2024 07 gg measure validation (#1687)

* Fix for validator using wrong property for list determination when parsing json

* Fix for R2B Resource.id cardinality problem

* Improve MeasureReport validation for checking subject count

* work around THO 6.0.0 problem (hack, to be reversed later)

* release notes

---------

Co-authored-by: Grahame Grieve <grahameg@gmail.ccom>

RELEASE_NOTES.md

@@ -1,7 +1,12 @@
 ## Validator Changes
 
-* no changes
+* work around THO 6.0.0 problem (hack, to be reversed later)
+* Improve MeasureReport validation for checking subject count
+* Fix for R2B Resource.id cardinality problem
+* Fix for validator using wrong property for list determination when parsing json
 
 ## Other code changes
 
 * no changes
+
+

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/context/BaseWorkerContext.java

@@ -564,6 +564,7 @@ public abstract class BaseWorkerContext extends I18nBase implements IWorkerConte
   public Map<String, NamingSystem> getNSUrlMap() {
     if (systemUrlMap == null) {
       systemUrlMap = new HashMap<>();
+      try {
       List<NamingSystem> nsl = systems.getList();
       for (NamingSystem ns : nsl) {
         for (NamingSystemUniqueIdComponent uid : ns.getUniqueId()) {
@@ -572,6 +573,12 @@ public abstract class BaseWorkerContext extends I18nBase implements IWorkerConte
           }
         }        
       }
+      } catch (Exception e) {
+        if (!nsFailHasFailed) {
+          e.printStackTrace();
+          nsFailHasFailed  = true;
+        }
+      }
     }
     return systemUrlMap;
   }
@@ -2530,6 +2537,7 @@ public abstract class BaseWorkerContext extends I18nBase implements IWorkerConte
   protected IWorkerContextManager.IPackageLoadingTracker packageTracker;
   private boolean forPublication;
   private boolean cachingAllowed = true;
+  private static boolean nsFailHasFailed;
 
   public Resource fetchResourceById(String type, String uri, FhirPublication fhirVersion) {
     return fetchResourceById(type, uri);

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/elementmodel/Property.java

@@ -280,7 +280,7 @@ public class Property {
 	}
 
   public boolean isList() {
-    return !"1".equals(definition.getMax());
+    return !"1".equals(definition.getBase().hasMax() ? definition.getBase().getMax() : definition.getMax());
   }
 
   public boolean isBaseList() {

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/renderers/DataRenderer.java

@@ -828,7 +828,6 @@ public class DataRenderer extends Renderer implements CodeResolver {
         x.tx(context.formatPhrase(RenderingContext.DATA_REND_BASE64, length));
       } else {
         x.code(type.primitiveValue());
-        
       }
       break;
     default:

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/utils/PackageHackerR5.java

@@ -78,6 +78,16 @@ public class PackageHackerR5 {
        }
      }
    }
+   // work around an r2b issue
+   if (packageInfo.getId().equals("hl7.fhir.r2b.core") && r.getType().equals("StructureDefinition")) {
+     StructureDefinition sd = (StructureDefinition) r.getResource();
+     for (ElementDefinition ed : sd.getSnapshot().getElement()) {
+       if (ed.getPath().equals(sd.getType()+".id")) {
+         ed.getBase().setMax("1");
+       }
+     }
+   }
+   
    // work around a r4 version of extension pack issue
    if (packageInfo.getId().equals("hl7.fhir.uv.extensions.r4") && r.getType().equals("StructureDefinition")) {
      StructureDefinition sd = (StructureDefinition) r.getResource();

org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/i18n/I18nConstants.java

@@ -1093,4 +1093,9 @@ public class I18nConstants {
   public static final String IG_DEPENDENCY_EXCEPTION = "IG_DEPENDENCY_EXCEPTION";
   public static final String IG_DEPENDENCY_PACKAGE_UNKNOWN = "IG_DEPENDENCY_PACKAGE_UNKNOWN";
   public static final String NDJSON_EMPTY_LINE_WARNING = "NDJSON_EMPTY_LINE_WARNING";
+  public static final String MEASURE_MR_GRP_POP_COUNT_CANT_CHECK = "MEASURE_MR_GRP_POP_COUNT_CANT_CHECK";
+  public static final String MEASURE_MR_GRP_POP_COUNT_NO_REF = "MEASURE_MR_GRP_POP_COUNT_NO_REF";
+  public static final String MEASURE_MR_GRP_POP_COUNT_UNRESOLVED = "MEASURE_MR_GRP_POP_COUNT_UNRESOLVED";
+  public static final String MEASURE_MR_GRP_POP_COUNT_NO_REF_RES = "MEASURE_MR_GRP_POP_COUNT_NO_REF_RES";
+  public static final String MEASURE_MR_GRP_POP_COUNT_REF_UNPROCESSIBLE = "MEASURE_MR_GRP_POP_COUNT_REF_UNPROCESSIBLE";
 }

