@zakodium/nmrium-core 0.4.6 → 0.4.8

package/dist/nmrium-core.d.ts

@@ -140,9 +140,7 @@ export declare interface BaseNucleusPreferences<T> {
 
 declare interface BaseSpectrum {
     id: string;
-    sourceId?: string;
-    sourceSelector?: NmrLoaderSelectors;
-    fileCollectionId?: string;
+    selector?: NmrLoaderSelectors;
     meta: Metadata;
     customInfo: any;
 }
@@ -214,7 +212,7 @@ declare interface ContourOptions_2 {
 
 export declare type ContoursLevels = Record<string, Level>;
 
-export declare const CURRENT_EXPORT_VERSION = 10;
+export declare const CURRENT_EXPORT_VERSION = 12;
 
 export declare type CustomWorkspaces = Record<string, InnerWorkspace>;
 
@@ -477,9 +475,17 @@ export declare type MoleculesView = Record<string, MoleculeView>;
 export declare interface MoleculeView {
     floating: FloatingElement;
     /**
-     * Show/Hide atoms numbers on the molecule.
+     * Show/Hide molecule label.
      */
-    showAtomNumber: boolean;
+    showLabel: boolean;
+    /**
+     * Defines which type of annotation is displayed on atoms.
+     * "none": Show atoms only
+     * "atom-numbers": Show atom numbers
+     * "custom-labels": Show custom atom labels
+     * @default "none"
+     */
+    atomAnnotation: 'none' | 'atom-numbers' | 'custom-labels';
 }
 
 declare type MultipleSpectraAnalysis = Record<string, MultipleSpectraAnalysisPreferences>;
@@ -491,14 +497,14 @@ export declare interface MultipleSpectraAnalysisPreferences {
 
 export declare class NMRiumCore {
     #private;
-    readonly version = 10;
+    readonly version = 12;
     registerPlugin(plugin: NMRiumPlugin): void;
     registerPlugins(plugins: NMRiumPlugin[]): void;
     private migrate;
     read(input: FileCollection | FileItem, options?: Partial<ParsingOptions>): ReturnType<typeof read>;
     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]>;
+    readFromWebSource(source: Source, options?: ParsingOptions): Promise<[state: Partial<NmriumState>, fileCollection: FileCollection, selectorRoot: string]>;
     /**
      * Serialize a state to nmrium object.
      * It can be serialized to json then,
@@ -712,7 +718,7 @@ export declare interface NMRiumPluginOnReadProcess {
      * 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.
+     * Spectra contained must include a selector with subset files used to extract the spectra.
      *
      * @param files
      * @param options
@@ -729,9 +735,9 @@ export declare interface NMRiumPluginOnReadProcess {
      * 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.
+     * Each spectrum contained must include a selector 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.
+     * selector must have extra metadata to link to this specific spectrum.
      *
      * @param file
      * @param options
@@ -804,8 +810,13 @@ export declare interface NMRiumToolBarPreferences {
 
 /**
  * Plugins should use Declaration Merging on this interface
+ * `NmrLoaderSelectors` is a selector used by nmrium loaders to filter the data to load
  */
 export declare interface NmrLoaderSelectors {
+    /**
+     * Read methods take a file-collection input, the root is used to call `fileCollection.subroot(selector.root)`.
+     */
+    root?: string;
     general?: GeneralLoadersSelector;
     files?: string[];
 }
@@ -851,10 +862,11 @@ export declare interface PanelsPreferences {
 export declare interface ParsingOptions {
     name?: string;
     converter?: Partial<ParsingOptionsConverter>;
-    sourceSelector?: Partial<NmrLoaderSelectors>;
+    selector?: Partial<NmrLoaderSelectors>;
     onLoadProcessing?: OnLoadProcessing;
     experimentalFeatures?: boolean;
     logger?: Logger;
+    selectorRoot?: string;
 }
 
 /**
@@ -1053,7 +1065,7 @@ export declare interface RangesViewState {
 
 declare function read(_options: ReadOptions): Promise<ReadReturn>;
 
