qpp-measures-data - npm Package Compare versions

Comparing version 1.0.0-alpha.14 to 1.0.0-alpha.15

package.json

 {
   "name": "qpp-measures-data",
-  "version": "1.0.0-alpha.14",
+  "version": "1.0.0-alpha.15",
   "description": "Quality Payment Program Measures Data Repository",
@@ -5,0 +5,0 @@ "repository": {

scripts/measures/enrich-measures-data.js

@@ -8,4 +8,6 @@ const fs = require('fs');
 
-const qpp = fs.readFileSync(path.join(__dirname, '../../staging/measures-data.json'), 'utf8');
-fs.writeFileSync(path.join(__dirname, '../../measures/measures-data.json'), enrichMeasures(JSON.parse(qpp)));
+const measuresDataPath = process.argv[2];
+const outputPath = process.argv[3];
+const qpp = fs.readFileSync(path.join(__dirname, measuresDataPath), 'utf8');
+fs.writeFileSync(path.join(__dirname, outputPath), enrichMeasures(JSON.parse(qpp)));
 
@@ -12,0 +14,0 @@ function enrichMeasures(measures) {

scripts/measures/import-qcdr-measures.js

 const parse = require('csv-parse/lib/sync');
+const _ = require('lodash');
+const fs = require('fs');
+const path = require('path');
 
 /**
- * `import-qcdr-measures` reads a QCDR CSV file and outputs valid measures
- * using `convertCsvToMeasures` and a config object.
- *
- * example:
- * $ cat util/measures/20170825-PIMMS-non-mips_measure_specifications.csv | node ./scripts/measures/import-qcdr-measures.js
- *
- * test:
- * $ cat util/measures/20170825-PIMMS-non-mips_measure_specifications.csv | node ./scripts/measures/import-qcdr-measures.js | node scripts/validate-data.js measures
-*/
+ * `import-qcdr-measures` reads a QCDR CSV file and creates valid measures,
+ * then merges the result into an existing set of measures, throwing an error
+ * if any existing measures with the same measureId has different values
+ * for any existing properties.
+ */
 
@@ -28,3 +27,2 @@ /**
     lastPerformanceYear: null,
-    metricType: 'singlePerformanceRate',
     eMeasureId: null,
@@ -38,7 +36,6 @@ nqfEMeasureId: null,
     ],
-    measureSets: []
+    measureSets: [],
+    isRegistryMeasure: true
   },
   sourced_fields: {
-    vendorId: 0,
-    primarySteward: 1,
     measureId: 2,
@@ -87,3 +84,6 @@ title: 3,
       }
-    }
+    },
+    primarySteward: 22
+    // `metricType` is a sourced field but not represented here since it maps from
+    // multiple columns-- you can find it by searching in the code below
   }
@@ -97,2 +97,4 @@ };
  * @return {array}            Returns an array of measures objects
+ *
+ * We trim all data sourced from CSVs because people sometimes unintentionally include spaces or linebreaks
  */
@@ -111,7 +113,7 @@ const convertCsvToMeasures = function(records, config) {
           // measure data maps directly to data in csv
-          newMeasure[measureKey] = record[columnObject];
+          newMeasure[measureKey] = _.trim(record[columnObject]);
         }
       } else {
         // measure data requires mapping CSV data to new value, e.g. Y, N -> true, false
-        const mappedValue = columnObject.mappings[record[columnObject.index]];
+        const mappedValue = columnObject.mappings[_.trim(record[columnObject.index])];
         newMeasure[measureKey] = mappedValue || columnObject.mappings['default'];
@@ -123,2 +125,18 @@ }
     });
+
+    // If the 'proportion' column (col 17) is Y and the other two columns
+    // (continuous and ratio, cols 18 and 19) are N, metricType should be
+    // 'singlePerformanceRate'. Otherwise it should be 'nonProportion'
+    //
+    // Note: if the 'proportion' column is Y *and* there are multiple
+    // strata, then the metricType should be 'multiPerformanceRate'
+    // TODO(kalvin): implement multiPerformanceRate;
+    if (record[17] === 'Y' &&
+        record[18] === 'N' &&
+        record[19] === 'N') {
+      newMeasure['metricType'] = 'singlePerformanceRate';
+    } else {
+      newMeasure['metricType'] = 'nonProportion';
+    }
+
     return newMeasure;
@@ -130,18 +148,86 @@ });
 
