Merge pull request #1821 from hapifhir/2024-11-gg-various-fixes

2024 11 gg various fixes

org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/conv40_50/resources40_50/NamingSystem40_50.java

@@ -97,9 +97,10 @@ public static org.hl7.fhir.r4.model.NamingSystem convertNamingSystem(org.hl7.fhi
     if (src == null)
       return null;
     org.hl7.fhir.r4.model.NamingSystem tgt = new org.hl7.fhir.r4.model.NamingSystem();
-    ConversionContext40_50.INSTANCE.getVersionConvertor_40_50().copyDomainResource(src, tgt);
-    if (src.hasUrlElement()) 
+    ConversionContext40_50.INSTANCE.getVersionConvertor_40_50().copyDomainResource(src, tgt, VersionConvertorConstants.EXT_NAMINGSYSTEM_URL);
+    if (src.hasUrlElement()) {
       tgt.getExtension().add(new Extension().setUrl(VersionConvertorConstants.EXT_NAMINGSYSTEM_URL).setValue(Uri40_50.convertUri(src.getUrlElement())));
+    }
     if (src.hasVersionElement()) 
       tgt.getExtension().add(new Extension().setUrl(VersionConvertorConstants.EXT_NAMINGSYSTEM_VERSION).setValue(String40_50.convertString(src.getVersionElement())));
     if (src.hasName())

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

@@ -2718,18 +2718,24 @@ else if (trimDifferential)
       // profiles cannot change : isModifier, defaultValue, meaningWhenMissing
       // but extensions can change isModifier
       if (isExtension) {
-        if (derived.hasIsModifierElement() && !(base.hasIsModifierElement() && Base.compareDeep(derived.getIsModifierElement(), base.getIsModifierElement(), false)))
+        if (derived.hasIsModifierElement() && !(base.hasIsModifierElement() && Base.compareDeep(derived.getIsModifierElement(), base.getIsModifierElement(), false))) {
           base.setIsModifierElement(derived.getIsModifierElement().copy());
-        else if (trimDifferential)
+        } else if (trimDifferential) {
           derived.setIsModifierElement(null);
-        else if (derived.hasIsModifierElement())
+        } else if (derived.hasIsModifierElement()) {
           derived.getIsModifierElement().setUserData(UserDataNames.SNAPSHOT_DERIVATION_EQUALS, true);
-        if (derived.hasIsModifierReasonElement() && !(base.hasIsModifierReasonElement() && Base.compareDeep(derived.getIsModifierReasonElement(), base.getIsModifierReasonElement(), false)))
+        }
+        if (derived.hasIsModifierReasonElement() && !(base.hasIsModifierReasonElement() && Base.compareDeep(derived.getIsModifierReasonElement(), base.getIsModifierReasonElement(), false))) {
           base.setIsModifierReasonElement(derived.getIsModifierReasonElement().copy());
-        else if (trimDifferential)
+        } else if (trimDifferential) {
           derived.setIsModifierReasonElement(null);
-        else if (derived.hasIsModifierReasonElement())
+        } else if (derived.hasIsModifierReasonElement()) {
           derived.getIsModifierReasonElement().setUserData(UserDataNames.SNAPSHOT_DERIVATION_EQUALS, true);
+        }
+        if (base.getIsModifier() && !base.hasIsModifierReason()) {
+          // we get here because modifier extensions don't get a modifier reason from the type
+          base.setIsModifierReason("Modifier extensions are labelled as such because they modify the meaning or interpretation of the resource or element that contains them");
+        }
       }
 
       boolean hasBinding = derived.hasBinding();

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

@@ -1110,6 +1110,20 @@ public Element getExtension(String url) {
     return null;
   }
 
+  public String getExtensionString(String url) {
+    if (children != null) {
+      for (Element child : children) {
+        if (extensionList.contains(child.getName())) {
+          String u = child.getChildValue("url");
+          if (url.equals(u)) {
+            return child.getNamedChildValue("value");
+          }
+        }
+      }
+    }
+    return null;
+  }
+
   public List<Element> getExtensions(String url) {
     List<Element> list = new ArrayList<>();
     if (children != null) {

