2023 10 gg template

org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/loaders/loaderR5/R4BToR5Loader.java

@@ -123,7 +123,7 @@ public org.hl7.fhir.r5.model.Resource loadResource(InputStream stream, boolean i
     if (killPrimitives) {
       throw new FHIRException("Cannot kill primitives when using deferred loading");
     }
-    if (r5 instanceof StructureDefinition && VersionUtilities.isR4BVer(version)) {
+    if (r5 instanceof StructureDefinition) {
       r5 = new StructureDefinitionHacker(version).fixSD((StructureDefinition) r5);
     }
     if (patchUrls) {

org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/loaders/loaderR5/R4ToR5Loader.java

@@ -123,7 +123,7 @@ public org.hl7.fhir.r5.model.Resource loadResource(InputStream stream, boolean i
     if (killPrimitives) {
       throw new FHIRException("Cannot kill primitives when using deferred loading");
     }
-    if (r5 instanceof StructureDefinition && VersionUtilities.isR4Ver(version)) {
+    if (r5 instanceof StructureDefinition) {
       r5 = new StructureDefinitionHacker(version).fixSD((StructureDefinition) r5);
     }
     if (patchUrls) {

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/conformance/StructureDefinitionHacker.java

@@ -49,9 +49,29 @@ public Resource fixSD(StructureDefinition sd) {
         }
       }
     }    
+    if (sd.getUrl().startsWith("http://hl7.org/fhir/uv/subscriptions-backport")) {
+      for (ElementDefinition ed : sd.getDifferential().getElement()) {
+        fixMarkdownR4BURLs(ed);
+      }
+      for (ElementDefinition ed : sd.getSnapshot().getElement()) {
+        fixMarkdownR4BURLs(ed);
+      }
+    }
     return sd;
   }
 
+  private void fixMarkdownR4BURLs(ElementDefinition ed) {
+    if (ed.hasDefinition()) {
+      ed.setDefinition(ed.getDefinition().replace("http://hl7.org/fhir/R4B/", "http://hl7.org/fhir/R4/"));
+    } 
+    if (ed.hasComment()) {
+      ed.setComment(ed.getComment().replace("http://hl7.org/fhir/R4B/", "http://hl7.org/fhir/R4/"));
+    }
+    if (ed.hasRequirements()) {
+      ed.setRequirements(ed.getRequirements().replace("http://hl7.org/fhir/R4B/", "http://hl7.org/fhir/R4/"));
+    }
+  }
+
   private void fixDocSecURL(ElementDefinition ed) {
     for (TypeRefComponent tr : ed.getType()) {
       for (CanonicalType c : tr.getProfile()) {

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/conformance/profile/ProfileUtilities.java

@@ -2356,6 +2356,9 @@ protected void updateFromDefinition(ElementDefinition dest, ElementDefinition so
       }
     }
     if (profile != null) {
+      if (profile.getSnapshot().getElement().isEmpty()) {
+        throw new DefinitionException(context.formatMessage(I18nConstants.SNAPSHOT_IS_EMPTY, profile.getVersionedUrl()));
+      }
       ElementDefinition e = profile.getSnapshot().getElement().get(0);
       String webroot = profile.getUserString("webroot");
 

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

@@ -2546,7 +2546,7 @@ public StructureDefinition fetchTypeDefinition(String typeName) {
         }
       } catch (Exception e) {
         // not sure what to do in this case?
-        System.out.println("Unable to generate snapshot @4 for "+p.getVersionedUrl()+": "+e.getMessage());
+        System.out.println("Unable to generate snapshot @5 for "+p.getVersionedUrl()+": "+e.getMessage());
         if (logger.isDebugLogging()) {
           e.printStackTrace();
         }

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

@@ -424,5 +424,16 @@ public StructureDefinition findType(String typeName) {
     return null;
   }
 
+  public StructureDefinition fetchProfileByIdentifier(String tid) {
+    for (StructureDefinition sd : context.fetchResourcesByType(StructureDefinition.class)) {
+      for (Identifier ii : sd.getIdentifier()) {
+        if (tid.equals(ii.getValue())) {
+          return sd;
+        }
+      }
+    }
+    return null;
+  }
+
 }
 

