refactor: move auto processing to nmr-load-save (#2737)

* feat: update nmr-load-save * feat: manage auto processing by nmr-load-save * fix: digitalFilter applied by nmr-load-save * chore: fix sourceSelector option --------- Co-authored-by: jobo322 <[email protected]>
cheminfo · Nov 7, 2023 · 2aeb9e1 · 2aeb9e1
1 parent 6deb455
commit 2aeb9e1
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Showing 10 changed files with 120 additions and 150 deletions.
diff --git a/package-lock.json b/package-lock.json
diff --git a/package.json b/package.json
@@ -86,7 +86,7 @@
     "ml-stat": "^1.3.3",
     "multiplet-analysis": "^2.1.2",
     "nmr-correlation": "^2.3.3",
-    "nmr-load-save": "^0.22.4",
+    "nmr-load-save": "^0.23.2",
     "nmr-processing": "^11.5.0",
     "nmredata": "^0.9.7",
     "numeral": "^2.0.6",
@@ -148,4 +148,4 @@
     "vite": "^4.5.0",
     "vitest": "^0.34.6"
   }
-}
+}
diff --git a/src/component/loader/DropZone.tsx b/src/component/loader/DropZone.tsx
@@ -14,6 +14,7 @@ import { LoaderProvider } from '../context/LoaderContext';
 import { useLogger } from '../context/LoggerContext';
 import { usePreferences } from '../context/PreferencesContext';
 import { useAlert } from '../elements/popup/Alert';
+import useCheckExperimentalFeature from '../hooks/useCheckExperimentalFeature';
 import { useCheckToolsVisibility } from '../hooks/useCheckToolsVisibility';
 import { useMetaInformationImportationModal } from '../modal/metaImportation/index';
 
@@ -59,6 +60,7 @@ function DropZone(props) {
   const openImportMetaInformationModal = useMetaInformationImportationModal();
   const alert = useAlert();
   const { logger } = useLogger();
+  const experimentalFeatures = useCheckExperimentalFeature();
 
   async function loadFilesHandler(files) {
     try {
@@ -73,13 +75,14 @@ function DropZone(props) {
         if (metaFile) {
           parseMetaFileResult = await parseMetaFile(metaFile);
         }
-
         const { nmrLoaders: sourceSelector } = preferences.current;
         const { nmriumState, containsNmrium } = await readDropFiles(
           fileCollection,
           {
             sourceSelector,
             logger: logger.child({ context: 'nmr-processing' }),
+            onLoadProcessing: current.onLoadProcessing,
+            experimentalFeatures,
           },
         );
 
@@ -97,7 +100,6 @@ function DropZone(props) {
           payload: {
             nmriumState,
             containsNmrium,
-            onLoadProcessing: current.onLoadProcessing,
             parseMetaFileResult,
           },
         });

diff --git a/src/component/modal/setting/settings-tabs/OnLoadProcessingTabContent.tsx b/src/component/modal/setting/settings-tabs/OnLoadProcessingTabContent.tsx
@@ -1,27 +1,46 @@
 import { useFormikContext } from 'formik';
-import { OnLoadProcessing, WorkspacePreferences } from 'nmr-load-save';
+import { WorkspacePreferences } from 'nmr-load-save';
+import { BaseFilter } from 'nmr-processing';
 import { useState } from 'react';
 import { TabItem, Tabs } from 'react-science/ui';
 
 import { Nucleus } from '../../../../data/types/common/Nucleus';
 import { CheckBoxCell } from '../../../elements/CheckBoxCell';
 import IsotopesViewer from '../../../elements/IsotopesViewer';
+import Label from '../../../elements/Label';
 import ReactTable from '../../../elements/ReactTable/ReactTable';
 import { CustomColumn } from '../../../elements/ReactTable/utility/addCustomColumn';
+import FormikCheckBox from '../../../elements/formik/FormikCheckBox';
 
 function OnLoadProcessingTabContent() {
   const { values } = useFormikContext<WorkspacePreferences>();
-  const [activeTab, setActiveTab] = useState<Nucleus>('1H');
+  const isExperimentalFeatures =
+    values.display?.general?.experimentalFeatures?.display || false;
 