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

@@ -788,8 +788,9 @@ public void compose(Element e, OutputStream stream, OutputStyle style, String id
     }
     checkComposeComments(e);
     json.beginObject();
-//    if (!isSuppressResourceType())
+    if (!isSuppressResourceType(e.getProperty())) {
       prop("resourceType", e.getType(), null);
+    }
     Set<String> done = new HashSet<String>();
     for (Element child : e.getChildren()) {
       compose(e.getName(), e, done, child);
@@ -799,6 +800,15 @@ public void compose(Element e, OutputStream stream, OutputStyle style, String id
     osw.flush();
   }
 
+  private boolean isSuppressResourceType(Property property) {
+    StructureDefinition sd = property.getStructure();
+    if (sd != null && sd.hasExtension(ToolingExtensions.EXT_SUPPRESS_RESOURCE_TYPE)) {
+      return ToolingExtensions.readBoolExtension(sd, ToolingExtensions.EXT_SUPPRESS_RESOURCE_TYPE);
+    } else {
+      return false;
+    }
+  }
+
   private void checkComposeComments(Element e) {
     for (String s : e.getComments()) {
       json.comment(s);
@@ -814,8 +824,9 @@ public void compose(Element e, JsonCreator json) throws Exception {
     checkComposeComments(e);
     json.beginObject();
 
-//    if (!isSuppressResourceType())
+    if (!isSuppressResourceType(e.getProperty())) {
       prop("resourceType", e.getType(), linkResolver == null ? null : linkResolver.resolveProperty(e.getProperty()));
+    }
     Set<String> done = new HashSet<String>();
     for (Element child : e.getChildren()) {
       compose(e.getName(), e, done, child);
@@ -931,7 +942,7 @@ else if (item.hasValue()) {
           json.elide();
         else if (item.hasChildren()) {
           open(null,null);
-          if (item.getProperty().isResource()) {
+          if (item.getProperty().isResource() && !isSuppressResourceType(item.getProperty())) {
             prop("resourceType", item.getType(), linkResolver == null ? null : linkResolver.resolveType(item.getType()));
           }
           if (linkResolver != null && item.getProperty().isReference()) {
@@ -987,7 +998,7 @@ private void compose(String path, Element element) throws IOException {
     }
     if (element.hasChildren()) {
       open(name, linkResolver == null ? null : linkResolver.resolveProperty(element.getProperty()));
-      if (element.getProperty().isResource()) {
+      if (element.getProperty().isResource() && !isSuppressResourceType(element.getProperty())) {
         prop("resourceType", element.getType(), linkResolver == null ? null : linkResolver.resolveType(element.getType()));
       }
       if (linkResolver != null && element.getProperty().isReference()) {

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/fhirpath/FHIRPathEngine.java

@@ -6572,8 +6572,13 @@ private boolean hasDataType(ElementDefinition ed) {
   }
 
   private ElementDefinitionMatch getElementDefinitionById(StructureDefinition sd, String ref) {
-    if (ref.startsWith(sd.getUrl()+"#")) {
-      ref = ref.replace(sd.getUrl()+"#", "#"); 
+    StructureDefinition sdt = sd; 
+    while (sdt != null) {
+      if (ref.startsWith(sdt.getUrl()+"#")) {
+        ref = ref.replace(sdt.getUrl()+"#", "#");
+        break;
+      }
+      sdt = worker.fetchResource(StructureDefinition.class, sdt.getBaseDefinition());
     }
     for (ElementDefinition ed : sd.getSnapshot().getElement()) {
       if (ref.equals("#"+ed.getId())) {

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

@@ -289,7 +289,7 @@ private ResourceWrapper resolveReference(List<ResourceWrapper> entries, Resource
 
   public static boolean allEntriesAreHistoryProvenance(List<ResourceWrapper> entries) throws UnsupportedEncodingException, FHIRException, IOException {
     for (ResourceWrapper be : entries) {
-      if (!"Provenance".equals(be.child("resource").fhirType())) {
+      if (!be.has("child") || !"Provenance".equals(be.child("resource").fhirType())) {
         return false;
       }
     }

