Merge pull request #1434 from synthetichealth/code_versions

Add support for code system versions

src/main/java/org/mitre/synthea/export/FhirDstu2.java

@@ -1809,6 +1809,7 @@ private static CodeableConceptDt mapCodeToCodeableConcept(Code from, String syst
     } else {
       coding.setSystem(from.system);
     }
+    coding.setVersion(from.version); // may be null
 
     to.addCoding(coding);
 

src/main/java/org/mitre/synthea/export/FhirR4.java

@@ -3440,6 +3440,7 @@ private static CodeableConcept mapCodeToCodeableConcept(Code from, String system
     } else {
       coding.setSystem(from.system);
     }
+    coding.setVersion(from.version); // may be null
 
     to.addCoding(coding);
 

src/main/java/org/mitre/synthea/export/FhirStu3.java

@@ -2662,6 +2662,7 @@ private static CodeableConcept mapCodeToCodeableConcept(Code from, String system
     } else {
       coding.setSystem(from.system);
     }
+    coding.setVersion(from.version); // may be null
 
     to.addCoding(coding);
 

src/main/java/org/mitre/synthea/world/concepts/HealthRecord.java

@@ -85,6 +85,8 @@ public boolean equals(Object obj) {
     public String code;
     /** The human-readable description of the code. */
     public String display;
+    /** An identifier for the version of the code system that this code is part of. */
+    public String version;
     /**
      * A ValueSet URI that defines a set of possible codes, one of which should be selected at
      * random.
@@ -116,9 +118,13 @@ public Code(JsonObject definition) {
       this.display = definition.get("display").getAsString();
     }
 
+    /**
+     * {@inheritDoc}
+     */
     public String toString() {
-      return String
-          .format("system=%s, code=%s, display=%s, valueSet=%s", system, code, display, valueSet);
+      return String.format(
+          "system=%s, code=%s, display=%s, version=%s, valueSet=%s",
+          system, code, display, version, valueSet);
     }
 
     /**

src/main/javascript/update_code_display.js

@@ -152,7 +152,7 @@ function inventoryCode(codeObj) {
 
 function buildDictionary() {
   for (const codeObj of allCodes) {
-    let { system, code, display } = codeObj;
+    let { system, code, display, version } = codeObj;
     code = code.toString();
     if (!codeDictionary[system]) {
       codeDictionary[system] = {};
@@ -163,8 +163,10 @@ function buildDictionary() {
       console.log(`Unexpected code system ${system} may not be supported by tx.fhir.org`);
     }
     // http://hl7.org/fhir/R4/terminology-service.html#validation
-    const requestUrl = `http://tx.fhir.org/r4/CodeSystem/$validate-code?system=${systemUri}&code=${code}&display=${display}`
-
+    let requestUrl = `http://tx.fhir.org/r4/CodeSystem/$validate-code?system=${systemUri}&code=${code}&display=${display}`
+    if (version) {
+      requestUrl += `&version=${version}`
+    }
     const res = fetch(requestUrl, { headers: { "Accept": "application/fhir+json" } }).json();
 
     const displayParam = res.parameter.find(p => p.name === 'display');
@@ -195,7 +197,7 @@ function selectBestCode(system, inventory, aPreferredDisplay, currentDisplay) {
     for (const option of inventory) {
       // if we already use the preferred display with a snomed semantic tag, use that.
       // some codes aren't regex safe
-      const regexSafeDisplay = display.replaceAll('+', '\\+').replaceAll('(', '\\(').replaceAll(')', '\\)');
+      const regexSafeDisplay = aPreferredDisplay.replaceAll('+', '\\+').replaceAll('(', '\\(').replaceAll(')', '\\)');
       if (option.match(new RegExp(`^${regexSafeDisplay} \\([a-z\\+/ ]+\\)$`, 'i'))) {
         return option;
       }
@@ -255,7 +257,7 @@ function handleErrorOrExit(requestUrl, res) {
     const message = messageParam.valueString;
 
     if (message.startsWith("Unable to find code ") 
-      || message.startsWith("Unknown Code '")) {
+      || message.startsWith("Unknown code '")) {
       console.log(message);
       return;
     }

