feat: adapt to flat nmrium archive structure (#3811)

Author: tpoisseau

package-lock.json

@@ -69,8 +69,8 @@
     "@emotion/styled": "^11.14.1",
     "@hookform/resolvers": "^5.2.2",
     "@zakodium/nmr-types": "^0.4.1",
-    "@zakodium/nmrium-core": "^0.4.7",
-    "@zakodium/nmrium-core-plugins": "^0.6.6",
+    "@zakodium/nmrium-core": "^0.4.8",
+    "@zakodium/nmrium-core-plugins": "^0.6.8",
     "@zakodium/pdnd-esm": "^1.0.2",
     "@zip.js/zip.js": "^2.8.10",
     "cheminfo-font": "^1.13.1",
@@ -82,7 +82,7 @@
     "dlv": "^1.1.3",
     "eventemitter3": "^5.0.1",
     "fifo-logger": "^2.0.1",
-    "file-collection": "^6.2.0",
+    "file-collection": "^6.2.1",
     "file-saver": "^2.0.5",
     "immer": "^10.2.0",
     "lodash": "^4.17.21",

package.json

@@ -94,7 +94,7 @@ export function useExport() {
             const archive = await core.serializeNmriumArchive({
               molecules: state.molecules,
               spectra: state.data,
-              fileCollections: state.fileCollections,
+              aggregator: state.aggregator,
               includeData: options.include.dataType === 'SELF_CONTAINED',
               serializedState: blob,
             });

src/component/hooks/useExport.tsx

@@ -42,23 +42,28 @@ export function useLoadFiles(onOpenMetaInformation?: (file: File) => void) {
         let parseMetaFileResult: ParseResult<any> | null = null;
         const { onLoadProcessing, spectraColors, defaultMoleculeSettings } =
           workspacePreferences;
-        const { nmrLoaders: sourceSelector } = preferences.current;
+        const { nmrLoaders: selector } = preferences.current;
 
         const parsingOptions: Partial<ParsingOptions> = {
-          sourceSelector,
+          selector,
           logger: logger.child({ context: 'nmr-processing' }),
           onLoadProcessing,
           experimentalFeatures,
         };
 
+        let aggregator: FileCollection | undefined;
         let fileCollection: FileCollection | undefined;
-        let fileCollections: Map<string, FileCollection> | undefined;
+        let selectorRoot: string | undefined;
+        let resetSourceObject = false;
+
         if (files.length === 1 && files[0].name.endsWith('.nmrium.zip')) {
-          [nmriumState, fileCollections] = await core.readNMRiumArchive(
+          const [state, ium] = await core.readNMRiumArchive(
             files[0].stream(),
             parsingOptions,
           );
+          nmriumState = state;
           containsNmrium = true;
+          aggregator = ium;
         } else {
           for (const file of files) {
             if (file.name.endsWith('.nmrium.zip')) {
@@ -85,10 +90,13 @@ export function useLoadFiles(onOpenMetaInformation?: (file: File) => void) {
           if (metaFile) {
             parseMetaFileResult = await parseMetaFile(metaFile);
           }
-          ({ nmriumState, containsNmrium } = await core.read(
+          ({ nmriumState, containsNmrium, selectorRoot } = await core.read(
             fileCollection,
             parsingOptions,
           ));
+          if (containsNmrium) {
+            resetSourceObject = true;
+          }
         }
 
         if (nmriumState.settings) {
@@ -107,8 +115,10 @@ export function useLoadFiles(onOpenMetaInformation?: (file: File) => void) {
             containsNmrium,
             parseMetaFileResult,
             spectraColors,
+            aggregator,
             fileCollection,
-            fileCollections,
+            selectorRoot,
+            resetSourceObject,
             defaultMoleculeSettings,
           },
         });

src/component/loader/useLoadFiles.ts

@@ -78,7 +78,6 @@ export default function NMRiumStateProvider(props: NMRiumStateProviderProps) {
         sources,
         view,
         actionType,
-        fileCollections: {},
       },
       { current: workspaces[workspace.current] },
       { serialize: false, exportTarget: 'onChange' },
@@ -120,7 +119,7 @@ export default function NMRiumStateProvider(props: NMRiumStateProviderProps) {
       void core
         .readNMRiumObject(nmriumData)
         .then((result) => {
-          const [nmriumState, fileCollections] = result;
+          const [nmriumState, aggregator] = result;
           if (nmriumState?.settings) {
             dispatchPreferences({
               type: 'SET_WORKSPACE',
@@ -132,7 +131,7 @@ export default function NMRiumStateProvider(props: NMRiumStateProviderProps) {
           }
           dispatch({
             type: 'INITIATE',
-            payload: { nmriumState, fileCollections },
+            payload: { nmriumState, aggregator },
           });
         })
         .catch((error: unknown) => {

