updated readme; exporting baseCSVExtractor; added tests

Author: Dtphelan1

README.md

@@ -92,8 +92,9 @@ Examples files for these extractor can be found in the [`test/sample-client-data
 
 After exporting your CSV files to the `data` directory, kickstart the creation of a configuration file by renaming the provided `csv.config.example.json` to `csv.config.json`. Then, ensure the following configuration parameters are properly set:
 
-1. `patientIdCsvPath` should provide a file path to a CSV file containing MRN's for relevant patients;
-2. For each extractor, `filePath:` should provide a file path to a CSV file containing that corresponding extractor's data;
+1. `patientIdCsvPath` should correspond to an absolute file path to a CSV file containing MRN's for relevant patients;
+2. `commonExtractorArgs.dataDirectory` should correspond to an absolute path to the dataDirectory containing all your exported CSV files;
+3. For each extractor, `fileName` should correspond to the file name this extractor should be reading from. Note: combining the `dataDirectory` above and `fileName` should resolve to a file on disk containing this corresponding extractor's data;
 
 For instructions on setting up an email notification trigger whenever an error is encountered in extraction, see the [Email Notification](#Email-Notification) section below.
 

src/extractors/BaseCSVExtractor.js

@@ -29,7 +29,7 @@ class BaseCSVExtractor extends Extractor {
       logger.debug(
         'Could not instantiate a CSVExtractor with the provided constructor args',
       );
-      throw new Error('Trying to instantiate a CSVExtractor without a filePath, url, or fileName+dataDirectory combination');
+      throw new Error('Trying to instantiate a CSVExtractor without a valid filePath, url, or fileName+dataDirectory combination');
     }
   }
 

src/extractors/index.js

@@ -1,3 +1,4 @@
+const { BaseCSVExtractor } = require('./BaseCSVExtractor');
 const { BaseFHIRExtractor } = require('./BaseFHIRExtractor');
 const { CSVAdverseEventExtractor } = require('./CSVAdverseEventExtractor');
 const { CSVCancerDiseaseStatusExtractor } = require('./CSVCancerDiseaseStatusExtractor');
@@ -26,6 +27,7 @@ const { FHIRProcedureExtractor } = require('./FHIRProcedureExtractor');
 const { MCODESurgicalProcedureExtractor } = require('./MCODESurgicalProcedureExtractor');
 
 module.exports = {
+  BaseCSVExtractor,
   BaseFHIRExtractor,
   CSVAdverseEventExtractor,
   CSVCancerDiseaseStatusExtractor,

test/extractors/BaseCSVExtractor.test.js

@@ -0,0 +1,64 @@
+const { BaseCSVExtractor } = require('../../src/extractors');
+
+// Tests
+describe('BaseCSVExtractor', () => {
+  describe('constructor', () => {
+    test('Should create a CSVURLModule when provided a filePath', () => {
+      const filePathExtractor = new BaseCSVExtractor({ filePath: '/Users/dphelan/Development/mcode-extraction-framework/test/extractors/fixtures/example.csv' });
+      expect(filePathExtractor.csvModule).not.toBeUndefined();
+      expect(filePathExtractor.csvModule.constructor.name).toEqual('CSVFileModule');
+    });
+    test('Should create a CSVFileModule when provided a URL', () => {
+      const urlExtractor = new BaseCSVExtractor({ url: 'http://example.com' });
+      expect(urlExtractor.csvModule).not.toBeUndefined();
+      expect(urlExtractor.csvModule.constructor.name).toEqual('CSVURLModule');
+    });
+    test('Should create a CSVFileModule when provided a fileName and a dataDirectory', () => {
+      const fileNameDataDirectoryExtractor = new BaseCSVExtractor({ fileName: 'example.csv', dataDirectory: '/Users/dphelan/Development/mcode-extraction-framework/test/extractors/fixtures/' });
+      expect(fileNameDataDirectoryExtractor.csvModule).not.toBeUndefined();
+      expect(fileNameDataDirectoryExtractor.csvModule.constructor.name).toEqual('CSVFileModule');
+    });
+    test('Should fail when provided only provided a fileName and no dataDirectory', () => {
+      expect(() => new BaseCSVExtractor({ fileName: 'example.csv' })
+        .toThrowError('Trying to instantiate a CSVExtractor without a valid filePath, url, or fileName+dataDirectory combination'));
+    });
+    test('Should fail when provided only provided a dataDirectory and no fileName', () => {
+      expect(() => new BaseCSVExtractor({ dataDirectory: '/Users/dphelan/Development/mcode-extraction-framework/test/extractors/fixtures/' })
+        .toThrowError('Trying to instantiate a CSVExtractor without a valid filePath, url, or fileName+dataDirectory combination'));
+    });
+    test('Should fail when provided none of the three options above', () => {
+      expect(() => new BaseCSVExtractor({})
+        .toThrowError('Trying to instantiate a CSVExtractor without a valid filePath, url, or fileName+dataDirectory combination'));
+    });
+  });
+  // test('updateRequestHeaders calls its modules updateRequestHeaders function', () => {
+  //   moduleRequestHeadersSpy.mockClear();
+  //   baseFHIRExtractor.updateRequestHeaders(MOCK_REQUEST_HEADERS);
+  //   expect(moduleRequestHeadersSpy).toHaveBeenCalledWith(MOCK_REQUEST_HEADERS);
+  // });
+
+  // test('parametrizeArgsForFHIRModule parses data off of context if available', async () => {
+  //   baseFHIRModuleSearchSpy.mockClear();
+  //   const paramsBasedOnContext = await baseFHIRExtractor.parametrizeArgsForFHIRModule({ context: MOCK_CONTEXT });
+  //   expect(baseFHIRModuleSearchSpy).not.toHaveBeenCalled();
+  //   expect(paramsBasedOnContext).toHaveProperty('patient');
+  //   expect(paramsBasedOnContext.patient).toEqual(MOCK_CONTEXT.entry[0].resource.id);
+  // });
+
+  // test('parametrizeArgsForFHIRModule throws an error if context has no relevant ID', async () => {
+  //   baseFHIRModuleSearchSpy.mockClear();
+  //   await expect(baseFHIRExtractor.parametrizeArgsForFHIRModule({ context: {} })).rejects.toThrow();
+  //   expect(baseFHIRModuleSearchSpy).not.toHaveBeenCalled();
+  // });
+
+  // test('get should return a condition resource', async () => {
+  //   const data = await baseFHIRExtractor.get({ context: MOCK_CONTEXT });
+  //   expect(data.resourceType).toEqual('Bundle');
+  //   expect(data.entry).toBeDefined();
+  //   expect(data.entry.length).toBeGreaterThan(0);
+  //   expect(data.entry[0].resource.resourceType).toEqual('Condition');
+
+  //   // expect data to contain every element in the example
+  //   expect(data.entry).toEqual(expect.arrayContaining(exampleConditionBundle.entry));
+  // });
+});