-declare function readNMRiumArchive(_options: ReadNMRiumArchiveOptions): Promise<readonly [NmriumState, Map<string, FileCollection>]>;
+declare function readNMRiumArchive(_options: ReadNMRiumArchiveOptions): Promise<readonly [NmriumState, FileCollection]>;
 
 declare interface ReadNMRiumArchiveOptions {
     input: ZipFileContent;
@@ -1077,9 +1089,10 @@ declare type ReadNMRiumObjectReturn = [
  */
 state: Partial<NmriumState>,
 /**
- * A map of file collection where the key is the source id
+ * A file collection where each subfolder is
+ * an uuid of a file collection from sources.
  */
-fileCollections: Map<string, FileCollection>
+aggregator: FileCollection
 ];
 
 declare interface ReadOptions {
@@ -1093,6 +1106,7 @@ declare interface ReadReturn {
     nmriumState: Partial<NmriumState>;
     containsNmrium: boolean;
     fileCollection: FileCollection;
+    selectorRoot: string;
 }
 
 export declare type SerializedNmriumState = Omit<Partial<NmriumState>, 'data'> & {
@@ -1119,7 +1133,7 @@ export declare interface SerializeNmriumArchiveOptions {
      * Key can be orphan (no related source).
      *  It generally means that data was imported from a local file.
      * */
-    fileCollections: Record<string, FileCollection>;
+    aggregator: 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).
@@ -1235,9 +1249,7 @@ export declare interface StateMolecule {
     id?: string;
     molfile: string;
     label?: string;
-    sourceId?: string;
-    sourceSelector?: NmrLoaderSelectors;
-    fileCollectionId?: string;
+    selector?: NmrLoaderSelectors;
 }
 
 declare interface StructuresPreferences {
@@ -1421,6 +1433,7 @@ export declare interface WorkspacePreferences {
     export?: ExportPreferences;
     peaksLabel?: PeaksLabel;
     acsExportSettings?: ACSExportSettings;
+    defaultMoleculeSettings?: MoleculeView;
 }
 
