Merge remote-tracking branch 'nlm/master' into bugfix/ts-import

Author: yuriy-sedinkin

CHANGELOG.md

@@ -3,6 +3,12 @@
 This log documents significant changes for each release.  This project follows
 [Semantic Versioning](http://semver.org/).
 
+## [2.6.0] - 2020-09-01
+### Added
+Limited support for types (see README.md for details):
+- Function is(type) and operator "is"
+- Function ofType(type)
+
 ## [2.5.0] - 2020-08-26
 ### Added
 - Function union(other: collection)

README.md

@@ -125,9 +125,9 @@ some behavior may still be following the previous version, STU1.
 The core parser was generated from the FHIRPath ANTLR grammar.
 
 Completed sections:
-- 3 (Path selection) - except that "is" and "as" are not supported yet
+- 3 (Path selection)
 - 5.1 (Existence)
-- 5.2 (Filtering and Projection) "ofType" - basic support for primitives
+- 5.2 (Filtering and Projection) "ofType" - limited support for types (see below)
 - 5.3 (Subsetting)
 - 5.4 (Combining)
 - 5.6 (String Manipulation)
@@ -149,13 +149,23 @@ Almost completed sections:
 We are deferring handling information about FHIR resources, as much as
 possible, with the exception of support for choice types.  This affects
 implementation of the following sections:
-- 6.3 (Types) - deferred
+- 6.3 (Types) - "is" - limited support for types(see below),
+                "as" is not supported yet
 
 Also, because in JSON DateTime and Time types are represented as strings, if a
 string in a resource looks like a DateTime or Time (matches the regular
 expression defined for those types in FHIR), the string will be interpreted as a
 DateTime or Time.
 
+### Limited support for types:
+Currently, the type of the resource property value is used to determine the type,
+without using the FHIR specification. This shortcut causes the following issues:
+- Type hierarchy is not supported;
+- FHIR.uri, FHIR.code, FHIR.oid, FHIR.id, FHIR.uuid, FHIR.sid, FHIR.markdown, FHIR.base64Binary are treated as FHIR.string;
+- FHIR.unsignedInt, FHIR.positiveInt are treated as FHIR.integer;
+- Also, a property could be specified as FHIR.decimal, but treated as FHIR.integer;
+- For date-time related types, only FHIR.dateTime, FHIR.time, System.DateTime and System.Time are supported.
+
 ## Development Notes
 
 This section is for people doing development on this package (as opposed to

converter/bin/index.js

@@ -5,6 +5,8 @@ const sourceDir = __dirname + '/../dataset/';
 // Directory for converter output(for YAML and JSON files)
 const destDir = __dirname + '/../../test/';
 
+// FHIR model used for test cases
+const model = 'r4';
 // Descriptions for file generation:
 // [<relative path to XML source file>, <relative path to YAML/JSON output file>, <download URL>]
 const sources = [
@@ -64,7 +66,7 @@ commander
 
       for (let i = 0; i < testFiles.length; i++) {
         const [xmlFilename, yamlFilename] = testFiles[i];
-        await convert.testsXmlFileToYamlFile(sourceDir + xmlFilename, destDir + yamlFilename);
+        await convert.testsXmlFileToYamlFile(sourceDir + xmlFilename, destDir + yamlFilename, model);
       }
     } catch(e) {
       console.error(e);

converter/converter.js

@@ -57,28 +57,35 @@ 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
+ * @param {string} model - model name, e.g. 'r4','stu3', 'dstu2'
  * @return {Object}
  */
-const transform = (node) => {
+const transform = (node, model = null) => {
 
   return Object.keys(node).reduce((acc, key) => {
 
     switch(key) {
       case 'tests':
-        return { tests: transform(_.pick(node[key], 'group')) };
+        return { tests: transform(_.pick(node[key], 'group'), model) };
 
       case 'group':
         return [...acc, ...node[key].map(item =>
-          ({ [`group: ${item['$'].description || item['$'].name}`]: transform(_.pick(item, 'test')) }))];
+          ({ [`group: ${item['$'].description || item['$'].name}`]: transform(_.pick(item, 'test'), model) }))];
 
       case 'test':
         return [...acc, ...node[key].map(item => {
-          let test = transform(item);
+          let test = transform(item, model);
           if (!test.hasOwnProperty('result') && !test.error) {
             test.result = [];
           }
           if (!validateTest(test)) {
-            test.disable = true;
+            if (model && validateTest(Object.assign({}, test, { model }))) {
+              // if the test cannot be passed without set the model, we set the model
+              test.model = model;
+            } else {
+              // if the test cannot be passed at all, we disable it
+              test.disable = true;
+            }
           }
           return test;
         })];
@@ -120,14 +127,15 @@ module.exports = {
   /**
    * Serializes an XML test cases to YAML
    * @param {string} xmlData
+   * @param {string} model - model name, e.g. 'r4','stu3', 'dstu2'
    * @returns {string}
    */
-  testsXmlStringToYamlString: async (xmlData) => {
+  testsXmlStringToYamlString: async (xmlData, model) => {
     const parser = new xml2js.Parser({ explicitCharkey: true });
     const parseString = util.promisify(parser.parseString);
 
     const parsed = await parseString(xmlData);
-    const transformed = transform(parsed);
+    const transformed = transform(parsed, model);
     transformed.tests.forEach(group => {
       const groupKey = Object.keys(group)[0];
       const groupTests = group[groupKey];

converter/index.js

@@ -6,14 +6,27 @@ const readFile = util.promisify(fs.readFile);
 const writeFile = util.promisify(fs.writeFile);
 
 module.exports = {
+  /**
+   * Converts XML resource to the YAML format
+   * @param {string} from - path to XML file
+   * @param {string} to - path to YAML file
+   */
   resourceXmlFileToJsonFile: async (from, to) => {
     const xmlData = await readFile(from);
     const ymlData = await convert.resourceXmlStringToJsonString(xmlData);
     await writeFile(to, ymlData);
   },
-  testsXmlFileToYamlFile: async (from, to) => {
+
+
+  /**
+   * Converts XML test cases to the YAML format
+   * @param {string} from - path to XML file
+   * @param {string} to - path to YAML file
+   * @param {string} model - model name, e.g. 'r4','stu3', 'dstu2'
+   */
+  testsXmlFileToYamlFile: async (from, to, model) => {
     const xmlData = await readFile(from);
-    const ymlData = await convert.testsXmlStringToYamlString(xmlData);
+    const ymlData = await convert.testsXmlStringToYamlString(xmlData, model);
     await writeFile(to, ymlData);
   }
 };

package-lock.json

@@ -1,6 +1,6 @@
 {
   "name": "fhirpath",
-  "version": "2.5.0",
+  "version": "2.6.0",
   "description": "A FHIRPath engine",
   "main": "src/fhirpath.js",
   "dependencies": {
@@ -15,7 +15,7 @@
     "@babel/preset-env": "^7.5.5",
     "babel-eslint": "^9.0.0",
     "babel-loader": "^8.0.6",
-    "bestzip": "^2.1.4",
+    "bestzip": "^2.1.7",
     "copy-webpack-plugin": "^6.0.3",
     "eslint": "^5.2.0",
     "fhir": "^4.7.10",