Merge pull request #13 in LFOR/fhirpath.js from feature/LF-1485/updat…

…e-test-converter to master * commit 'ed74194ff0c1ecc4d74871eb9e4388134c21f647': Update FHIRPath test converter Update FHIRPath test converter Update FHIRPath test converter
HL7 · Jun 9, 2020 · 01c7e18 · 01c7e18
2 parents 8da56ba + ed74194
commit 01c7e18
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,6 +3,10 @@
 This log documents significant changes for each release.  This project follows
 [Semantic Versioning](http://semver.org/).
 
+## [2.2.2] - 2020-06-05
+### Fixed
+- Updated FHIRPath test cases
+
 ## [2.2.1] - 2020-06-03
 ### Fixed
 - Issue with substring function without a second parameter

diff --git a/converter/README.md b/converter/README.md
@@ -1,14 +1,13 @@
 # FHIR-r4 test converter
 
-CLI-tool for converting fhirpath [XML test cases](https://github.com/hl7-fhir/fhir-svn/blob/master/tests/resources/tests-fhir-r4.xml)
-into fhirpath.js yaml test cases format.
+CLI-tool for converting fhirpath [XML test cases](https://github.com/HL7/FHIRPath/tree/master/tests/r4/)
+into fhirpath.js yaml test cases format with json resource files.
 
 ### Installing:
 ```npm ci```
 
-
-### Convert test file:
-```converter/bin/index.js converter/dataset/fhir-r4.xml(path to xml file)  converter/dataset/tests-r4.yaml(path to save result data)```
+### Download and convert test file and resource files:
+```converter/bin/index.js```
 
 ### Converter test in whole test scope:
 ```npm run test```
diff --git a/converter/bin/index.js b/converter/bin/index.js
@@ -1,12 +1,74 @@
 #! /usr/bin/env node
 
+// Directory for downloading XML source files
+const sourceDir = __dirname + '/../dataset/';
+// Directory for converter output(for YAML and JSON files)
+const destDir = __dirname + '/../../test/';
+
+// Descriptions for file generation:
+// [<relative path to XML source file>, <relative path to YAML/JSON output file>, <download URL>]
+const sources = [
+  ['fhir-r4.xml', 'cases/fhir-r4.yaml', 'https://raw.githubusercontent.com/HL7/FHIRPath/master/tests/r4/tests-fhir-r4.xml'],
+  ['input/observation-example.xml', 'resources/observation-example.json', 'https://raw.githubusercontent.com/HL7/FHIRPath/master/tests/r4/input/observation-example.xml'],
+  ['input/patient-example.xml', 'resources/patient-example.json', 'https://raw.githubusercontent.com/HL7/FHIRPath/master/tests/r4/input/patient-example.xml'],
+  ['input/questionnaire-example.xml', 'resources/questionnaire-example.json', 'https://raw.githubusercontent.com/HL7/FHIRPath/master/tests/r4/input/questionnaire-example.xml'],
+  ['input/valueset-example-expansion.xml', 'resources/valueset-example-expansion.json', 'https://raw.githubusercontent.com/HL7/FHIRPath/master/tests/r4/input/valueset-example-expansion.xml']
+];
+
 const commander = require('commander');
-const run = require('../index');
+const convert = require('../index');
+
+const https = require('https');
+const fs = require('fs');
+
+function downloadFile(url, dest) {
+  return new Promise((resolve, reject) => {
+    const file = fs.createWriteStream(dest);
+    https.get(url, function(res) {
+      const { statusCode } = res;
+
+      if (statusCode !== 200) {
+        // Consume response data to free up memory
+        res.resume();
+        reject(`Failed to download ${url}.\n` +
+          `Status Code: ${statusCode}`);
+      } else {
+        res.pipe(file);
+        file.on('finish', function () {
+          resolve();
+        });
+      }
+    });
+  });
+}
 
 commander
-  .arguments('<path_from> <path_to>')
-  .description('Convert xml test cases to yaml')
-  .action(async (from, to) =>
-    await run(from, to))
+  .option('-s, --skip-download', 'skip downloading sources from FHIRPath repository')
+  .description('Convert xml test cases/resources to yaml/json')
+  .action(async (cmd) => {
+    try {
+      if (!cmd.skipDownload) {
+        for (let i = 0; i < sources.length; i++) {
+          const [xmlFilename,, url] = sources[i];
+          await downloadFile(url, sourceDir + xmlFilename);
+        }
+      }
+
+      const resourceFiles = sources.filter(([,target]) => target.endsWith('.json'));
+      const testFiles = sources.filter(([,target]) => target.endsWith('.yaml'));
+
+      for (let i = 0; i < resourceFiles.length; i++) {
+        const [xmlFilename, jsonFilename] = resourceFiles[i];
+        await convert.resourceXmlFileToJsonFile(sourceDir + xmlFilename, destDir + jsonFilename);
+      }
+
+      for (let i = 0; i < testFiles.length; i++) {
+        const [xmlFilename, yamlFilename] = testFiles[i];
+        await convert.testsXmlFileToYamlFile(sourceDir + xmlFilename, destDir + yamlFilename);
+      }
+    } catch(e) {
+      console.error(e);
+    }
+  })
   .parse(process.argv);
 
diff --git a/converter/converter.js b/converter/converter.js
@@ -4,15 +4,44 @@ const _ = require('lodash');
 const xml2js = require('xml2js');
 const yaml = require('js-yaml');
 
