0].to,delta:n,resolution:i,nucleus:p},y:{from:r[1].from,to:r[1].to,delta:s,resolution:a,nucleus:l}}}return o},[])),t),[])}var Fe={name:"apodization",label:"Apodization",value:{lineBroadening:1,gaussBroadening:0,lineBroadeningCenter:0}};function z(e){if(e?.version===3)return e;let t={...e,version:3};for(let o of t.spectra)if(Array.isArray(o?.filters)&&o?.filters.length>0){let r=o.filters.findIndex(n=>n.name==="lineBroadening");if(r!==-1){let n={...o.filters[r],...Fe};o.filters[r]=o.filters[r-1],o.filters[r-1]=n}}return t}function B(e){if(e?.version===4)return e;let{version:t,...o}=e,r=[],n={};for(let{source:s,...a}of o.spectra){let l={},{info:u={},display:c={}}=a;if(u?.dimension===2&&!s?.jcampURL)if(u.isFt)l.data={rr:a.data};else continue;if(s?.jcampURL){let{jcampURL:m,jcampSpectrumIndex:g}=s,S=m.match(/(?<baseURL>^\w+:\/{2}\w+\/)(?<relativePath>.*)/);n[m]||(n[m]={baseURL:S?.groups.baseURL||"",relativePath:S?.groups.relativePath||m.replace(/^\.\//,"")}),l.sourceSelector={files:[n[m].relativePath]},g!==void 0&&(l.sourceSelector.jcamp={index:g})}l.filters=Ee(a.filters);let{name:d,...f}=c;d&&(l.info={...u,name:d}),l.display=f,r.push({...a,...l})}let i={data:{...o,spectra:r},version:4},p={entries:Object.values(n)};return p.entries.length>0&&(i.data.source=p),i}function Ee(e=[]){let t=[];for(let o of e){let{name:r,value:n}=o;switch(r){case"zeroFilling":t.push({...o,value:{nbPoints:n}});break;case"shiftX":case"shift2DX":case"shift2DY":t.push({...o,value:{shift:n}});break;default:t.push({...o})}}return t}function K(e){if(e?.version===5)return e;let t={...e,version:5},o={originFrom:"originalFrom",originTo:"originalTo",originDelta:"originalDelta",originX:"originalX",originY:"originalY",originZ:"originalZ"};for(let r of t?.data?.spectra||[])for(let n of["peaks","ranges","zones"])r?.[n]&&(r[n]=x(r[n],o));return t}function X(e){if(e?.version===6)return e;let t={...e,version:6};for(let o of t?.data?.spectra||[]){let{digitalFilter:r,fft:n,phaseCorrection:i}=ke(o);n?.flag&&r?.flag&&i&&Math.floor(r.value.digitalFilterValue)%2>0&&(i.value.ph0-=180)}return t}function ke(e,t=["phaseCorrection","fft","digitalFilter"]){let{filters:o=[]}=e,r={};for(let n of t)r[n]=o.find(i=>i.name===n);return r}function I(e,t="localStorage"){if(e?.version===7)return e;if(t==="nmrium")return H(e);let o={...e,version:7};for(let r in e.workspaces)o.workspaces[r]=H(o.workspaces[r]);return o}function H(e){let{formatting:{nuclei:t,panels:o}={nuclei:null,panels:null},version:r,...n}=e,i={...n};return t&&(i.nuclei=je(t)),o&&(i.panels=o),i}function je(e){let t=[],o={name:"nucleus",ppm:"ppmFormat",hz:"hzFormat"};for(let r in e)t.push(x(e[r],o));return t}function Y(e){if(e?.version===7)return e;let t={...e,version:7};return t?.settings&&(t.settings=I(t.settings,"nmrium")),t}function C(e,t="localStorage"){if(e?.version===8)return e;if(t==="nmrium")return Q(e);let o={...e,version:8};for(let r in e.workspaces)o.workspaces[r]=Q(o.workspaces[r]);return o}function Q(e){let{version:t,...o}=e,r={...o};return