-  const tabItems: TabItem[] = Object.keys(values?.onLoadProcessing || {}).map(
+  return (
+    <div>
+      <Label
+        title="Enable auto processing"
+        htmlFor="onLoadProcessing.autoProcessing"
+        style={{ wrapper: { padding: '10px 0' } }}
+      >
+        <FormikCheckBox name="onLoadProcessing.autoProcessing" />
+      </Label>
+      {isExperimentalFeatures && <AutoProcessingFilters />}
+    </div>
+  );
+}
+
+function AutoProcessingFilters() {
+  const { values } = useFormikContext<WorkspacePreferences>();
+  const [activeTab, setActiveTab] = useState<Nucleus>('1H');
+  const autoProcessingFilters = values?.onLoadProcessing?.filters || {};
+  const tabItems: TabItem[] = Object.keys(autoProcessingFilters).map(
     (nucleus) => ({
       id: nucleus,
       title: <IsotopesViewer value={nucleus} />,
       content: (
-        <FiltersTable
-          data={values?.onLoadProcessing?.[nucleus]}
-          nucleus={nucleus}
-        />
+        <FiltersTable data={autoProcessingFilters[nucleus]} nucleus={nucleus} />
       ),
     }),
   );
@@ -37,7 +56,7 @@ function OnLoadProcessingTabContent() {
 }
 
 function FiltersTable({ data, nucleus }) {
-  const COLUMNS: Array<CustomColumn<OnLoadProcessing>> = [
+  const COLUMNS: Array<CustomColumn<BaseFilter>> = [
     {
       index: 1,
       Header: '#',
@@ -54,7 +73,7 @@ function FiltersTable({ data, nucleus }) {
       Header: 'Enable',
       Cell: ({ row }) => (
         <CheckBoxCell
-          name={`onLoadProcessing.${nucleus}.${row.index}.flag`}
+          name={`onLoadProcessing.filters.${nucleus}.${row.index}.flag`}
           defaultValue={false}
         />
       ),

diff --git a/src/component/reducer/actions/LoadActions.ts b/src/component/reducer/actions/LoadActions.ts
@@ -2,12 +2,7 @@ import { Draft } from 'immer';
 import lodashMerge from 'lodash/merge';
 import lodashMergeWith from 'lodash/mergeWith';
 import { buildCorrelationData, CorrelationData } from 'nmr-correlation';
-import {
-  Spectrum,
-  OnLoadProcessing,
-  ViewState,
-  NmriumState,
-} from 'nmr-load-save';
+import { Spectrum, ViewState, NmriumState } from 'nmr-load-save';
 import { ParseResult } from 'papaparse';
 
 import { initiateDatum1D } from '../../../data/data1d/Spectrum1D';
@@ -17,7 +12,6 @@ import * as MoleculeManager from '../../../data/molecules/MoleculeManager';
 import { linkMetaWithSpectra } from '../../../data/parseMeta/linkMetaWithSpectra';
 import { UsedColors } from '../../../types/UsedColors';
 import { DefaultTolerance } from '../../panels/SummaryPanel/CorrelationTable/Constants';
-import nucleusToString from '../../utility/nucleusToString';
 import { getDefaultViewState, getInitialState, State } from '../Reducer';
 import { ActionType } from '../types/ActionType';
 
@@ -32,7 +26,6 @@ interface InitiateProps {
 interface InputProps extends InitiateProps {
   containsNmrium?: boolean;
   usedColors?: UsedColors;
-  onLoadProcessing?: OnLoadProcessing;
   parseMetaFileResult?: ParseResult<any> | null;
   resetSourceObject?: boolean;
 }
@@ -87,23 +80,15 @@ function setCorrelation(draft: Draft<State>, correlations: CorrelationData) {
   }
 }
 
-function setData(
-  draft: Draft<State>,
-  input: InputProps,
-  options: {
-    autoOnLoadProcessing?: boolean;
-  } = {},
-) {
+function setData(draft: Draft<State>, input: InputProps) {
   const {
     nmriumState: { data, view },
-    onLoadProcessing = {},
     parseMetaFileResult = null,
   } = input || {
     nmriumState: { data: { spectra: [], molecules: [], correlations: {} } },
     multipleAnalysis: {},
   };
 
