@zakodium/nmrium-core 0.6.8 → 0.7.1

package/README.md

@@ -52,7 +52,7 @@ console.log(result);
 // readSource function accept a partial FileCollectionItems and a baseURL to generate a
 // data structure with a source object inside with { files, filter, baseURL }
 
-const nmriumObject = await core.readFromWebSource(
+const { state } = await core.readFromWebSource(
   {
     baseURL: 'https://cheminfo.github.io',
     files: [

package/dist/nmrium-core.d.ts

@@ -1,6 +1,6 @@
 import type { CorrelationData } from 'nmr-correlation';
 import type { FifoLoggerOptions } from 'fifo-logger';
-import { FileCollection } from 'file-collection';
+import type { FileCollection } from 'file-collection';
 import type { FileItem } from 'file-collection';
 import type { Filter1DEntry } from '@zakodium/nmr-types';
 import type { Filter1DOptions } from '@zakodium/nmr-types';
@@ -197,25 +197,34 @@ export declare interface ContourItem {
     numberOfLayers: number;
 }
 
-export declare interface ContourOptions {
+export declare interface ContourLevel {
     positive: ContourItem;
     negative: ContourItem;
 }
 
-declare interface ContourOptions_2 {
-    positive: {
-        contourLevels: [number, number];
-        numberOfLayers: number;
-    };
-    negative: {
-        contourLevels: [number, number];
-        numberOfLayers: number;
-    };
+export declare interface CoreReadReturn {
+    /**
+     * Common state representation between NMRium component and NMRium apps
+     */
+    state: Partial<NmriumState>;
+    /**
+     * Meta file collection.
+     * Each user source of data is placed in his dedicated uuid folder.
+     * In the UI, it means one drag n drop (with possibly multiple files) = one uuid folder.
+     */
+    aggregator: FileCollection;
+    /**
+     * Is input given to the read method contains a nmrium file?
+     * This also means that the reader ignored the rest of the content.
+     * Or the reading method read a nmrium object / file.
+     *
+     * This information is generally used by the NMRium component
+     * or an NMRium app to know if it should merge state and aggregator or replace them.
+     */
+    containsNmrium: boolean;
 }
 
-export declare type ContoursLevels = Record<string, Level>;
-
-export declare const CURRENT_EXPORT_VERSION: 13;
+export declare const CURRENT_EXPORT_VERSION: 14;
 
 export declare type CustomWorkspaces = Record<string, InnerWorkspace>;
 
@@ -289,7 +298,6 @@ export declare interface Display1D extends Display {
 export declare interface Display2D extends Color2D, Display {
     isPositiveVisible: boolean;
     isNegativeVisible: boolean;
-    contourOptions: ContourOptions_2;
 }
 
 declare interface DisplayPreferences {
@@ -437,11 +445,6 @@ export declare type Layout = 'portrait' | 'landscape';
 
 export declare type LegendField = JpathLegendField | PredefinedLegendField;
 
-export declare interface Level {
-    positive: ContourItem;
-    negative: ContourItem;
-}
-
 declare interface LoadersPreferences {
     general: GeneralLoadersSelector;
     bruker: BrukerLoaderSelector;
@@ -504,7 +507,7 @@ export declare interface MultipleSpectraAnalysisPreferences {
 