r.display.panels=Le(e),r}function Le(e){let t={},o=e.display.panels;for(let r of Object.keys(o)){let{display:n,open:i}=o[r];t[r]={display:n,visible:n,open:i}}return t}function W(e){if(e?.version===8)return e;let t={...e,version:8};t?.settings&&(t.settings=C(t.settings,"nmrium"));for(let o of t?.data?.spectra||[]){let{filters:r=[]}=o;for(let s=0;s<r.length;s++){let{flag:a,isDeleteAllow:l,label:u,...c}=r[s];r[s]={...c,enabled:a}}let n=r.findIndex(s=>s.name==="apodization");if(n!==-1){let s=r[n],{lineBroadening:a,gaussBroadening:l,lineBroadeningCenter:u}=s.value;s.value={exponential:{apply:!0,options:{lineBroadening:l>0?-a:a}}},l>0&&(s.value.gaussian={apply:!0,options:{lineBroadening:.6*l,lineBroadeningCenter:u}}),r[n]=s}let i=r.findIndex(s=>s.name==="apodizationDimension1"),p=r.findIndex(s=>s.name==="apodizationDimension2");if(i!==-1){let s=r[i],{shapes:a}=s.value.compose;s.value=ee(a)}if(p!==-1){let s=r[p],{shapes:a}=s.value.compose;s.value=ee(a)}}return t}function ee(e){let t={};for(let{shape:o}of e){let{kind:r,options:n}=o;if(r==="sineBell"){let{exponent:i,offset:p}=n,s=i===2?"sineSquare":"sineBell";t[s]={apply:!0,options:{offset:p}}}}return t}function $(e){let{version:t,plugins:o,...r}=e;return t===9?e:{version:9,plugins:{},...r}}var Ue=[V,_,z,B,K,X,Y,W,$];function te(e,t,o){let r=structuredClone(e),n=Object.entries(e?.plugins??{});for(let[s,{version:a}]of n){let l=o.get(s);if(!(l&&l.version>=a)){if(l){console.warn(`Plugin "${l.id}" is loaded with a version older (${l.version}) than the one used to save the state (${a}).
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NMRium may fail to load the state.
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Please update the plugin to the latest version.`);continue}console.warn(`Plugin "${s}@${a}" is not registered. NMRium may fail to load the state.
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Please consider open this file with the plugin installed.`)}}let i=new Set,p=()=>{let s=r.version;for(let a of o.values())for(let l of a.migrations){if(i.has(l)||s<l.minCore||l.maxCore&&s>l.maxCore)continue;if((r.plugins?.[a.id]?.version||0)===a.version)break;r=l.up(r),i.add(l)}};for(let s=e?.version||0;s<t;s++){let a=
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+
Please consider open this file with the plugin installed.`)}}let i=new Set,p=()=>{let s=r.version;for(let a of o.values())for(let l of a.migrations){if(i.has(l)||s<l.minCore||l.maxCore&&s>l.maxCore)continue;if((r.plugins?.[a.id]?.version||0)===a.version)break;r=l.up(r),i.add(l)}};for(let s=e?.version||0;s<t;s++){let a=Ue[s];r=a(r),p()}return p(),R(r,o),r}import{FileCollection as $e}from"file-collection";var re={SDF:"sdf",MOL:"mol",NMRIUM:"nmrium",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 w(e,t={},o){let{data:r,...n}=e;if(!r)return e;let{spectra:i=[]}=r,{keep1D:p=!0,keep2D:s=!0,onlyReal:a}=t,l=a?"ft":t.dataSelection||"both",u=[];for(let c of i){if(!c.info){u.push(c);continue}let{isFid:d,dimension:f,name:m}=c.info;if(!T(f===1&&!p,m,o)&&!T(f===2&&!s,m,o)&&!T(d&&l==="ft",m,o)&&!T(!d&&l==="fid",m,o))if(a&&!d)if(c.info.isComplex=!1,Ve(c)){let{rr:g}=c.data;u.push({...c,data:{rr:g}})}else{let{re:g,x:S}=c.data;u.push({...c,data:{re:g,x:S}})}else u.push(c)}return{data:{...r,spectra:u},...n}}function T(e,t,o){return e?