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

@@ -1488,4 +1488,15 @@ public Element setNativeObject(Object nativeObject) {
     return this;
   }
 
+  public void removeExtension(String url) {
+    List<Element> rem = new ArrayList<>();
+    for (Element e : children) {
+      if ("extension".equals(e.getName()) && url.equals(e.getChildValue("url"))) {
+        rem.add(e);
+      }
+    }
+    children.removeAll(rem);
+  }
+
+
 }

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/model/Base.java

@@ -541,7 +541,17 @@ public ValidationInfo addDefinition(StructureDefinition structure, ElementDefini
     return vi;
   }
 
-
+
+  public boolean hasValidated(StructureDefinition sd, ElementDefinition ed) {
+    if (validationInfo != null) {
+      for (ValidationInfo vi : validationInfo) {
+        if (vi.definition == ed && vi.structure == sd) {
+          return true;
+        }
+      }
+    }
+    return false;
+  }
 
   // validation messages: the validator does not populate these (yet)
   public Base addValidationMessage(ValidationMessage msg) {

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/model/ExpressionNode.java

@@ -721,9 +721,9 @@ public List<String> getDistalNames() {
     } else if (group != null) {
       names.addAll(group.getDistalNames());
     } else if (function != null) {
-      names.addAll(null);
+      names.add(null);
     } else if (constant != null) {
-      names.addAll(null);
+      names.add(null);
     } else {
       names.add(name);
     }    

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

@@ -258,6 +258,10 @@ public class ToolingExtensions {
   public static final String EXT_ID_CHOICE_GROUP = "http://hl7.org/fhir/tools/StructureDefinition/xml-choice-group";
   public static final String EXT_DATE_RULES = "http://hl7.org/fhir/tools/StructureDefinition/elementdefinition-date-rules";
   public static final String EXT_PROFILE_STYLE = "http://hl7.org/fhir/tools/StructureDefinition/type-profile-style";
+  public static final String EXT_RESOURCE_NAME = "http://hl7.org/fhir/StructureDefinition/resource-instance-name";
+  public static final String EXT_RESOURCE_DESC = "http://hl7.org/fhir/StructureDefinition/resource-instance-description";
+  public static final String EXT_ARTIFACT_NAME = "http://hl7.org/fhir/StructureDefinition/artifact-name";
+  public static final String EXT_ARTIFACT_DESC = "http://hl7.org/fhir/StructureDefinition/artifact-description";
 
   // specific extension helpers
 

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/utils/sql/Validator.java

@@ -226,26 +226,28 @@ private void checkColumn(String path, JsonObject column, TypeDetails t) {
             warning(path+".path", expression, s);
           }
           String columnName = null;
-          JsonElement aliasJ = column.get("alias");
-          if (aliasJ != null) {
-            if (aliasJ instanceof JsonString) {
-              columnName = aliasJ.asString();
+          JsonElement nameJ = column.get("name");
+          if (nameJ != null) {
+            if (nameJ instanceof JsonString) {
+              columnName = nameJ.asString();
               if (!isValidName(columnName)) {      
-                error(path+".name", aliasJ, "The name '"+columnName+"' is not valid", IssueType.VALUE);
+                error(path+".name", nameJ, "The name '"+columnName+"' is not valid", IssueType.VALUE);
               }
             } else {
-              error(path+".alias", aliasJ, "alias must be a string", IssueType.INVALID);
+              error(path+".name", nameJ, "name must be a string", IssueType.INVALID);
             }
           }
           if (columnName == null) {
             List<String> names = node.getDistalNames();
             if (names.size() == 1 && names.get(0) != null) {
               columnName = names.get(0);
               if (!isValidName(columnName)) {      
-                error(path+".path", expression, "The name '"+columnName+"' found in the path expression is not a valid column name, so an alias is required", IssueType.INVARIANT);
+                error(path+".path", expression, "A column name is required. The natural name to chose is '"+columnName+"' (from the path)", IssueType.INVARIANT);
+              } else {
+                error(path, column, "A column name is required", IssueType.REQUIRED);
               }
             } else {
-              error(path, column, "The path does not resolve to a name, so an alias is required", IssueType.REQUIRED);
+              error(path, column, "A column name is required", IssueType.REQUIRED);
             }
           }
           // ok, name is sorted!

