Merge branch 'master' into do-20230602-refactor-cli-params

.github/workflows/codeql.yml

@@ -0,0 +1,73 @@
+# For most projects, this workflow file will not need changing; you simply need
+# to commit it to your repository.
+#
+# You may wish to alter this file to override the set of languages analyzed,
+# or to provide custom queries or build logic.
+#
+# ******** NOTE ********
+# We have attempted to detect the languages in your repository. Please check
+# the `language` matrix defined below to confirm you have the correct set of
+# supported CodeQL languages.
+#
+name: "CodeQL"
+
+on:
+  schedule:
+    - cron: '0 0 * * *'
+
+  workflow_dispatch:
+
+jobs:
+  analyze:
+    name: Analyze
+    runs-on: ${{ (matrix.language == 'swift' && 'macos-latest') || 'ubuntu-latest' }}
+    permissions:
+      actions: read
+      contents: read
+      security-events: write
+
+    strategy:
+      fail-fast: false
+      matrix:
+        language: [ 'java' ]
+        module: [ 'org.hl7.fhir.utilities','org.hl7.fhir.dstu2','org.hl7.fhir.dstu2016may', 'org.hl7.fhir.dstu3', 'org.hl7.fhir.r4', 'org.hl7.fhir.r4b','org.hl7.fhir.r5','org.hl7.fhir.convertors','org.hl7.fhir.validation' ]
+        # CodeQL supports [ 'cpp', 'csharp', 'go', 'java', 'javascript', 'python', 'ruby' ]
+        # Use only 'java' to analyze code written in Java, Kotlin or both
+        # Use only 'javascript' to analyze code written in JavaScript, TypeScript or both
+        # Learn more about CodeQL language support at https://aka.ms/codeql-docs/language-support
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v3
+
+    # Initializes the CodeQL tools for scanning.
+    - name: Initialize CodeQL
+      uses: github/codeql-action/init@v2
+      with:
+        languages: ${{ matrix.language }}
+        # If you wish to specify custom queries, you can do so here or in a config file.
+        # By default, queries listed here will override any specified in a config file.
+        # Prefix the list here with "+" to use these queries and those in the config file.
+
+        # For more details on CodeQL's query packs, refer to: https://docs.github.com/en/code-security/code-scanning/automatically-scanning-your-code-for-vulnerabilities-and-errors/configuring-code-scanning#using-queries-in-ql-packs
+        # queries: security-extended,security-and-quality
+
+
+    # Autobuild attempts to build any compiled languages  (C/C++, C#, Go, or Java).
+    # If this step fails, then you should remove it and run the build manually (see below)
+    # - name: Autobuild
+    #  uses: github/codeql-action/autobuild@v2
+
+    # ℹ️ Command-line programs to run using the OS shell.
+    # 📚 See https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idstepsrun
+
+    #   If the Autobuild fails above, remove it and uncomment the following three lines.
+    #   modify them (or add more) to build your code if your project, please refer to the EXAMPLE below for guidance.
+
+    - run: |
+        mvn install -DskipTests -pl ${{ matrix.module }}
+
+    - name: Perform CodeQL Analysis
+      uses: github/codeql-action/analyze@v2
+      with:
+        category: "/language:${{matrix.language}}:${{ matrix.module }}"

.github/workflows/trivy.yml

@@ -0,0 +1,35 @@
+name: Trivy Security Scans
+
+on:
+  push:
+    branches: [ "master" ]
+  pull_request:
+    branches: [ "master" ]
+    
+  workflow_dispatch:
+
+jobs:
+  build:
+    name: build
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v3
+
+      - name: Run static analysis
+        uses: aquasecurity/trivy-action@master
+        with:
+          scan-type: 'fs'
+          vuln-type: 'library'
+          scanners: 'vuln,secret,config'
+          ignore-unfixed: true
+          format: 'sarif'
+          output: 'trivy-results.sarif'
+          severity: 'MEDIUM,HIGH,CRITICAL'
+
+
+      - name: Upload Trivy scan results to GitHub Security tab
+        uses: github/codeql-action/upload-sarif@v2
+        with:
+          sarif_file: 'trivy-results.sarif'
+          category: 'code'

org.hl7.fhir.convertors/pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <groupId>ca.uhn.hapi.fhir</groupId>
         <artifactId>org.hl7.fhir.core</artifactId>
-        <version>6.0.12-SNAPSHOT</version>
+        <version>6.0.16-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 
@@ -91,7 +91,6 @@
         <dependency>
           <groupId>com.squareup.okhttp3</groupId>
           <artifactId>okhttp</artifactId>
-          <version>${okhttp.version}</version>
           <optional>true</optional>
         </dependency>
 

