Merge pull request #1814 from hapifhir/2024-11-gg-vs-filter-fix

2024 11 gg vs filter fix

org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/conv40_50/resources40_50/ConceptMap40_50.java

@@ -208,6 +208,9 @@ public static org.hl7.fhir.r5.model.ConceptMap.SourceElementComponent convertSou
       if (t.getEquivalence() == org.hl7.fhir.r4.model.Enumerations.ConceptMapEquivalence.UNMATCHED) {
         tgt.setNoMap(true);
         if (t.hasComment()) {
+          if (tgt.hasExtension("http://hl7.org/fhir/4.0/StructureDefinition/extension-ConceptMap.group.element.target.comment")) {
+            throw new FHIRException("A source can only have one 'unmatched' relationship. Consider using 'disjoint' ");
+          }
           tgt.addExtension("http://hl7.org/fhir/4.0/StructureDefinition/extension-ConceptMap.group.element.target.comment", ConversionContext40_50.INSTANCE.getVersionConvertor_40_50().convertType(t.getCommentElement()));
         }
       } else {

org.hl7.fhir.r4/src/main/java/org/hl7/fhir/r4/profilemodel/gen/PECodeGenerator.java

@@ -845,7 +845,7 @@ private void w(StringBuilder b, String line) {
 
   private PEGenClass genClass(PEDefinition source) {
     PEGenClass cls = new PEGenClass();
-    cls.name = source.getProfile().getName();
+    cls.name = Utilities.javaTokenize(source.getProfile().getName(), true);
     cls.base = source.getProfile().getType();
     cls.doco = source.documentation();
     cls.url = source.getProfile().getVersionedUrl();

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/profilemodel/gen/PECodeGenerator.java

@@ -343,6 +343,7 @@ private String generateEnum(PEDefinition source, PEDefinition field) {
       }
       return null;
     }
+
     private void defineField(PEDefinition source, PEDefinition field) {
       if (field.types().size() == 1) {
         StructureDefinition sd = workerContext.fetchTypeDefinition(field.types().get(0).getUrl());
@@ -846,7 +847,7 @@ private void w(StringBuilder b, String line) {
 
   private PEGenClass genClass(PEDefinition source) {
     PEGenClass cls = new PEGenClass();
-    cls.name = source.getProfile().getName();
+    cls.name = Utilities.javaTokenize(source.getProfile().getName(), true);
     cls.base = source.getProfile().getType();
     cls.doco = source.documentation();
     cls.url = source.getProfile().getVersionedUrl();

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/terminologies/validation/ValueSetValidator.java

@@ -96,6 +96,7 @@ WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWIS
 import org.hl7.fhir.r5.utils.validation.ValidationContextCarrier;
 import org.hl7.fhir.r5.utils.validation.ValidationContextCarrier.ValidationContextResourceProxy;
 import org.hl7.fhir.utilities.CommaSeparatedStringBuilder;
+import org.hl7.fhir.utilities.DebugUtilities;
 import org.hl7.fhir.utilities.FhirPublication;
 import org.hl7.fhir.utilities.Utilities;
 import org.hl7.fhir.utilities.VersionUtilities;
@@ -183,6 +184,22 @@ private void analyseValueSet() {
       for (Extension s : valueset.getExtensionsByUrl(ExtensionConstants.EXT_VSSUPPLEMENT)) {
         requiredSupplements.add(s.getValue().primitiveValue());
       }
+
+      if (!requiredSupplements.isEmpty()) {
+        for (ConceptSetComponent inc : valueset.getCompose().getInclude()) {
+          if (inc.hasSystem()) {
+            checkCodeSystemResolves(inc);
+          }
+        }
+        for (ConceptSetComponent inc : valueset.getCompose().getExclude()) {
+          if (inc.hasSystem()) {
+            checkCodeSystemResolves(inc);
+          }
+        }
+        if (!requiredSupplements.isEmpty()) {
+          DebugUtilities.breakpoint();
+        }
+      }
     } else {
       opContext.note("vs = null");
     }
@@ -202,6 +219,15 @@ private void analyseValueSet() {
     opContext.note("analysed");
   }
 