 export declare class NMRiumCore {
     #private;
-    readonly version: 13;
+    readonly version: 14;
     registerPlugin(plugin: NMRiumPlugin): void;
     registerPlugins(plugins: NMRiumPlugin[]): void;
     private getPlugin;
@@ -518,8 +521,8 @@ export declare class NMRiumCore {
      */
     read(input: FileCollection | FileItem, options?: Partial<ParsingOptions>, fromSourceOptions?: {
         baseURL?: string;
-    }): ReturnType<typeof read>;
-    readNMRiumArchive(input: ZipFileContent, options?: Partial<ParsingOptions>): ReturnType<typeof readNMRiumArchive>;
+    }): Promise<CoreReadReturn>;
+    readNMRiumArchive(input: ZipFileContent, options?: Partial<ParsingOptions>): Promise<CoreReadReturn>;
     /**
      * Read a nmrium state, migrate it to the current version,
      * fetch data from sources contained, and format spectra and molecules.
@@ -530,7 +533,7 @@ export declare class NMRiumCore {
      */
     readNMRiumObject(nmriumObjectInput: object, options?: ParsingOptions, fromSourceOptions?: {
         baseURL?: string;
-    }): ReturnType<typeof readNMRiumObject>;
+    }): Promise<CoreReadReturn>;
     /**
      * Same than `readNMRiumObject` but from a file from `FileCollection`
      * @param file - supports nmrium state file with any extension, compressed or not.
@@ -539,8 +542,8 @@ export declare class NMRiumCore {
      */
     readNMRiumFile(file: FileItem, options?: Partial<ParsingOptions>, fromSourceOptions?: {
         baseURL?: string;
-    }): ReturnType<typeof readNMRiumObject>;
-    readFromWebSource(source: Source, options?: ParsingOptions): Promise<[state: Partial<NmriumState>, fileCollection: FileCollection, selectorRoot: string]>;
+    }): Promise<CoreReadReturn>;
+    readFromWebSource(source: Source, options?: ParsingOptions): Promise<CoreReadReturn>;
     /**
      * Serialize a state to nmrium object.
      * It can be serialized to json then,
@@ -1100,58 +1103,6 @@ export declare interface RangesViewState {
     rangesBounding: BoundingBox;
 }
 
-declare function read(_options: ReadOptions): Promise<ReadReturn>;
-
-declare function readNMRiumArchive(_options: ReadNMRiumArchiveOptions): Promise<readonly [NmriumState, 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;
-    fromSourceOptions?: {
-        baseURL?: string;
-    };
-}
-
-declare type ReadNMRiumObjectReturn = [
-/**
- * State read from `nmriumObjectInput`
- */
-state: Partial<NmriumState>,
-/**
- * A file collection where each subfolder is
- * an uuid of a file collection from sources.
- */
-aggregator: FileCollection
-];
-
-declare interface ReadOptions {
-    input: FileCollection | FileItem;
-    migrator: (state: object) => any;
-    plugins: Map<string, NMRiumPlugin>;
-    options?: ParsingOptions;
-    fromSourceOptions?: {
-        baseURL?: string;
-    };
-}
-
-declare interface ReadReturn {
-    nmriumState: Partial<NmriumState>;
-    containsNmrium: boolean;
-    fileCollection: FileCollection;
-    selectorRoot: string;
-}
-
 export declare type SerializedNmriumState = Omit<Partial<NmriumState>, 'data'> & {
     version: number;
     data?: NmriumData | NmriumDataSource;
@@ -1236,6 +1187,8 @@ export declare interface SpectraColors {
     indicatorLineColor: string;
 }
 
+export declare type SpectraContourLevels = Record<string, ContourLevel>;
+
 declare type SpectraPredictionOptions = Record<Experiment, boolean>;
 
 export declare interface SpectraPreferences {
@@ -1445,9 +1398,7 @@ export declare interface ViewState {
          */
         showSimilarityTree: boolean;
     };
-    zoom: {
-        levels: ContoursLevels;
-    };
+    spectraContourLevels: SpectraContourLevels;
     /**
      * options to control spectra vertical alignment
      * @default  'bottom'
@@ -1465,8 +1416,8 @@ export declare interface ViewState {
 
 export declare interface WheelOptions {
     shiftKey: boolean;
-    contourOptions: ContourOptions;
-    currentLevel: Level;
+    contourLevel: ContourLevel;
+    currentContourLevel: ContourLevel;
 }
 
 export declare type Workspace = WorkspaceMeta & Required<WorkspacePreferences>;