src/main/resources/modules/encounter/depression_screening.json

@@ -108,7 +108,8 @@
         {
           "system": "SNOMED-CT",
           "code": 454711000124102,
-          "display": "Depression screening using Patient Health Questionnaire Two-Item score (procedure)"
+          "display": "Depression screening using Patient Health Questionnaire Two-Item score (procedure)",
+          "version": "http://snomed.info/sct/731000124108"
         }
       ],
       "distribution": {

src/main/resources/modules/encounter/sdoh_hrsn.json

@@ -1229,7 +1229,7 @@
           "system": "SNOMED-CT",
           "code": 5251000175109,
           "display": "Received certificate of high school equivalency (finding)",
-          "value_set": ""
+          "version": "http://snomed.info/sct/731000124108"
         }
       ],
       "direct_transition": "Q11",

src/main/resources/modules/heart/avrr/outcomes.json

@@ -756,8 +756,8 @@
       "codes": [
         {
           "system": "SNOMED-CT",
-          "code": 457551000124104,
-          "display": "Acute cerebrovascular accident (disorder)"
+          "code": "230690007",
+          "display": "Cerebrovascular accident (disorder)"
         }
       ],
       "direct_transition": "End Stroke"

src/main/resources/modules/heart/avrr/sequence.json

@@ -51,7 +51,8 @@
         {
           "system": "SNOMED-CT",
           "code": 452331000124102,
-          "display": "Review of imaging finding (procedure)"
+          "display": "Review of imaging finding (procedure)",
+          "version": "http://snomed.info/sct/731000124108"
         }
       ],
       "distribution": {

src/main/resources/modules/heart/cabg/outcomes.json

@@ -839,8 +839,8 @@
       "codes": [
         {
           "system": "SNOMED-CT",
-          "code": 457551000124104,
-          "display": "Acute cerebrovascular accident (disorder)"
+          "code": "230690007",
+          "display": "Cerebrovascular accident (disorder)"
         }
       ],
       "target_encounter": "CABG_Postop",

src/main/resources/modules/heart/tavr/outcomes.json

@@ -756,8 +756,8 @@
       "codes": [
         {
           "system": "SNOMED-CT",
-          "code": 457551000124104,
-          "display": "Acute cerebrovascular accident (disorder)"
+          "code": "230690007",
+          "display": "Cerebrovascular accident (disorder)"
         }
       ],
       "direct_transition": "End Stroke"

src/main/resources/modules/injuries.json

@@ -428,11 +428,6 @@
         }
       ],
       "activities": [
-        {
-          "system": "SNOMED-CT",
-          "code": "231181000000100",
-          "display": "Delivery of rehabilitation for spinal cord injury"
-        },
         {
           "system": "SNOMED-CT",
           "code": "77476009",

src/main/resources/modules/self_harm.json

@@ -480,7 +480,7 @@
       "activities": [
         {
           "system": "SNOMED-CT",
-          "code": "784051000000106",
+          "code": "768835002",
           "display": "Depression care management"
         },
         {

src/main/resources/modules/snf/skilled_nursing_facility.json

@@ -27,7 +27,8 @@
         {
           "system": "SNOMED-CT",
           "code": "449411000124106",
-          "display": "Admission to skilled nursing facility (procedure)"
+          "display": "Admission to skilled nursing facility (procedure)",
+          "version": "http://snomed.info/sct/731000124108"
         }
       ],
       "conditional_transition": [
@@ -298,7 +299,8 @@
         {
           "system": "SNOMED-CT",
           "code": "449381000124108",
-          "display": "Discharge from skilled nursing facility (procedure)"
+          "display": "Discharge from skilled nursing facility (procedure)",
+          "version": "http://snomed.info/sct/731000124108"
         }
       ],
       "direct_transition": "Return_Wheelchair"

src/main/resources/modules/veteran_self_harm.json

@@ -153,7 +153,7 @@
       "activities": [
         {
           "system": "SNOMED-CT",
-          "code": "784051000000106",
+          "code": "768835002",
           "display": "Depression care management"
         },
         {