+  private void checkCodeSystemResolves(ConceptSetComponent c) {
+    VersionInfo vi = new VersionInfo(this);
+    CodeSystem cs = resolveCodeSystem(c.getSystem(), vi.getVersion(c.getSystem(), c.getVersion()));
+    if (cs == null) {
+      // well, it doesn't really matter at this point. Mainly we're triggering the supplement analysis to happen 
+      opContext.note("Unable to resolve "+c.getSystem()+"#"+vi.getVersion(c.getSystem(), c.getVersion()));
+    }
+  }
+
   private void analyseComponent(ConceptSetComponent i, String name) {
     opContext.deadCheck("analyse Component "+name);
     if (i.getSystemElement().hasExtension(ToolingExtensions.EXT_VALUESET_SYSTEM)) {
@@ -446,7 +472,7 @@ private int checkValueSetLoad(ConceptSetComponent inc, ValidationProcessInfo inf
 
   private boolean checkRequiredSupplements(ValidationProcessInfo info) {
     if (!requiredSupplements.isEmpty()) {
-      String msg= context.formatMessagePlural(requiredSupplements.size(), I18nConstants.VALUESET_SUPPLEMENT_MISSING, CommaSeparatedStringBuilder.build(requiredSupplements));
+      String msg = context.formatMessagePlural(requiredSupplements.size(), I18nConstants.VALUESET_SUPPLEMENT_MISSING, CommaSeparatedStringBuilder.build(requiredSupplements));
       throw new TerminologyServiceProtectionException(msg, TerminologyServiceErrorClass.BUSINESS_RULE, IssueType.NOTFOUND);
     }
     return requiredSupplements.isEmpty();
@@ -492,6 +518,17 @@ public CodeSystem resolveCodeSystem(String system, String version) {
     if (cs == null) {
       cs = findSpecialCodeSystem(system, version);
     }
+    if (cs != null) {
+      if (cs.hasUserData("supplements.installed")) {
+        for (String s : cs.getUserString("supplements.installed").split("\\,")) {
+          requiredSupplements.remove(s);
+          if (s.contains("|")) {
+            s = s.substring(0, s.indexOf("|"));
+            requiredSupplements.remove(s);
+          }
+        }
+      }
+    }
     return cs;
   }
 

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/utils/validation/IValidationPolicyAdvisor.java

@@ -16,6 +16,10 @@
 
 public interface IValidationPolicyAdvisor {
 
+
+  public IValidationPolicyAdvisor getPolicyAdvisor();
+  public IValidationPolicyAdvisor setPolicyAdvisor(IValidationPolicyAdvisor policyAdvisor);
+
   /** 
    * Internal use, for chaining advisors
    * 

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

@@ -1142,4 +1142,6 @@ public class I18nConstants {
   public static final String VIEWDEFINITION_TYPE_MISMATCH = "VIEWDEFINITION_TYPE_MISMATCH";
   public static final String VIEWDEFINITION_UNABLE_TO_TYPE = "VIEWDEFINITION_UNABLE_TO_TYPE";
   public static final String VIEWDEFINITION_COMPLEX_TYPE = "VIEWDEFINITION_COMPLEX_TYPE";
+  public static final String CODESYSTEM_PROPERTY_ABSOLUTE_URI = "CODESYSTEM_PROPERTY_ABSOLUTE_URI";
+  public static final String CODESYSTEM_CS_SUPP_HIERARCHY_MEANING = "CODESYSTEM_CS_SUPP_HIERARCHY_MEANING";
 }

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

@@ -1172,3 +1172,5 @@ VIEWDEFINITION_COLLECTION_NEEDED2 = This column is defined to be not a collectio
 VIEWDEFINITION_TYPE_MISMATCH = The path expression ''{0}'' does not return a value of the type ''{1}'' - found ''{2}''{3}
 VIEWDEFINITION_UNABLE_TO_TYPE = Unable to determine a type (found ''{0}''){1}
 VIEWDEFINITION_COMPLEX_TYPE = Column from path ''{0}'' is a complex type (''{1}''){2}. This is not supported in some Runners
+CODESYSTEM_PROPERTY_ABSOLUTE_URI = A property URI must be an absolute URI, but ''{0}'' is not
+CODESYSTEM_CS_SUPP_HIERARCHY_MEANING = The supplement declares a heirarchyMeaning of ''{0}'' that doesn''t match that in the base code system ''{1}''

org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/cli/services/DisabledValidationPolicyAdvisor.java