-let csvFile = '';
+function mergeMeasures(allMeasures, qcdrMeasures, measuresDataPath) {
+  const addedMeasureIds = [];
+  const modifiedMeasureIds = [];
 
-process.stdin.setEncoding('utf8');
+  // If measure exists already, merge in keys from QCDR measures. If any existing
+  // non-empty keys have a different value, throw an error.
+  // If measure doesn't exist, create it.
+  _.each(qcdrMeasures, function(measure) {
+    const id = measure.measureId;
+    const existingMeasure = _.find(allMeasures, {'measureId': id});
 
-process.stdin.on('readable', function() {
-  var chunk = process.stdin.read();
-  if (chunk !== null) {
-    csvFile += chunk;
+    if (existingMeasure && !_.isEqual(existingMeasure, measure)) {
+      const conflictingValues = _.reduce(measure, function(result, value, key) {
+        const existingValue = existingMeasure[key];
+        // isEqual does a deep comparison so this works with strata as well
+        if (!_.isNil(existingValue) && !_.isEqual(value, existingValue)) {
+          result.push({
+            'existingKey': key,
+            'existingValue': existingValue,
+            'conflictingQcdrValue': value
+          });
+        }
+        return result;
+      }, []);
+
+      if (!_.isEmpty(conflictingValues)) {
+        throw TypeError('QCDR measure with measureId: "' + id + '" conflicts' +
+        ' with existing measure. See below:\n' + JSON.stringify(conflictingValues, null, 2));
+      } else {
+        _.assign(existingMeasure, measure);
+        modifiedMeasureIds.push(id);
+      }
+    } else if (!existingMeasure) {
+      allMeasures.push(measure);
+      addedMeasureIds.push(id);
+    }
+  });
+
+  if (_.isEmpty(addedMeasureIds) && _.isEmpty(modifiedMeasureIds)) {
+    console.log('Import complete. No measures added to or modified in ' + measuresDataPath);
+  } else {
+    console.log('Added measures with the following ids: ' +
+      addedMeasureIds + '\n');
+    console.log('Modified measures with the following ids: ' +
+      modifiedMeasureIds + '\n');
+    console.log('Successfully merged QCDR measures into ' + measuresDataPath);
   }
-});
 
-process.stdin.on('end', function() {
-  const records = parse(csvFile, 'utf8');
+  return allMeasures;
+}
+
+// We want to add the new isRegistryMeasure field to all quality measures,
+// not just the measures where it's true (aka qcdr measures)
+function addMissingRegistryFlags(measures) {
+  _.each(measures, function(measure) {
+    if (measure.category === 'quality' && !_.isBoolean(measure.isRegistryMeasure)) {
+      measure.isRegistryMeasure = false;
+    }
+  });
+  return measures;
+}
+
+function importMeasures(measuresDataPath, qcdrMeasuresDataPath, outputPath) {
+  const qpp = fs.readFileSync(path.join(__dirname, measuresDataPath), 'utf8');
+  const allMeasures = JSON.parse(qpp);
+
+  const csv = fs.readFileSync(path.join(__dirname, qcdrMeasuresDataPath), 'utf8');
+  const records = parse(csv, 'utf8');
   // remove header
   records.shift();
-  process.stdout.write(JSON.stringify(convertCsvToMeasures(records, config), null, 2));
-});
+  // If there's more than one QCDR measure with the same measure, we can
+  // arbitrarily pick one and ignore the others (they should all be
+  // identical except for the QCDR Organization Name which we don't care about)
+  const qcdrMeasures = _.uniqBy(convertCsvToMeasures(records, config), 'measureId');
+
+  const mergedMeasures = mergeMeasures(allMeasures, qcdrMeasures, outputPath);
+  return JSON.stringify(addMissingRegistryFlags(mergedMeasures), null, 2);
+}
+
+const measuresDataPath = process.argv[2];
+const qcdrMeasuresDataPath = process.argv[3];
+const outputPath = process.argv[4];
+
+const newMeasures = importMeasures(measuresDataPath, qcdrMeasuresDataPath, outputPath);
+fs.writeFileSync(path.join(__dirname, outputPath), newMeasures);