package/dist/nmrium-core.js

@@ -1,6 +1,6 @@
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e.version!="number"||Number.isNaN(e.version))throw new Error("Not a valid NMRium archive, no version specified");if(e.version===0)throw new Error("NMRium Archive generated behind experimental flag are not supported.");if(!e.state)throw new Error("NMRium Archive corrupted, state.json is missing")}function be(e){return e.filter(t=>!Pt(t.relativePath))}function Pt(e){return e.startsWith("META-INF/")||e==="state.json"||e==="index.txt"}async function Ne(e){let{options:t,plugins:o,migrator:r}=e,i=await xt.fromIum(e.input),n=await xe(i);he(n);let c=be(i),s=r(n.state),l={...s,data:{...s.data,spectra:[],molecules:[]}},a=l.data.spectra,p=l.data.molecules,m=s.data?.spectra??[],u=s.data?.molecules??[],f=ht(i),d=[];for(let g of m)d.push(bt({subRoots:f,unserializedSpectrum:g,spectraResult:a,options:t,plugins:o,migrator:r}));for(let g of u)d.push(Nt({subRoots:f,unserializedMolecule:g,moleculesResult:p,options:t,plugins:o,migrator:r}));return await Promise.allSettled(d),{state:l,aggregator:c,containsNmrium:!0}}function ht(e){let t=new Map;return{get(o){let r=t.get(o);return r||(r=e.subroot(o),t.set(o,r)),r},[Symbol("debug")]:{ium:e,views:t}}}async function bt(e){let{subRoots:t}=e,{unserializedSpectrum:o,spectraResult:r}=e,{options:i,plugins:n,migrator:c}=e,{selector:s}=o,l=await Re({subRoots:t,selector:s});if(!l)return k({spectrum:o,spectraResult:r,logger:i?.logger});await z({input:l,unserializedSpectrum:o,spectraResult:r,options:i,plugins:n,migrator:c})}async function Nt(e){let{subRoots:t}=e,{unserializedMolecule:o,moleculesResult:r}=e,{options:i,plugins:n,migrator:c}=e,{selector:s}=o,l=await Re({subRoots:t,selector:s});if(!l)return V({molecule:o,moleculesResult:r,logger:i?.logger});await U({input:l,unserializedMolecule:o,moleculesResult:r,options:i,plugins:n,migrator:c})}async function Re(e){let{subRoots:t,selector:o}=e;if(!o)return;let{root:r}=o;if(r)return t.get(r)}import{FileCollection as Oe}from"file-collection";async function Ie(e){let{source:t,plugins:o,options:r={}}=e,{converter:i,...n}=r,{selectorRoot:c=x()}=r,s={...t,id:c},l={spectra:[],molecules:[]},a=await Oe.fromSource(s,{unzip:{zipExtensions:["zip","nmredata"]}}),{spectra:p=[],molecules:m=[]}=await L(a,o,{converter:{...i,bruker:{keepFiles:!0,...Reflect.get(i??{},"bruker")}},...n});l.spectra.push(...p),l.molecules.push(...m);for(let S of l.spectra)S.selector??={root:c},S.selector.root=c;for(let S of l.molecules)S.selector??={root:c},S.selector.root=c;l.sources??=[],l.sources.push(s);let u=T({version:14,data:l},r?.selector?.general),{onLoadProcessing:f}=n,d={filters:f?.filters,autoProcessing:f?.autoProcessing??!1,experimentalFeatures:r.experimentalFeatures};E({nmriumState:u,plugins:o,options:d});let g=new Oe().appendFileCollection(a,c);return{state:u,aggregator:g,containsNmrium:!1}}function D(e,t){let o={};for(let r in e)t.includes(r)||(o[r]=e[r]);return o}var Rt=["data","originalData","info","originalInfo","meta","customInfo"],Ot=["data","originalData","info","originalInfo","meta","customInfo"],It=["selector","originalData","originalInfo"];function ve(e,t,o={}){let{version:r,data:i}=e;if(i.actionType)return e;let n={version:r,plugins:e.plugins},{includeData:c,forceRawSpectra:s=[]}=o;c!