Proper error checking for parsing, naming changes, readme updates

- DOMParser did not throw errors, so extra error checking functionality was needed
- changes argument names to be more clearer
- adds new test cases to handle error checking for invalid inputs

README.md

@@ -27,7 +27,25 @@ fetch('some-sbgnml-file.xml').then( fileString => {
 
 For a holistic view on how to use this module, take a look at the [example](https://github.com/PathwayCommons/sbgnml-to-cytoscape/tree/master/example) folder.
 
-## Tests
+## Errors
+
+Feeding invalid sbgnml text to the converter will result in an error being thrown.
+
+```js
+let convert = require('sbgnml-to-cytoscape')
+
+let graph = convert(null);  //  error:  Could not convert the following text to xml: null
+```
+
+## Commands
+
+#### Development
+Run the following commands to spin up a test server:
+```sh
+gulp
+```
+
+#### Tests
 Run the tests with:
 ```sh
 npm test

src/sbgnmlConverter.js

@@ -12,6 +12,12 @@ var sbgnmlConverter = {
       var parser = new DOMParser();
       doc = parser.parseFromString(text, 'text/xml');
     }
+
+    var parseError = doc.getElementsByTagName('parsererror');
+    if (parseError.length > 0) {
+      throw new Error('Could not convert the following text to xml: ' + JSON.stringify(text));
+    }
+
     return doc;
   },
   sbgnmlTags: {
@@ -411,12 +417,12 @@ var sbgnmlConverter = {
     var cytoscapeJsEdge = {data: edgeObj};
     jsonArray.push(cytoscapeJsEdge);
   },
-  convert: function (filestring) {
+  convert: function (sbgnmlText) {
     var self = this;
     var cytoscapeJsNodes = [];
     var cytoscapeJsEdges = [];
 
-    var xmlObject = this.loadXMLFromString(filestring);
+    var xmlObject = this.loadXMLFromString(sbgnmlText);
 
     var compartments = self.getAllCompartments(xmlObject);
 

test/sbgnmlConverter.spec.js

@@ -13,7 +13,10 @@ var fixtureFiles = [
   './fixtures/input/mapk_cascade.xml',
   './fixtures/input/neuronal_muscle_signalling.xml',
   './fixtures/input/polyq_proteins_interference.xml',
-  './fixtures/input/vitamins_b6_activation_to_pyridoxal_phosphate.xml'
+  './fixtures/input/vitamins_b6_activation_to_pyridoxal_phosphate.xml',
+
+
+  './fixtures/input/broken.xml'
 ];
 
 var outputFiles = [
@@ -25,7 +28,10 @@ var outputFiles = [
   require('./fixtures/output/mapk_cascade.json'),
   require('./fixtures/output/neuronal_muscle_signalling.json'),
   require('./fixtures/output/polyq_proteins_interference.json'),
-  require('./fixtures/output/vitamins_b6_activation_to_pyridoxal_phosphate.json')
+  require('./fixtures/output/vitamins_b6_activation_to_pyridoxal_phosphate.json'),
+
+
+  require('./fixtures/output/broken.json')
 ];
 
 var getFileText = function (filename) {
@@ -53,4 +59,18 @@ describe('sbgnmlConverter', function () {
       assert.deepEqual(expected, actual);
     }
   });
+  it('should throw an error when the text to xml conversion function fails', function () {
+    var garbageInputs = [null, 'blah', true, false, {'stuff': 'stuff'}];
+
+    var c = function (input) {
+      converter.convert(input);
+    };
+
+    /* eslint-disable */
+    for (var i = 0; i < garbageInputs.length; i++) {
+      assert.throws(function () { c(garbageInputs[i]) }, Error); // show invalid argument in the error message
+    }
+
+    /* eslint-enable */
+  });
 });