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

@@ -1010,6 +1010,8 @@ public class I18nConstants {
   public static final String XSI_TYPE_WRONG = "XSI_TYPE_WRONG";
   public static final String XSI_TYPE_UNNECESSARY = "XSI_TYPE_UNNECESSARY";
   public static final String TERMINOLOGY_TX_OID_MULTIPLE_MATCHES = "TERMINOLOGY_TX_OID_MULTIPLE_MATCHES";
+  public static final String CDA_UNKNOWN_TEMPLATE = "CDA_UNKNOWN_TEMPLATE";
+  public static final String CDA_UNKNOWN_TEMPLATE_EXT = "CDA_UNKNOWN_TEMPLATE_EXT";
 }
 
 

org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/npm/FilesystemPackageCacheManager.java

@@ -242,6 +242,11 @@ public String getFolder() {
   }
 
   private NpmPackage loadPackageInfo(String path) throws IOException {
+    File f = new File(Utilities.path(path, "usage.ini"));
+    JsonObject j = f.exists() ? JsonParser.parseObject(f) : new JsonObject();
+    j.set("date", new SimpleDateFormat("yyyy-MM-dd").format(new Date()));
+    JsonParser.compose(j, f, true);
+
     NpmPackage pi = minimalMemory ?  NpmPackage.fromFolderMinimal(path) : NpmPackage.fromFolder(path);
     return pi;
   }

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

@@ -976,7 +976,7 @@ ED_INVARIANT_KEY_ALREADY_USED = The constraint key ''{0}'' already exists in the
 ED_INVARIANT_NO_EXPRESSION = The constraint ''{0}'' has no computable expression, so validators will not be able to check it
 ED_INVARIANT_EXPRESSION_CONFLICT = The constraint ''{0}'' has an expression ''{1}'', which differs from the earlier expression provided of ''{2}'' (invariants are allowed to repeat, but cannot differ)
 ED_INVARIANT_EXPRESSION_ERROR = Error in constraint ''{0}'' with expression ''{1}'': {2}
-SNAPSHOT_IS_EMPTY = The snapshot for the profile ''{0}'' is empty (which should not happen)
+SNAPSHOT_IS_EMPTY = The snapshot for the profile ''{0}'' is empty. This is usually due to a processing logged elsewhere
 TERMINOLOGY_TX_HINT = {1}
 TERMINOLOGY_TX_WARNING = {1}
 SD_ED_TYPE_WRONG_TYPE_one = The element has a type {0} which is different to the type {1} on the base profile {2}
@@ -1062,8 +1062,10 @@ LOGICAL_MODEL_QNAME_MISMATCH = The QName ''{0}'' does not match the expected QNa
 FHIRPATH_CHOICE_NO_TYPE_SPECIFIER = The expression ''{0}'' refers to an element that is a choice, but doesn''t have an .ofType() so that SQL view runners can pre-determine the full element name
 FHIRPATH_CHOICE_SPURIOUS_TYPE_SPECIFIER = The expression ''{0}'' refers to an element that is not a choice, but has an .ofType(). SQL view runners are likely to pre-determine an incorrect full element name
 FHIRPATH_NOT_A_COLLECTION = Found a use of a collection operator on something that is not a collection at ''{0}'' - check that there's no mistakes in the expression syntax
-TERMINOLOGY_TX_UNKNOWN_OID = The OID ''{0}'' is not known
+TERMINOLOGY_TX_UNKNOWN_OID = The OID ''{0}'' is not known, so the code can't be validated
 TERMINOLOGY_TX_SYSTEM_NO_CODE = A code with no system has no defined meaning, and it cannot be validated. A system should be provided
 XSI_TYPE_WRONG = The xsi:type value ''{0}'' is wrong (should be ''{1}''). Note that xsi:type is unnecessary at this point
 XSI_TYPE_UNNECESSARY = xsi:type is unnecessary at this point
 TERMINOLOGY_TX_OID_MULTIPLE_MATCHES = The OID ''{0}'' matches multiple code systems ({1})
+CDA_UNKNOWN_TEMPLATE = The CDA Template {0} is not known
+CDA_UNKNOWN_TEMPLATE_EXT = The CDA Template {0} / {1} is not known