(o?.warn(`Skipping ${t} because it didn't match the import filters.`),!0):!1}function Ve(e){let{info:t}=e;return t?.dimension===2}function A(e){let{nmriumState:t,plugins:o,options:r}=e;for(let n of o.values()){let i=n.onReadProcess?.onProcessing;i&&i(t,r)}}async function M(e,t,o={}){let{sourceSelector:r,converter:n,keepSource:i,logger:p}=o,s=[],a=[];for(let f of t.values()){let{onReadProcess:m}=f;m&&(m?.onFiles&&s.push(f),m?.supportedExtensions?.length&&m?.onFile&&a.push(f))}let l=await Promise.allSettled(s.map(f=>f.onReadProcess.onFiles(e,o))),u=[],c=await Promise.allSettled(e.files.flatMap(f=>{let m=v(f.name).toLowerCase();return a.flatMap(g=>{let{supportedExtensions:S,onFile:P}=g.onReadProcess;return S.includes(m)?(u.push({file:f,plugin:g}),P(f,{logger:p,sourceSelector:r,converter:n,keepSource:i})):[]})})),d={spectra:[],molecules:[]};for(let f=0;f<l.length;f++){let m=l[f];switch(m.status){case"fulfilled":{let{spectra:g=[],molecules:S=[]}=m.value||{};d.spectra.push(...g),d.molecules.push(...S);break}case"rejected":{let g=m.reason,S=s[f];o.logger?.error(`Load file collection with plugin ${S.id}@${S.version} fails with: ${g}`);break}}}for(let f=0;f<c.length;f++){let m=c[f];switch(m.status){case"fulfilled":{let{spectra:g=[],molecules:S=[]}=m.value||{};d.spectra.push(...g),d.molecules.push(...S);break}case"rejected":{let g=m.reason,{file:S,plugin:P}=u[f];o.logger?.error(`Load file ${S.relativePath} with plugin ${P.id}@${P.version} fails with: ${g}`);break}}}return d}import{FileCollection as Xe}from"file-collection";import{FileCollection as _e}from"file-collection";import oe from"lodash.merge";import{xIsEquallySpaced as ze}from"ml-spectra-processing";async function F(e){let{nmriumObjectInput:t,options:o={},migrator:r,plugins:n}=e,i=r(t),{data:p,...s}=i;if(!p)return{...s};let a={data:{...p,spectra:[]},...s},l=a.data,{source:u,spectra:c,molecules:d}=l,f;u&&(f=await _e.fromSource(u,{unzip:{zipExtensions:["zip","nmredata"]}}));let m=[];for(let g of p.spectra)if(f){let{sourceSelector:S}=g,P=E({input:f,migrator:r,plugins:n,options:{...o,sourceSelector:S}}).then(h=>{let{nmriumState:{data:D}}=h,{spectra:pe=[],molecules:q=[]}=D||{};q.length>0&&d.length===0&&d.push(...q);for(let ce of pe)c.push(Be(g,Ke(ce)))});m.push(P)}else{let{dimension:S}=g.info;if(S===1){if(!ze(g.data)){o.logger?.error('The ".nmrium" file is corrupted; the X-axis values are not equally distant.');continue}c.push(N(g))}else S===2&&c.push(O(g))}return await Promise.allSettled(m),a}function Be(e,t){let{data:o,...r}=e;if("ranges"in t){let{data:n,...i}=t;return{...oe(i,r),data:n}}else if("zones"in t){let{data:n,...i}=t;return{...oe(i,r),data:n}}else return t}function Ke(e){return{...e,id:b()}}async