WIP bump core.

gradle.properties

@@ -1,4 +1,4 @@
-fhirCoreVersion = 6.4.1-SNAPSHOT
+fhirCoreVersion = 6.5.3-SNAPSHOT
 apachePoiVersion = 5.2.1
 jacksonVersion = 2.16.0
 apacheHttpcomponentsVersion = 4.5.13
@@ -8,7 +8,7 @@ log4jVersion = 2.17.1
 
 slf4jVersion = 1.7.36
 jettyVersion = 11.0.20
-logbackVersion = 1.2.13
+logbackVersion = 1.5.15
 nettyConstrainedVersion = 4.1.101.Final
 
 ## Leave the subsequent line blank for additional properties appended by azure builds

src/main/java/org/hl7/fhir/definitions/generators/specification/DictHTMLGenerator.java

@@ -44,7 +44,6 @@ WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWIS
 import org.hl7.fhir.definitions.model.Invariant;
 import org.hl7.fhir.definitions.model.TypeRef;
 import org.hl7.fhir.exceptions.FHIRException;
-import org.hl7.fhir.r5.conformance.profile.ProfileUtilities;
 import org.hl7.fhir.r5.formats.IParser.OutputStyle;
 import org.hl7.fhir.r5.formats.XmlParser;
 import org.hl7.fhir.r5.model.DataType;
@@ -64,6 +63,7 @@ WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWIS
 import org.hl7.fhir.r5.model.StructureDefinition.StructureDefinitionKind;
 import org.hl7.fhir.r5.model.StructureDefinition.StructureDefinitionMappingComponent;
 import org.hl7.fhir.r5.utils.ToolingExtensions;
+import org.hl7.fhir.r5.utils.UserDataNames;
 import org.hl7.fhir.tools.publisher.PageProcessor;
 import org.hl7.fhir.utilities.CommaSeparatedStringBuilder;
 import org.hl7.fhir.utilities.StandardsStatus;
@@ -84,7 +84,6 @@ public DictHTMLGenerator(OutputStream out, PageProcessor page, String prefix) th
 	}
 
 	public void generate(StructureDefinition profile) throws Exception {
-	  int i = 1;
 	  write("<table class=\"dict\">\r\n");
 
 	  for (ElementDefinition ec : profile.getSnapshot().getElement()) {
@@ -112,7 +111,7 @@ public void generate(StructureDefinition profile) throws Exception {
 	    }
 	  }
 	  write("</table>\r\n");
-	  i++;      
+
     flush();
     close();
   }
@@ -152,7 +151,7 @@ public void generateExtension(StructureDefinition ed) throws Exception {
       }
     }
     write("</table>\r\n");
-    i++;      
+    i++;
     flush();
     close();
   }
@@ -391,7 +390,7 @@ public int compare(String s0, String s1) {
       return s0.compareTo(s1);
     int comp = parts0[0].compareTo(parts1[0]);
     if (comp == 0 && Utilities.isInteger(parts0[1]) && Utilities.isInteger(parts1[1]))
-      return new Integer(parts0[1]).compareTo(new Integer(parts1[1]));
+      return Integer.valueOf(parts0[1]).compareTo(Integer.valueOf(parts1[1]));
     else
       return parts0[1].compareTo(parts1[1]);
     }
@@ -428,8 +427,8 @@ private String presentLevel(ElementDefinitionConstraintComponent inv) {
   }
 
   private boolean isInherited(ElementDefinitionConstraintComponent id, StructureDefinition sd) {
-    if (id.hasUserData(ProfileUtilities.UD_IS_DERIVED)) {
-      Boolean b = (Boolean) id.getUserData(ProfileUtilities.UD_IS_DERIVED);
+    if (id.hasUserData(UserDataNames.SNAPSHOT_IS_DERIVED)) {
+      Boolean b = (Boolean) id.getUserData(UserDataNames.SNAPSHOT_IS_DERIVED);
       return b.booleanValue();
     } else {
       //  if it was snapshotted in process? can't happen? - only happens on extensions... no id too, and then definitely inherited. see https://xkcd.com/2200/

src/main/java/org/hl7/fhir/definitions/model/Definitions.java

@@ -591,7 +591,7 @@ public void checkContextValid(StructureDefinitionContextComponent ec, String con
       throw new Error("The element context '"+ec.getExpression()+"' is not valid @ "+context);      
     } else if (ec.getType() == ExtensionContextType.FHIRPATH) {
       FHIRPathEngine fpe = new FHIRPathEngine(worker);
-      TypeDetails td = fpe.check(null, null, null, ec.getExpression());
+      TypeDetails td = fpe.check(null, null, null,null, ec.getExpression());
       if (td.hasNoTypes())
         throw new Error("The resource context '"+ec.getExpression()+"' is not valid @ "+context);
       else