 /**

package/dist/nmrium-core.js

@@ -1,6 +1,6 @@
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dt(e){let{archive:t,externalSources:o,embedFiles:r}=e,{unserializedSpectrum:i,spectraResult:n}=e,{options:a,plugins:s,migrator:c}=e,l=await Se({archive:t,externalSources:o,embedFiles:r,pickableInput:i});if(!l)return T({spectrum:i,spectraResult:n,logger:a?.logger});await E({input:l,unserializedSpectrum:i,spectraResult:n,options:a,plugins:s,migrator:c})}async function gt(e){let{archive:t,externalSources:o,embedFiles:r}=e,{unserializedMolecule:i,moleculesResult:n}=e,{options:a,plugins:s,migrator:c}=e,l=await Se({archive:t,externalSources:o,embedFiles:r,pickableInput:i});if(!l)return k({molecule:i,moleculesResult:n,logger:a?.logger});await z({input:l,unserializedMolecule:i,moleculesResult:n,options:a,plugins:s,migrator:c})}async function Se(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 St}from"file-collection";async function ye(e){let{source:t,plugins:o,options:r={}}=e,{converter:i,...n}=r,a={spectra:[],molecules:[]},s=await St.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=F({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]}function I(e,t){let o={};for(let r in e)t.includes(r)||(o[r]=e[r]);return o}var 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I(e,Pt)}function Ct(e){let{data:t,info:o,originalData:r,originalInfo:i}=e,n=I(e,xt);return n.data=r||t,n.info=i||o,n}import{FileCollection as Ot}from"file-collection";async function Ne(e){let{spectra:t,molecules:o,fileCollections:r,serializedState:i,includeData:n=!0}=e,a=new Ot({filter:{ignoreDotfiles:!1}}),s=new Set,c=[];for(let l of t)xe({builder:a,fileCollections:r,fileCollectionId:l.fileCollectionId,includeData:n,alreadyAdded:s,asyncTasks:c});for(let l of o)xe({builder:a,fileCollections:r,fileCollectionId:l.fileCollectionId,includeData:n,alreadyAdded:s,asyncTasks:c});return await 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rt(e){let{info:t}=e;return t?.dimension===2}function T(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{selector:r,converter:n,logger:i}=o,c=[],s=[];for(let u of t.values()){let{onReadProcess:f}=u;f&&(f?.onFiles&&c.push(u),f?.supportedExtensions?.length&&f?.onFile&&s.push(u))}let l=await Promise.allSettled(c.map(u=>u.onReadProcess.onFiles(e,o))),a=[],p=await Promise.allSettled(e.files.flatMap(u=>{let f=A(u.name).toLowerCase();return s.flatMap(d=>{let{supportedExtensions:g,onFile:y}=d.onReadProcess;return g.includes(f)?(a.push({file:u,plugin:d}),y(u,{logger:i,selector:r,converter:n})):[]})})),m={spectra:[],molecules:[]};for(let u=0;u<l.length;u++){let f=l[u];switch(f.status){case"fulfilled":{let{spectra:d=[],molecules:g=[]}=f.value||{};m.spectra.push(...d),m.molecules.push(...g);break}case"rejected":{let d=f.reason,g=c[u];o.logger?.error(`Load file collection with plugin 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it.fromZip(e);if(t.files.length===0)throw new Error("compressed nmrium file is corrupted");return t.files[0].text()}function at(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 I(e){let{options:t={},input:o,migrator:r,plugins:n}=e,{selectorRoot:i=crypto.randomUUID()}=t,c=pt(await ct(o),t.selector?.files),s=mt(c);if(s){let[f]=await fe({file:s,migrator:r,plugins:n,options:t});return ge(f,i),{nmriumState:f,containsNmrium:!0,fileCollection:c,selectorRoot:i}}let l=await E(c,n,t),a=F({version:12,data:l},t?.selector?.general,t.logger),{onLoadProcessing:p,experimentalFeatures:m}=t,u={...p,autoProcessing:p?.autoProcessing??!1,experimentalFeatures:m};return T({nmriumState:a,plugins:n,options:u}),ge(a,i),{nmriumState:a,containsNmrium:!1,fileCollection:c,selectorRoot:i}}function ct(e){return Array.isArray(e)?Promise.reject(new Error("For a set of fileCollectionItems pass a FileCollection 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r||(r=e.subroot(o),t.set(o,r)),r},[Symbol("debug")]:{ium:e,views:t}}}async function St(e){let{subRoots:t}=e,{unserializedSpectrum:o,spectraResult:r}=e,{options:n,plugins:i,migrator:c}=e,{selector:s}=o,l=await xe({subRoots:t,selector:s});if(!l)return k({spectrum:o,spectraResult:r,logger:n?.logger});await L({input:l,unserializedSpectrum:o,spectraResult:r,options:n,plugins:i,migrator:c})}async function yt(e){let{subRoots:t}=e,{unserializedMolecule:o,moleculesResult:r}=e,{options:n,plugins:i,migrator:c}=e,{selector:s}=o,l=await xe({subRoots:t,selector:s});if(!l)return j({molecule:o,moleculesResult:r,logger:n?.logger});await U({input:l,unserializedMolecule:o,moleculesResult:r,options:n,plugins:i,migrator:c})}async function xe(e){let{subRoots:t,selector:o}=e;if(!o)return;let{root:r}=o;if(r)return t.get(r)}import{FileCollection as Pt}from"file-collection";async function Ne(e){let{source:t,plugins:o,options:r={},sourceId:n=crypto.randomUUID()}=e,{converter:i,...c}=r,s={...t,id:n},l={spectra:[],molecules:[]},a=await Pt.fromSource(s,{unzip:{zipExtensions:["zip","nmredata"]}}),{spectra:p=[],molecules:m=[]}=await E(a,o,{converter:{...i,bruker:{keepFiles:!0,...Reflect.get(i??