test/measures/examples/quality/019.json

@@ -16,2 +16,3 @@ [
     "isInverse": false,
+    "isRegistryMeasure": false,
     "strata": [
@@ -18,0 +19,0 @@ {

test/measures/examples/quality/052.json

@@ -15,2 +15,3 @@ [
     "nqfId": "0102",
+    "isRegistryMeasure": false,
     "isInverse": false,
@@ -146,2 +147,2 @@ "strata": [
   }
-]
+]

test/measures/examples/quality/141.json

@@ -15,2 +15,3 @@ [
     "nqfId": "0563",
+    "isRegistryMeasure": false,
     "isInverse": false,
@@ -141,2 +142,2 @@ "strata": [
   }
-]
+]

test/measures/examples/quality/204.json

@@ -15,2 +15,3 @@ [
     "nqfId": "0068",
+    "isRegistryMeasure": false,
     "isInverse": false,
@@ -196,2 +197,2 @@ "strata": [
   }
-]
+]

test/measures/examples/quality/254.json

@@ -15,2 +15,3 @@ [
     "nqfId": "0651",
+    "isRegistryMeasure": false,
     "isInverse": false,
@@ -165,3 +166,3 @@ "strata": [
             "code": "G8807"
-          } 
+          }
         ]
@@ -182,2 +183,2 @@ },
   }
-]
+]

test/scripts/measures/fixtures/expected-measures.json

@@ -14,3 +14,3 @@ [
     "title": "Asthma: Assessment of Asthma Control – Ambulatory Care Setting",
-    "description": "Percentage of patients aged 5 years and older with a diagnosis of asthma who were evaluated at least once during the measurement period for asthma control (comprising asthma impairment and asthma risk). National Quality Strategy Domain: Effective Clinical Care Process Measure ",
+    "description": "Percentage of patients aged 5 years and older with a diagnosis of asthma who were evaluated at least once during the measurement period for asthma control (comprising asthma impairment and asthma risk). National Quality Strategy Domain: Effective Clinical Care Process Measure",
     "nationalQualityStrategyDomain": "Effective Clinical Care",
@@ -20,3 +20,4 @@ "measureType": "process",
     "isInverse": false,
-    "isRiskAdjusted": false
+    "isRiskAdjusted": false,
+    "isRegistryMeasure": true
   },
@@ -35,3 +36,3 @@ {
     "title": "Allergen Immunotherapy Treatment: Allergen Specific Immunoglobulin E (IgE) Sensitivity Assessed and Documented Prior to Treatment",
-    "description": "Percentage of patients aged 5 years and older who were assessed for IgE sensitivity to allergens prior to initiating allergen immunotherapy AND results documented in the medical record.National Quality Strategy Domain: Patient Safety Process Measure ",
+    "description": "Percentage of patients aged 5 years and older who were assessed for IgE sensitivity to allergens prior to initiating allergen immunotherapy AND results documented in the medical record.National Quality Strategy Domain: Patient Safety Process Measure",
     "nationalQualityStrategyDomain": "Patient Safety",
@@ -41,4 +42,5 @@ "measureType": "process",
     "isInverse": false,
-    "isRiskAdjusted": false
+    "isRiskAdjusted": false,
+    "isRegistryMeasure": true
   }
-]
+]

test/scripts/measures/import-qcdr-measures-spec.js

@@ -5,6 +5,12 @@ // Libraries
 const { execSync } = require('child_process');
+const fs = require('fs');
+const path = require('path');
 