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

@@ -29,8 +29,9 @@ public class PackageMinifier {
     for (PackageResourceInformation pri : src.listIndexedResources()) {
       if (min.isMinified(pri.getResourceType())) {
         Resource res = new JsonParser().parse(src.load(pri));
-        min.minify(res);
+        if (min.minify(res)) {
-        tgt.addFile("package", res.fhirType()+"-"+res.getIdPart()+".json", new JsonParser().composeBytes(res), null);
+          tgt.addFile("package", res.fhirType()+"-"+res.getIdPart()+".json", new JsonParser().composeBytes(res), null);
+        }
       }
     }
     tgt.save(new FileOutputStream(target));

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

@@ -91,7 +91,9 @@ public class ResourceDependencyPackageBuilder {
         ResourceMinifier min = new ResourceMinifier();
         if (min.isMinified(resource.fhirType())) {
           resource = resource.copy();
-          min.minify(resource);
+          if (!min.minify(resource)) {
+            return;
+          }
         } else {
           return;
         }

org.hl7.fhir.dstu2/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>org.hl7.fhir.core</artifactId>
-		<version>6.0.12-SNAPSHOT</version>
+		<version>6.0.16-SNAPSHOT</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 
@@ -59,25 +59,16 @@
         <dependency>
             <groupId>org.apache.poi</groupId>
             <artifactId>poi</artifactId>
-            <version>${apache_poi_version}</version>
             <optional>true</optional>
         </dependency>
         <dependency>
             <groupId>org.apache.poi</groupId>
             <artifactId>poi-ooxml</artifactId>
-            <version>${apache_poi_version}</version>
             <optional>true</optional>
         </dependency>
         <dependency>
             <groupId>org.apache.poi</groupId>
-            <artifactId>poi-ooxml-schemas</artifactId>
+            <artifactId>poi-ooxml-full</artifactId>
-            <version>${apache_poi_version}</version>
-            <optional>true</optional>
-        </dependency>
-        <dependency>
-            <groupId>org.apache.poi</groupId>
-            <artifactId>ooxml-schemas</artifactId>
-            <version>1.4</version>
             <optional>true</optional>
         </dependency>
 

org.hl7.fhir.dstu2016may/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>org.hl7.fhir.core</artifactId>
-		<version>6.0.12-SNAPSHOT</version>
+		<version>6.0.16-SNAPSHOT</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 
@@ -73,25 +73,16 @@
         <dependency>
             <groupId>org.apache.poi</groupId>
             <artifactId>poi</artifactId>
-            <version>${apache_poi_version}</version>
             <optional>true</optional>
         </dependency>
         <dependency>
             <groupId>org.apache.poi</groupId>
             <artifactId>poi-ooxml</artifactId>
-            <version>${apache_poi_version}</version>
             <optional>true</optional>
         </dependency>
         <dependency>
             <groupId>org.apache.poi</groupId>
-            <artifactId>poi-ooxml-schemas</artifactId>
+            <artifactId>poi-ooxml-full</artifactId>
-            <version>${apache_poi_version}</version>
-            <optional>true</optional>
-        </dependency>
-        <dependency>
-            <groupId>org.apache.poi</groupId>
-            <artifactId>ooxml-schemas</artifactId>
-            <version>1.4</version>
             <optional>true</optional>
         </dependency>
 

org.hl7.fhir.dstu3/pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <groupId>ca.uhn.hapi.fhir</groupId>
         <artifactId>org.hl7.fhir.core</artifactId>
-        <version>6.0.12-SNAPSHOT</version>
+        <version>6.0.16-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 
@@ -59,7 +59,6 @@
         <dependency>
             <groupId>com.squareup.okhttp3</groupId>
             <artifactId>okhttp</artifactId>
-            <version>${okhttp.version}</version>
             <optional>true</optional>
         </dependency>
 
@@ -67,25 +66,16 @@
         <dependency>
             <groupId>org.apache.poi</groupId>
             <artifactId>poi</artifactId>
-            <version>${apache_poi_version}</version>
             <optional>true</optional>
         </dependency>
         <dependency>
             <groupId>org.apache.poi</groupId>
             <artifactId>poi-ooxml</artifactId>
-            <version>${apache_poi_version}</version>
             <optional>true</optional>
         </dependency>
         <dependency>
             <groupId>org.apache.poi</groupId>
-            <artifactId>poi-ooxml-schemas</artifactId>
+            <artifactId>poi-ooxml-full</artifactId>
-            <version>${apache_poi_version}</version>
-            <optional>true</optional>
-        </dependency>
-        <dependency>
-            <groupId>org.apache.poi</groupId>
-            <artifactId>ooxml-schemas</artifactId>
-            <version>1.4</version>
             <optional>true</optional>
         </dependency>
 