src/main/java/org/hl7/fhir/definitions/validation/ResourceValidator.java

@@ -93,7 +93,7 @@ public static class UsageT {
 
 
   public ResourceValidator(Definitions definitions, Translations translations, CanonicalResourceManager<CodeSystem> map, String srcFolder, List<FHIRPathUsage> fpUsages, List<String> suppressedMessages, IWorkerContext context) throws IOException {
-    super(context, null, true);
+    super(context, null, true, null);
     source = Source.ResourceValidator;
     this.definitions = definitions;
     this.translations = translations;

src/main/java/org/hl7/fhir/definitions/validation/ValueSetValidator.java

@@ -74,7 +74,7 @@ public VSDuplicateList(ValueSet vs) {
   private Map<String, CodeSystem> codeSystems = new HashMap<String, CodeSystem>();
 
   public ValueSetValidator(BuildWorkerContext context, List<String> fixups, Set<String> styleExemptions) {
-    super(context, null, true);
+    super(context, null, true, null);
     this.context = context;
     this.fixups = fixups;
     this.styleExemptions = styleExemptions;
@@ -354,7 +354,7 @@ private boolean isKnownCodeSystem(String system) {
         "http://www.radlex.org",  "http://www.whocc.no/atc",   
         "urn:ietf:bcp:47",  "urn:ietf:bcp:13",  "urn:ietf:rfc:3986", 
         "urn:iso:std:iso:4217",  "urn:iso:std:iso:11073:10101",  "urn:iso-astm:E1762-95:2013", 
-        "urn:iso:std:iso:3166",  "urn:iso:std:iso:3166:-2",  "urn:iso:std:iso:3166:-3",  "http://nucc.org/provider-taxonomy", 
+        "urn:iso:std:iso:3166",  "urn:iso:std:iso:3166:-2",  "urn:iso:std:iso:3166:-3",  "http://nucc.org/provider-taxonomy", 
         "http://example.com",  "http://example.org", "https://precision.fda.gov/files/", "http://www.ebi.ac.uk/ipd/imgt/hla", 
         "https://www.iana.org/time-zones", "https://precision.fda.gov/jobs/"))
       return true;

src/main/java/org/hl7/fhir/tools/publisher/ExampleInspector.java

@@ -221,7 +221,7 @@ public ExampleInspector(IWorkerContext context, Logger logger, String rootDir, S
   private FHIRVersion version;
 
   public void prepare() throws Exception {
-    validator = new InstanceValidator(context, hostServices, null);
+    validator = new InstanceValidator(context, hostServices, null, null);
     validator.setSuppressLoincSnomedMessages(true);
     validator.setResourceIdRule(IdStatus.REQUIRED);
     validator.setBestPracticeWarningLevel(BestPracticeWarningLevel.Warning);
@@ -882,6 +882,16 @@ public boolean isSuppressMessageId(String path, String messageId) {
     return false;
   }
 
+  @Override
+  public IValidationPolicyAdvisor getPolicyAdvisor() {
+    return this;
+  }
+
+  @Override
+  public IValidationPolicyAdvisor setPolicyAdvisor(IValidationPolicyAdvisor iValidationPolicyAdvisor) {
+    return this;
+  }
+
   @Override
   public ReferenceValidationPolicy getReferencePolicy() {
     return ReferenceValidationPolicy.IGNORE;

src/main/java/org/hl7/fhir/tools/publisher/PageProcessor.java

@@ -237,6 +237,7 @@ WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWIS
 import org.hl7.fhir.r5.utils.TypesUtilities;
 import org.hl7.fhir.r5.utils.TypesUtilities.TypeClassification;
 import org.hl7.fhir.r5.utils.TypesUtilities.WildcardInformation;
+import org.hl7.fhir.r5.utils.UserDataNames;
 import org.hl7.fhir.r5.utils.structuremap.StructureMapUtilities;
 import org.hl7.fhir.r5.utils.validation.IResourceValidator;
 import org.hl7.fhir.tools.converters.MarkDownPreProcessor;
@@ -9704,7 +9705,7 @@ private boolean parentChainHasOptional(ElementDefinition ed, StructureDefinition
     if (!ed.getPath().contains("."))
       return false;
 