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

@@ -276,6 +276,7 @@ public class ToolingExtensions {
   public static final String EXT_TYPE_PARAMETER = "http://hl7.org/fhir/tools/StructureDefinition/type-parameter";
   public static final String EXT_ALTERNATE_CANONICAL = "http://hl7.org/fhir/StructureDefinition/alternate-canonical";
   public static final String EXT_SUPPRESSED = "http://hl7.org/fhir/StructureDefinition/elementdefinition-suppress";
+  public static final String EXT_SUPPRESS_RESOURCE_TYPE = "http://hl7.org/fhir/tools/StructureDefinition/json-suppress-resourcetype";
 
   // specific extension helpers
 

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

@@ -1043,8 +1043,6 @@ public class I18nConstants {
   public static final String VALUESET_TOO_COSTLY = "VALUESET_TOO_COSTLY";
   public static final String VALUESET_TOO_COSTLY_COUNT = "VALUESET_TOO_COSTLY_COUNT";
   public static final String VALUESET_TOO_COSTLY_TIME = "VALUESET_TOO_COSTLY_TIME";
-  public static final String TX_SERVER_NOT_READY = "TX_SERVER_NOT_READY";
-  public static final String REQUEST_TOO_COSTLY_TIME = "REQUEST_TOO_COSTLY_TIME";
   public static final String VALUESET_UNC_SYSTEM_WARNING = "VALUESET_UNC_SYSTEM_WARNING";
   public static final String VALUESET_UNC_SYSTEM_WARNING_VER = "VALUESET_UNC_SYSTEM_WARNING_VER";
   public static final String VALUESET_UNKNOWN_FILTER_PROPERTY = "VALUESET_UNKNOWN_FILTER_PROPERTY";
@@ -1123,6 +1121,7 @@ public class I18nConstants {
   public static final String PRIMITIVE_TOO_SHORT = "PRIMITIVE_TOO_SHORT";
   public static final String CANONICAL_MULTIPLE_VERSIONS_KNOWN = "CANONICAL_MULTIPLE_VERSIONS_KNOWN";
   public static final String SD_PATH_NO_SLICING = "SD_PATH_NO_SLICING";
+  public static final String SD_PATH_SLICING_DEPRECATED_R5 = "SD_PATH_SLICING_DEPRECATED_R5";
   public static final String SD_PATH_SLICING_DEPRECATED = "SD_PATH_SLICING_DEPRECATED";
   public static final String SD_PATH_NOT_VALID = "SD_PATH_NOT_VALID";
   public static final String SD_PATH_ERROR = "SD_PATH_ERROR";
@@ -1144,4 +1143,8 @@ public class I18nConstants {
   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";
+  public static final String HTA_SCT_DESC = "HTA_SCT_DESC";
+  public static final String HTA_SCT_MESSAGE = "HTA_SCT_MESSAGE";
+  public static final String HTA_LOINC_DESC = "HTA_LOINC_DESC";
+  public static final String HTA_LOINC_MESSAGE = "HTA_LOINC_MESSAGE";
 }

org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/i18n/RenderingI18nContext.java

@@ -185,8 +185,6 @@ public class RenderingI18nContext extends I18nBase {
   public static final String CONC_MAP_FROM = "CONC_MAP_FROM";
   public static final String CONC_MAP_GRP = "CONC_MAP_GRP";
   public static final String CONC_MAP_NOT_SPEC = "CONC_MAP_NOT_SPEC";
-  public static final String CONC_MAP_NO_PROD_USE = "CONC_MAP_NO_PROD_USE";
-  public static final String CONC_MAP_PUB_ON = "CONC_MAP_PUB_ON"; 
   public static final String CONC_MAP_REL = "CONC_MAP_REL";
   public static final String CONC_MAP_SOURCE = "CONC_MAP_SOURCE";
   public static final String CONC_MAP_SRC_DET = "CONC_MAP_SRC_DET";
@@ -300,7 +298,6 @@ public class RenderingI18nContext extends I18nBase {
   public static final String EX_SCEN_TIME = "EX_SCEN_TIME";
   public static final String EX_SCEN_UN = "EX_SCEN_UN";
   public static final String EX_SCEN_UN_ACT = "EX_SCEN_UN_ACT";
-  public static final String EX_SCEN_UN_INST = "EX_SCEN_UN_INST";
   public static final String GENERAL_VER_LOW = "GENERAL_VER_LOW";
   public static final String IMP_GUIDE_URL = "IMP_GUIDE_URL";
   public static final String LIB_REND_ART = "LIB_REND_ART";

