Merge pull request #52 in LFOR/fhirpath.js from feature/LF-2586/add-version-R5-support to master

* commit 'abadcceedd68770958130401590a9c3261494339':
  npm audit fix
  Updated version in package-lock.json
  Minor changes
  LInux case sensitivity on the output parameter in the upgrade guidance
  Include additional guidance on the version upgrade process
  Update the package version and changelog
  Missed including the min.r5.js file from the build step
  Unit test the R5 Observation model and various other updates to support building the content also.
  #137 Add support for FHIR R5

Author: yuriy-sedinkin

CHANGELOG.md

@@ -3,6 +3,10 @@
 This log documents significant changes for each release.  This project follows
 [Semantic Versioning](http://semver.org/).
 
+## [3.4.0] - 2023-04-26
+### Added
+- support for FHIR R5 publication.
+
 ## [3.3.2] - 2023-03-29
 ### Fixed
 - toQuantity() now works with subclasses of Quantity.

README.md

@@ -260,6 +260,39 @@ npm install && npm run build && npm run start
 
 open browser on localhost:8080
 
+### Updating the FHIR module on a FHIR release
+* Download the FHIR StructureDefinitions (into the `fhir-context` directory - *don't check these in*)
+  ```
+  > wget http://hl7.org/fhir/profiles-types.json -O profiles-types.json
+  > wget http://hl7.org/fhir/profiles-others.json -O profiles-others.json
+  > wget http://hl7.org/fhir/profiles-resources.json -O profiles-resources.json
+  ```
+* Create the new folder for the version you are importing
+  ```
+  > mkdir r5
+  ```
+* Run the script `` with NodeJS
+  ```
+  > node ./extract-model-info.js --outputDir r5 --fhirDefDir .
+  ```
+* Compare the output files in the new folder to those of the last release
+  (looking for issues that might be due to changes in the StructureDefinition format)
+* Copy the `index.js` file from the last release into the new folder
+  ```
+  > cp ../r4/index.js r5
+  ```
+* Update the `/index.d.ts` file to include the new module as an export
+  ``` js
+  declare module "fhirpath/fhir-context/r5" {
+    export const {
+      choiceTypePaths,
+      pathsDefinedElsewhere,
+      type2Parent,
+      path2Type
+    }: Model;
+  }
+  ```
+
 ## Credits
 This implemention of the FHIRPath specification was developed as a joint project
 between the U.S. National Library of Medicine (NLM) and Health Samurai, and was

bin/fhirpath

@@ -10,7 +10,7 @@ options.option('-e, --expression <expr>', 'FHIRPath expression.');
 options.option('-f, --resourceFile <path name>', 'A file containing the JSON resource or part of it, if basePath is passed.');
 options.option('-r, --resourceJSON <JSON>', 'JSON resource or part of it, if basePath is passed.');
 options.option('-v, --variables <JSON>', 'JSON hash of variables.');
-options.option('-m, --model <dstu2 | stu3 | r4>', 'Include FHIR model data.');
+options.option('-m, --model <dstu2 | stu3 | r4 | r5>', 'Include FHIR model data.');
 options.parse(process.argv);
 
 // this cli util is part of public interface of fhirpath
@@ -42,7 +42,7 @@ else {
     let resource = JSON.parse(resourceJSON);
     let model;
     if (options.model) {
-      let supportedVersions = ['dstu2', 'stu3', 'r4'];
+      let supportedVersions = ['dstu2', 'stu3', 'r4', 'r5'];
       if (supportedVersions.indexOf(options.model) < 0)
         throw new Error('FHIR model must be one of '+supportedVersions);
       model = require('../fhir-context/'+options.model);

browser-build/test/index.html

@@ -25,10 +25,12 @@
 <textarea id="result"></textarea>
 <br>
 FHIR model:
+<input id="r5" name="model" type="radio" value="r5" onclick="evaluateFP()"> R5
 <input id="r4" name="model" type="radio" value="r4" onclick="evaluateFP()"> R4
 <input id="stu3" name="model" type="radio" value="stu3" onclick="evaluateFP()"> STU3
 <input id="dstu2" name="model" type="radio" value="dstu2" onclick="evaluateFP()"> DSTU2
 <script src="../fhirpath.min.js"></script>
+<script src="../fhirpath.r5.min.js"></script>
 <script src="../fhirpath.r4.min.js"></script>
 <script src="../fhirpath.stu3.min.js"></script>
 <script src="../fhirpath.dstu2.min.js"></script>
@@ -39,6 +41,7 @@
   var modelChoices = document.getElementsByName('model');
   var model;
   var models = {
+    r5: fhirpath_r5_model,
     r4: fhirpath_r4_model,
     stu3: fhirpath_stu3_model,
     dstu2: fhirpath_dstu2_model

browser-build/webpack.config.js

@@ -63,7 +63,7 @@ config.plugins = [
 module.exports.push(config);
 
 // FHIR model files
-for (let fhirVers of ['dstu2', 'stu3', 'r4']) {
+for (let fhirVers of ['dstu2', 'stu3', 'r4', 'r5']) {
   config = makeBaseConfig();
   config.entry = '../fhir-context/'+fhirVers+'/index';
   config.output.filename = './fhirpath.'+fhirVers+'.min.js';

converter/converter.js

@@ -57,7 +57,7 @@ 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'
+ * @param {string} model - model name, e.g. 'r5', 'r4','stu3', 'dstu2'
  * @return {Object}
  */
 const transform = (node, model = null) => {
@@ -127,7 +127,7 @@ module.exports = {
   /**
    * Serializes an XML test cases to YAML
    * @param {string} xmlData
-   * @param {string} model - model name, e.g. 'r4','stu3', 'dstu2'
+   * @param {string} model - model name, e.g. 'r5', 'r4','stu3', 'dstu2'
    * @returns {string}
    */
   testsXmlStringToYamlString: async (xmlData, model) => {

converter/index.js

@@ -22,7 +22,7 @@ module.exports = {
    * 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'
+   * @param {string} model - model name, e.g. 'r5', 'r4','stu3', 'dstu2'
    */
   testsXmlFileToYamlFile: async (from, to, model) => {
     const xmlData = await readFile(from);

fhir-context/extract-model-info.js

@@ -1,4 +1,4 @@
-// Takes a directory of JSON FHIR definitions (DSTU2, STU3 or R4) and extracts the information
+// Takes a directory of JSON FHIR definitions (DSTU2, STU3, R4 or R5) and extracts the information
 // about "choice types" (polymorphic fields).
 
 const path = require('path');