-    ElementDefinition match = (ElementDefinition) ed.getUserData(ProfileUtilities.UD_DERIVATION_POINTER);
+    ElementDefinition match = (ElementDefinition) ed.getUserData(UserDataNames.SNAPSHOT_DERIVATION_POINTER);
     if (match == null)
       return true; // really, we shouldn't get here, but this appears to be common in the existing profiles?
     // throw new Error("no matches for "+ed.getPath()+"/"+ed.getName()+" in "+profile.getUrl());

src/main/java/org/hl7/fhir/tools/publisher/Publisher.java

@@ -1015,9 +1015,9 @@ private boolean testSearchParameter(SearchParameter sp, StructureDefinition rd)
         String exp = sp.getExpression().replace("{{name}}", rd.getType()); // for templates  
         TypeDetails td = null;
         if (sp.getBase().size() > 1) {
-          td = fpe.check(null, rd.getType(), page.getWorkerContext().getResourceNames(), fpe.parse(exp), set);
+          td = fpe.check(null, rd.getType(), rd.getType(), page.getWorkerContext().getResourceNames(), fpe.parse(exp), set);
         } else {
-          td = fpe.check(null, rd.getType(), rd.getType(), fpe.parse(exp), set);
+          td = fpe.check(null, rd.getType(), rd.getType(), rd.getType(), fpe.parse(exp), set);
         }
         if (!Utilities.existsInList(sp.getCode(), "_id", "_in") && sp.getType() != SearchParamType.COMPOSITE) {
           String types = page.getDefinitions().getAllowedSearchTypes().get(sp.getType().toCode());
@@ -1189,9 +1189,9 @@ private boolean checkInvariant(FHIRPathEngine fpe, StructureDefinition sd,
     try {
       Set<ElementDefinition> set = new HashSet<>();
       if (sd.getKind() == StructureDefinitionKind.RESOURCE) {
-        fpe.check(null, sd.getType(), ed.getPath(), fpe.parse(inv.getExpression()), set);
+        fpe.check(null, sd.getType(), sd.getType(), ed.getPath(), fpe.parse(inv.getExpression()), set);
       } else {
-        fpe.check(null, "Resource", ed.getPath(), fpe.parse(inv.getExpression()), set);
+        fpe.check(null, "Resource", "DomainResource", ed.getPath(), fpe.parse(inv.getExpression()), set);
       }
       for (ElementDefinition edt : set) {
         if (!edt.getPath().equals(ed.getPath()) && map.containsKey(edt.getPath())) {
@@ -1494,7 +1494,7 @@ private void checkExpression(StringBuilder b, FHIRPathEngine fp, FHIRPathUsage p
     b.append(p.getResource() + " (" + p.getContext() + "): " + p.getExpression()+"\r\n");
     try {
       if (!"n/a".equals(p.getExpression())) {
-        fp.check(null, p.getResource(), p.getContext(), p.getExpression()); 
+        fp.check(null, p.getResource(), p.getResource(), p.getContext(), p.getExpression());
       }
     } catch (Exception e) {
       ValidationMessage validationMessage = new ValidationMessage(Source.Publisher, IssueType.STRUCTURE, -1, -1, p.getLocation(), 
@@ -1532,7 +1532,7 @@ private Profile makeConformancePack(ResourceDefn r) {
 
   private void validateProfile(ConstraintStructure p) throws Exception {
     if (pv == null) {
-      pv = new ProfileValidator(page.getWorkerContext(), null);
+      pv = new ProfileValidator(page.getWorkerContext(), null, null);
     }
     page.getValidationErrors().addAll(pv.validate(p.getResource(), true));
   }
@@ -2534,7 +2534,7 @@ private void validate() throws Exception {
     page.log("Validating", LogMessageType.Process);
     ResourceValidator val = new ResourceValidator(page.getDefinitions(), page.getTranslations(), page.getCodeSystems(), page.getFolders().srcDir, fpUsages, page.getSuppressedMessages(), page.getWorkerContext());
     val.resolvePatterns();
-    ProfileValidator valp = new ProfileValidator(page.getWorkerContext(), null);
+    ProfileValidator valp = new ProfileValidator(page.getWorkerContext(), null, null);
 
     for (String n : page.getDefinitions().getTypes().keySet())
       page.getValidationErrors().addAll(val.checkStucture(n, page.getDefinitions().getTypes().get(n)));

src/main/java/org/hl7/fhir/tools/publisher/WinRegistry.java

@@ -369,10 +369,10 @@ private static String readString(Preferences root, int hkey, String key, String
         new Integer(hkey), toCstr(key), new Integer(KEY_ALL_ACCESS) });
 
     regSetValueEx.invoke(root,  
-        new Object[] { 
-          new Integer(handles[0]), toCstr(valueName), toCstr(value) 
+        new Object[] {
+                handles[0], toCstr(valueName), toCstr(value)
           }); 
-    regCloseKey.invoke(root, new Object[] { new Integer(handles[0]) });
+    regCloseKey.invoke(root, new Object[] {handles[0]});
   }
 
   // utility