@@ -0,0 +1,86 @@
+package org.hl7.fhir.validation.cli.services;
+
+import java.util.EnumSet;
+import java.util.List;
+
+import org.hl7.fhir.r5.elementmodel.Element;
+import org.hl7.fhir.r5.elementmodel.Element.SpecialElement;
+import org.hl7.fhir.r5.model.ElementDefinition;
+import org.hl7.fhir.r5.model.StructureDefinition;
+import org.hl7.fhir.r5.model.ValueSet;
+import org.hl7.fhir.r5.utils.validation.IMessagingServices;
+import org.hl7.fhir.r5.utils.validation.IResourceValidator;
+import org.hl7.fhir.r5.utils.validation.IValidationPolicyAdvisor;
+import org.hl7.fhir.r5.utils.validation.IValidationPolicyAdvisor.AdditionalBindingPurpose;
+import org.hl7.fhir.r5.utils.validation.IValidationPolicyAdvisor.CodedContentValidationAction;
+import org.hl7.fhir.r5.utils.validation.IValidationPolicyAdvisor.ElementValidationAction;
+import org.hl7.fhir.r5.utils.validation.IValidationPolicyAdvisor.ResourceValidationAction;
+import org.hl7.fhir.r5.utils.validation.constants.BindingKind;
+import org.hl7.fhir.r5.utils.validation.constants.ContainedReferenceValidationPolicy;
+import org.hl7.fhir.r5.utils.validation.constants.ReferenceValidationPolicy;
+import org.hl7.fhir.utilities.validation.ValidationMessage;
+
+public class DisabledValidationPolicyAdvisor implements IValidationPolicyAdvisor {
+
+  private IValidationPolicyAdvisor policyAdvisor;
+
+  @Override
+  public ReferenceValidationPolicy getReferencePolicy() {
+    return ReferenceValidationPolicy.CHECK_TYPE_IF_EXISTS;
+  }
+
+  @Override
+  public boolean isSuppressMessageId(String path, String messageId) {
+    return policyAdvisor.isSuppressMessageId(path, messageId);
+  }
+
+  @Override
+  public ContainedReferenceValidationPolicy policyForContained(IResourceValidator validator, Object appContext,
+      StructureDefinition structure, ElementDefinition element, String containerType, String containerId,
+      SpecialElement containingResourceType, String path, String url) {
+    return policyAdvisor.policyForContained(validator, appContext, structure, element, containerType, containerId, containingResourceType, path, url);
+  }
+
+  @Override
+  public EnumSet<ResourceValidationAction> policyForResource(IResourceValidator validator, Object appContext,
+      StructureDefinition type, String path) {
+    return policyAdvisor.policyForResource(validator, appContext, type, path);
+  }
+
+  @Override
+  public EnumSet<ElementValidationAction> policyForElement(IResourceValidator validator, Object appContext,
+      StructureDefinition structure, ElementDefinition element, String path) {
+    return policyAdvisor.policyForElement(validator, appContext, structure, element, path);
+  }
+
+  @Override
+  public EnumSet<CodedContentValidationAction> policyForCodedContent(IResourceValidator validator, Object appContext,
+      String stackPath, ElementDefinition definition, StructureDefinition structure, BindingKind kind,
+      AdditionalBindingPurpose purpose, ValueSet valueSet, List<String> systems) {
+    return policyAdvisor.policyForCodedContent(validator, appContext, stackPath, definition, structure, kind, purpose, valueSet, systems);
+  }
+
+  @Override
+  public List<StructureDefinition> getImpliedProfilesForResource(IResourceValidator validator, Object appContext,
+      String stackPath, ElementDefinition definition, StructureDefinition structure, Element resource, boolean valid,
+      IMessagingServices msgServices, List<ValidationMessage> messages) {
+    return policyAdvisor.getImpliedProfilesForResource(validator, appContext, stackPath, definition, structure, resource, valid, msgServices, messages);
+  }
+
+  public IValidationPolicyAdvisor getPolicyAdvisor() {
+    return policyAdvisor;
+  }
+
+  public IValidationPolicyAdvisor setPolicyAdvisor(IValidationPolicyAdvisor policyAdvisor) {
+    this.policyAdvisor = policyAdvisor;
+    return this;
+  }
+
+  @Override
+  public ReferenceValidationPolicy policyForReference(IResourceValidator validator,
+                                                      Object appContext,
+                                                      String path,
+                                                      String url) {
+    return ReferenceValidationPolicy.IGNORE;
+  }
+}

org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/cli/services/StandAloneValidatorFetcher.java

@@ -348,8 +348,9 @@ public IValidationPolicyAdvisor getPolicyAdvisor() {
     return policyAdvisor;
   }
 
-  public void setPolicyAdvisor(IValidationPolicyAdvisor policyAdvisor) {
+  public IValidationPolicyAdvisor setPolicyAdvisor(IValidationPolicyAdvisor policyAdvisor) {
     this.policyAdvisor = policyAdvisor;
+    return this;
   }
 
 }

org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/cli/services/ValidationService.java

@@ -44,6 +44,7 @@
 import org.hl7.fhir.r5.terminologies.CodeSystemUtilities;
 import org.hl7.fhir.r5.terminologies.client.TerminologyClientManager.InternalLogEvent;
 import org.hl7.fhir.r5.terminologies.utilities.TerminologyCache;
+import org.hl7.fhir.r5.utils.validation.constants.ReferenceValidationPolicy;
 import org.hl7.fhir.utilities.FhirPublication;
 import org.hl7.fhir.utilities.SystemExitManager;
 import org.hl7.fhir.utilities.TextFile;
@@ -72,6 +73,7 @@
 import org.hl7.fhir.validation.cli.utils.Common;
 import org.hl7.fhir.validation.cli.utils.EngineMode;
 import org.hl7.fhir.validation.cli.utils.VersionSourceInformation;
+import org.hl7.fhir.validation.instance.advisor.BasePolicyAdvisorForFullValidation;
 import org.hl7.fhir.validation.instance.advisor.JsonDrivenPolicyAdvisor;
 import org.hl7.fhir.validation.instance.advisor.TextDrivenPolicyAdvisor;
 