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

@@ -502,12 +502,14 @@ public FHIRPathEngine getFHIRPathEngine() {
   public boolean testMode;
   private boolean example ;
   private IDigitalSignatureServices signatureServices;
+  private ContextUtilities cu;
 
   public InstanceValidator(@Nonnull IWorkerContext theContext, @Nonnull IEvaluationContext hostServices, @Nonnull XVerExtensionManager xverManager) {
     super(theContext, xverManager, false);
     start = System.currentTimeMillis();
     this.externalHostServices = hostServices;
     this.profileUtilities = new ProfileUtilities(theContext, null, null);
+    cu = new ContextUtilities(theContext);
     fpe = new FHIRPathEngine(context);
     validatorServices = new ValidatorHostServices();
     fpe.setHostServices(validatorServices);
@@ -1662,7 +1664,7 @@ private boolean convertCDACodeToCodeableConcept(List<ValidationMessage> errors,
           c.setSystem("urn:oid:"+oid);
           ok = false;
           if (urls.size() == 0) {
-            rule(errors, "2023-10-11", IssueType.CODEINVALID, element.line(), element.col(), path, false, I18nConstants.TERMINOLOGY_TX_UNKNOWN_OID, oid);
+            warning(errors, "2023-10-11", IssueType.CODEINVALID, element.line(), element.col(), path, false, I18nConstants.TERMINOLOGY_TX_UNKNOWN_OID, oid);
           } else {
             rule(errors, "2023-10-11", IssueType.CODEINVALID, element.line(), element.col(), path, false, I18nConstants.TERMINOLOGY_TX_OID_MULTIPLE_MATCHES, oid, CommaSeparatedStringBuilder.join(",", urls));
           }
@@ -5799,6 +5801,25 @@ private boolean validateElement(ValidationContext valContext, List<ValidationMes
       ok = checkChild(valContext, errors, profile, definition, resource, element, actualType, stack, inCodeableConcept, checkDisplayInContext, ei, extensionUrl, pct, mode) && ok;
     }
     vi.setValid(ok);
+
+
+    if (!definition.getPath().contains(".") && profile.hasExtension(ToolingExtensions.EXT_PROFILE_STYLE) && "cda".equals(ToolingExtensions.readStringExtension(profile, ToolingExtensions.EXT_PROFILE_STYLE))) {
+      List<Element> templates = element.getChildren("templateId");
+      for (Element t : templates) {
+        String tid = "urn:hl7ii:"+t.getChildValue("root")+(t.hasChild("extension") ? ":"+t.getChildValue("extension") : "");
+        StructureDefinition sd = cu.fetchProfileByIdentifier(tid);
+        if (sd == null) {
+          ok = rule(errors, "2023-10-20", IssueType.INVALID, element.line(), element.col(), stack.getLiteralPath(), false, t.hasChild("extension") ? I18nConstants.CDA_UNKNOWN_TEMPLATE_EXT : I18nConstants.CDA_UNKNOWN_TEMPLATE, t.getChildValue("root"), t.getChildValue("extension")) && ok;
+        } else {
+          ElementDefinition ed = sd.getSnapshot().getElementFirstRep();
+          if (!element.hasValidated(sd, ed)) {
+            element.addMessage(signpost(errors, NO_RULE_DATE, IssueType.INFORMATIONAL, element.line(), element.col(), stack.getLiteralPath(), I18nConstants.VALIDATION_VAL_PROFILE_SIGNPOST, sd.getVersionedUrl()));
+            ok = validateElement(valContext, errors, sd, ed, null, null, resource, element, actualType, stack, inCodeableConcept, checkDisplayInContext, extensionUrl, pct, mode) && ok;
+          }
+        }
+      }
+    }      
+
     return ok;
   }
 
