@zakodium/nmrium-core 0.6.2 → 0.6.3

package/dist/nmrium-core.d.ts

@@ -395,6 +395,8 @@ export declare interface InfoBlockField extends JpathTableColumn {
     format: string;
 }
 
+export declare function injectDeprecatedUiToSupportedUiSlots(dts: Record<string, string>, std: Record<string, string[]>): void;
+
 export declare type InnerWorkspace = WorkspaceMeta & WorkspacePreferences;
 
 declare interface IntegralsNucleusPreferences {
@@ -503,6 +505,7 @@ export declare class NMRiumCore {
     readonly version: 13;
     registerPlugin(plugin: NMRiumPlugin): void;
     registerPlugins(plugins: NMRiumPlugin[]): void;
+    private getPlugin;
     migrate(state: any): any;
     /**
      * Try to read any kind of files to build a NMRiumState
@@ -758,6 +761,7 @@ export declare interface NMRiumPluginOnReadProcess {
     /**
      * Filter file loader by extension.
      * Extensions should be in lowercase.
+     * The extensions does not include the dot.
      */
     supportedExtensions?: readonly string[];
     /**
@@ -1331,7 +1335,7 @@ export declare interface SumOptions {
 export declare const SUPPORTED_UI_SLOTS: readonly ["topbar.right", "topbar.about_us.modal"];
 
 /**
- * Cache inverted relationship between deprecated and supported.
+ * Cache inverted the relationship between deprecated and supported.
  */
 export declare const SUPPORTED_UI_TO_DEPRECATED_UI_SLOTS: Partial<Record<SupportedUISlot, DeprecatedUISlot[]>>;
 

