@zakodium/nmrium-core 0.2.2 → 0.3.0

package/dist/nmrium-core.d.ts

@@ -1,4 +1,5 @@
 import type { CorrelationData } from 'nmr-correlation';
+import type { ExtraFileContent } from 'file-collection';
 import type { FifoLoggerOptions } from 'fifo-logger';
 import { FileCollection } from 'file-collection';
 import type { FileItem } from 'file-collection';
@@ -17,6 +18,7 @@ import type { Peaks } from '@zakodium/nmr-types';
 import type { Ranges } from '@zakodium/nmr-types';
 import type { ReactNode } from 'react';
 import type { Source } from 'file-collection';
+import type { ZipFileContent } from 'file-collection';
 import type { Zones } from '@zakodium/nmr-types';
 
 export declare interface ACSExportOptions {
@@ -138,7 +140,9 @@ export declare interface BaseNucleusPreferences<T> {
 
 declare interface BaseSpectrum {
     id: string;
+    sourceId?: string;
     sourceSelector?: NmrLoaderSelectors;
+    fileCollectionId?: string;
     meta: Metadata;
     customInfo: any;
 }
@@ -210,7 +214,7 @@ declare interface ContourOptions_2 {
 
 export declare type ContoursLevels = Record<string, Level>;
 
-export declare const CURRENT_EXPORT_VERSION = 9;
+export declare const CURRENT_EXPORT_VERSION = 10;
 
 export declare type CustomWorkspaces = Record<string, InnerWorkspace>;
 
@@ -375,7 +379,7 @@ export declare const generateID: () => `${string}-${string}-${string}-${string}-
  */
 export declare function getOneIfArray<T extends PosibleInput>(data: T | T[], index?: number): T;
 
-declare type IncludeData = 'rawData' | 'dataSource' | 'noData';
+export declare type IncludeData = 'rawData' | 'dataSource' | 'noData' | 'selfContained' | 'selfContainedExternalDatasource';
 
 declare interface InfoBlock {
     visible: boolean;
@@ -487,25 +491,43 @@ export declare interface MultipleSpectraAnalysisPreferences {
 
 export declare class NMRiumCore {
     #private;
-    readonly version = 9;
+    readonly version = 10;
     registerPlugin(plugin: NMRiumPlugin): void;
     registerPlugins(plugins: NMRiumPlugin[]): void;
     private migrate;
     read(input: FileCollection | FileItem, options?: Partial<ParsingOptions>): ReturnType<typeof read>;
-    readNMRiumObject(nmriumObjectInput: object, options?: ParsingOptions): Promise<Partial<NmriumState>>;
-    readFromWebSource(source: Source, options?: ParsingOptions): Promise<Partial<NmriumState>>;
+    readNMRiumArchive(input: ZipFileContent, options?: Partial<ParsingOptions>): ReturnType<typeof readNMRiumArchive>;
+    readNMRiumObject(nmriumObjectInput: object, options?: ParsingOptions): ReturnType<typeof readNMRiumObject>;
+    readFromWebSource(source: Source, options?: ParsingOptions): Promise<[state: Partial<NmriumState>, fileCollection: FileCollection]>;
+    /**
+     * Serialize a state to nmrium object.
+     * It can be serialized to json then,
+     * it should be saved in a file with the extension ".nmrium"
+     * And served with the content-type "application/nmrium+json"
+     *  or "application/nmrium+json+zip" if it is a single .nmrium file in a zip archive.
+     * @param nmriumState
+     * @param options
+     */
     serializeNmriumState(nmriumState: NmriumState, options?: SerializeNmriumStateOptions): SerializedNmriumState;
+    /**
+     * Serialize nmrium state to nmrium archive.
+     * It should be save in a file with the extension ".nmrium.zip"
+     * and served with the content-type "application/nmrium+zip".
+     * @param options
+     */
+    serializeNmriumArchive(options: SerializeNmriumArchiveOptions): Promise<Uint8Array<ArrayBuffer>>;
+    serializePlugins(): NmriumStatePlugins;
     slot(slot: SupportedUISlot): IteratorObject<[pluginId: string, Component: PluginUIComponent], void>;
 }
 
 export declare interface NmriumData extends BaseNmriumData {
     spectra: Spectrum[];
-    source?: Source;
+    sources?: SourceNmriumData[];
 }
 
 export declare interface NmriumDataSource extends BaseNmriumData {
     spectra: SpectraSource[];
-    source: Source;
+    sources: SourceNmriumData[];
 }
 
 export declare interface NMRiumGeneralPreferences {
@@ -686,8 +708,12 @@ export declare interface NMRiumPluginMigration {
 
