netcdf-gcms - npm Package Compare versions

Comparing version 1.1.0 to 1.2.0

package.json

 {
   "name": "netcdf-gcms",
-  "version": "1.1.0",
+  "version": "1.2.0",
   "description": "Parser from NetCDF files to JSON usable for GCMS",
@@ -34,11 +34,13 @@ "main": "./src/index.js",
   "devDependencies": {
-    "cheminfo-tools": "^1.5.0",
-    "eslint": "^4.10.0",
-    "eslint-config-cheminfo": "^1.2.0",
-    "eslint-plugin-no-only-tests": "^2.0.0",
+    "cheminfo-tools": "^1.21.1",
+    "eslint": "^4.19.1",
+    "eslint-config-cheminfo": "^1.18.0",
+    "eslint-plugin-import": "^2.14.0",
+    "eslint-plugin-jest": "^21.27.1",
+    "eslint-plugin-no-only-tests": "^2.0.1",
     "jest": "^21.2.1"
   },
   "dependencies": {
-    "netcdfjs": "^0.3.0"
+    "netcdfjs": "^0.6.0"
   }
 }

src/aiaTemplate.js

 'use strict';
 
 function aiaTemplate(reader) {
-    var time = [];
-    const tic = reader.getDataVariable('ordinate_values');
+  var time = [];
+  const tic = reader.getDataVariable('ordinate_values');
 
-    // variables to get the time
-    const delayTime = Number(reader.getDataVariable('actual_delay_time'));
-    const interval = Number(reader.getDataVariable('actual_sampling_interval'));
+  // variables to get the time
+  const delayTime = Number(reader.getDataVariable('actual_delay_time'));
+  const interval = Number(reader.getDataVariable('actual_sampling_interval'));
 
-    var currentTime = delayTime;
-    for (var i = 0; i < tic.length; i++) {
-        time.push(currentTime);
-        currentTime += interval;
-    }
+  var currentTime = delayTime;
+  for (var i = 0; i < tic.length; i++) {
+    time.push(currentTime);
+    currentTime += interval;
+  }
 
-    return {
-        times: time,
-        series: [{
-            name: 'tic',
-            dimension: 1,
-            data: tic
-        }]
-    };
+  return {
+    times: time,
+    series: [
+      {
+        name: 'tic',
+        dimension: 1,
+        data: tic
+      }
+    ]
+  };
 }
 
 module.exports = aiaTemplate;

src/index.js

 'use strict';
 
 const NetCDFReader = require('netcdfjs');
-const agilent = require('./agilent');
-const finnigan = require('./finnigan');
+
+const agilentGCMS = require('./agilentGCMS');
+const agilentHPLC = require('./agilentHPLC');
+const finniganGCMS = require('./finniganGCMS');
 const aiaTemplate = require('./aiaTemplate');
@@ -11,29 +13,66 @@
  * @param {ArrayBuffer} data - ArrayBuffer or any Typed Array (including Node.js' Buffer from v4) with the data
+ * @param {object} [options={}]
+ * @param {boolean} [options.meta] - add meta information
+ * @param {boolean} [options.variables] -add variables information
  * @return {{times, series}} - JSON with the time, TIC and mass spectra values
  */
-function netcdfGcms(data) {
-    let reader = new NetCDFReader(data);
-    const globalAttributes = reader.globalAttributes;
+function netcdfGcms(data, options) {
+  let reader = new NetCDFReader(data);
 