package/dist/nmrium-core.js

@@ -1,6 +1,6 @@
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Ct(e,t){return!("selector"in e)||t?.includes(e.id)?Oe(e):M(e,Rt)}function Oe(e){let{data:t,info:o,originalData:r,originalInfo:i}=e,n=M(e,Ot);return n.data=r||t,n.info=i||o,n}import{FileCollection as At}from"file-collection";async function Ie(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:wt(e,o,r,{externalData:i,includeData:n,includeView:s,includeSettings:c})},yield{relativePath:"index.txt",data:Ft({aggregator:r,spectra:l,molecules:a,index:m})}}})}function wt(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 Ft(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 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p={data:{...s,spectra:[],molecules:[]},...l},m=p.data,{sources:u=[],spectra:f,molecules:d}=m,g=await Promise.all(u.map(async P=>{let h=await ge.fromSource(P,{unzip:{zipExtensions:["zip","nmredata"]}},n);if(!P.baseURL)for(let R of P.entries)R.baseURL||(R.baseURL=n?.baseURL);return[P.id,h]})),S=new Map(g),y=[];for(let P of s.spectra){let h=P.selector?.root??"",R=S.get(h);if(!R){k({spectrum:P,spectraResult:f,logger:o.logger});continue}y.push(z({input:R,spectraResult:f,unserializedSpectrum:P,migrator:r,plugins:i,options:o}))}for(let P of s.molecules??[]){let h=P.selector?.root??"",R=S.get(h);if(!R){j({molecule:P,moleculesResult:d,logger:o.logger});continue}y.push(U({input:R,unserializedMolecule:P,moleculesResult:d,migrator:r,plugins:i,options:o}))}await Promise.allSettled(y);for(let[P,h]of S.entries())a.appendFileCollection(h,P);return[p,a]}async function _(e){let{file:t,options:o={},migrator:r,plugins:i,fromSourceOptions:n}=e,c="byteLength"in t?t:await t.arrayBuffer(),s=Se.isZip(c)?await 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Promise.all(o),t}function Pe(e){if(!e.archive)throw new Error("Not a valid NMRium archive");if(typeof 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 xe(e){return e.filter(t=>!yt(t.relativePath))}function yt(e){return e.startsWith("META-INF/")||e==="state.json"||e==="index.txt"}async function he(e){let{options:t,plugins:o,migrator:r}=e,i=await Pt.fromIum(e.input),n=await ye(i);Pe(n);let c=xe(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=xt(i),d=[];for(let g of m)d.push(ht({subRoots:f,unserializedSpectrum:g,spectraResult:a,options:t,plugins:o,migrator:r}));for(let g of 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Ne(e){let{subRoots:t,selector:o}=e;if(!o)return;let{root:r}=o;if(r)return t.get(r)}import{FileCollection as bt}from"file-collection";async function be(e){let{source:t,plugins:o,options:r={},sourceId:i=x()}=e,{converter:n,...c}=r,s={...t,id:i},l={spectra:[],molecules:[]},a=await bt.fromSource(s,{unzip:{zipExtensions:["zip","nmredata"]}}),{spectra:p=[],molecules:m=[]}=await L(a,o,{converter:{...n,bruker:{keepFiles:!0,...Reflect.get(n??{},"bruker")}},...c});l.spectra.push(...p),l.molecules.push(...m);for(let g of l.spectra)g.selector??={root:i},g.selector.root=i;for(let g of l.molecules)g.selector??={root:i},g.selector.root=i;l.sources??=[],l.sources.push(s);let u=T({version:13,data:l},r?.selector?.general),{onLoadProcessing:f}=c,d={filters:f?.filters,autoProcessing:f?.autoProcessing??!1,experimentalFeatures:r.experimentalFeatures};return E({nmriumState:u,plugins:o,options:d}),[u,a,i]}function M(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 Re(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=Dt({...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 Dt(e,t="rawData",o){let{spectra:r}=e;switch(t){case"dataSource":return vt(e);case"selfContained":case"selfContainedExternalDatasource":return Mt(e,o);case"rawData":return{...M(e,["sources"]),spectra:r.map(Oe)};default:return e}}function vt(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=>At(n,t))}}function Ct(e){return M(e,Rt)}function At(e,t){return!("selector"in e)||t?.includes(e.id)?Oe(e):M(e,Ot)}function Oe(e){let{data:t,info:o,originalData:r,originalInfo:i}=e,n=M(e,It);return n.data=r||t,n.info=i||o,n}import{FileCollection as wt}from"file-collection";async function Ie(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 wt({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 se=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)}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 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 O(t,this.#e),t.plugins}slot(t){return me({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 De=[{version:6,fun:A},{version:7,fun:w}];function Et(e){let{version:t}=e||{},o=Tt(De,t);if(o===-1)return{...e,version:13};let r=De.slice(o);for(let i of r)e=i.fun(e);return e}export{ve as ANALYSIS_COLUMN_TYPES,Me as ANALYSIS_COLUMN_VALUES_KEYS,h as CURRENT_EXPORT_VERSION,Ae as EXTERNAL_API_KEYS,se as NMRiumCore,Ze as defineNMRiumPlugin,Ye as formatSpectra,b as generateID,W as getOneIfArray,Et as migrateSettings,Ce as units};
+`)}var se=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 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 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 me({slot:t,plugins:this.#e})}};function Et(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 De=[{version:6,fun:A},{version:7,fun:w}];function Lt(e){let{version:t}=e||{},o=Et(De,t);if(o===-1)return{...e,version:13};let r=De.slice(o);for(let i of r)e=i.fun(e);return e}export{ve as ANALYSIS_COLUMN_TYPES,Me as ANALYSIS_COLUMN_VALUES_KEYS,N as CURRENT_EXPORT_VERSION,Ae as EXTERNAL_API_KEYS,se as NMRiumCore,Ze as defineNMRiumPlugin,Ye as formatSpectra,x as generateID,W as getOneIfArray,Lt as migrateSettings,Ce as units};

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@zakodium/nmrium-core",
-  "version": "0.6.2",
+  "version": "0.6.3",
   "description": "The core of NMRium: types, state, state migration and plugin system.",
   "author": "Zakodium Sàrl",
   "license": "CC-BY-NC-SA-4.0",
@@ -29,10 +29,11 @@
     "@zakodium/nmr-types": "^0.5.1",
     "esbuild": "^0.27.0",
     "jest-matcher-deep-close-to": "^3.0.2",
+    "msw": "^2.12.7",
     "react-science": "^19.7.1",
     "rimraf": "^6.1.2",
     "typescript": "~5.9.3",
-    "vitest": "^4.0.17"
+    "vitest": "^4.0.18"
   },
   "dependencies": {
     "cheminfo-types": "^1.8.1",
@@ -46,5 +47,5 @@
   "volta": {
     "extends": "../../../package.json"
   },
-  "gitHead": "e66cb34d09917e88a12148a89951e2705f4321c9"
+  "gitHead": "bff4790ea356055b08d716cd063eb0815c59e7e7"
 }