-module.exports = async (xmlData) => {
-  const parser = new xml2js.Parser({ explicitCharkey: true });
-  const parseString = util.promisify(parser.parseString);
+const fhir = new (require('fhir').Fhir);
+const fhirpath = require('../src/fhirpath');
+const { getFHIRModel, calcExpression } = require("../test/test_utils");
+const FP_DateTime = require('../src/types').FP_DateTime;
+const equals = _.isEqual;
 
-  const parsed = await parseString(xmlData);
-  const transformed = transform(parsed);
-  const formatted = yaml.dump(transformed);
-  return formatted;
-};
+/**
+ * Validates a test to determine whether to disable it
+ * @param {Object} test
+ * @return {boolean}
+ */
+function validateTest(test) {
+  if (!test.error && test.expression) {
+    try {
+      const result = calcExpression(test.expression, test);
+      // Run the result through JSON so the FP_Type quantities get converted to
+      // strings.  Also , if the result is an FP_DateTime, convert to a Date
+      // object so that timezone differences are handled.
+      if (result.length === 1 && result[0] instanceof FP_DateTime)
+        return equals(new Date(result[0]), new Date(test.result[0]));
+      else
+        return equals(JSON.parse(JSON.stringify(result)), test.result);
+    } catch (e) {
+      return false;
+    }
+  }
+  else if (test.error) {
+    let exception = null;
+    try {
+      fhirpath.evaluate({}, test.expression, null,
+        getFHIRModel(test.model));
+    }
+    catch (error) {
+      exception = error;
+    }
+    return exception !== null;
+  }
+}
 
 const mapper = {
   boolean: (v) => v === 'true',
@@ -25,24 +54,38 @@ const mapper = {
 
 const castValue = (value, type) => mapper[type](value);
 
+/**
+ * Converts Object representing test cases from XML to Object that can be serialized to YAML
+ * @param {Object} node - result of xml2js.parseString
+ * @return {Object}
+ */
 const transform = (node) => {
 
   return Object.keys(node).reduce((acc, key) => {
 
     switch(key) {
       case 'tests':
-        return { tests: transform(node[key]) };
+        return { tests: transform(_.pick(node[key], 'group')) };
 
       case 'group':
         return [...acc, ...node[key].map(item =>
-          ({ [`group: ${item['$'].name}`]: transform(_.pick(item, 'test')) }))];
+          ({ [`group: ${item['$'].description || item['$'].name}`]: transform(_.pick(item, 'test')) }))];
 
       case 'test':
-        return [...acc, ...node[key].map(item => transform(item))];
+        return [...acc, ...node[key].map(item => {
+          let test = transform(item);
+          if (!test.hasOwnProperty('result') && !test.error) {
+            test.result = [];
+          }
+          if (!validateTest(test)) {
+            test.disable = true;
+          }
+          return test;
+        })];
 
       case '$': {
         const value = node[key];
-        const updated = { desc: `** ${node[key].name || 'test'}` };
+        const updated = { desc: `** ${node[key].description || node[key].name || 'test'}` };
         if (_.has(value, 'inputfile')) {
           updated.inputfile = value.inputfile.replace(/.xml$/, '.json');
         }
@@ -64,3 +107,35 @@ const transform = (node) => {
     }
   }, []);
 };
+
+module.exports = {
+  /**
+   * Serializes an XML resource to JSON
+   * @param {string} xmlData
+   * @returns {string}
+   */
+  resourceXmlStringToJsonString: async (xmlData) => {
+    return fhir.xmlToJson(xmlData).replace(/\t/g, '  ');
+  },
+  /**
+   * Serializes an XML test cases to YAML
+   * @param {string} xmlData
+   * @returns {string}
+   */
+  testsXmlStringToYamlString: async (xmlData) => {
+    const parser = new xml2js.Parser({ explicitCharkey: true });
+    const parseString = util.promisify(parser.parseString);
+
+    const parsed = await parseString(xmlData);
+    const transformed = transform(parsed);
+    transformed.tests.forEach(group => {
+      const groupKey = Object.keys(group)[0];
+      const groupTests = group[groupKey];
+      if (groupTests.some(test => test.disable) && groupTests.every(test => test.disable || test.error)) {
+        group.disable = true;
+        groupTests.forEach(test => delete test.disable);
+      }
+    });
+    return yaml.dump(transformed);
+  }
+};