=="noData"&&(n.data=vt({...i},c,s));let{includeSettings:l,includeView:a}=o;return l&&(n.settings=e.settings),a&&(n.view=e.view),I(n,t),n}function vt(e,t="rawData",o){let{spectra:r}=e;switch(t){case"dataSource":return Dt(e);case"selfContained":case"selfContainedExternalDatasource":return Mt(e,o);case"rawData":return{...D(e,["sources"]),spectra:r.map(De)};default:return e}}function Dt(e){let{spectra:t}=e;if(!e.sources)throw new Error("sources property should exists for dataSource serialization");return{...e,spectra:t.map(Ct)}}function Mt(e,t){let{spectra:o,sources:r,...i}=e;return{...i,spectra:o.map(n=>wt(n,t))}}function Ct(e){return D(e,Rt)}function wt(e,t){return!("selector"in e)||t?.includes(e.id)?De(e):D(e,Ot)}function De(e){let{data:t,info:o,originalData:r,originalInfo:i}=e,n=D(e,It);return n.data=r||t,n.info=i||o,n}import{FileCollection as At}from"file-collection";async function Me(e,t){let{state:o,aggregator:r,externalData:i="embedded",includeData:n=!0,includeSettings:c,includeView:s}=t,{spectra:l,molecules:a}=o.data,p=new At({filter:{ignoreDotfiles:!1}});return n&&p.appendFileCollection(r),p.toIum({includeData:i==="embedded",mimetype:"chemical/x-nmrium+zip",*getExtraFiles(m){yield{relativePath:"META-INF/NMRIUM_ARCHIVE",data:""},yield{relativePath:"META-INF/VERSION",data:"1"},yield{relativePath:"state.json",data:Ft(e,o,r,{externalData:i,includeData:n,includeView:s,includeSettings:c})},yield{relativePath:"index.txt",data:Tt({aggregator:r,spectra:l,molecules:a,index:m})}}})}function Ft(e,t,o,r){let{includeData:i,includeView:n,includeSettings:c,externalData:s="embedded"}=r,l="noData";i&&(l=s==="embedded"?"selfContained":"selfContainedExternalDatasource");let a=[];if(l!=="noData")for(let u of t.data?.spectra??[]){let f=u.selector?.root;f&&o.subroot(f).files.length>0||a.push(u.id)}let p=e(t,{includeData:l,includeView:n,includeSettings:c,forceRawSpectra:a}),m=JSON.stringify(p,(u,f)=>ArrayBuffer.isView(f)?Array.from(f):f,2);return new Blob([m],{type:"application/json"})}function Tt(e){let{aggregator:t,spectra:o,molecules:r,index:i}=e,n=new Map,c=new Map(i.sources.map(l=>[l.uuid,l]));for(let l of o){let a=l.selector?.root;a&&(n.has(a)||n.set(a,t.subroot(a)))}for(let l of r){let a=l.selector?.root;a&&(n.has(a)||n.set(a,t.subroot(a)))}let s=[];for(let[l,a]of n.entries()){let p=new Map(a.sources.map(u=>[u.uuid,u])),m=`data/${l}/`;s.push(m);for(let u of a.files){let f=c.get(u.sourceUUID),d=p.get(u.sourceUUID),g=f?.baseURL?.startsWith("ium:/")?"embedded":"linked",y=i.paths[u.sourceUUID]?.replace(m,""),P=u.relativePath.replace(d?.relativePath??"",""),h=y?y+P:u.relativePath;s.push(`	${h}	(${g})`)}s.push(`
 `)}return s.join(`