-    if (globalAttributes.find(val => val.name === 'dataset_origin')) {
-        return agilent(reader);
-    } else if (globalAttributes.find(val => val.name === 'source_file_format')) {
-        return finnigan(reader);
-    } else if (globalAttributes.find(val => val.name === 'aia_template_revision')) {
-        return aiaTemplate(reader);
-    } else {
-        throw new TypeError('Unknown file format');
-    }
+  let instrument_mfr = reader.getDataVariableAsString('instrument_mfr');
+  let dataset_origin = reader.attributeExists('dataset_origin');
+  let mass_values = reader.dataVariableExists('mass_values');
+  let detector_name = reader.getAttribute('detector_name');
+  let aia_template_revision = reader.attributeExists('aia_template_revision');
+  const globalAttributes = reader.globalAttributes;
+
+  let ans;
+
+  if (mass_values && dataset_origin) {
+    ans = agilentGCMS(reader);
+  } else if (
+    mass_values &&
+    instrument_mfr &&
+    instrument_mfr.match(/finnigan/i)
+  ) {
+    ans = finniganGCMS(reader);
+  } else if (detector_name && detector_name.match(/dad/i)) {
+    // diode array agilent HPLC
+    ans = agilentHPLC(reader);
+  } else if (aia_template_revision) {
+    ans = aiaTemplate(reader);
+  } else {
+    throw new TypeError('Unknown file format');
+  }
+
+  if (options && options.meta) {
+    ans.meta = addMeta(globalAttributes);
+  }
+
+  if (options && options.variables) {
+    ans.variables = addVariables(reader);
+  }
+
+  return ans;
 }
 
 /**
- * Reads a NetCDF file with Agilent format and returns a formatted JSON with the data from it
+ * Reads a NetCDF file with Agilent GCMS format and returns a formatted JSON with the data from it
  * @param {ArrayBuffer} data - ArrayBuffer or any Typed Array (including Node.js' Buffer from v4) with the data
  * @return {{times, series}} - JSON with the time, TIC and mass spectra values
  */
-function fromAgilent(data) {
-    return agilent(new NetCDFReader(data));
+function fromAgilentGCMS(data) {
+  return agilentGCMS(new NetCDFReader(data));
 }
 
 /**
+ * Reads a NetCDF file with Agilent HPLC format and returns a formatted JSON with the data from it
+ * @param {ArrayBuffer} data - ArrayBuffer or any Typed Array (including Node.js' Buffer from v4) with the data
+ * @return {{times, series}} - JSON with the time, TIC and mass spectra values
+ */
+function fromAgilentHPLC(data) {
+  return agilentHPLC(new NetCDFReader(data));
+}
+
+/**
  * Reads a NetCDF file with Finnigan format and returns a formatted JSON with the data from it
@@ -43,13 +82,29 @@ * @param {ArrayBuffer} data - ArrayBuffer or any Typed Array (including Node.js' Buffer from v4) with the data
  */
-function fromFinnigan(data) {
-    return finnigan(new NetCDFReader(data));
+function fromFinniganGCMS(data) {
+  return finniganGCMS(new NetCDFReader(data));
 }
 
 function fromAiaTemplate(data) {
-    return aiaTemplate(new NetCDFReader(data));
+  return aiaTemplate(new NetCDFReader(data));
 }
 
+function addMeta(globalAttributes) {
+  var ans = {};
+  for (const item of globalAttributes) {
+    ans[item.name] = item.value;
+  }
+  return ans;
+}
+
+function addVariables(reader) {
+  for (let variable of reader.variables) {
+    variable.value = reader.getDataVariable(variable);
+  }
+  return reader.variables;
+}
+
 module.exports = netcdfGcms;
-module.exports.fromAgilent = fromAgilent;
-module.exports.fromFinnigan = fromFinnigan;
+module.exports.fromAgilentGCMS = fromAgilentGCMS;
+module.exports.fromAgilentHPLC = fromAgilentHPLC;
+module.exports.fromFinniganGCMS = fromFinniganGCMS;
 module.exports.fromAiaTemplate = fromAiaTemplate;

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Found 1 instance in 1 package

Major refactor

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Package has recently undergone a major refactor. It may be unstable or indicate significant internal changes. Use caution when updating to versions that include significant changes.

Found 1 instance in 1 package

Fixed alerts

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This package is not allowed per your license policy. Review the package's license to ensure compliance.

Found 1 instance in 1 package

Improved metrics

Total package byte prevSize

23110

increased by163.06%

Number of package files

9

increased by12.5%

Lines of code

389

increased by192.48%

Worsened metrics

Dev dependency count

7

increased by40%

Number of medium supply chain risk alerts

2

increased by100%

Dependency changes

• + Addednetcdfjs@0.6.0(transitive)

• - Removednetcdfjs@0.3.3(transitive)

• Updatednetcdfjs@^0.6.0