feat: use refactored nmr-correlation package (#1025)

* chore: modifications regarding new nmr-correlation version * chore: put optional previous correlation data into options * fix: put previous correlations into options parameter * chore: use nmr-correlation@1.3.2
cheminfo · May 6, 2021 · 990eb54 · 990eb54
1 parent aa04eef
commit 990eb54
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Showing 8 changed files with 166 additions and 178 deletions.
diff --git a/package-lock.json b/package-lock.json
diff --git a/package.json b/package.json
@@ -71,7 +71,7 @@
     "ml-spectra-processing": "^6.3.0",
     "ml-stat": "^1.3.3",
     "multiplet-analysis": "^1.0.0",
-    "nmr-correlation": "^1.2.0",
+    "nmr-correlation": "^1.3.2",
     "nmr-parser": "^1.1.0",
     "nmr-processing": "^1.2.0",
     "nmredata": "^0.4.0",

diff --git a/src/component/panels/SummaryPanel/CorrelationTable/AdditionalColumnField.jsx b/src/component/panels/SummaryPanel/CorrelationTable/AdditionalColumnField.jsx
@@ -1,8 +1,9 @@
 import lodashCloneDeep from 'lodash/cloneDeep';
 import {
-  CorrelationUtilities,
-  GeneralUtilities,
-  LinkUtilities,
+  addLink,
+  buildLink,
+  getCorrelationIndex,
+  removeLink,
 } from 'nmr-correlation';
 import { useCallback, useEffect, useMemo, useRef, useState } from 'react';
 
@@ -83,7 +84,7 @@ function AdditionalColumnField({
       if (action === 'add') {
         const pseudoLinkID = generateID();
         const pseudoExperimentID = generateID();
-        const pseudoCommonLink = LinkUtilities.buildLink({
+        const pseudoCommonLink = buildLink({
           experimentType,
           experimentID: pseudoExperimentID,
           atomType: [_columnCorrelation.atomType, _rowCorrelation.atomType],
@@ -92,38 +93,28 @@ function AdditionalColumnField({
           signal: { id: generateID(), sign: 0 }, // pseudo signal
         });
 
-        CorrelationUtilities.addLink(
+        addLink(
           _columnCorrelation,
-          LinkUtilities.buildLink({
+          buildLink({
             ...pseudoCommonLink,
             axis: 'x',
-            match: [
-              GeneralUtilities.getCorrelationIndex(
-                correlations,
-                _rowCorrelation,
-              ),
-            ],
+            match: [getCorrelationIndex(correlations, _rowCorrelation)],
           }),
         );
-        CorrelationUtilities.addLink(
+        addLink(
           _rowCorrelation,
-          LinkUtilities.buildLink({
+          buildLink({
             ...pseudoCommonLink,
             axis: 'y',
-            match: [
-              GeneralUtilities.getCorrelationIndex(
-                correlations,
-                _columnCorrelation,
-              ),
-            ],
+            match: [getCorrelationIndex(correlations, _columnCorrelation)],
           }),
         );
         if (!_rowCorrelation.edited.protonsCount) {
           _rowCorrelation.protonsCount = [pseudoLinkCountHSQC + 1];
         }
       } else if (action === 'remove') {
-        CorrelationUtilities.removeLink(_rowCorrelation, commonLink.id);
-        CorrelationUtilities.removeLink(_columnCorrelation, commonLink.id);
+        removeLink(_rowCorrelation, commonLink.id);
+        removeLink(_columnCorrelation, commonLink.id);
         if (!_rowCorrelation.edited.protonsCount) {
           _rowCorrelation.protonsCount =
             pseudoLinkCountHSQC - 1 > 0 ? [pseudoLinkCountHSQC - 1] : [];

diff --git a/src/component/panels/SummaryPanel/CorrelationTable/CorrelationTableRow.jsx b/src/component/panels/SummaryPanel/CorrelationTable/CorrelationTableRow.jsx
@@ -1,5 +1,5 @@
 import lodashGet from 'lodash/get';
-import { LinkUtilities, GeneralUtilities } from 'nmr-correlation';
+import { buildLink, getLabel } from 'nmr-correlation';
 import { useCallback, useMemo } from 'react';
 
 import { buildID } from '../../../../data/utilities/Concatenation';
@@ -86,7 +86,7 @@ function CorrelationTableRow({
               experimentLabel += ' (edited)';
             }
             commonLinks.push(
-              LinkUtilities.buildLink({
+              buildLink({
                 ...link,
                 experimentLabel,
                 axis: undefined,
@@ -190,7 +190,7 @@ function CorrelationTableRow({
           style: { ...tableDataProps.style, styleLabel },
         }}
       >
-        {GeneralUtilities.getLabel(correlations, correlation)}
+        {getLabel(correlations, correlation)}
       </td>
       <td {...tableDataProps}>
         {lodashGet(correlation.signal, 'delta', false)

diff --git a/src/component/panels/SummaryPanel/Overview.jsx b/src/component/panels/SummaryPanel/Overview.jsx
@@ -1,4 +1,4 @@
-import { GeneralUtilities } from 'nmr-correlation';
+import { getAtomCounts } from 'nmr-correlation';
 import { memo } from 'react';
 
 import { ErrorColors, Errors } from './CorrelationTable/Constants';
@@ -7,7 +7,7 @@ function Overview({ correlationsData }) {
   if (!correlationsData) {
     return null;
   }
-  const atoms = GeneralUtilities.getAtomCounts(correlationsData.options.mf);
+  const atoms = getAtomCounts(correlationsData.options.mf);
 
   return Object.keys(atoms).length > 0 ? (
     Object.keys(atoms).map((atomType, i) => {

diff --git a/src/component/reducer/Reducer.ts b/src/component/reducer/Reducer.ts
@@ -1,5 +1,5 @@
 import { produce } from 'immer';
-import { Build, Types } from 'nmr-correlation';
+import { buildCorrelationData, Types } from 'nmr-correlation';
 import { predictionProton } from 'nmr-processing';
 import OCL from 'openchemlib/full';
 
