@zakodium/nmrium-core 0.2.0 → 0.2.2
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 +99 -6
- package/dist/nmrium-core.js +2 -2
- package/package.json +2 -2
package/dist/nmrium-core.d.ts
CHANGED
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@@ -19,7 +19,7 @@ import type { ReactNode } from 'react';
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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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export 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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@@ -62,6 +62,8 @@ declare interface ACSExportOptions {
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couplingFormat: string;
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}
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export declare type ACSExportSettings = Record<string, ACSExportOptions>;
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export declare interface ActiveSpectrum {
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id: string;
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index: number;
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@@ -536,9 +538,42 @@ export declare interface NMRiumPanelPreferences {
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}
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export declare interface NMRiumPlugin {
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/**
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* Unique identifier for the plugin across the plugins registered in the core.
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*
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* This should be a string in the format `<PackageName>#<PluginSymbol>`.
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* The `<PackageName>` should be the name of the package that defines the plugin.
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* The `<PluginSymbol>` could be a unique symbol that identifies the plugin and exported by the package.
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* Or could be the name of the plugin, unrelated to any usable symbol.
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*/
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id: string;
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/**
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* Version of the plugin.
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* Plugins must follow incremental versioning, like NMRium state versioning.
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* The version should be incremented when a migration is needed.
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*/
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version: number;
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/**
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* Migrations are applied in ascending order
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* and follow the `minCore` and `maxCore` conditions.
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*
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* Your migrations must be declared in ascending order.
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* Your migrations must update the plugin version in the state.
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* Your last migration must update the plugin version in the state to the current plugin version.
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*
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* For more information about how to write migrations
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* @see `NMRiumPluginMigration.up`
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*/
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migrations: NMRiumPluginMigration[];
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/**
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* A configuration option to control if the plugin definition should be serialized into the state.
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* Consider setting this option to true if the plugin is able to read or manipulate the state.
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* If your plugin is `ui` only, you can set this false to avoid unnecessary serialization.
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*/
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shouldSerialize: boolean;
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/**
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* Read hooks
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*/
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onReadProcess?: NMRiumPluginOnReadProcess;
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/**
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* UI components to render in nmrium components
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@@ -586,8 +621,66 @@ export declare interface NMRiumPlugin {
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}
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export declare interface NMRiumPluginMigration {
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/**
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* Migration function.
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*
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* It is called during `core.migrate(state)` (used by some core read methods)
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*
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* You could mutate the state to apply the migration, but you must return it.
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* If your migration returns nothing, the state will be lost, and it will break the core migration process.
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* The process ensures to call the migration once (if needed).
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* But you must update the plugin version in the state.
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* /!\ the plugin may not exist yet in the state on firsts' migration.
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*
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* @param state - the nmrium state to migrate to the next version
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* @returns the migrated nmrium state
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*
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* @example
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*
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* Your plugin was in version 1, and you have to update states to be compatible with version 2 of your plugin:
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*
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* ```ts
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* const id = 'my-package#MyProcessingPlugin';
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* defineNMRiumPlugin({
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* id,
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* version: 2,
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* shouldSerialize: true,
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* migrations: [
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* {
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* coreMin: 9,
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* up(state: any): any {
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* state.plugins[id] ??= { version: 1, id };
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* state.plugins[id].version = 2;
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*
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* // mutate anything else in the state about your migration
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*
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* return state;
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* },
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* }
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* ],
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* onReadProcess: {
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* onProcessing: (state, options) => {
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* // process the state here
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* },
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* },
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* });
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* ```
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*/
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up(state: any): any;
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/**
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* Minimum core version supported to apply the migration.
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* The lower nmrium core version supporting plugins is 9
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* In doubt, put the current core version.
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*
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* @see CURRENT_EXPORT_VERSION
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* @see NMRiumState.version
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*/
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minCore: number;
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/**
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* Maximum core version supported to apply the migration.