org.hl7.fhir.utilities/src/main/resources/Messages.properties

@@ -371,6 +371,11 @@ MEASURE_MR_GRP_NO_CODE = Group should have a code that matches the group definit
 MEASURE_MR_GRP_NO_USABLE_CODE = None of the codes provided are usable for comparison - need both system and code on at least one code
 MEASURE_MR_GRP_NO_WRONG_CODE = The code provided ({0}) does not match the code specified in the measure report ({1})
 MEASURE_MR_GRP_POP_COUNT_MISMATCH = Mismatch between count {0} and number of subjects {1}
+MEASURE_MR_GRP_POP_COUNT_CANT_CHECK = Unable to check the stated count {0} because the subject list cannot be fully processed ({1})
+MEASURE_MR_GRP_POP_COUNT_NO_REF = Subject reference has no actual reference
+MEASURE_MR_GRP_POP_COUNT_UNRESOLVED = Subject reference {0} could not be resolved, and the apparent type is {1} which could not be processed
+MEASURE_MR_GRP_POP_COUNT_NO_REF_RES = Subject reference {0} could not be resolved, and so could not be processed
+MEASURE_MR_GRP_POP_COUNT_REF_UNPROCESSIBLE = Subject reference {0} resolved to a {1}, which could not be processed
 MEASURE_MR_GRP_POP_DUPL_CODE = The code for this group population is duplicated with another group
 MEASURE_MR_GRP_POP_NO_CODE = Group should have a code that matches the group population definition in the measure
 MEASURE_MR_GRP_POP_NO_COUNT = Count should be present for reports where type is not ''subject-list''

org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/InstanceValidator.java

@@ -4564,7 +4564,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
     return true;
   }
 
-  private ResolvedReference localResolve(String ref, NodeStack stack, List<ValidationMessage> errors, String path, Element rootResource, Element groupingResource, Element source, BooleanHolder bh) {
+  public ResolvedReference localResolve(String ref, NodeStack stack, List<ValidationMessage> errors, String path, Element rootResource, Element groupingResource, Element source, BooleanHolder bh) {
     if (ref.startsWith("#")) {
       // work back through the parent list, tracking the stack as we go 
       // really, there should only be one level for this (contained resources cannot contain

org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/type/MeasureValidator.java

@@ -25,6 +25,7 @@ import org.hl7.fhir.r5.model.Measure.MeasureGroupStratifierComponent;
 import org.hl7.fhir.r5.model.Resource;
 import org.hl7.fhir.r5.renderers.DataRenderer;
 import org.hl7.fhir.r5.utils.ToolingExtensions;
+import org.hl7.fhir.utilities.CommaSeparatedStringBuilder;
 import org.hl7.fhir.utilities.FhirPublication;
 import org.hl7.fhir.utilities.Utilities;
 import org.hl7.fhir.utilities.i18n.I18nConstants;
@@ -32,7 +33,10 @@ import org.hl7.fhir.utilities.validation.ValidationMessage;
 import org.hl7.fhir.utilities.validation.ValidationMessage.IssueType;
 import org.hl7.fhir.utilities.xml.XMLUtil;
 import org.hl7.fhir.validation.BaseValidator;
+import org.hl7.fhir.validation.BaseValidator.BooleanHolder;
+import org.hl7.fhir.validation.instance.InstanceValidator;
 import org.hl7.fhir.validation.instance.utils.NodeStack;
+import org.hl7.fhir.validation.instance.utils.ResolvedReference;
 import org.hl7.fhir.validation.instance.utils.ValidationContext;
 import org.w3c.dom.Document;
 
