Add configuration to support including both uri and oid when parsing …

…valuesets (#31)

Squashed commits from PR #31:

* feat: add initial support for oid and url

* fix: refactor the logic

* fix: spelling mistake

* fix: remove unused option for fhir

* style: fix lint

* fix: update to a better option name and value

* fix: default option should be url when empty options passed

---------

Co-authored-by: Tyler J Cvetan <[email protected]>

src/CodeService.js

@@ -77,7 +77,8 @@ class CodeService {
   async ensureValueSetsWithAPIKey(
     valueSetList = [],
     umlsAPIKey = env['UMLS_API_KEY'],
-    caching = true
+    caching = true,
+    options = { svsCodeSystemType: 'url' }
   ) {
     // First, filter out the value sets we already have
     const filteredVSList = valueSetList.filter(vs => {
@@ -112,7 +113,7 @@ class CodeService {
         // Catch errors and convert to resolutions returning an error.  This ensures Promise.all waits for all promises.
         // See: http://stackoverflow.com/questions/31424561/wait-until-all-es6-promises-complete-even-rejected-promises
         return this.api
-          .downloadValueSet(umlsAPIKey, oid, version, output, this.valueSets, caching)
+          .downloadValueSet(umlsAPIKey, oid, version, output, this.valueSets, caching, options)
           .catch(err => {
             debug(
               `Error downloading valueset ${oid}${version != null ? ` version ${version}` : ''}`,
@@ -151,10 +152,11 @@ class CodeService {
     library,
     checkIncluded = true,
     umlsAPIKey = env['UMLS_API_KEY'],
-    caching = true
+    caching = true,
+    options = { svsCodeSystemType: 'url' }
   ) {
     const valueSets = extractSetOfValueSetsFromLibrary(library, checkIncluded);
-    return this.ensureValueSetsWithAPIKey(Array.from(valueSets), umlsAPIKey, caching);
+    return this.ensureValueSetsWithAPIKey(Array.from(valueSets), umlsAPIKey, caching, options);
   }
 
   /**

src/fhir.js

@@ -4,7 +4,17 @@ const fetch = require('node-fetch');
 const debug = require('debug')('vsac'); // To turn on DEBUG: $ export DEBUG=vsac
 const { Code, ValueSet } = require('cql-execution');
 
-async function downloadValueSet(apiKey, oid, version, output, vsDB = {}, caching = true) {
+async function downloadValueSet(
+  apiKey,
+  oid,
+  version,
+  output,
+  vsDB = {},
+  caching = true,
+  options = {
+    /* reserved for future use */
+  }
+) {
   const pages = await getValueSetPages(apiKey, oid, version);
   if (pages == null || pages.length === 0) {
     return;

src/svs.js

@@ -6,37 +6,56 @@ const debug = require('debug')('vsac'); // To turn on DEBUG: $ export DEBUG=vsac
 const { Code, ValueSet } = require('cql-execution');
 const vsacCS = require('./vsac-code-systems');
 
-async function downloadValueSet(apiKey, oid, version, output, vsDB = {}, caching = true) {
+async function downloadValueSet(
+  apiKey,
+  oid,
+  version,
+  output,
+  vsDB = {},
+  caching = true,
+  options = { svsCodeSystemType: 'url' }
+) {
   debug(`Getting ValueSet: ${oid}${version != null ? ` version ${version}` : ''}`);
   const params = new URLSearchParams({ id: oid });
   if (version != null) {
     params.append('version', version);
   }
-  const options = {
+  const requestOptions = {
     headers: {
       Authorization: `Basic ${Buffer.from(`apikey:${apiKey}`).toString('base64')}`
     }
   };
   const response = await fetch(
     `https://vsac.nlm.nih.gov/vsac/svs/RetrieveValueSet?${params}`,
-    options
+    requestOptions
   );
   if (!response.ok) {
     throw new Error(response.status);
   }
   const data = await response.text();
-  parseVSACXML(data, vsDB);
+  parseVSACXML(data, vsDB, options);
   if (caching) {
     const file = path.join(output, `${oid}.xml`);
     await fs.writeFile(file, data);
     return file;
   }
 }
 
+function getVSACCodeSystem(codeSystems, system) {
+  if (
+    typeof codeSystems[system] !== 'undefined' &&
+    typeof codeSystems[system].uri !== 'undefined'
+  ) {
+    return codeSystems[system];
+  }
+
+  return null;
+}
+
 // Take in a string containing a string of the XML response from a VSAC SVS
 // response and parse it into a vsDB object.  This code makes strong
 // assumptions about the structure of the message.  See code below.
-function parseVSACXML(xmlString, vsDB = {}) {
+function parseVSACXML(xmlString, vsDB = {}, options = { svsCodeSystemType: 'url' }) {
   if (typeof xmlString === 'undefined' || xmlString == null || xmlString.trim().length == 0) {
     return;
   }
@@ -59,16 +78,31 @@ function parseVSACXML(xmlString, vsDB = {}) {
   // Loop over the codes and build the JSON.
   const codeList = [];
   for (let concept in conceptList) {
-    let system;
-    const systemOID = conceptList[concept]['$']['codeSystem'];
-    if (typeof vsacCS[systemOID] !== 'undefined' && typeof vsacCS[systemOID].uri !== 'undefined') {
-      system = vsacCS[systemOID].uri;
+    let system = conceptList[concept]['$']['codeSystem'];
+    const code = conceptList[concept]['$']['code'];
+    const version = conceptList[concept]['$']['codeSystemVersion'];
+    const systemOid = `urn:oid:${system}`;
+    const systemUri = getVSACCodeSystem(vsacCS, system);
+
+    if (options.svsCodeSystemType === 'oid') {
+      // Keep the oid system as is
+      system = systemOid;
+    } else if (options.svsCodeSystemType === 'both') {
+      // Optionally include both if they exist
+      if (systemUri !== null) {
+        codeList.push({ code, system: systemUri.uri, version });
+      }
+      // Include the standard oid system
+      system = systemOid;
     } else {
-      system = `urn:oid:${systemOID}`;
+      // Replace oid system with the url system, if one exists
+      if (systemUri !== null) {
+        system = systemUri.uri;
+      } else {
+        system = systemOid;
+      }
     }
 
-    const code = conceptList[concept]['$']['code'];
-    const version = conceptList[concept]['$']['codeSystemVersion'];
     codeList.push({ code, system, version });
   }
 

test/fixtures/2.16.840.1.113883.3.526.3.1032-oid-uri-vsdb.json

@@ -0,0 +1,20 @@
+{
+  "2.16.840.1.113883.3.526.3.1032": {
+    "20170504": {
+      "oid": "2.16.840.1.113883.3.526.3.1032",
+      "version": "20170504",
+      "codes": [
+        {
+          "code": "8480-6",
+          "system": "http://loinc.org",
+          "version": "2.74"
+        },
+        {
+          "code": "8480-6",
+          "system": "urn:oid:2.16.840.1.113883.6.1",
+          "version": "2.74"
+        }
+      ]
+    }
+  }
+}

test/fixtures/2.16.840.1.113883.3.526.3.1032-oid-vsdb.json

@@ -0,0 +1,15 @@
+{
+  "2.16.840.1.113883.3.526.3.1032": {
+    "20170504": {
+      "oid": "2.16.840.1.113883.3.526.3.1032",
+      "version": "20170504",
+      "codes": [
+        {
+          "code": "8480-6",
+          "system": "urn:oid:2.16.840.1.113883.6.1",
+          "version": "2.74"
+        }
+      ]
+    }
+  }
+}