src/component/main/NMRiumStateProvider.tsx

@@ -66,13 +66,19 @@ function InnerLoadJCAMPModal({ onCloseDialog }: InnerLoadJCAMPModalProps) {
     });
     const { pathname, origin } = new URL(url);
     try {
-      const [nmriumState, fileCollection] = await core.readFromWebSource({
-        entries: [{ relativePath: pathname, baseURL: origin }],
-      });
+      const [nmriumState, fileCollection, selectorRoot] =
+        await core.readFromWebSource({
+          entries: [{ relativePath: pathname, baseURL: origin }],
+        });
 
       dispatch({
         type: 'LOAD_DROP_FILES',
-        payload: { nmriumState, resetSourceObject: false, fileCollection },
+        payload: {
+          nmriumState,
+          resetSourceObject: false,
+          fileCollection,
+          selectorRoot,
+        },
       });
     } catch {
       toaster.show({ message: `Failed to load ${url}`, intent: 'danger' });

src/component/modal/LoadJCAMPModal.tsx

@@ -5,6 +5,7 @@ import {
   Radio,
   RadioGroup,
 } from '@blueprintjs/core';
+import { useMemo } from 'react';
 import { Controller, useForm } from 'react-hook-form';
 
 import type { ExportOptions } from '../../data/SpectraManager.js';
@@ -58,7 +59,7 @@ function SaveAsModal(props: SaveAsModalProps) {
 }
 function InnerSaveAsModal(props: InnerSaveAsModalProps) {
   const { onCloseDialog } = props;
-  const { sources, data } = useChartData();
+  const { sources, data, aggregator } = useChartData();
   const { saveHandler } = useExport();
   const experimentalFlagEnabled = useCheckExperimentalFeature();
 
@@ -72,6 +73,11 @@ function InnerSaveAsModal(props: InnerSaveAsModalProps) {
   const { handleSubmit, control, register } = useForm({
     defaultValues: { ...INITIAL_VALUE, name: fileName },
   });
+
+  const containsLinkedFiles = useMemo(() => {
+    return aggregator.sources.some((s) => !s.baseURL?.startsWith('ium:'));
+  }, [aggregator]);
+
   return (
     <Dialog
       isOpen
@@ -129,7 +135,7 @@ function InnerSaveAsModal(props: InnerSaveAsModalProps) {
                   {experimentalFlagEnabled && (
                     <Radio
                       label="Full data (external data linked, experimental)"
-                      disabled={Object.keys(sources).length === 0}
+                      disabled={!containsLinkedFiles}
                       value={
                         DataExportOptions.SELF_CONTAINED_EXTERNAL_DATASOURCE
                       }

src/component/modal/SaveAsModal.tsx

@@ -1,6 +1,7 @@
 import type { BaselineCorrectionZone } from '@zakodium/nmr-types';
 import type { Spectrum, ViewState } from '@zakodium/nmrium-core';
-import type { FileCollection, Source } from 'file-collection';
+import type { Source } from 'file-collection';
+import { FileCollection } from 'file-collection';
 import type { Draft } from 'immer';
 import { original, produce } from 'immer';
 import type { CorrelationData } from 'nmr-correlation';
@@ -114,7 +115,7 @@ export function getDefaultViewState(): ViewState {
 export const getInitialState = (): State => ({
   actionType: 'INITIALIZE_NMRIUM',
   sources: {},
-  fileCollections: {},
+  aggregator: new FileCollection(),
   data: [],
   tempData: null,
   xDomain: [],
@@ -192,15 +193,20 @@ export interface State {
 
   /**
    * web source of data
-   * Record key is identifier of the source (stored in spectra)
+   * Record key is an identifier of the source (stored in spectra)
+   *
+   * Is needed until we remove the support of the old nmrium format
    */
   sources: Record<string, Source>;
 
   /**
-   * File collections of the loaded files
-   * Record key is identifier of the fileCollection (stored in spectra)
+   * Aggregation of file collections used to load the data
+   * - external data sources (web-source, import jdx from url, ...)
+   * - multiples files open / drag and drop
+   *
+   * Each of them is separated in an uuid folder
    */
-  fileCollections: Record<string, FileCollection>;
+  aggregator: FileCollection;
 
   /**
    * spectra list (1d and 2d)