Merge pull request #1546 from hapifhir/2024-01-gg-fix-debug

2024 01 gg fix debug

RELEASE_NOTES.md

@@ -1,7 +1,9 @@
 ## Validator Changes
 
-* no changes
+* Remove debugging code hiding error from server
 
 ## Other code changes
 
-* no changes
+* fix broken links rendering questionnaires
+* render target profiles on operation definition parameters
+* fix up cvx importer

org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/misc/CVXImporter.java

@@ -66,7 +66,7 @@ public class CVXImporter {
     Element cvxCodes = xml.getDocumentElement();
     for (Element cvsInfo : XMLUtil.getNamedChildren(cvxCodes, "CVXInfo")) {
       String desc = XMLUtil.getNamedChildText(cvsInfo, "ShortDescription").trim();
-      String name = XMLUtil.getNamedChildText(cvsInfo, "FullVaccinename").trim();
+      String fullName = XMLUtil.getNamedChildText(cvsInfo, "FullVaccinename").trim();
       String code = XMLUtil.getNamedChildText(cvsInfo, "CVXCode").trim();
       String notes = XMLUtil.getNamedChildText(cvsInfo, "Notes");
       String status = XMLUtil.getNamedChildText(cvsInfo, "Status").trim();
@@ -78,8 +78,8 @@ public class CVXImporter {
       } else {
         def.getDesignation().clear();
       }
-      def.setDisplay(name);
+      def.setDisplay(desc);
-      def.addDesignation().setValue(desc).setLanguage("en").setUse(new Coding().setSystem("http://snomed.info/sct").setCode("900000000000013009").setDisplay("Synonym"));
+      def.addDesignation().setValue(fullName).setLanguage("en").setUse(new Coding().setSystem("http://snomed.info/sct").setCode("900000000000013009").setDisplay("Synonym"));
       if (!Utilities.noString(notes)) {
         def.forceProperty("notes").setValue(new StringType(notes.trim()));
       }

org.hl7.fhir.r4/src/main/java/org/hl7/fhir/r4/utils/client/network/FhirRequestBuilder.java

@@ -295,7 +295,6 @@ public class FhirRequestBuilder {
     OperationOutcome error = null;
     try {
       byte[] body = response.body().bytes();
-      TextFile.bytesToFile(body, "/Users/grahamegrieve/temp/http-body.txt");
       String contentType = response.header("Content-Type");
       if (body != null) {
         if (contentType.contains(ResourceFormat.RESOURCE_XML.getHeader())

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

@@ -3449,10 +3449,12 @@ public class ProfileUtilities extends TranslatingUtilities {
 
     @Override
     public int compare(ElementDefinitionHolder o1, ElementDefinitionHolder o2) {
-      if (o1.getBaseIndex() == 0)
+      if (o1.getBaseIndex() == 0) {
         o1.setBaseIndex(find(o1.getSelf().getPath(), true));
-      if (o2.getBaseIndex() == 0)
+      }
+      if (o2.getBaseIndex() == 0) {
         o2.setBaseIndex(find(o2.getSelf().getPath(), true));
+      }
       return o1.getBaseIndex() - o2.getBaseIndex();
     }
 
@@ -3545,11 +3547,6 @@ public class ProfileUtilities extends TranslatingUtilities {
       }
       paths.add(elt.getPath());
     }
-    if(!hasSlicing) {
-      // if Differential does not have slicing then safe to pre-sort the list
-      // so elements and subcomponents are together
-      Collections.sort(diffList, new ElementNameCompare());
-    }
 
     processElementsIntoTree(edh, i, diff.getDifferential().getElement());
 

