Merge pull request #39 from onemedical/CHIRP-930/fix-gender-sex

CHIRP-930 fix birthsex value

.editorconfig

@@ -0,0 +1,15 @@
+# editorconfig.org
+
+root = true
+
+[*]
+charset = utf-8
+end_of_line = lf
+indent_size = 4
+indent_style = space
+max_line_length = 120
+insert_final_newline = true
+trim_trailing_whitespace = true
+
+[*.{diff,md,mdx}]
+trim_trailing_whitespace = false

.gitignore

@@ -1,78 +1,80 @@
-# Logs
-logs
-*.log
-npm-debug.log*
-yarn-debug.log*
-yarn-error.log*
-
-# Runtime data
-pids
-*.pid
-*.seed
-*.pid.lock
-
-# Directory for instrumented libs generated by jscoverage/JSCover
-lib-cov
-
-# Coverage directory used by tools like istanbul
-coverage
-!/src/**/Coverage
-
-# nyc test coverage
-.nyc_output
-.test_output
-
-# Grunt intermediate storage (http://gruntjs.com/creating-plugins#storing-task-files)
-.grunt
-
-# Bower dependency directory (https://bower.io/)
-bower_components
-
-# node-waf configuration
-.lock-wscript
-
-# Compiled binary addons (https://nodejs.org/api/addons.html)
-build/Release
-
-# Dependency directories
-node_modules/
-jspm_packages/
-
-# TypeScript v1 declaration files
-typings/
-
-# Optional npm cache directory
-.npm
-
-# Optional eslint cache
-.eslintcache
-
-# Optional REPL history
-.node_repl_history
-
-# Output of 'npm pack'
-*.tgz
-!hl7.fhir.r4.core-4.0.1.tgz
-
-# Yarn Integrity file
-.yarn-integrity
-
-# dotenv environment variables file
-.env
-
-# next.js build output
-.next
-
-# test temp data
-.temp*
-
-# app runtime data
-service-templates
-tmp/
-
-# autogen files
-src/lib/outputProcessor/autogen/*.interp
-src/lib/outputProcessor/autogen/*.tokens
-
-.idea
-*.DS_Store
+.DS_Store
+
+# Logs
+logs
+*.log
+npm-debug.log*
+yarn-debug.log*
+yarn-error.log*
+
+# Runtime data
+pids
+*.pid
+*.seed
+*.pid.lock
+
+# Directory for instrumented libs generated by jscoverage/JSCover
+lib-cov
+
+# Coverage directory used by tools like istanbul
+coverage
+!/src/**/Coverage
+
+# nyc test coverage
+.nyc_output
+.test_output
+
+# Grunt intermediate storage (http://gruntjs.com/creating-plugins#storing-task-files)
+.grunt
+
+# Bower dependency directory (https://bower.io/)
+bower_components
+
+# node-waf configuration
+.lock-wscript
+
+# Compiled binary addons (https://nodejs.org/api/addons.html)
+build/Release
+
+# Dependency directories
+node_modules/
+jspm_packages/
+
+# TypeScript v1 declaration files
+typings/
+
+# Optional npm cache directory
+.npm
+
+# Optional eslint cache
+.eslintcache
+
+# Optional REPL history
+.node_repl_history
+
+# Output of 'npm pack'
+*.tgz
+!hl7.fhir.r4.core-4.0.1.tgz
+
+# Yarn Integrity file
+.yarn-integrity
+
+# dotenv environment variables file
+.env
+
+# next.js build output
+.next
+
+# test temp data
+.temp*
+
+# app runtime data
+service-templates
+tmp/
+
+# autogen files
+src/lib/outputProcessor/autogen/*.interp
+src/lib/outputProcessor/autogen/*.tokens
+
+.idea
+*.DS_Store

.node-version

@@ -1 +1 @@
-14.19.3
+14.21.3

.prettierrc

@@ -0,0 +1,4 @@
+{
+  "printWidth": 120,
+  "tabWidth": 4
+}

.vscode/launch.json

@@ -0,0 +1,17 @@
+{
+  // Use IntelliSense to learn about possible attributes.
+  // Hover to view descriptions of existing attributes.
+  // For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387
+  "version": "0.2.0",
+  "configurations": [
+    {
+      "name": "Attach",
+      "port": 9229,
+      "request": "attach",
+      "skipFiles": [
+        "<node_internals>/**"
+      ],
+      "type": "node"
+    }
+  ]
+}

