Merge pull request #172 from mcode/data-directory-round-2

Improving dataDirectory approach

Author: jafeltra

src/application/app.js

@@ -30,7 +30,8 @@ async function mcodeApp(Client, fromDate, toDate, config, pathToRunLogs, debug,
   await mcodeClient.init();
 
   // Parse CSV for list of patient mrns
-  const patientIds = parsePatientIds(config.patientIdCsvPath);
+  const dataDirectory = config.commonExtractorArgs && config.commonExtractorArgs.dataDirectory;
+  const patientIds = parsePatientIds(config.patientIdCsvPath, dataDirectory);
 
   // Get RunInstanceLogger for recording new runs and inferring dates from previous runs
   const runLogger = allEntries ? null : new RunInstanceLogger(pathToRunLogs);

src/helpers/appUtils.js

@@ -1,25 +1,40 @@
 const fs = require('fs');
 const path = require('path');
 const { csvParse } = require('./csvParsingUtils');
+const logger = require('./logger');
+
+/**
+ * Loads the patientIdCSV data from disk, with some helpful hints logged in case of failure
+ *
+ * @returns file corresponding to the patient data
+ */
+function getPatientIdCSVData(patientIdCsvPath, dataDirectory) {
+  try {
+    const patientIdsCsvPath = path.resolve(patientIdCsvPath);
+    return fs.readFileSync(patientIdsCsvPath, 'utf8');
+  } catch (e) {
+    if (dataDirectory) {
+      logger.error(`Could not resolve ${patientIdCsvPath}; even with a dataDirectory, the config.patientIdCsvPath variable needs to be a resolvable path to the patientID file on disk.`);
+    }
+    throw e;
+  }
+}
 
 /**
  * Parses a provided CSV with MRN column into string array of IDs
  *
- * @param {string} pathToCSV filePath to the CSV content to be parsed to get IDs
+ * @param {string} patientIdCsvPath filePath to the CSV content to be parsed to get IDs
+ * @param {string} dataDirectory optional argument for if a dataDirectory was specified by the config
  * @returns array of parsed IDs from the CSV
  */
-function parsePatientIds(pathToCSV) {
-  // Parse CSV for list of patient IDs
-  const patientIdsCsvPath = path.resolve(pathToCSV);
-  const patientIds = csvParse(fs.readFileSync(patientIdsCsvPath, 'utf8')).map((row) => {
+function parsePatientIds(patientIdCsvPath, dataDirectory) {
+  const csvData = getPatientIdCSVData(patientIdCsvPath, dataDirectory);
+  return csvParse(csvData).map((row) => {
     if (!row.mrn) {
-      throw new Error(`${pathToCSV} has no "mrn" column`);
+      throw new Error(`${patientIdCsvPath} has no "mrn" column`);
     }
-
     return row.mrn;
   });
-
-  return patientIds;
 }
 
 module.exports = {