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

@@ -4,6 +4,7 @@ import java.io.IOException;
 import java.io.UnsupportedEncodingException;
 
 import org.hl7.fhir.exceptions.FHIRException;
+import org.hl7.fhir.r5.model.CanonicalType;
 import org.hl7.fhir.r5.model.CodeType;
 import org.hl7.fhir.r5.model.Enumeration;
 import org.hl7.fhir.r5.model.Enumerations.FHIRTypes;
@@ -141,6 +142,20 @@ public class OperationDefinitionRenderer extends TerminologyRenderer {
       }
     } else
       td.ah(sd.getWebPath()).tx(actualType);
+    if (p.hasTargetProfile()) {
+      td.tx(" (");
+      boolean first = true;
+      for (CanonicalType tp : p.getTargetProfile()) {
+        if (first) { first = false;} else {td.tx(", ");};
+        StructureDefinition sdt = context.getWorker().fetchTypeDefinition(tp.asStringValue());
+        if (sdt == null || !sdt.hasWebPath()) {
+          td.code().tx(tp.asStringValue());
+        } else {
+          td.ah(sdt.getWebPath(), tp.asStringValue()).tx(sdt.present());
+        }
+      }
+      td.tx(")");
+    }
     if (p.hasSearchType()) {
       td.br();
       td.tx("(");

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

@@ -282,7 +282,7 @@ public class QuestionnaireRenderer extends TerminologyRenderer {
       if (i.hasExtension(ToolingExtensions.EXT_Q_DISPLAY_CAT)) {
         CodeableConcept cc = i.getExtensionByUrl(ToolingExtensions.EXT_Q_DISPLAY_CAT).getValueCodeableConcept();
         String code = cc.getCode("http://hl7.org/fhir/questionnaire-display-category");
-        flags.addPiece(gen.new Piece(getSDCLink("StructureDefinition-sdc-questionnaire-displayCategory.html"), null, "Category: "+code).addHtml(new XhtmlNode(NodeType.Element, "img").attribute("alt", "icon").attribute("src", getImgPath("icon-qi-" + code + ".png"))));
+        flags.addPiece(gen.new Piece("https://hl7.org/fhir/R4/extension-questionnaire-displayCategory.html", null, "Category: "+code).addHtml(new XhtmlNode(NodeType.Element, "img").attribute("alt", "icon").attribute("src", getImgPath("icon-qi-" + code + ".png"))));
       }
     }    
     Cell defn = gen.new Cell();
@@ -731,7 +731,7 @@ public class QuestionnaireRenderer extends TerminologyRenderer {
       CodeableConcept cc = i.getExtensionByUrl(ToolingExtensions.EXT_Q_DISPLAY_CAT).getValueCodeableConcept();
       String code = cc.getCode("http://hl7.org/fhir/questionnaire-display-category");
       hasFlag = true;
-      flags.ah(getSDCLink("http://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire-displayCategory"), "Category: "+code).img(getImgPath("icon-qi-" + code + ".png"), "icon");
+      flags.ah("https://hl7.org/fhir/R4/extension-questionnaire-displayCategory.html", "Category: "+code).img(getImgPath("icon-qi-" + code + ".png"), "icon");
     }
 
     if (i.hasMaxLength()) {

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

@@ -470,7 +470,7 @@ public class QuestionnaireResponseRenderer extends ResourceRenderer {
 //      CodeableConcept cc = i.getExtensionByUrl("http://hl7.org/fhir/StructureDefinition/QuestionnaireResponse-displayCategory").getValueCodeableConcept();
 //      String code = cc.getCode("http://hl7.org/fhir/QuestionnaireResponse-display-category");
 //      hasFlag = true;
-//      flags.ah(getSDCLink("http://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-QuestionnaireResponse-displayCategory", "Category: "+code).img(Utilities.path(context.getLocalPrefix(), "icon-qi-"+code+".png"));
+//      flags.ah("https://hl7.org/fhir/R4/extension-questionnaire-displayCategory.html", "Category: "+code).img(Utilities.path(context.getLocalPrefix(), "icon-qi-"+code+".png"));
 //    }
 //
 //    if (i.hasMaxLength()) {
@@ -742,7 +742,7 @@ public class QuestionnaireResponseRenderer extends ResourceRenderer {
 //      render(tr.td(), qi.getExtensionByUrl("http://hl7.org/fhir/StructureDefinition/QuestionnaireResponse-displayCategory").getValue());
 //    }
 //    if (ToolingExtensions.readBoolExtension(qi, "http://hl7.org/fhir/StructureDefinition/QuestionnaireResponse-hidden")) {
-//      defn(tbl, "Hidden Item", "http://hl7.org/fhir/StructureDefinition/QuestionnaireResponse-displayCategory", "This item is a hidden question", null);
+//      defn(tbl, "Hidden Item", "https://hl7.org/fhir/R4/extension-questionnaire-displayCategory.html", "This item is a hidden question", null);
 //    }
 //    if (ToolingExtensions.readBoolExtension(qi, "http://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-QuestionnaireResponse-optionalDisplay")) {
 //      defn(tbl, "Hidden Item", "http://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-QuestionnaireResponse-optionalDisplay", "This item is optional to display", null);