README.md

@@ -109,3 +109,10 @@ provided by the bot. You will only need to do this once across all repos using o
 This project has adopted the [Microsoft Open Source Code of Conduct](https://opensource.microsoft.com/codeofconduct/).
 For more information see the [Code of Conduct FAQ](https://opensource.microsoft.com/codeofconduct/faq/) or
 contact [[email protected]](mailto:[email protected]) with any additional questions or comments.
+
+## M2 Macs
+
+```shell
+arch -x86_64 zsh
+nodenv install 14.21.3
+```

src/convert-xml-to-fhir-resource.js

@@ -4,10 +4,14 @@ const WorkerPool = require("./lib/workers/workerPool");
 function createAndUploadFhirResource()  {
     let filePath, newPath;
     const generateChirpTestFile = process.argv.slice(2)[0] == '--chirp-test-file';
+    const filePathArg = process.argv.slice(2).find(value => /^--filePath=/.test(value));
 
     if (generateChirpTestFile) {
         filePath = "src/sample-data/cda/Chirp_CCD.cda";
         newPath = "test/e2e-test/regression-test/data/cda/ccd.hbs/ccd.hbs-Chirp_CCD.cda.json";
+    } else if(filePathArg) {
+        filePath = filePathArg.split("=")[1].trim();
+        newPath = filePath.replace(".xml", "--FHIR-RESOURCE.json");
     } else {
         if ((process.env.npm_config_filepath || '') === '') {
             console.log("Must specify file path");

src/lib/handlebars-converter/handlebars-helpers.js

@@ -643,35 +643,56 @@ module.exports.external = [
             }
         }
     },
-
     {
         name: 'getBirthSexInfo',
         description: "Returns first instance of birthSex id e.g. getBirthSexInfo msg '2.16.840.1.113883.10.20.22.2.14'",
+        // FIXME: (anti-pattern) the arrow pattern here has been slightly improved but is still really bad
+        // FIXME: (code smell) long method - the function is way too long, but the structure of this file is terrible
+        // there isn't an obvious way to extract a method without introducing a new pattern and that's not the goal here
         func: function getBirthSexInfo(msg, templateId) {
             try {
-                var birthSexValue ;
+                var birthSexValue;
                 let structuredBody = msg.ClinicalDocument.component.structuredBody;
-                if(structuredBody && structuredBody.component) {
-                    for(var i=0; i< structuredBody.component.length; i++) {
-                        let sectionObj = structuredBody.component[i].section;
-                        if(sectionObj && sectionObj.templateId && JSON.stringify(sectionObj.templateId).includes('2.16.840.1.113883.10.20.22.2.17')){
-                            let entryObjs = sectionObj.entry;
-                            for(var j=0; j < entryObjs.length; j++) {
-                                let entryObj = entryObjs[j];
-                                if(entryObj){
-                                    let observation = entryObj.observation;
-                                    if(observation && observation.templateId && JSON.stringify(observation.templateId).includes(templateId)){
-                                        birthSexValue = observation.value.code;
-                                        break;
-                                    }
-                                }
+
+                // return undefined when there is no structured body component
+                if (!structuredBody || !structuredBody.component) return birthSexValue;
+
+                sectionLoop: for (var i = 0; i < structuredBody.component.length; i++) {
+                    let sectionObj = structuredBody.component[i].section;
+                    if (!sectionObj || !sectionObj.templateId) continue;
+                    if (!JSON.stringify(sectionObj.templateId).includes("2.16.840.1.113883.10.20.22.2.17")) continue;
+
+                    if (Array.isArray(sectionObj.entry)) {
+                        let entries = sectionObj.entry;
+                        for (var j = 0; j < entries.length; j++) {
+                            let entry = entries[j];
+                            if (!entry) continue;
+
+                            let observation = entry.observation;
+                            if (
+                                observation &&
+                                observation.templateId &&
+                                JSON.stringify(observation.templateId).includes(templateId)
+                            ) {
+                                birthSexValue = observation.value.code;
+                                break sectionLoop;
                             }
                         }
+                    } else {
+                        let entry = sectionObj.entry;
+                        if (
+                            entry &&
+                            entry.observation &&
+                            entry.observation.templateId &&
+                            JSON.stringify(entry.observation.templateId).includes(templateId)
+                        ) {
+                            birthSexValue = entry.observation.value.code;
+                            break sectionLoop;
+                        }
                     }
                 }
                 return birthSexValue;
-            }
-            catch (err) {
+            } catch (err) {
                 throw `helper "getBirthSexInfo" : ${err}`;
             }
         }

src/templates/cda/Resources/Patient.hbs

@@ -50,14 +50,14 @@
                         [
                           	{
                                	"system":"urn:ietf:bcp:47",
-                               	"code":"{{this.languageCode.code}}", 
+                               	"code":"{{this.languageCode.code}}",
                                 "display":{{>ValueSet/Language.hbs code=this.languageCode.code}},
                             },
                         ],
-                    },           
+                    },
                 	"preferred":{{this.preferenceInd.value}},
                 },
-            {{/each}}         
+            {{/each}}
         ],
     },
     "request":{