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*
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* @see NMRiumState.version
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*/
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maxCore?: number;
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}
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@@ -636,10 +729,10 @@ export declare interface NmriumState {
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*
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* @example Minimal plugin declaration
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* ```ts
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* declare module '@zakodium/nmrium-core' {
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* export interface NmriumStatePlugins {
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* ['my-package#MyPlugin']?: NmriumStateBasePlugin & { config: object };
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* }
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* }
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* ```
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*/
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@@ -1228,7 +1321,7 @@ 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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acsExportSettings?: ACSExportSettings;
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}
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/**
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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 P=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=ye(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 ye(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 Pe,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=Pe(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 y in p)u[y]=U(p[y]);let{z:c,maxX:d,minX:f}=i[l],m=Oe({from:f,to:d,size:c[0].length}),[g,S]=Ie(o);for(let y=0;y<s.length;y++){let h={re:m,x:m};for(let D in i)h[Ce(D)]=i[D].z.at(g*(y+S));t.push(N({data:h,info:{...u,name:`${u.name}_${s[y]}`,dimension:1,vd:s[y]}}))}}return t}function Ce(e){return["rr","re"].includes(e)?"re":["im","ri","ir","ii"].includes(e)?"im":"x"}function Ie(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,Ae=1;function Te(e){let{spectra:t=[],molecules:o}=e,r=[];for(let n of t){let{info:i}=n;switch(i.dimension){case Ae: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 we(e){return e}function R(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}}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=Ee(r.zones.values));return t}function Ee(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 Me={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],...Me};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=Fe(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 Fe(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 C(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=C(t.settings,"nmrium")),t}function I(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=I(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 (${a}).
|
|
2
2
|
NMRium may fail to load the state.
|
|
3
3
|
Please update the plugin to the latest version.`);continue}console.warn(`Plugin "${s}@${a}" is not registered. NMRium may fail to load the state.
|
|
4
|
-
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
|
|
4
|
+
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 T(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(!A(f===1&&!p,m,o)&&!A(f===2&&!s,m,o)&&!A(d&&l==="ft",m,o)&&!A(!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 A(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 w(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 E(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:y}=g.onReadProcess;return S.includes(m)?(u.push({file:f,plugin:g}),y(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:y}=u[f];o.logger?.error(`Load file ${S.relativePath} with plugin ${y.id}@${y.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 M(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,y=F({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(y)}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 M({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 F(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 E(i,n,t),a=T({version:9,data:s},t?.sourceSelector?.general,t.logger),{onLoadProcessing:l,experimentalFeatures:u}=t,c={...l,autoProcessing:l?.autoProcessing??!1,experimentalFeatures:u};return w({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 E(a,o,{keepSource:n,converter:{...i,bruker:{keepFiles:!0,...Reflect.get(i??{},"bruker")}},...p});s.spectra.push(...l),s.molecules.push(...u);let c=T({version:9,data:s},r?.sourceSelector?.general),{onLoadProcessing:d}=p,f={filters:d?.filters,autoProcessing:d?.autoProcessing??!1,experimentalFeatures:r.experimentalFeatures};return w({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 F({input:t,migrator:this.migrate.bind(this),plugins:this.#e,options:o})}readNMRiumObject(t,o){return M({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:C},{version:7,fun:I}];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,P as CURRENT_EXPORT_VERSION,ge as EXTERNAL_API_KEYS,Z as NMRiumCore,we as defineNMRiumPlugin,Te 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": "0.2.
|
|
3
|
+
"version": "0.2.2",
|
|
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",
|
|
@@ -44,5 +44,5 @@
|
|
|
44
44
|
"volta": {
|
|
45
45
|
"extends": "../../../package.json"
|
|
46
46
|
},
|
|
47
|
-
"gitHead": "
|
|
47
|
+
"gitHead": "53cd32cbf4a73e576f5ef817bb5d5939f411e900"
|
|
48
48
|
}
|