 export declare interface NMRiumPluginOnReadProcess {
     /**
-     * Hooks on processFileCollection, in first steps, to extract data from file collection.
+     * Hooks on processFileCollection, in first steps, to extract data from a file collection.
      * Usefully to parse files like nmredata, jcamp, bruker, etc.
+     *
+     * Plugins implementing this hook must return a nmrium data object.
+     * Spectra contained must include a sourceSelector with subset files used to extract the spectra.
+     *
      * @param files
      * @param options
      */
@@ -701,6 +727,12 @@ export declare interface NMRiumPluginOnReadProcess {
      * Hooks on processFileCollection, on file iteration.
      * Each file could be processed by all plugins to load and merge to nmrium data.
      * use `supportedExtensions` to filter files to be processed by the plugin.
+     *
+     * Plugins implementing this hook must return a nmrium data object.
+     * Each spectrum contained must include a sourceSelector with the file used to extract spectra.
+     * If the file contains multiple spectra,
+     * sourceSelector must explain have extra metadata to link to this specific spectrum.
+     *
      * @param file
      * @param options
      */
@@ -820,11 +852,6 @@ export declare interface ParsingOptions {
     name?: string;
     converter?: Partial<ParsingOptionsConverter>;
     sourceSelector?: Partial<NmrLoaderSelectors>;
-    /**
-     * if it is true the source object with files will be keeped
-     * @default false
-     */
-    keepSource?: boolean;
     onLoadProcessing?: OnLoadProcessing;
     experimentalFeatures?: boolean;
     logger?: Logger;
@@ -1026,6 +1053,35 @@ export declare interface RangesViewState {
 
 declare function read(_options: ReadOptions): Promise<ReadReturn>;
 
+declare function readNMRiumArchive(_options: ReadNMRiumArchiveOptions): Promise<readonly [NmriumState, Map<string, FileCollection>]>;
+
+declare interface ReadNMRiumArchiveOptions {
+    input: ZipFileContent;
+    options?: Partial<ParsingOptions>;
+    plugins: Map<string, NMRiumPlugin>;
+    migrator: (state: object) => any;
+}
+
+declare function readNMRiumObject(_options: ReadNMRiumObjectOptions): Promise<ReadNMRiumObjectReturn>;
+
+declare interface ReadNMRiumObjectOptions {
+    nmriumObjectInput: object;
+    migrator: (state: object) => any;
+    plugins: Map<string, NMRiumPlugin>;
+    options?: ParsingOptions;
+}
+
+declare type ReadNMRiumObjectReturn = [
+/**
+ * State read from `nmriumObjectInput`
+ */
+state: Partial<NmriumState>,
+/**
+ * A map of file collection where the key is the source id
+ */
+fileCollections: Map<string, FileCollection>
+];
+
 declare interface ReadOptions {
     input: FileCollection | FileItem;
     migrator: (state: object) => any;
@@ -1036,19 +1092,59 @@ declare interface ReadOptions {
 declare interface ReadReturn {
     nmriumState: Partial<NmriumState>;
     containsNmrium: boolean;
+    fileCollection: FileCollection;
 }
 
-declare type SerializedNmriumState = Omit<Partial<NmriumState>, 'data'> & {
+export declare type SerializedNmriumState = Omit<Partial<NmriumState>, 'data'> & {
     version: number;
     data?: NmriumData | NmriumDataSource;
 };
 
-declare interface SerializeNmriumStateOptions {
+export declare interface SerializeNmriumArchiveOptions {
+    /**
+     * Spectra to include in the archive.
+     * Must be tracked by nmrium applications to be able to serialize them into a nmrium archive.
+     */
+    spectra: Spectrum[];
+    /**
+     * Molecules to include in the archive.
+     * Must be tracked by nmrium applications to be able to serialize them into a nmrium archive.
+     */
+    molecules: StateMolecule[];
+    /**
+     * FileCollections to include in the archive.
+     * Applications managing a NMRium State are in charge to memorize files collections aside the state,
+     *  to be able to serialize them into a nmrium archive.
+     * Record key is linked to source id
+     * Key can be orphan (no related source).
+     *  It generally means that data was imported from a local file.
+     * */
+    fileCollections: Record<string, FileCollection>;
+    /**
+     * If true, it will include all the data in to the archive even if they are referenced sources as external files.
+     * If false, it will include only the data not referenced by sources as external files (index.json sources).
+     * @default true
+     * */
+    includeData?: boolean;
+    /**
+     * Serialized state of nmrium. Produced by core.serializeNmriumState() or a transformation to NMRiumState.
+     * As a blob or buffer ready to be put into an archive.
+     * */
+    serializedState: ExtraFileContent;
+}
+
+export declare function serializeNmriumState(nmriumState: NmriumState, plugins: Map<string, NMRiumPlugin>, options?: SerializeNmriumStateOptions): SerializedNmriumState;
+
+export declare interface SerializeNmriumStateOptions {
     includeData?: IncludeData;
     includeSettings?: boolean;
     includeView?: boolean;
 }
 
