Merge branch 'synthetichealth:master' into master

Author: Ritakoubeh

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

@@ -198,9 +198,10 @@ public class FhirR4 {
   private static final Table<String, String, String> US_CORE_4_MAPPING;
   private static final Table<String, String, String> US_CORE_5_MAPPING;
   private static final Table<String, String, String> US_CORE_6_MAPPING;
+  private static final Table<String, String, String> US_CORE_7_MAPPING;
 
   public static enum USCoreVersion {
-    v311, v400, v501, v610
+    v311, v400, v501, v610, v700
   }
 
   protected static boolean useUSCore3() {
@@ -235,6 +236,14 @@ protected static boolean useUSCore6() {
     return useUSCore6;
   }
 
+  protected static boolean useUSCore7() {
+    boolean useUSCore7 = USE_US_CORE_IG && US_CORE_VERSION.startsWith("7");
+    if (useUSCore7) {
+      US_CORE_MAPPING = US_CORE_7_MAPPING;
+    }
+    return useUSCore7;
+  }
+
   private static final String COUNTRY_CODE = Config.get("generate.geography.country_code");
   private static final String PASSPORT_URI = Config.get("generate.geography.passport_uri", "http://hl7.org/fhir/sid/passport-USA");
 
@@ -245,12 +254,13 @@ protected static boolean useUSCore6() {
     reloadIncludeExclude();
 
     Map<String, Table<String, String, String>> usCoreMappings =
-        loadMappingWithVersions("us_core_mapping.csv", "3", "4", "5", "6");
+        loadMappingWithVersions("us_core_mapping.csv", "3", "4", "5", "6", "7");
 
     US_CORE_3_MAPPING = usCoreMappings.get("3");
     US_CORE_4_MAPPING = usCoreMappings.get("4");
     US_CORE_5_MAPPING = usCoreMappings.get("5");
     US_CORE_6_MAPPING = usCoreMappings.get("6");
+    US_CORE_7_MAPPING = usCoreMappings.get("7");
 
     if (US_CORE_VERSION.startsWith("3")) {
       US_CORE_MAPPING = US_CORE_3_MAPPING;
@@ -260,6 +270,8 @@ protected static boolean useUSCore6() {
       US_CORE_MAPPING = US_CORE_5_MAPPING;
     } else if (US_CORE_VERSION.startsWith("6")) {
       US_CORE_MAPPING = US_CORE_6_MAPPING;
+    } else if (US_CORE_VERSION.startsWith("7")) {
+      US_CORE_MAPPING = US_CORE_7_MAPPING;
     }
   }
 
@@ -370,7 +382,7 @@ private static Map loadLanguageLookup() {
 
         if (StringUtils.isBlank(version) || version.contains(versionKey)) {
           // blank means applies to ALL versions
-          // version.contains allows for things like "4,5,6"
+          // version.contains allows for things like "4+5+6"
           mappingTable.put(system, code, url);
         }
       }
@@ -1404,6 +1416,7 @@ private static BundleEntryComponent explanationOfBenefit(BundleEntryComponent pe
     eob.addContained(referral);
     eob.setReferral(new Reference().setReference("#referral"));
 
+    // TODO: Make Coverage separate resources for US Core 6 & 7?
     // Get the insurance info at the time that the encounter occurred.
     Payer payer = claim.getPayer();
     Coverage coverage = new Coverage();
@@ -1639,7 +1652,7 @@ private static BundleEntryComponent condition(
 
     if (USE_US_CORE_IG) {
       Meta meta = new Meta();
-      if (useUSCore5() || useUSCore6()) {
+      if (useUSCore5() || useUSCore6() || useUSCore7()) {
         meta.addProfile(
             "http://hl7.org/fhir/us/core/StructureDefinition/us-core-condition-encounter-diagnosis");
       } else {
@@ -1867,14 +1880,20 @@ private static BundleEntryComponent observation(
         meta.addProfile("http://hl7.org/fhir/us/core/StructureDefinition/us-core-observation-lab");
       }
 
+
       if (observation.category != null) {
-        if (useUSCore6()) {
+        if (useUSCore6() || useUSCore7()) {
           switch (observation.category) {
             case "imaging":
               meta.addProfile("http://hl7.org/fhir/us/core/StructureDefinition/us-core-observation-clinical-result");
               break;
             case "social-history":
-              meta.addProfile("http://hl7.org/fhir/us/core/StructureDefinition/us-core-simple-observation");
+              if (code.code.equals("82810-3")) {
+                meta.addProfile("http://hl7.org/fhir/us/core/StructureDefinition/us-core-observation-pregnancystatus");
+              } else {
+                meta.addProfile("http://hl7.org/fhir/us/core/StructureDefinition/us-core-simple-observation");
+              }
+
               break;
             case "survey":
               meta.addProfile("http://hl7.org/fhir/us/core/StructureDefinition/us-core-observation-screening-assessment");
@@ -3476,4 +3495,4 @@ protected static String getUrlPrefix(String resourceType) {
       return "urn:uuid:";
     }
   }
-}
+}

src/main/javascript/update_code_display.js

@@ -31,7 +31,7 @@ const codeDictionary = {};
 // codeDictionary[system][code] = "display to use"
 