@@ -604,18 +606,25 @@ protected ValidationEngine buildValidationEngine(CliContext cliContext, String d
     validationEngine.setForPublication(cliContext.isForPublication());
     validationEngine.setShowTimes(cliContext.isShowTimes());
     validationEngine.setAllowExampleUrls(cliContext.isAllowExampleUrls());
+    ReferenceValidationPolicy refpol = ReferenceValidationPolicy.CHECK_VALID;
     if (!cliContext.isDisableDefaultResourceFetcher()) {
       StandAloneValidatorFetcher fetcher = new StandAloneValidatorFetcher(validationEngine.getPcm(), validationEngine.getContext(), validationEngine);
       validationEngine.setFetcher(fetcher);
       validationEngine.getContext().setLocator(fetcher);
       validationEngine.setPolicyAdvisor(fetcher);
-      if (cliContext.getAdvisorFile() != null) {
-        if (cliContext.getAdvisorFile().endsWith(".json")) {
-          fetcher.setPolicyAdvisor(new JsonDrivenPolicyAdvisor(fetcher.getPolicyAdvisor(), new File(cliContext.getAdvisorFile())));
-        } else {
-          fetcher.setPolicyAdvisor(new TextDrivenPolicyAdvisor(fetcher.getPolicyAdvisor(), new File(cliContext.getAdvisorFile())));          
-        }
+    } else {
+      DisabledValidationPolicyAdvisor fetcher = new DisabledValidationPolicyAdvisor();
+      validationEngine.setPolicyAdvisor(fetcher);
+      refpol = ReferenceValidationPolicy.CHECK_TYPE_IF_EXISTS;
+    }
+    if (cliContext.getAdvisorFile() != null) {
+      if (cliContext.getAdvisorFile().endsWith(".json")) {
+        validationEngine.getPolicyAdvisor().setPolicyAdvisor(new JsonDrivenPolicyAdvisor(validationEngine.getPolicyAdvisor().getPolicyAdvisor(), new File(cliContext.getAdvisorFile())));
+      } else {
+        validationEngine.getPolicyAdvisor().setPolicyAdvisor(new TextDrivenPolicyAdvisor(validationEngine.getPolicyAdvisor().getPolicyAdvisor(), new File(cliContext.getAdvisorFile())));          
       }
+    } else {
+      validationEngine.getPolicyAdvisor().setPolicyAdvisor(new BasePolicyAdvisorForFullValidation(validationEngine.getPolicyAdvisor() == null ? refpol : validationEngine.getPolicyAdvisor().getReferencePolicy()));
     }
     validationEngine.getBundleValidationRules().addAll(cliContext.getBundleValidationRules());
     validationEngine.setJurisdiction(CodeSystemUtilities.readCoding(cliContext.getJurisdiction()));

org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/codesystem/LoincChecker.java

@@ -214,8 +214,12 @@ public PropertyValidationRules rulesForFilter(String property, EnumSet<PropertyO
 
       if (Utilities.existsInList(property, 
         "concept")) {
-        return new PropertyValidationRules(PropertyFilterType.Code, CodeValidationRule.None, addToOps(ops, PropertyOperation.IsA));      
+        return new PropertyValidationRules(PropertyFilterType.Code, CodeValidationRule.None, addToOps(ops, PropertyOperation.Equals, PropertyOperation.IsA, PropertyOperation.IsNotA));      
       }
+      if (Utilities.existsInList(property, 
+          "code")) {
+          return new PropertyValidationRules(PropertyFilterType.Code, CodeValidationRule.None, addToOps(ops, PropertyOperation.Equals, PropertyOperation.IsA, PropertyOperation.IsNotA));      
+        }
       return null;
   }
 }

org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/advisor/BasePolicyAdvisorForFullValidation.java

@@ -25,6 +25,14 @@
 public class BasePolicyAdvisorForFullValidation implements IValidationPolicyAdvisor {
 
   private ReferenceValidationPolicy refpol = ReferenceValidationPolicy.CHECK_VALID;
+
+  public IValidationPolicyAdvisor getPolicyAdvisor() {
+    return null;
+  }
+
+  public IValidationPolicyAdvisor setPolicyAdvisor(IValidationPolicyAdvisor policyAdvisor) {
+    throw new Error("This policy advisor is the end of the chain");
+  }
 
   public BasePolicyAdvisorForFullValidation(ReferenceValidationPolicy refpol) {
     super();