jcampconverter - npm Package Compare versions

Comparing version 7.6.5 to 7.6.6

CHANGELOG.md

 # Changelog
 
+### [7.6.6](https://www.github.com/cheminfo/jcampconverter/compare/v7.6.5...v7.6.6) (2021-01-18)
+
+
+### Bug Fixes
+
+* deal with 2D jcamp without all .nucleus ([3cf7cc0](https://www.github.com/cheminfo/jcampconverter/commit/3cf7cc0907866505f430f4cf359d3b6e0f711878))
+
 ### [7.6.5](https://www.github.com/cheminfo/jcampconverter/compare/v7.6.4...v7.6.5) (2020-10-27)
@@ -4,0 +11,0 @@

lib/index.js

@@ -667,2 +667,17 @@ 'use strict';
 
+      // we will check if some nucleus are missing ...
+      if (entry.ntuples && entry.ntuples.nucleus && entry.ntuples.symbol) {
+        for (let i = 0; i < entry.ntuples.nucleus.length; i++) {
+          let symbol = entry.ntuples.symbol[i];
+          let nucleus = entry.ntuples.nucleus[i];
+          if (symbol.startsWith('F') && !nucleus) {
+            if (symbol === 'F1') entry.ntuples.nucleus[i] = entry.tmp.$NUC2;
+            if (symbol === 'F2') entry.ntuples.nucleus[i] = entry.tmp.$NUC1;
+          }
+          if (symbol === 'F2') {
+            entry.yType = entry.ntuples.nucleus[0];
+          }
+        }
+      }
+
       if (
@@ -757,2 +772,3 @@ observeFrequency &&
     }
+    delete entry.tmp;
   }
@@ -1001,2 +1017,3 @@ }
         meta: {},
+        tmp: {}, // tmp information we need to keep for postprocessing
       };
@@ -1101,5 +1118,2 @@ parentEntry.children.push(currentEntry);
       }
-      if (currentEntry.twoD) {
-        currentEntry.yType = dataValue.split(ntuplesSeparatorRegExp)[0];
-      }
     } else if (canonicDataLabel === 'PAGE') {
@@ -1115,2 +1129,6 @@ spectrum.page = dataValue.trim();
       spectrum.sampleDescription = dataValue;
+    } else if (canonicDataLabel.startsWith('$NUC')) {
+      if (!currentEntry.tmp[canonicDataLabel] && !dataValue.includes('off')) {
+        currentEntry.tmp[canonicDataLabel] = dataValue.replace(/[<>]/g, '');
+      }
     } else if (canonicDataLabel === 'END') {
@@ -1117,0 +1135,0 @@ currentEntry = parentsStack.pop();

package.json

 {
   "name": "jcampconverter",
-  "version": "7.6.5",
+  "version": "7.6.6",
   "description": "Parse and convert JCAMP data",
@@ -50,20 +50,20 @@ "main": "lib/index.js",
     "@babel/plugin-transform-modules-commonjs": "^7.12.1",
-    "@types/jest": "^26.0.15",
+    "@types/jest": "^26.0.20",
     "benchmark": "^2.1.4",
-    "cheminfo-build": "^1.1.8",
-    "eslint": "^7.12.1",
+    "cheminfo-build": "^1.1.9",
+    "eslint": "^7.18.0",
     "eslint-config-cheminfo": "^5.2.2",
     "eslint-plugin-import": "^2.22.1",
-    "eslint-plugin-jest": "^24.1.0",
-    "eslint-plugin-prettier": "^3.1.4",
+    "eslint-plugin-jest": "^24.1.3",
+    "eslint-plugin-prettier": "^3.3.1",
     "esm": "^3.2.25",
-    "jest": "^26.6.1",
+    "jest": "^26.6.3",
     "jest-matcher-deep-close-to": "^2.0.1",
-    "prettier": "^2.1.2",
-    "rollup": "^2.32.1"
+    "prettier": "^2.2.1",
+    "rollup": "^2.36.2"
   },
   "dependencies": {
     "ml-array-median": "^1.1.4",
-    "nmr-processing": "^0.3.0"
+    "nmr-processing": "^0.5.0"
   }
 }

src/convert.js

@@ -160,2 +160,3 @@ import { isMSField, convertMSFieldToLabel } from './complexChromatogram';
         meta: {},
+        tmp: {}, // tmp information we need to keep for postprocessing
       };
@@ -267,5 +268,2 @@ parentEntry.children.push(currentEntry);
       }
-      if (currentEntry.twoD) {
-        currentEntry.yType = dataValue.split(ntuplesSeparatorRegExp)[0];
-      }
     } else if (canonicDataLabel === 'PAGE') {
@@ -281,2 +279,6 @@ spectrum.page = dataValue.trim();
       spectrum.sampleDescription = dataValue;
+    } else if (canonicDataLabel.startsWith('$NUC')) {
+      if (!currentEntry.tmp[canonicDataLabel] && !dataValue.includes('off')) {
+        currentEntry.tmp[canonicDataLabel] = dataValue.replace(/[<>]/g, '');
+      }
     } else if (canonicDataLabel === 'END') {
@@ -283,0 +285,0 @@ currentEntry = parentsStack.pop();

src/postProcessing.js

@@ -45,3 +45,4 @@ import add2D from './2d/add2D';
     }
+    delete entry.tmp;
   }
 }

src/postProcessingNMR.js

@@ -43,2 +43,17 @@ import { gyromagneticRatio } from 'nmr-processing';
 
+      // we will check if some nucleus are missing ...
+      if (entry.ntuples && entry.ntuples.nucleus && entry.ntuples.symbol) {
+        for (let i = 0; i < entry.ntuples.nucleus.length; i++) {
+          let symbol = entry.ntuples.symbol[i];
+          let nucleus = entry.ntuples.nucleus[i];
+          if (symbol.startsWith('F') && !nucleus) {
+            if (symbol === 'F1') entry.ntuples.nucleus[i] = entry.tmp.$NUC2;
+            if (symbol === 'F2') entry.ntuples.nucleus[i] = entry.tmp.$NUC1;
+          }
+          if (symbol === 'F2') {
+            entry.yType = entry.ntuples.nucleus[0];
+          }
+        }
+      }
+
       if (
@@ -45,0 +60,0 @@ observeFrequency &&

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Improved metrics

Total package byte prevSize

91444

increased by2.14%

Lines of code

2187

increased by1.58%

Dependency changes

• + Addednmr-processing@0.5.0(transitive)

• - Removedis-any-array@0.1.1(transitive)

• - Removedml-gsd@5.0.2(transitive)

• - Removedml-levenberg-marquardt@2.1.1(transitive)

• - Removedml-optimize-lorentzian@0.2.0(transitive)

• - Removedml-savitzky-golay-generalized@2.0.2(transitive)

• - Removednmr-processing@0.3.1(transitive)

• Updatednmr-processing@^0.5.0