 // systems to skip because tx.fhir.org doesn't know about them
-const SYSTEMS_TO_SKIP = ['NUBC', 'DICOM-DCM', 'DICOM-SOP'];
+const SYSTEMS_TO_SKIP = ['NUBC', 'DICOM-DCM', 'DICOM-SOP', 'NullFlavor'];
 
 // codes used in Synthea as placeholders that we know aren't real
 const PLACEHOLDER_CODES = ['999999',

src/main/resources/costs/medications.csv

@@ -187,4 +187,4 @@ CODE,MIN,MODE,MAX,COMMENTS
 966222,0.25,0.28,0.43,Levothyroxine Sodium 0.075 MG Oral Tablet - https://data.medicaid.gov/Drug-Pricing-and-Payment/NADAC-National-Average-Drug-Acquisition-Cost-/a4y5-998d
 979092,0.1,0.28,2.62,Hydroxychloroquine Sulfate 200 MG Oral Tablet - https://data.medicaid.gov/Drug-Pricing-and-Payment/NADAC-National-Average-Drug-Acquisition-Cost-/a4y5-998d
 979485,0.03,0.08,0.09,Losartan Potassium 25 MG Oral Tablet - https://data.medicaid.gov/Drug-Pricing-and-Payment/NADAC-National-Average-Drug-Acquisition-Cost-/a4y5-998d
-993452,816.12,1014.45,1237.68,1 ML denosumab 60 MG/ML Prefilled Syringe (Prolia) - https://data.medicaid.gov/d/a4y5-998d/visualization
+993452,816.12,1014.45,1237.68,1 ML denosumab 60 MG/ML Prefilled Syringe (Prolia) - https://data.medicaid.gov/d/a4y5-998d/visualization

src/main/resources/immunization_schedule.json

@@ -102,7 +102,7 @@
     "code": {
       "system": "http://hl7.org/fhir/sid/cvx",
       "code": "140",
-      "display": "Influenza, seasonal, injectable, preservative free"
+      "display": "Influenza, split virus, trivalent, PF"
     },
     "remark": "This should really only happen Aug - Feb (preferring earlier). That may take some trickery. Since this is annual administration just populate the array with every 12 months, starting at 6 months.",
     "at_months": [

src/main/resources/keep_modules/keep_diabetes_no_dr.json

@@ -30,7 +30,7 @@
                     {
                       "system": "SNOMED-CT",
                       "code": "1551000119108",
-                      "display": "Nonproliferative diabetic retinopathy due to type 2 diabetes mellitus (disorder)"
+                      "display": "Nonproliferative diabetic retinopathy due to type II diabetes mellitus"
                     }
                   ]
                 }

src/main/resources/keep_modules/keep_npdr.json

@@ -13,7 +13,7 @@
               {
                 "system": "SNOMED-CT",
                 "code": "1551000119108",
-                "display": "Nonproliferative diabetic retinopathy due to type 2 diabetes mellitus (disorder)"
+                "display": "Nonproliferative diabetic retinopathy due to type II diabetes mellitus"
               }
             ]
           }

src/main/resources/keep_modules/keep_npdr_no_pdr.json

@@ -18,7 +18,7 @@
                   {
                     "system": "SNOMED-CT",
                     "code": "1551000119108",
-                    "display": "Nonproliferative diabetic retinopathy due to type 2 diabetes mellitus (disorder)"
+                    "display": "Nonproliferative diabetic retinopathy due to type II diabetes mellitus"
                   }
                 ]
               },
@@ -30,7 +30,7 @@
                     {
                       "system": "SNOMED-CT",
                       "code": "1501000119109",
-                      "display": "Proliferative diabetic retinopathy due to type II diabetes mellitus (disorder)"
+                      "display": "Proliferative diabetic retinopathy due to type II diabetes mellitus"
                     }
                   ]
                 }

src/main/resources/keep_modules/keep_pdr.json

@@ -13,7 +13,7 @@
               {
                 "system": "SNOMED-CT",
                 "code": "1501000119109",
-                "display": "Proliferative diabetic retinopathy due to type II diabetes mellitus (disorder)"
+                "display": "Proliferative diabetic retinopathy due to type II diabetes mellitus"
               }
             ]
           }

src/main/resources/language_lookup.json

@@ -47,7 +47,7 @@
   "russian": {
     "code": "ru-RU",
     "system": "urn:ietf:bcp:47",
-    "display": "Russian (Russia)"
+    "display": "Russian (Region=Russian Federation)"
   },
   "vietnamese": {
     "code": "vi",

src/main/resources/modules/acute_myeloid_leukemia.json

@@ -720,7 +720,7 @@
         {
           "system": "RxNorm",
           "code": 199885,
-          "display": "levofloxacin 500MG Oral tablet"
+          "display": "levofloxacin 500 MG Oral Tablet"
         }
       ]
     },