-`)}var ne=class{version=13;#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)}getPlugin(t){return this.#e.get(t)}migrate(t){return ue(t,this.version,this.#e)}read(t,o={},r){return v({input:t,options:o,fromSourceOptions:r,migrator:this.migrate.bind(this),plugins:this.#e})}readNMRiumArchive(t,o={}){return he({input:t,options:o,plugins:this.#e,migrator:this.migrate.bind(this)})}readNMRiumObject(t,o,r){return V({nmriumObjectInput:t,options:o,fromSourceOptions:r,plugins:this.#e,migrator:this.migrate.bind(this)})}readNMRiumFile(t,o={},r){return _({file:t,options:o,fromSourceOptions:r,plugins:this.#e,migrator:this.migrate.bind(this)})}readFromWebSource(t,o){return be({source:t,options:o,plugins:this.#e})}serializeNmriumState(t,o){return Re(t,this.#e,o)}serializeNmriumArchive(t){let o=this.serializeNmriumState.bind(this);return Ie(o,t)}serializePlugins(){let t={plugins:{}};return I(t,this.#e),t.plugins}slot(t){return pe({slot:t,plugins:this.#e})}};function Tt(e,t){if(t>13)return 0;let o=-1;for(let r=0;r<e.length;r++)if(e[r].version>t){o=r;break}return o}var ve=[{version:6,fun:C},{version:7,fun:A}];function Et(e){let{version:t}=e||{},o=Tt(ve,t);if(o===-1)return{...e,version:13};let r=ve.slice(o);for(let i of r)e=i.fun(e);return e}export{De as ANALYSIS_COLUMN_TYPES,Me as ANALYSIS_COLUMN_VALUES_KEYS,N as CURRENT_EXPORT_VERSION,Ae as EXTERNAL_API_KEYS,ne as NMRiumCore,Ze as defineNMRiumPlugin,Ye as formatSpectra,x as generateID,W as getOneIfArray,Et as migrateSettings,Ce as units};
+`)}var se=class{version=14;#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)}getPlugin(t){return this.#e.get(t)}migrate(t){return pe(t,this.version,this.#e)}read(t,o={},r){return v({input:t,options:o,fromSourceOptions:r,migrator:this.migrate.bind(this),plugins:this.#e})}readNMRiumArchive(t,o={}){return Ne({input:t,options:o,plugins:this.#e,migrator:this.migrate.bind(this)})}readNMRiumObject(t,o,r){return j({nmriumObjectInput:t,options:o,fromSourceOptions:r,plugins:this.#e,migrator:this.migrate.bind(this)})}readNMRiumFile(t,o={},r){return _({file:t,options:o,fromSourceOptions:r,plugins:this.#e,migrator:this.migrate.bind(this)})}readFromWebSource(t,o){return Ie({source:t,options:o,plugins:this.#e})}serializeNmriumState(t,o){return ve(t,this.#e,o)}serializeNmriumArchive(t){let o=this.serializeNmriumState.bind(this);return Me(o,t)}serializePlugins(){let t={plugins:{}};return I(t,this.#e),t.plugins}slot(t){return me({slot:t,plugins:this.#e})}};function Et(e,t){if(t>14)return 0;let o=-1;for(let r=0;r<e.length;r++)if(e[r].version>t){o=r;break}return o}var Ce=[{version:6,fun:C},{version:7,fun:w}];function Lt(e){let{version:t}=e||{},o=Et(Ce,t);if(o===-1)return{...e,version:14};let r=Ce.slice(o);for(let i of r)e=i.fun(e);return e}export{we as ANALYSIS_COLUMN_TYPES,Ae as ANALYSIS_COLUMN_VALUES_KEYS,b as CURRENT_EXPORT_VERSION,Te as EXTERNAL_API_KEYS,se as NMRiumCore,Je as defineNMRiumPlugin,Ge as formatSpectra,x as generateID,W as getOneIfArray,Lt as migrateSettings,Fe as units};

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@zakodium/nmrium-core",
-  "version": "0.6.8",
+  "version": "0.7.1",
   "description": "The core of NMRium: types, state, state migration and plugin system.",
   "author": "Zakodium Sàrl",
   "license": "CC-BY-NC-SA-4.0",
@@ -47,5 +47,5 @@
   "volta": {
     "extends": "../../../package.json"
   },
-  "gitHead": "f50e6395c4e57d9b01016e7138889a24b4b22ec3"
+  "gitHead": "176a331e9d92d157e0f7cbdc11bf37c7f334c4dd"
 }