+declare interface SourceNmriumData extends Source {
+    id: string;
+}
+
 export declare interface SpectraAnalysisColumn {
     type: AnalysisColumnsTypes;
     valueKey: AnalysisColumnsValuesKeys;
@@ -1139,6 +1235,9 @@ export declare interface StateMolecule {
     id?: string;
     molfile: string;
     label?: string;
+    sourceId?: string;
+    sourceSelector?: NmrLoaderSelectors;
+    fileCollectionId?: string;
 }
 
 declare interface StructuresPreferences {

package/dist/nmrium-core.js

@@ -1,4 +1,6 @@
-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 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Mt(e){let{archive:t,externalSources:o,embedFiles:r}=e,{unserializedMolecule:i,moleculesResult:n}=e,{options:a,plugins:s,migrator:c}=e,l=await xe({archive:t,externalSources:o,embedFiles:r,pickableInput:i});if(!l)return z({molecule:i,moleculesResult:n,logger:a?.logger});await j({input:l,unserializedMolecule:i,moleculesResult:n,options:a,plugins:s,migrator:c})}async function xe(e){let{archive:t,externalSources:o,embedFiles:r,pickableInput:i}=e,{fileCollectionId:n,sourceId:a}=i,s;return t.external&&a&&(s=await o.get(a)),!s&&t.external&&a&&n&&(s=await r.get(n)),!s&&t.embed&&n&&(s=await r.get(n)),s}import{FileCollection as Dt}from"file-collection";async function Ne(e){let{source:t,plugins:o,options:r={}}=e,{converter:i,...n}=r,a={spectra:[],molecules:[]},s=await Dt.fromSource(t,{unzip:{zipExtensions:["zip","nmredata"]}}),{spectra:c=[],molecules:l=[]}=await w(s,o,{converter:{...i,bruker:{keepFiles:!0,...Reflect.get(i??{},"bruker")}},...n});a.spectra.push(...c),a.molecules.push(...l);let p=crypto.randomUUID(),m={...t,id:p};for(let g of a.spectra)g.sourceId=p;for(let g of a.molecules)g.sourceId=p;a.sources??=[],a.sources.push(m);let u=v({version:10,data:a},r?.sourceSelector?.general),{onLoadProcessing:d}=n,f={filters:d?.filters,autoProcessing:d?.autoProcessing??!1,experimentalFeatures:r.experimentalFeatures};return A({nmriumState:u,plugins:o,options:f}),[u,s]}var ee=class{version=10;#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 ae(t,this.version,this.#e)}read(t,o={}){return R({input:t,migrator:this.migrate.bind(this),plugins:this.#e,options:o})}readNMRiumArchive(t,o={}){return Pe({input:t,options:o,plugins:this.#e,migrator:this.migrate.bind(this)})}readNMRiumObject(t,o){return k({nmriumObjectInput:t,options:o,plugins:this.#e,migrator:this.migrate.bind(this)})}readFromWebSource(t,o){return Ne({source:t,options:o,plugins:this.#e})}serializeNmriumState(t,o){return me(t,this.#e,o)}serializeNmriumArchive(t){return de(t)}serializePlugins(){let t={plugins:{}};return b(t,this.#e),t.plugins}slot(t){return ge({slot:t,plugins:this.#e})}};function Ft(e,t){if(t>10)return 0;let o=-1;for(let r=0;r<e.length;r++)if(e[r].version>t){o=r;break}return o}var he=[{version:6,fun:O},{version:7,fun:M}];function vt(e){let{version:t}=e||{},o=Ft(he,t);if(o===-1)return{...e,version:10};let r=he.slice(o);for(let i of r)e=i.fun(e);return e}export{be as ANALYSIS_COLUMN_TYPES,Re as ANALYSIS_COLUMN_VALUES_KEYS,P as CURRENT_EXPORT_VERSION,Ie as EXTERNAL_API_KEYS,ee as NMRiumCore,Be as defineNMRiumPlugin,_e as formatSpectra,N as generateID,_ as getOneIfArray,vt as migrateSettings,Ce as units};

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@zakodium/nmrium-core",
-  "version": "0.2.2",
+  "version": "0.3.0",
   "description": "The core of NMRium: types, state, state migration and plugin system.",
   "author": "Zakodium Sàrl",
   "license": "CC-BY-NC-SA-4.0",
@@ -24,18 +24,19 @@
   },
   "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": {
     "cheminfo-types": "^1.8.1",
     "fifo-logger": "^2.0.1",
-    "file-collection": "^5.1.1",
+    "file-collection": "^5.4.0",
     "is-any-array": "^2.0.1",
     "lodash.merge": "^4.6.2",
     "ml-spectra-processing": "^14.17.1",
@@ -44,5 +45,5 @@
   "volta": {
     "extends": "../../../package.json"
   },
-  "gitHead": "53cd32cbf4a73e576f5ef817bb5d5939f411e900"
+  "gitHead": "30b6c308027caff1d01e896dae5f61c7c9196d1a"
 }