 // Test data
-const testCsv = './test/scripts/measures/fixtures/test-qcdr.csv';
-const testCsv2Cols = './test/scripts/measures/fixtures/test-qcdr-2cols.csv';
+const testMeasures = '../../test/scripts/measures/fixtures/test-measures-data.json';
+const testMeasures2 = '../../test/scripts/measures/fixtures/test-measures-data2.json';
+const testCsv = '../../test/scripts/measures/fixtures/test-qcdr.csv';
+const testCsv2Cols = '../../test/scripts/measures/fixtures/test-qcdr-2cols.csv';
+const outputArg = '../../test/scripts/measures/fixtures/test-measures-data-output.json';
+const output = '../' + outputArg;
 
@@ -14,20 +20,24 @@ // Expected new measures
 
-// Function which executes script and converts output to a JS object.
-const runTest = function(file) {
-  const cmd = 'cat ' + file + ' | node ./scripts/measures/import-qcdr-measures.js';
-  const measuresJson = execSync(cmd, {stdio: 'pipe'}).toString();
-  return JSON.parse(measuresJson);
+// Function which executes script and reads in output file to a JS object.
+const runTest = function(measuresFile, measuresCsv) {
+  const cmd = 'node ./scripts/measures/import-qcdr-measures.js ' +
+    measuresFile + ' ' + measuresCsv + ' ' + outputArg;
+  console.log(execSync(cmd, {stdio: 'pipe'}).toString());
+
+  const qpp = fs.readFileSync(path.join(__dirname, output), 'utf8');
+
+  return JSON.parse(qpp);
 };
 
-describe('convertCsvToMeasures', function() {
-  it('should create new measures', () => {
-    const newMeasures = runTest(testCsv);
-    assert.equal(newMeasures.length, 2);
+describe('import measures', function() {
+  it('should create new measures and ignore duplicate measureIds', () => {
+    const measures = runTest(testMeasures, testCsv);
+    assert.equal(measures.length, 2);
   });
 
   it('should overwrite fields with the right csv data', () => {
-    const newMeasures = runTest(testCsv);
+    const measures = runTest(testMeasures, testCsv);
     expectedMeasures.forEach(function(expectedMeasure, measureIdx) {
       Object.entries(expectedMeasure).forEach(function([measureKey, measureValue]) {
-        assert.deepEqual(newMeasures[measureIdx][measureKey], measureValue);
+        assert.deepEqual(measures[measureIdx][measureKey], measureValue);
       });
@@ -40,5 +50,25 @@ });
     // assert.throws expects a function as its first parameter
-    const errFunc = () => { runTest(testCsv2Cols); };
+    const errFunc = () => {
+      runTest(testMeasures, testCsv2Cols);
+    };
     assert.throws(errFunc, Error, errorMessage);
   });
+
+  it('throws an informative error when a value in the qcdr csv for an existing ' +
+    'measureId conflicts with an existing measure', function() {
+    const errorMessage = /conflicts with existing measure/;
+    // assert.throws expects a function as its first parameter
+    const errFunc = () => {
+      runTest(testMeasures2, testCsv);
+    };
+    assert.throws(errFunc, Error, errorMessage);
+  });
 });
+
+after(function() {
+  try {
+    fs.unlinkSync(path.join(__dirname, output));
+  } catch (err) {
+    console.log('Warning: ', output, ' should have been deleted but was not.');
+  }
+});

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Found 1 instance in 1 package

Fixed alerts

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Improved metrics

Total package byte prevSize

5734100

increased by77.86%

Number of package files

67

increased by4.69%

Lines of code

53734

increased by42.89%

Worsened metrics

Number of low supply chain risk alerts

15

increased by15.38%

No dependency changes