@zakodium/nmrium-core 0.2.1 → 0.2.3

package/dist/nmrium-core.d.ts

@@ -538,9 +538,42 @@ export declare interface NMRiumPanelPreferences {
 }
 
 export declare interface NMRiumPlugin {
+    /**
+     * Unique identifier for the plugin across the plugins registered in the core.
+     *
+     * This should be a string in the format `<PackageName>#<PluginSymbol>`.
+     * The `<PackageName>` should be the name of the package that defines the plugin.
+     * The `<PluginSymbol>` could be a unique symbol that identifies the plugin and exported by the package.
+     *  Or could be the name of the plugin, unrelated to any usable symbol.
+     */
     id: string;
+    /**
+     * Version of the plugin.
+     * Plugins must follow incremental versioning, like NMRium state versioning.
+     * The version should be incremented when a migration is needed.
+     */
     version: number;
+    /**
+     * Migrations are applied in ascending order
+     * and follow the `minCore` and `maxCore` conditions.
+     *
+     * Your migrations must be declared in ascending order.
+     * Your migrations must update the plugin version in the state.
+     * Your last migration must update the plugin version in the state to the current plugin version.
+     *
+     * For more information about how to write migrations
+     * @see `NMRiumPluginMigration.up`
+     */
     migrations: NMRiumPluginMigration[];
+    /**
+     * A configuration option to control if the plugin definition should be serialized into the state.
+     * Consider setting this option to true if the plugin is able to read or manipulate the state.
+     * If your plugin is `ui` only, you can set this false to avoid unnecessary serialization.
+     */
+    shouldSerialize: boolean;
+    /**
+     * Read hooks
+     */
     onReadProcess?: NMRiumPluginOnReadProcess;
     /**
      * UI components to render in nmrium components
@@ -588,8 +621,66 @@ export declare interface NMRiumPlugin {
 }
 
 export declare interface NMRiumPluginMigration {
+    /**
+     * Migration function.
+     *
+     * It is called during `core.migrate(state)` (used by some core read methods)
+     *
+     * You could mutate the state to apply the migration, but you must return it.
+     *  If your migration returns nothing, the state will be lost, and it will break the core migration process.
+     * The process ensures to call the migration once (if needed).
+     *  But you must update the plugin version in the state.
+     *  /!\ the plugin may not exist yet in the state on firsts' migration.
+     *
+     * @param state - the nmrium state to migrate to the next version
+     * @returns the migrated nmrium state
+     *
+     * @example
+     *
+     * Your plugin was in version 1, and you have to update states to be compatible with version 2 of your plugin:
+     *
+     * ```ts
+     * const id = 'my-package#MyProcessingPlugin';
+     * defineNMRiumPlugin({
+     *  id,
+     *  version: 2,
+     *  shouldSerialize: true,
+     *  migrations: [
+     *    {
+     *      coreMin: 9,
+     *      up(state: any): any {
+     *        state.plugins[id] ??= { version: 1, id };
+     *        state.plugins[id].version = 2;
+     *
+     *        // mutate anything else in the state about your migration
+     *
+     *        return state;
+     *      },
+     *    }
+     *  ],
+     *  onReadProcess: {
+     *    onProcessing: (state, options) => {
+     *      // process the state here
+     *    },
+     *  },
+     * });
+     * ```
+     */
     up(state: any): any;
+    /**
+     * Minimum core version supported to apply the migration.
+     * The lower nmrium core version supporting plugins is 9
+     * In doubt, put the current core version.
+     *
+     * @see CURRENT_EXPORT_VERSION
+     * @see NMRiumState.version
+     */
     minCore: number;
+    /**
+     * Maximum core version supported to apply the migration.
+     *
+     * @see NMRiumState.version
+     */
     maxCore?: number;
 }
 
@@ -638,10 +729,10 @@ export declare interface NmriumState {
  *
  * @example Minimal plugin declaration
  * ```ts
- * import type { NmriumStatePlugins, NmriumStateBasePlugin } from 'nmrium-core';
- *
- * export interface NmriumStatePlugins {
- *  '@zakodium/nmrium-core-plugins#BrukerLoaderPlugin': NmriumStateBasePlugin;
+ * declare module '@zakodium/nmrium-core' {
+ *   export interface NmriumStatePlugins {
+ *     ['my-package#MyPlugin']?: NmriumStateBasePlugin & { config: object };
+ *   }
  * }
  * ```
  */

package/dist/nmrium-core.js

@@ -1,4 +1,4 @@
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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}).
 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=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: ${g}`);break}}}return d}import{FileCollection as Xe}from"file-collection";import{FileCollection as _e}from"file-collection";import oe from"lodash.merge";import{xIsEquallySpaced as ze}from"ml-spectra-processing";async function M(e){let{nmriumObjectInput:t,options:o={},migrator:r,plugins:n}=e,i=r(t),{data:p,...s}=i;if(!p)return{...s};let a={data:{...p,spectra:[]},...s},l=a.data,{source:u,spectra:c,molecules:d}=l,f;u&&(f=await _e.fromSource(u,{unzip:{zipExtensions:["zip","nmredata"]}}));let m=[];for(let g of p.spectra)if(f){let{sourceSelector:S}=g,y=F({input:f,migrator:r,plugins:n,options:{...o,sourceSelector:S}}).then(h=>{let{nmriumState:{data:D}}=h,{spectra:pe=[],molecules:q=[]}=D||{};q.length>0&&d.length===0&&d.push(...q);for(let ce of pe)c.push(Be(g,Ke(ce)))});m.push(y)}else{let{dimension:S}=g.info;if(S===1){if(!ze(g.data)){o.logger?.error('The ".nmrium" file is corrupted; 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Please update this plugin to use "${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

@@ -1,6 +1,6 @@
 {
   "name": "@zakodium/nmrium-core",
-  "version": "0.2.1",
+  "version": "0.2.3",
   "description": "The core of NMRium: types, state, state migration and plugin system.",
   "author": "Zakodium Sàrl",
   "license": "CC-BY-NC-SA-4.0",
@@ -24,12 +24,13 @@
   },
   "devDependencies": {
     "@types/lodash.merge": "^4.6.9",
-    "@types/node": "^24.5.2",
+    "@types/node": "^24.7.2",
     "@types/react": "^18.3.13",
-    "@zakodium/nmr-types": "^0.2.0",
+    "@zakodium/nmr-types": "^0.2.1",
     "esbuild": "^0.25.10",
     "jest-matcher-deep-close-to": "^3.0.2",
     "rimraf": "^6.0.1",
+    "typescript": "~5.9.3",
     "vitest": "^3.2.4"
   },
   "dependencies": {
@@ -44,5 +45,5 @@
   "volta": {
     "extends": "../../../package.json"
   },
-  "gitHead": "3ae265679edc9e722d29dc66f3338d9fb8ab2062"
+  "gitHead": "590a8e4b1d464902733151fcefa7c9a739fddccf"
 }