function ne(e){let{file:t,options:o={},migrator:r,plugins:n}=e,i=await t.arrayBuffer(),p=await(We(i)?Ye(i):t.text());return F({nmriumObjectInput:JSON.parse(p),plugins:n,migrator:r,options:o})}async function Ye(e){let t=await Xe.fromZip(e);if(t.files.length===0)throw new Error("compressed nmrium file is corrupted");return t.files[0].text()}function We(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 E(e){let{options:t={},input:o,migrator:r,plugins:n}=e,i=qe(await Ge(o),t.sourceSelector?.files),p=Je(i);if(p)return{nmriumState:await ne({file:p,migrator:r,plugins:n,options:t}),containsNmrium:!0};let s=await M(i,n,t),a=w({version:9,data:s},t?.sourceSelector?.general,t.logger),{onLoadProcessing:l,experimentalFeatures:u}=t,c={...l,autoProcessing:l?.autoProcessing??!1,experimentalFeatures:u};return A({nmriumState:a,plugins:n,options:c}),{nmriumState:a,containsNmrium:!1}}function Ge(e){return Array.isArray(e)?Promise.reject(new Error("For a set of fileCollectionItems pass a FileCollection instance")):Ze(e)?Promise.resolve(e):new $e().appendExtendedSource({...e,uuid:crypto.randomUUID()})}function Ze(e){return typeof e=="object"&&"files"in e}function qe(e,t){if(!t)return e;let o=new Set(t);return e.filter(r=>o.has(r.relativePath))}function Je(e){return e.files.find(t=>v(t.name).toLowerCase()===re.NMRIUM)}function k(e,t){let o={};for(let r in e)t.includes(r)||(o[r]=e[r]);return o}var He=["data","originalData","info","originalInfo","meta","customInfo"],Qe=["sourceSelector","originalData","originalInfo"];function ie(e,t,o={}){let{version:r,data:n}=e;if(n.actionType)return e;let i={version:r,plugins:e.plugins},{includeData:p}=o;p!=="noData"&&(i.data=et({...n},p));let{includeSettings:s,includeView:a}=o;return s&&(i.settings=e.settings),a&&(i.view=e.view),R(i,t),i}function et(e,t="rawData"){let{spectra:o}=e;switch(t){case"dataSource":return tt(e);case"rawData":return{...k(e,["source"]),spectra:o.map(ot)};default:return e}}function tt(e){let{spectra:t}=e;if(!e.source)throw new Error("source property should exists for dataSource serialization");return{...e,spectra:t.map(rt)}}function rt(e){return k(e,He)}function ot(e){let{data:t,info:o,originalData:r,originalInfo:n}=e,i=k(e,Qe);return i.data=r||t,i.info=n||o,i}var nt=["topbar.right","topbar.about_us.modal"],it=[],qr=[...nt,...it],st={},G={};{let e=st,t=G;for(let[o,r]of Object.entries(e))t[r]||(t[r]=[]),t[r]?.push(o)}function*se(e){let{slot:t,plugins:o,supportedToDeprecatedSlots:r=G}=e,n=r[t];for(let[i,p]of o.entries()){let s=p.ui;if(!s)continue;let a=s[t];if(a){yield[i,a];continue}if(n)for(let l of n){let u=p.ui?.[l];if(u){yield[i,u],console.warn(`Plugin ${p.id} used deprecated slot "${l}". Please update this plugin to use "${t}" instead.`);break}}}}import{FileCollection as at}from"file-collection";async function ae(e){let{source:t,plugins:o,options:r={}}=e,{keepSource:n=!0,converter:i,...p}=r,s={source:t,spectra:[],molecules:[]},a=await at.fromSource(t,{unzip:{zipExtensions:["zip","nmredata"]}}),{spectra:l=[],molecules:u=[]}=await M(a,o,{keepSource:n,converter:{...i,bruker:{keepFiles:!0,...Reflect.get(i??