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

@@ -6,6 +6,6 @@ public class CommonPackages {
   public static final String VER_XVER = "0.1.0";
 
   public static final String ID_PUBPACK = "hl7.fhir.pubpack";
-  public static final String VER_PUBPACK = "0.1.8";
+  public static final String VER_PUBPACK = "0.1.9";
 
 }

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

@@ -439,7 +439,7 @@ NO_VALID_DISPLAY_FOUND_other = No valid Display Names found for {1}#{2} in the l
 NO_VALID_DISPLAY_FOUND_LANG_SOME_one = ''{5}'' is the default display; no valid Display Names found for {1}#{2} in the language {4}
 NO_VALID_DISPLAY_FOUND_LANG_SOME_other = ''{5}'' is the default display; no valid Display Names found for {1}#{2} in the language {4}
 NO_VALID_DISPLAY_FOUND_LANG_NONE_one = ''{5}'' is the default display; the code system {1} has no Display Names for the language {4}
-NO_VALID_DISPLAY_FOUND_LANG_NINE_other = ''{5}'' is the default display; the code system {1} has no Display Names found for the language {4}
+NO_VALID_DISPLAY_FOUND_LANG_NONE_other = ''{5}'' is the default display; the code system {1} has no Display Names found for the language {4}
 Named_items_are_out_of_order_in_the_slice = Named items are out of order in the slice
 No_ExpansionProfile_provided = No ExpansionProfile provided
 No_Expansion_Parameters_provided = No Expansion Parameters provided
@@ -1153,7 +1153,8 @@ CODESYSTEM_CS_COMPLETE_AND_EMPTY = When a CodeSystem has content = ''complete'',
 VALIDATION_VAL_VERSION_NOHASH = Version ''{0}'' contains a ''#'', which as this character is used in some URLs to separate the version and the fragment id. When version does include '#', systems will not be able to parse the URL
 PRIMITIVE_TOO_SHORT = Value ''{0}'' is shorter than permitted minimum length of {1}
 CANONICAL_MULTIPLE_VERSIONS_KNOWN = The version {2} for the {0} {1} is not known. These versions are known: {3}
-SD_PATH_SLICING_DEPRECATED = The discriminator type ''{0}'' has been deprecated. Use type=value with a pattern[x] instead
+SD_PATH_SLICING_DEPRECATED = The discriminator type ''{0}'' is been deprecated in R5+. For future compatibility, you could consider using type=value with a pattern[x] instead (if this is not an inherited slicing)
+SD_PATH_SLICING_DEPRECATED_R5 = The discriminator type ''{0}'' has been deprecated. Use type=value with a pattern[x] instead (if this is not an inherited slicing)
 SD_PATH_NOT_VALID = The discriminator path ''{0}'' does not appear to be valid for the element that is being sliced ''{1}''
 SD_PATH_ERROR = The discriminator path ''{0}'' does not appear to be valid for the element that is being sliced ''{1}'': {2}
 VIEWDEFINITION_SHOULD_HAVE_NAME = No name provided. A name is required in many contexts where a ViewDefinition is used
@@ -1174,3 +1175,8 @@ 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}''
+HTA_SCT_DESC = SNOMED Clinical Terms® (SNOMED CT®)
+HTA_SCT_MESSAGE = This material contains content that is copyright of SNOMED International. Implementers of these specifications must have the appropriate SNOMED CT Affiliate license - for more information contact <a href=\"https://www.snomed.org/get-snomed\">https://www.snomed.org/get-snomed</a> or <a href=\"mailto:[email protected]\">[email protected]</a>.
+HTA_LOINC_DESC = LOINC
+HTA_LOINC_MESSAGE = This material contains content from <a href=\"http://loinc.org\">LOINC</a>. LOINC is copyright &copy; 1995-2020, Regenstrief Institute, Inc. and the Logical Observation Identifiers Names and Codes (LOINC) Committee and is available at no cost under the <a href=\"http://loinc.org/license\">license</a>. LOINC&reg; is a registered United States trademark of Regenstrief Institute, Inc.
+SD_PATH_NO_SLICING = Slicing is not allowed at ''{0}''