@@ -6060,13 +6081,15 @@ public boolean checkChildByDefinition(ValidationContext valContext, List<Validat
         if (defn != null && defn.hasExtension(ToolingExtensions.EXT_BINDING_STYLE)) {
           String style = ToolingExtensions.readStringExtension(defn, ToolingExtensions.EXT_BINDING_STYLE);
           if ("CDA".equals(style)) {
-            if (cdaTypeIs(defn, "CS")) {
-              ok = checkCDACodeSimple(valContext, errors, ei.getPath(), ei.getElement(), profile, checkDefn, stack, defn) && ok;              
-            } else if (cdaTypeIs(defn, "CV") || cdaTypeIs(defn, "PQ")) {
-              ok = checkCDACoding(errors, ei.getPath(), cdaTypeIs(defn, "PQ"), ei.getElement(), profile, checkDefn, stack, defn, inCodeableConcept, checkDisplayInContext) && ok;
-            } else if (cdaTypeIs(defn, "CD") || cdaTypeIs(defn, "CE")) {
-              ok = checkCDACodeableConcept(errors, ei.getPath(), ei.getElement(), profile, checkDefn, stack, defn) && ok;
-              thisIsCodeableConcept = true;
+            if (!ei.getElement().hasChild("nullFlavor")) {
+              if (cdaTypeIs(defn, "CS")) {
+                ok = checkCDACodeSimple(valContext, errors, ei.getPath(), ei.getElement(), profile, checkDefn, stack, defn) && ok;              
+              } else if (cdaTypeIs(defn, "CV") || cdaTypeIs(defn, "PQ")) {
+                ok = checkCDACoding(errors, ei.getPath(), cdaTypeIs(defn, "PQ"), ei.getElement(), profile, checkDefn, stack, defn, inCodeableConcept, checkDisplayInContext) && ok;
+              } else if (cdaTypeIs(defn, "CD") || cdaTypeIs(defn, "CE")) {
+                ok = checkCDACodeableConcept(errors, ei.getPath(), ei.getElement(), profile, checkDefn, stack, defn) && ok;
+                thisIsCodeableConcept = true;
+              }
             }
           }
         }
@@ -6180,15 +6203,15 @@ private boolean checkCDACoding(List<ValidationMessage> errors, String path, bool
     boolean ok = true;
     String system = null;
     String code = element.getNamedChildValue(isPQ ? "unit" : "code");
-    String oid = element.getNamedChildValue("codeSystem");
+    String oid = isPQ ? "2.16.840.1.113883.6.8" : element.getNamedChildValue("codeSystem");
     if (oid != null) {
       Set<String> urls = context.urlsForOid(true, oid);
       if (urls.size() != 1) {
         system = "urn:oid:"+oid;
         ok = false;
 
         if (urls.size() == 0) {
-          rule(errors, "2023-10-11", IssueType.CODEINVALID, element.line(), element.col(), path, false, I18nConstants.TERMINOLOGY_TX_UNKNOWN_OID, oid);
+          warning(errors, "2023-10-11", IssueType.CODEINVALID, element.line(), element.col(), path, false, I18nConstants.TERMINOLOGY_TX_UNKNOWN_OID, oid);
         } else {
           rule(errors, "2023-10-11", IssueType.CODEINVALID, element.line(), element.col(), path, false, I18nConstants.TERMINOLOGY_TX_OID_MULTIPLE_MATCHES, oid, CommaSeparatedStringBuilder.join(",", urls));
         }

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

@@ -329,7 +329,7 @@ private boolean validateGroupElementTarget(List<ValidationMessage> errors, Eleme
             }
           }
         } else {
-          ok = (ctxt.source.cs.getContent() != CodeSystemContentMode.COMPLETE) & ok;
+          ok = (ctxt.target.cs.getContent() != CodeSystemContentMode.COMPLETE) & ok;
         }
       } else {
         addToBatch(code, cstack, ctxt.target, ctxt.targetScope);

org.hl7.fhir.validation/src/test/java/org/hl7/fhir/terminology/tests/ExternalTerminologyServiceTests.java

@@ -47,8 +47,6 @@ public JsonObjectPair(JsonObject suite, JsonObject test) {
   }
 
   private static final String SERVER = FhirSettings.getTxFhirDevelopment();  
-// private static final String SERVER = FhirSettings.getTxFhirLocal();  
-// private static final String SERVER = "https://r4.ontoserver.csiro.au/fhir";
 
 
   @Parameters(name = "{index}: id {0}")