{},"bruker")}},...c});l.spectra.push(...p),l.molecules.push(...m);for(let g of l.spectra)g.selector??={root:n},g.selector.root=n;for(let g of l.molecules)g.selector??={root:n},g.selector.root=n;l.sources??=[],l.sources.push(s);let u=F({version:12,data:l},r?.selector?.general),{onLoadProcessing:f}=c,d={filters:f?.filters,autoProcessing:f?.autoProcessing??!1,experimentalFeatures:r.experimentalFeatures};return T({nmriumState:u,plugins:o,options:d}),[u,a,n]}function M(e,t){let o={};for(let r in e)t.includes(r)||(o[r]=e[r]);return o}var xt=["data","originalData","info","originalInfo","meta","customInfo"],Nt=["data","originalData","info","originalInfo","meta","customInfo"],ht=["selector","originalData","originalInfo"];function he(e,t,o={}){let{version:r,data:n}=e;if(n.actionType)return e;let i={version:r,plugins:e.plugins},{includeData:c}=o;c!=="noData"&&(i.data=bt({...n},c));let{includeSettings:s,includeView:l}=o;return s&&(i.settings=e.settings),l&&(i.view=e.view),R(i,t),i}function bt(e,t="rawData"){let{spectra:o}=e;switch(t){case"dataSource":return Rt(e);case"selfContained":case"selfContainedExternalDatasource":return Ot(e);case"rawData":return{...M(e,["sources"]),spectra:o.map(vt)};default:return e}}function Rt(e){let{spectra:t}=e;if(!e.sources)throw new Error("sources property should exists for dataSource serialization");return{...e,spectra:t.map(It)}}function Ot(e){let{spectra:t,sources:o,...r}=e;return{...r,spectra:t.map(Mt)}}function It(e){return M(e,xt)}function Mt(e){return M(e,Nt)}function vt(e){let{data:t,info:o,originalData:r,originalInfo:n}=e,i=M(e,ht);return i.data=r||t,i.info=n||o,i}import{FileCollection as Dt}from"file-collection";async function be(e){let{spectra:t,molecules:o,aggregator:r,serializedState:n,includeData:i=!0}=e;return Dt.fromCollection(r,{filter:{ignoreDotfiles:!1}}).toIum({includeData:i,*getExtraFiles(s){yield{relativePath:".META-NMRIUM/NMRIUM_ARCHIVE",data:""},yield{relativePath:".META-NMRIUM/VERSION",data:"0"},yield{relativePath:"state.json",data:n},yield{relativePath:"index.txt",data:Ct({aggregator:r,spectra:t,molecules:o,index:s})}}})}function Ct(e){let{aggregator:t,spectra:o,molecules:r,index:n}=e,i=new Map,c=new Map(n.sources.map(l=>[l.uuid,l]));for(let l of o){let a=l.selector?.root;a&&(i.has(a)||i.set(a,t.subroot(a)))}for(let l of r){let a=l.selector?.root;a&&(i.has(a)||i.set(a,t.subroot(a)))}let s=[];for(let[l,a]of i.entries()){s.push(`data/${l}/`);for(let p of a.files){let u=c.get(p.sourceUUID)?.baseURL?.startsWith("ium:/")?"embedded":"linked";s.push(`	${p.relativePath}	(${u})`)}s.push(`
+`)}return s.join(`
+`)}var re=class{version=12;#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 I({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 z({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 he(t,this.#e,o)}serializeNmriumArchive(t){return be(t)}serializePlugins(){let t={plugins:{}};return R(t,this.#e),t.plugins}slot(t){return le({slot:t,plugins:this.#e})}};function At(e,t){if(t>12)return 0;let o=-1;for(let r=0;r<e.length;r++)if(e[r].version>t){o=r;break}return o}var Re=[{version:6,fun:D},{version:7,fun:C}];function wt(e){let{version:t}=e||{},o=At(Re,t);if(o===-1)return{...e,version:12};let r=Re.slice(o);for(let n of r)e=n.fun(e);return e}export{Oe as ANALYSIS_COLUMN_TYPES,Ie as ANALYSIS_COLUMN_VALUES_KEYS,x as CURRENT_EXPORT_VERSION,ve as EXTERNAL_API_KEYS,re as NMRiumCore,We as defineNMRiumPlugin,Ke as formatSpectra,h as generateID,B as getOneIfArray,wt as migrateSettings,Me as units};

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@zakodium/nmrium-core",
-  "version": "0.4.6",
+  "version": "0.4.8",
   "description": "The core of NMRium: types, state, state migration and plugin system.",
   "author": "Zakodium Sàrl",
   "license": "CC-BY-NC-SA-4.0",
@@ -31,12 +31,12 @@
     "jest-matcher-deep-close-to": "^3.0.2",
     "rimraf": "^6.0.1",
     "typescript": "~5.9.3",
-    "vitest": "^4.0.4"
+    "vitest": "^4.0.7"
   },
   "dependencies": {
     "cheminfo-types": "^1.8.1",
     "fifo-logger": "^2.0.1",
-    "file-collection": "^6.0.0",
+    "file-collection": "^6.2.1",
     "is-any-array": "^2.0.1",
     "lodash.merge": "^4.6.2",
     "ml-spectra-processing": "^14.18.0",
@@ -45,5 +45,5 @@
   "volta": {
     "extends": "../../../package.json"
   },
-  "gitHead": "95e420a71f11d29f770b0b2d71ac1b9ba0b45ac2"
+  "gitHead": "8a0482bab49d93f192dabb48f8b78903939d3990"
 }