netcdf-gcms - npm Package Compare versions

Comparing version 1.3.1 to 1.4.0

History.md

@@ -0,1 +1,10 @@
+# [1.4.0](https://github.com/cheminfo-js/netcdf-gcms/compare/v1.3.1...v1.4.0) (2020-03-03)
+
+
+### Features
+
+* add advion format ([8f866ee](https://github.com/cheminfo-js/netcdf-gcms/commit/8f866ee88e5116165c35b7f72a9f29084d9daa87))
+
+
+
 <a name="1.0.0"></a>
@@ -2,0 +11,0 @@ # 1.0.0 (2016-11-23)

package.json

 {
   "name": "netcdf-gcms",
-  "version": "1.3.1",
+  "version": "1.4.0",
   "description": "Parser from NetCDF files to JSON usable for GCMS",
@@ -34,13 +34,15 @@ "main": "./src/index.js",
   "devDependencies": {
-    "cheminfo-tools": "^1.22.4",
-    "eslint": "^5.15.1",
-    "eslint-config-cheminfo": "^1.20.0",
-    "eslint-plugin-import": "^2.16.0",
-    "eslint-plugin-jest": "^22.3.2",
-    "eslint-plugin-no-only-tests": "^2.1.0",
-    "jest": "^24.5.0"
+    "cheminfo-tools": "^1.23.3",
+    "eslint": "^6.8.0",
+    "eslint-config-cheminfo": "^2.0.4",
+    "eslint-plugin-import": "^2.20.1",
+    "eslint-plugin-jest": "^23.8.1",
+    "eslint-plugin-no-only-tests": "^2.4.0",
+    "eslint-plugin-prettier": "^3.1.2",
+    "jest": "^25.1.0",
+    "prettier": "^1.19.1"
   },
   "dependencies": {
-    "netcdfjs": "^0.7.0"
+    "netcdfjs": "^1.0.0"
   }
 }

src/agilentGCMS.js

@@ -74,9 +74,9 @@ 'use strict';
 
-  var ms = new Array(pointCount.length);
-  var index = 0;
-  for (var i = 0; i < ms.length; i++) {
-    var size = pointCount[i];
+  let ms = new Array(pointCount.length);
+  let index = 0;
+  for (let i = 0; i < ms.length; i++) {
+    let size = pointCount[i];
     ms[i] = [new Array(size), new Array(size)];
 
-    for (var j = 0; j < size; j++) {
+    for (let j = 0; j < size; j++) {
       ms[i][0][j] = massValues[index];
@@ -93,3 +93,3 @@ ms[i][1][j] = intensityValues[index++];
         dimension: 1,
-        data: tic
+        data: tic,
       },
@@ -99,5 +99,5 @@ {
         dimension: 2,
-        data: ms
-      }
-    ]
+        data: ms,
+      },
+    ],
   };
@@ -104,0 +104,0 @@ }

src/agilentHPLC.js

@@ -71,3 +71,3 @@ 'use strict';
       throw new Error(
-        'The expected last time does not correspond to the runtimeLength'
+        'The expected last time does not correspond to the runtimeLength',
       );
@@ -92,5 +92,5 @@ }
         dimension: 1,
-        data: intensities
-      }
-    ]
+        data: intensities,
+      },
+    ],
   };
@@ -97,0 +97,0 @@ }

src/aiaTemplate.js

 'use strict';
 
 function aiaTemplate(reader) {
-  var time = [];
+  let time = [];
   const tic = reader.getDataVariable('ordinate_values');
@@ -11,4 +11,4 @@
 
-  var currentTime = delayTime;
-  for (var i = 0; i < tic.length; i++) {
+  let currentTime = delayTime;
+  for (let i = 0; i < tic.length; i++) {
     time.push(currentTime);
@@ -24,5 +24,5 @@ currentTime += interval;
         dimension: 1,
-        data: tic
-      }
-    ]
+        data: tic,
+      },
+    ],
   };
@@ -29,0 +29,0 @@ }

src/brukerGCMS.js

@@ -76,9 +76,9 @@ 'use strict';
 
-  var ms = new Array(time.length);
-  var index = 0;
-  for (var i = 0; i < ms.length; i++) {
-    var size = scanIndex[i + 1] - scanIndex[i];
+  let ms = new Array(time.length);
+  let index = 0;
+  for (let i = 0; i < ms.length; i++) {
+    let size = scanIndex[i + 1] - scanIndex[i];
     ms[i] = [new Array(size), new Array(size)];
 