@@ -85,10 +85,8 @@ export const initialState = {
   displayerMode: DISPLAYER_MODE.DM_1D,
   tabActiveSpectrum: {},
   spectraAnalysis: {},
-  correlations: Build.init({
-    values: [],
-    options: { tolerance: DefaultTolerance, mf: '' },
-    state: {},
+  correlations: buildCorrelationData([], {
+    tolerance: DefaultTolerance,
   }),
   displayerKey: '',
   ZoomHistory: {},

diff --git a/src/component/reducer/actions/CorrelationsActions.ts b/src/component/reducer/actions/CorrelationsActions.ts
@@ -1,16 +1,15 @@
 import { original, Draft } from 'immer';
 import lodashCloneDeep from 'lodash/cloneDeep';
-import { Build, CorrelationUtilities, Types } from 'nmr-correlation';
+import { buildCorrelationData, setCorrelation, Types } from 'nmr-correlation';
 
 import { State } from '../Reducer';
 
 function handleUpdateCorrelations(draft: Draft<State>) {
   const { data: spectra, correlations } = draft;
-  draft.correlations = Build.build(
-    spectra as Types.Spectra,
-    correlations.options,
-    lodashCloneDeep(correlations.values),
-  );
+  draft.correlations = buildCorrelationData(spectra as Types.Spectra, {
+    ...correlations.options,
+    values: lodashCloneDeep(correlations.values),
+  });
 }
 
 function handleSetMF(draft: Draft<State>, payload: { mf: string }) {
@@ -19,11 +18,11 @@ function handleSetMF(draft: Draft<State>, payload: { mf: string }) {
   const { mf } = payload;
   // update of correlation data is needed only if the following is true
   if (correlations.options.mf === '' || correlations.options.mf !== mf) {
-    draft.correlations = Build.build(
-      spectra as Types.Spectra,
-      { ...correlations.options, mf },
-      lodashCloneDeep(correlations.values),
-    );
+    draft.correlations = buildCorrelationData(spectra as Types.Spectra, {
+      ...correlations.options,
+      mf,
+      values: lodashCloneDeep(correlations.values),
+    });
   }
 }
 
@@ -34,11 +33,11 @@ function handleSetTolerance(
   const state = original(draft) as State;
   const { data: spectra, correlations } = state;
   const { tolerance } = payload;
-  draft.correlations = Build.build(
-    spectra as Types.Spectra,
-    { ...correlations.options, tolerance },
-    lodashCloneDeep(correlations.values),
-  );
+  draft.correlations = buildCorrelationData(spectra as Types.Spectra, {
+    ...correlations.options,
+    tolerance,
+    values: lodashCloneDeep(correlations.values),
+  });
 }
 
 function handleSetCorrelation(
@@ -48,11 +47,7 @@ function handleSetCorrelation(
   const state = original(draft) as State;
   const { correlations } = state;
   const { id, correlation } = payload;
-  draft.correlations = CorrelationUtilities.setCorrelation(
-    correlations,
-    id,
-    correlation,
-  );
+  draft.correlations = setCorrelation(correlations, id, correlation);
   handleUpdateCorrelations(draft);
 }
 
@@ -63,11 +58,7 @@ function handleSetCorrelations(
   const { ids, correlations } = payload;
   ids.forEach((id, i) => {
     const { correlations: correlationsData } = draft;
-    draft.correlations = CorrelationUtilities.setCorrelation(
-      correlationsData,
-      id,
-      correlations[i],
-    );
+    draft.correlations = setCorrelation(correlationsData, id, correlations[i]);
   });
   handleUpdateCorrelations(draft);
 }

diff --git a/src/component/reducer/actions/LoadActions.ts b/src/component/reducer/actions/LoadActions.ts
@@ -1,6 +1,6 @@
 import { Draft } from 'immer';
 import lodashGet from 'lodash/get';
-import { Build, Types } from 'nmr-correlation';
+import { buildCorrelationData, Types } from 'nmr-correlation';
 
 import { addJcamps, addJDFs } from '../../../data/SpectraManager';
 import * as MoleculeManager from '../../../data/molecules/MoleculeManager';
@@ -47,13 +47,11 @@ function setData(
   draft.exclusionZones = exclusionZones;
 
   if (!correlations || Object.keys(correlations).length === 0) {
-    draft.correlations = Build.init({
-      values: [],
-      options: { tolerance: DefaultTolerance, mf: '' },
-      state: {},
+    draft.correlations = buildCorrelationData([], {
+      tolerance: DefaultTolerance,
     });
   } else {
-    draft.correlations = Build.init(correlations);
+    draft.correlations = correlations;
   }
 
   // const spectraAnalysis = AnalysisObj.getMultipleAnalysis();