-  const { autoOnLoadProcessing = true } = options;
   const {
     source,
     spectra = [],
@@ -133,7 +118,6 @@ function setData(
   draft.data = draft.data.concat(
     initSpectra(spectra, {
       usedColors: draft.usedColors,
-      onLoadProcessing: autoOnLoadProcessing ? onLoadProcessing : {},
       molecules: draft.molecules,
     }),
   );
@@ -153,19 +137,15 @@ function initSpectra(
   inputSpectra: Spectrum[],
   options: {
     usedColors: UsedColors;
-    onLoadProcessing: OnLoadProcessing;
     molecules: StateMoleculeExtended[];
   },
 ) {
   const spectra: any = [];
-  const { usedColors, onLoadProcessing, molecules } = options;
+  const { usedColors, molecules } = options;
   for (const spectrum of inputSpectra) {
     const { info } = spectrum;
     if (info.dimension === 1) {
-      const filters = onLoadProcessing?.[nucleusToString(info.nucleus)] || [];
-      spectra.push(
-        initiateDatum1D(spectrum, { usedColors, filters, molecules }),
-      );
+      spectra.push(initiateDatum1D(spectrum, { usedColors, molecules }));
     } else if (info.dimension === 2) {
       spectra.push(initiateDatum2D({ ...spectrum }, { usedColors }));
     }
@@ -195,10 +175,9 @@ function initData(
   action: LoadDropFilesAction | InitiateAction,
   options: {
     forceInitialize?: boolean;
-    autoOnLoadProcessing?: boolean;
   } = {},
 ) {
-  const { forceInitialize = false, autoOnLoadProcessing = true } = options;
+  const { forceInitialize = false } = options;
 
   const {
     nmriumState: { data, view },
@@ -207,7 +186,7 @@ function initData(
   const viewState = view as ViewState;
   if (data?.spectra?.length || forceInitialize) {
     const state = getInitialState();
-    setData(state, action.payload, { autoOnLoadProcessing });
+    setData(state, action.payload);
     setActiveTab(state, { tab: viewState?.spectra?.activeTab || '' });
     state.width = draft.width;
     state.height = draft.height;
@@ -234,7 +213,6 @@ function handleSetIsLoading(draft: Draft<State>, action: SetIsLoadingAction) {
 function handleInitiate(draft: Draft<State>, action: InitiateAction) {
   return initData(draft, action, {
     forceInitialize: true,
-    autoOnLoadProcessing: false,
   });
 }
 
@@ -249,7 +227,7 @@ function handleLoadDropFiles(draft: Draft<State>, action: LoadDropFilesAction) {
   } = payload;
 
   if (containsNmrium) {
-    return initData(draft, action, { autoOnLoadProcessing: false });
+    return initData(draft, action);
   } else {
     setData(draft, payload);
     setActiveTab(draft);

diff --git a/src/component/workspaces/exercise.ts b/src/component/workspaces/exercise.ts
@@ -34,6 +34,7 @@ export const exercise: InnerWorkspace = {
     verticalSplitterCloseThreshold: 600,
     spectraRendering: 'auto',
     loggingLevel: 'info',
+    invert: false,
   },
   formatting: {
     nuclei: {},

diff --git a/src/component/workspaces/prediction.ts b/src/component/workspaces/prediction.ts
@@ -9,6 +9,7 @@ export const prediction: InnerWorkspace = {
     verticalSplitterCloseThreshold: 600,
     spectraRendering: 'auto',
     loggingLevel: 'info',
+    invert: false,
   },
   display: {
     panels: {

diff --git a/src/component/workspaces/simulation.ts b/src/component/workspaces/simulation.ts
@@ -9,6 +9,7 @@ export const simulation: InnerWorkspace = {
     verticalSplitterCloseThreshold: 600,
     spectraRendering: 'auto',
     loggingLevel: 'info',
+    invert: false,
   },
   display: {
     panels: {