@@ -493,21 +497,95 @@ public class MeasureValidator extends BaseValidator {
   
   private boolean validateMeasureReportGroupPopulation(ValidationContext hostContext, MeasureContext m, MeasureGroupPopulationComponent mgp, List<ValidationMessage> errors, Element mrgp, NodeStack ns, boolean inProgress) {
     boolean ok = true;
-    List<Element> sr = mrgp.getChildrenByName("subjectResults");
+    List<Element> srl = mrgp.getChildrenByName("subjectResults");
     if ("subject-list".equals(m.reportType())) {
       try {
+        int subCount = 0;
+        CommaSeparatedStringBuilder b = new CommaSeparatedStringBuilder("; ");
+        for (Element sr : srl) {
+          subCount = addToSubjectCount(subCount, hostContext, sr, m, ns, b);
+        }
+        if (mrgp.hasChild("count")) {
           int c = Integer.parseInt(mrgp.getChildValue("count"));
-        ok = rule(errors, NO_RULE_DATE, IssueType.BUSINESSRULE, mrgp.line(), mrgp.col(), ns.getLiteralPath(), c == sr.size(), I18nConstants.MEASURE_MR_GRP_POP_COUNT_MISMATCH, c, sr.size()) && ok;
+          if (subCount > -1) {
+            ok = rule(errors, NO_RULE_DATE, IssueType.BUSINESSRULE, mrgp.line(), mrgp.col(), ns.getLiteralPath(), c == subCount, I18nConstants.MEASURE_MR_GRP_POP_COUNT_MISMATCH, c, subCount) && ok;
+          } else {
+            hint(errors, NO_RULE_DATE, IssueType.BUSINESSRULE, mrgp.line(), mrgp.col(), ns.getLiteralPath(), false, I18nConstants.MEASURE_MR_GRP_POP_COUNT_CANT_CHECK, c, b.toString());          
+          }
+        }
       } catch (Exception e) {
         // nothing; that'll be because count is not valid, and that's a different error or its missing and we don't care
       }
     } else {
-      ok = rule(errors, NO_RULE_DATE, IssueType.BUSINESSRULE, mrgp.line(), mrgp.col(), ns.getLiteralPath(), sr.size() == 0, I18nConstants.MEASURE_MR_GRP_POP_NO_SUBJECTS) && ok;
+      ok = rule(errors, NO_RULE_DATE, IssueType.BUSINESSRULE, mrgp.line(), mrgp.col(), ns.getLiteralPath(), srl.size() == 0, I18nConstants.MEASURE_MR_GRP_POP_NO_SUBJECTS) && ok;
       warning(errors, NO_RULE_DATE, IssueType.BUSINESSRULE, mrgp.line(), mrgp.col(), ns.getLiteralPath(), mrgp.hasChild("count", false), I18nConstants.MEASURE_MR_GRP_POP_NO_COUNT);      
     }
       return ok;
   }
 
+  private int addToSubjectCount(int subCount, ValidationContext valContext, Element sr, MeasureContext m, NodeStack ns, CommaSeparatedStringBuilder b) throws FHIRException, IOException {
+    if (subCount < 0) {
+      return -1;
+    }
+
+    String ref = sr.getNamedChildValue("reference");
+    if (ref == null) {
+      b.append(context.formatMessage(I18nConstants.MEASURE_MR_GRP_POP_COUNT_NO_REF));
+      return -1;
+    }
+    BooleanHolder bh = new BooleanHolder();
+    ResolvedReference rr = ((InstanceValidator) parent).localResolve(ref, ns, new ArrayList<>(), ns.getLiteralPath(), valContext.getRootResource(), valContext.getGroupingResource(), sr, bh);
+    Element tgt;
+    if (rr != null) {
+      tgt = rr.getResource();
+    } else {
+      tgt = fetcher.fetch(((InstanceValidator) parent), valContext.getAppContext(), ref);
+    }
+    if (tgt == null) {
+      // we couldn't resolve it, but we'll draw our own conclusion from the literal URL if we can. 
+      String[] parts = ref.split("\\/");
+      if (parts.length == 2 && context.getResourceNamesAsSet().contains(parts[0])) {
+        switch (parts[0]) {
+        case "Patient":
+        case "Practitioner":
+        case "Person":
+        case "PractitionerRole":
+        case "RelatedPerson":
+          return subCount + 1;
+        case "List": 
+          b.append(context.formatMessage(I18nConstants.MEASURE_MR_GRP_POP_COUNT_UNRESOLVED, "List", ref));
+          return -1; // for now
+        case "Group":
+          b.append(context.formatMessage(I18nConstants.MEASURE_MR_GRP_POP_COUNT_UNRESOLVED, "Group", ref));
+          return -1; // for now
+        default: 
+          b.append(context.formatMessage(I18nConstants.MEASURE_MR_GRP_POP_COUNT_UNRESOLVED, parts[0], ref));
+          return -1;
+        }
+      } else {
+        // add information / hint?
+        b.append(context.formatMessage(I18nConstants.MEASURE_MR_GRP_POP_COUNT_NO_REF_RES, ref));
+        return -1;
+      }
+    }
+    switch (tgt.fhirType()) {
+    case "Patient":
+    case "Practitioner":
+    case "Person":
+    case "PractitionerRole":
+    case "RelatedPerson":
+      return subCount + 1;
+    case "List": 
+      return subCount + tgt.getChildren("entry").size();
+    case "Group":
+      b.append(context.formatMessage(I18nConstants.MEASURE_MR_GRP_POP_COUNT_REF_UNPROCESSIBLE, "Group", ref));
+      return -1; // for now
+    default: 
+      b.append(context.formatMessage(I18nConstants.MEASURE_MR_GRP_POP_COUNT_REF_UNPROCESSIBLE, tgt.fhirType(), ref));
+      return -1;
+    }
+  }
+
   private boolean validateMeasureReportGroupStratifiers(ValidationContext hostContext, MeasureContext m, MeasureGroupComponent mg, List<ValidationMessage> errors, Element mrg, NodeStack stack, boolean inProgress) {
     boolean ok = true;
     

org.hl7.fhir.validation/src/test/resources/txCache/org.hl7.fhir.validation/4.0.1/all-systems.cache