-    for (var j = 0; j < size; j++) {
+    for (let j = 0; j < size; j++) {
       ms[i][0][j] = massValues[index];
@@ -95,3 +95,3 @@ ms[i][1][j] = intensityValues[index++];
         dimension: 1,
-        data: tic
+        data: tic,
       },
@@ -101,5 +101,5 @@ {
         dimension: 2,
-        data: ms
-      }
-    ]
+        data: ms,
+      },
+    ],
   };
@@ -106,0 +106,0 @@ }

src/finniganGCMS.js

@@ -77,9 +77,9 @@ 'use strict';
 
-  var ms = new Array(time.length);
-  var index = 0;
-  for (var i = 0; i < ms.length; i++) {
-    var size = scanIndex[i + 1] - scanIndex[i];
+  let ms = new Array(time.length);
+  let index = 0;
+  for (let i = 0; i < ms.length; i++) {
+    let size = scanIndex[i + 1] - scanIndex[i];
     ms[i] = [new Array(size), new Array(size)];
 
-    for (var j = 0; j < size; j++) {
+    for (let j = 0; j < size; j++) {
       ms[i][0][j] = massValues[index];
@@ -96,3 +96,3 @@ ms[i][1][j] = intensityValues[index++];
         dimension: 1,
-        data: tic
+        data: tic,
       },
@@ -102,5 +102,5 @@ {
         dimension: 2,
-        data: ms
-      }
-    ]
+        data: ms,
+      },
+    ],
   };
@@ -107,0 +107,0 @@ }

src/index.js

@@ -10,2 +10,3 @@ 'use strict';
 const shimadzuGCMS = require('./shimadzuGCMS');
+const advionGCMS = require('./advionGCMS');
 const aiaTemplate = require('./aiaTemplate');
@@ -25,3 +26,5 @@
 
-  let instrument_mfr = reader.getDataVariableAsString('instrument_mfr');
+  let instrument_mfr =
+    reader.dataVariableExists('instrument_mfr') &&
+    reader.getDataVariableAsString('instrument_mfr');
   let dataset_origin = reader.attributeExists('dataset_origin');
@@ -45,2 +48,4 @@ let mass_values = reader.dataVariableExists('mass_values');
     ans = brukerGCMS(reader);
+  } else if (mass_values && instrument_mfr && instrument_mfr.match(/bruker/i)) {
+    ans = brukerGCMS(reader);
   } else if (
@@ -52,2 +57,8 @@ mass_values &&
     ans = shimadzuGCMS(reader);
+  } else if (
+    mass_values &&
+    source_file_format &&
+    source_file_format.match(/advion/i)
+  ) {
+    ans = advionGCMS(reader);
   } else if (detector_name && detector_name.match(/(dad|tic)/i)) {
@@ -105,3 +116,3 @@ // diode array agilent HPLC
 function addMeta(globalAttributes) {
-  var ans = {};
+  let ans = {};
   for (const item of globalAttributes) {
@@ -108,0 +119,0 @@ ans[item.name] = item.value;

src/shimadzuGCMS.js

@@ -84,9 +84,9 @@ 'use strict';
 
-  var ms = new Array(time.length);
-  var index = 0;
-  for (var i = 0; i < ms.length; i++) {
-    var size = scanIndex[i + 1] - scanIndex[i];
+  let ms = new Array(time.length);
+  let index = 0;
+  for (let i = 0; i < ms.length; i++) {
+    let size = scanIndex[i + 1] - scanIndex[i];
     ms[i] = [new Array(size), new Array(size)];
 
-    for (var j = 0; j < size; j++) {
+    for (let j = 0; j < size; j++) {
       ms[i][0][j] = massValues[index];
@@ -103,3 +103,3 @@ ms[i][1][j] = intensityValues[index++];
         dimension: 1,
-        data: tic
+        data: tic,
       },
@@ -109,5 +109,5 @@ {
         dimension: 2,
-        data: ms
-      }
-    ]
+        data: ms,
+      },
+    ],
   };
@@ -114,0 +114,0 @@ }

New alerts

New author

Supply chain risk

A new npm collaborator published a version of the package for the first time. New collaborators are usually benign additions to a project, but do indicate a change to the security surface area of a package.

Found 1 instance in 1 package

Improved metrics

Total package byte prevSize

40807

increased by15.7%

Number of package files

12

increased by9.09%

Lines of code

717

increased by17.35%

Worsened metrics

Dev dependency count

9

increased by28.57%

Number of medium supply chain risk alerts

2

increased by100%

Dependency changes

• + Added@types/utf8@2.1.6(transitive)

• + Addediobuffer@4.0.1(transitive)

• + Addednetcdfjs@1.0.0(transitive)

• + Addedutf8@3.0.0(transitive)

• - Removediobuffer@3.2.0(transitive)

• - Removednetcdfjs@0.7.0(transitive)

• - Removedutf8@2.1.2(transitive)

• Updatednetcdfjs@^1.0.0