{},"bruker")}},...p});s.spectra.push(...l),s.molecules.push(...u);let c=w({version:9,data:s},r?.sourceSelector?.general),{onLoadProcessing:d}=p,f={filters:d?.filters,autoProcessing:d?.autoProcessing??!1,experimentalFeatures:r.experimentalFeatures};return A({nmriumState:c,plugins:o,options:f}),c}var Z=class{version=9;#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)}migrate(t){return te(t,this.version,this.#e)}read(t,o={}){return E({input:t,migrator:this.migrate.bind(this),plugins:this.#e,options:o})}readNMRiumObject(t,o){return F({nmriumObjectInput:t,options:o,plugins:this.#e,migrator:this.migrate.bind(this)})}readFromWebSource(t,o){return ae({source:t,options:o,plugins:this.#e})}serializeNmriumState(t,o){return ie(t,this.#e,o)}slot(t){return se({slot:t,plugins:this.#e})}};function lt(e,t){if(t>9)return 0;let o=-1;for(let r=0;r<e.length;r++)if(e[r].version>t){o=r;break}return o}var le=[{version:6,fun:I},{version:7,fun:C}];function pt(e){let{version:t}=e||{},o=lt(le,t);if(o===-1)return{...e,version:9};let r=le.slice(o);for(let n of r)e=n.fun(e);return e}export{ue as ANALYSIS_COLUMN_TYPES,me as ANALYSIS_COLUMN_VALUES_KEYS,y as CURRENT_EXPORT_VERSION,ge as EXTERNAL_API_KEYS,Z as NMRiumCore,Ae as defineNMRiumPlugin,we as formatSpectra,b as generateID,U as getOneIfArray,pt as migrateSettings,fe as units};
|
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "@zakodium/nmrium-core",
|
|
3
|
-
"version": "0.
|
|
3
|
+
"version": "0.2.0",
|
|
4
4
|
"description": "The core of NMRium: types, state, state migration and plugin system.",
|
|
5
5
|
"author": "Zakodium Sàrl",
|
|
6
6
|
"license": "CC-BY-NC-SA-4.0",
|
|
@@ -15,19 +15,19 @@
|
|
|
15
15
|
"dist"
|
|
16
16
|
],
|
|
17
17
|
"scripts": {
|
|
18
|
-
"bundle": "node scripts/esbuild.js &&
|
|
19
|
-
"bundle-types": "
|
|
18
|
+
"bundle": "node scripts/esbuild.js && yarn bundle-types",
|
|
19
|
+
"bundle-types": "yarn tsc && yarn g:api-extractor",
|
|
20
20
|
"clean": "rimraf types dist coverage",
|
|
21
|
-
"prepack": "
|
|
21
|
+
"prepack": "yarn clean && yarn bundle",
|
|
22
22
|
"test": "yarn g:test-only && yarn g:check-types && yarn g:eslint && yarn g:prettier",
|
|
23
23
|
"tsc": "tsc --project tsconfig.types.json"
|
|
24
24
|
},
|
|
25
25
|
"devDependencies": {
|
|
26
26
|
"@types/lodash.merge": "^4.6.9",
|
|
27
|
-
"@types/node": "^24.
|
|
27
|
+
"@types/node": "^24.5.2",
|
|
28
28
|
"@types/react": "^18.3.13",
|
|
29
|
-
"@zakodium/nmr-types": "^0.
|
|
30
|
-
"esbuild": "^0.25.
|
|
29
|
+
"@zakodium/nmr-types": "^0.2.0",
|
|
30
|
+
"esbuild": "^0.25.10",
|
|
31
31
|
"jest-matcher-deep-close-to": "^3.0.2",
|
|
32
32
|
"rimraf": "^6.0.1",
|
|
33
33
|
"vitest": "^3.2.4"
|
|
@@ -43,5 +43,6 @@
|
|
|
43
43
|
},
|
|
44
44
|
"volta": {
|
|
45
45
|
"extends": "../../../package.json"
|
|
46
|
-
}
|
|
47
|
-
|
|
46
|
+
},
|
|
47
|
+
"gitHead": "1fe1f91e225b5c3140ff63df99a74ad8e88d87b8"
|
|
48
|
+
}
|