@@ -3587,10 +3587,67 @@ v: {
   "code" : "en-AU",
   "system" : "urn:ietf:bcp:47",
   "server" : "http://tx-dev.fhir.org/r4",
-  "unknown-systems" : "",
   "issues" : {
   "resourceType" : "OperationOutcome"
 }
 
 }
 -------------------------------------------------------------------------------------
+{"code" : {
+  "system" : "urn:oid:1.2.840.114350.1.72.1.7.7.10.696784.13260",
+  "code" : "1",
+  "display" : "Surgery Case"
+}, "url": "http://terminology.hl7.org/ValueSet/v3-ActEncounterCode", "version": "3.0.0", "langs":"", "useServer":"true", "useClient":"true", "guessSystem":"false", "activeOnly":"false", "membershipOnly":"false", "displayWarningMode":"false", "versionFlexible":"false", "profile": {
+  "resourceType" : "Parameters",
+  "parameter" : [{
+    "name" : "profile-url",
+    "valueString" : "http://hl7.org/fhir/ExpansionProfile/dc8fd4bc-091a-424a-8a3b-6198ef146891"
+  }]
+}}####
+v: {
+  "code" : "1",
+  "severity" : "error",
+  "error" : "A definition for CodeSystem 'urn:oid:1.2.840.114350.1.72.1.7.7.10.696784.13260' could not be found, so the code cannot be validated; The provided code 'urn:oid:1.2.840.114350.1.72.1.7.7.10.696784.13260#1 ('Surgery Case')' was not found in the value set 'http://terminology.hl7.org/ValueSet/v3-ActEncounterCode|3.0.0'",
+  "class" : "UNKNOWN",
+  "server" : "http://tx-dev.fhir.org/r4",
+  "unknown-systems" : "urn:oid:1.2.840.114350.1.72.1.7.7.10.696784.13260",
+  "issues" : {
+  "resourceType" : "OperationOutcome",
+  "issue" : [{
+    "extension" : [{
+      "url" : "http://hl7.org/fhir/StructureDefinition/operationoutcome-issue-server",
+      "valueUrl" : "http://tx-dev.fhir.org/r4"
+    }],
+    "severity" : "error",
+    "code" : "not-found",
+    "details" : {
+      "coding" : [{
+        "system" : "http://hl7.org/fhir/tools/CodeSystem/tx-issue-type",
+        "code" : "not-found"
+      }],
+      "text" : "A definition for CodeSystem 'urn:oid:1.2.840.114350.1.72.1.7.7.10.696784.13260' could not be found, so the code cannot be validated"
+    },
+    "location" : ["Coding.system"],
+    "expression" : ["Coding.system"]
+  },
+  {
+    "extension" : [{
+      "url" : "http://hl7.org/fhir/StructureDefinition/operationoutcome-issue-server",
+      "valueUrl" : "http://tx-dev.fhir.org/r4"
+    }],
+    "severity" : "error",
+    "code" : "code-invalid",
+    "details" : {
+      "coding" : [{
+        "system" : "http://hl7.org/fhir/tools/CodeSystem/tx-issue-type",
+        "code" : "not-in-vs"
+      }],
+      "text" : "The provided code 'urn:oid:1.2.840.114350.1.72.1.7.7.10.696784.13260#1 ('Surgery Case')' was not found in the value set 'http://terminology.hl7.org/ValueSet/v3-ActEncounterCode|3.0.0'"
+    },
+    "location" : ["Coding.code"],
+    "expression" : ["Coding.code"]
+  }]
+}
+
+}
+-------------------------------------------------------------------------------------

pom.xml

@@ -21,7 +21,7 @@
         <commons_compress_version>1.26.0</commons_compress_version>
         <guava_version>32.0.1-jre</guava_version>
         <hapi_fhir_version>6.4.1</hapi_fhir_version>
-        <validator_test_case_version>1.5.15</validator_test_case_version>
+        <validator_test_case_version>1.5.16-SNAPSHOT</validator_test_case_version>
         <jackson_version>2.17.0</jackson_version>
         <junit_jupiter_version>5.9.2</junit_jupiter_version>
         <junit_platform_launcher_version>1.8.2</junit_platform_launcher_version>