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

@@ -65,6 +65,7 @@ public class I18nConstants {
   public static final String CODESYSTEM_CS_UNK_EXPANSION = "CODESYSTEM_CS_UNK_EXPANSION";
   public static final String CODE_FOUND_IN_EXPANSION_HOWEVER_ = "Code_found_in_expansion_however_";
   public static final String CODING_HAS_NO_SYSTEM__CANNOT_VALIDATE = "Coding_has_no_system__cannot_validate";
+  public static final String Coding_has_no_system__cannot_validate_NO_INFER = "Coding_has_no_system__cannot_validate_NO_INFER";
   public static final String CONTAINED_RESOURCE_DOES_NOT_APPEAR_TO_BE_A_FHIR_RESOURCE_UNKNOWN_NAME_ = "Contained_resource_does_not_appear_to_be_a_FHIR_resource_unknown_name_";
   public static final String Could_not_match_discriminator_for_slice_in_profile = "Could_not_match_discriminator_for_slice_in_profile";
   public static final String DEFINED_IN_THE_PROFILE = "defined_in_the_profile";

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

@@ -482,6 +482,7 @@ Code_found_in_expansion_however_ = Code found in expansion, however: {0}
 None_of_the_provided_codes_are_in_the_value_set_one = The provided code {2} was not found in the value set ''{1}''
 None_of_the_provided_codes_are_in_the_value_set_other = None of the provided codes [{2}] are in the value set ''{1}''
 Coding_has_no_system__cannot_validate = Coding has no system. A code with no system has no defined meaning, and it cannot be validated. A system should be provided
+Coding_has_no_system__cannot_validate_NO_INFER = Coding has no system, and inferring the code system is not possible in this context. A code with no system has no defined meaning, and it cannot be validated. A system should be provided
 Unable_to_handle_system__concept_filter_with_op__ = Unable to handle system {0} concept filter with op = {1}
 UNABLE_TO_HANDLE_SYSTEM__PROPERTY_FILTER_WITH_OP__ = Unable to handle system {0} property filter with op = {1}
 Unable_to_handle_system__filter_with_property__ = Unable to handle system {0} filter with property = {1}, op = {2}

org.hl7.fhir.validation/src/test/resources/txCache/org.hl7.fhir.r5/vs-externals.json

@@ -2,5 +2,7 @@
   "http://somewhere/something-else" : null,
   "http://loinc.org/vs/LL715-4" : null,
   "http://hl7.org/fhir/us/vrdr/ValueSet/vrdr-PlaceOfDeath" : null,
-  "http://somewhere/something" : null
+  "http://somewhere/something" : null,
+  "https://fhir.infoway-inforoute.ca/ValueSet/issuetype|20190415" : null,
+  "https://fhir.infoway-inforoute.ca/ValueSet/issueseverity|20190415" : null
 }

pom.xml

@@ -20,7 +20,7 @@
     <properties>
         <guava_version>32.0.1-jre</guava_version>
         <hapi_fhir_version>6.4.1</hapi_fhir_version>
-        <validator_test_case_version>1.4.24</validator_test_case_version>
+        <validator_test_case_version>1.4.25</validator_test_case_version>
         <jackson_version>2.16.0</jackson_version>
         <junit_jupiter_version>5.9.2</junit_jupiter_version>
         <junit_platform_launcher_version>1.8.2</junit_platform_launcher_version>