org.hl7.fhir.r4/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>org.hl7.fhir.core</artifactId>
-		<version>6.0.12-SNAPSHOT</version>
+		<version>6.0.16-SNAPSHOT</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 
@@ -71,7 +71,6 @@
 		<dependency>
 			<groupId>com.squareup.okhttp3</groupId>
 			<artifactId>okhttp</artifactId>
-			<version>${okhttp.version}</version>
 			<optional>true</optional>
 		</dependency>
 		<dependency>
@@ -80,29 +79,21 @@
 			<version>${validator_test_case_version}</version>
 			<scope>test</scope>
 		</dependency>
+
 		<!-- Apache POI -->
 		<dependency>
 			<groupId>org.apache.poi</groupId>
 			<artifactId>poi</artifactId>
-			<version>${apache_poi_version}</version>
 			<optional>true</optional>
 		</dependency>
 		<dependency>
 			<groupId>org.apache.poi</groupId>
 			<artifactId>poi-ooxml</artifactId>
-			<version>${apache_poi_version}</version>
 			<optional>true</optional>
 		</dependency>
 		<dependency>
 			<groupId>org.apache.poi</groupId>
-			<artifactId>poi-ooxml-schemas</artifactId>
+			<artifactId>poi-ooxml-full</artifactId>
-			<version>${apache_poi_version}</version>
-			<optional>true</optional>
-		</dependency>
-		<dependency>
-			<groupId>org.apache.poi</groupId>
-			<artifactId>ooxml-schemas</artifactId>
-			<version>1.4</version>
 			<optional>true</optional>
 		</dependency>
 

org.hl7.fhir.r4b/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>org.hl7.fhir.core</artifactId>
-		<version>6.0.12-SNAPSHOT</version>
+		<version>6.0.16-SNAPSHOT</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 
@@ -65,7 +65,6 @@
 		<dependency>
 			<groupId>com.squareup.okhttp3</groupId>
 			<artifactId>okhttp</artifactId>
-			<version>${okhttp.version}</version>
 			<optional>true</optional>
 		</dependency>
 		<dependency>
@@ -86,25 +85,16 @@
 		<dependency>
 			<groupId>org.apache.poi</groupId>
 			<artifactId>poi</artifactId>
-			<version>${apache_poi_version}</version>
 			<optional>true</optional>
 		</dependency>
 		<dependency>
 			<groupId>org.apache.poi</groupId>
 			<artifactId>poi-ooxml</artifactId>
-			<version>${apache_poi_version}</version>
 			<optional>true</optional>
 		</dependency>
 		<dependency>
 			<groupId>org.apache.poi</groupId>
-			<artifactId>poi-ooxml-schemas</artifactId>
+			<artifactId>poi-ooxml-full</artifactId>
-			<version>${apache_poi_version}</version>
-			<optional>true</optional>
-		</dependency>
-		<dependency>
-			<groupId>org.apache.poi</groupId>
-			<artifactId>ooxml-schemas</artifactId>
-			<version>1.4</version>
 			<optional>true</optional>
 		</dependency>
 

org.hl7.fhir.r4b/src/main/java/org/hl7/fhir/r4b/utils/GraphDefinitionEngine.java

@@ -8,7 +8,7 @@ import java.util.LinkedList;
 import java.util.List;
 import java.util.Map;
 
-import org.apache.xmlbeans.xml.stream.ReferenceResolver;
+
 import org.hl7.fhir.exceptions.FHIRException;
 import org.hl7.fhir.r4b.context.IWorkerContext;
 import org.hl7.fhir.r4b.model.Base;

org.hl7.fhir.r5/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>org.hl7.fhir.core</artifactId>
-		<version>6.0.12-SNAPSHOT</version>
+		<version>6.0.16-SNAPSHOT</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 
@@ -73,25 +73,16 @@
 		<dependency>
 			<groupId>org.apache.poi</groupId>
 			<artifactId>poi</artifactId>
-			<version>${apache_poi_version}</version>
 			<optional>true</optional>
 		</dependency>
 		<dependency>
 			<groupId>org.apache.poi</groupId>
 			<artifactId>poi-ooxml</artifactId>
-			<version>${apache_poi_version}</version>
 			<optional>true</optional>
 		</dependency>
 		<dependency>
 			<groupId>org.apache.poi</groupId>
-			<artifactId>poi-ooxml-schemas</artifactId>
+			<artifactId>poi-ooxml-full</artifactId>
-			<version>${apache_poi_version}</version>
-			<optional>true</optional>
-		</dependency>
-		<dependency>
-			<groupId>org.apache.poi</groupId>
-			<artifactId>ooxml-schemas</artifactId>
-			<version>1.4</version>
 			<optional>true</optional>
 		</dependency>
 
@@ -116,7 +107,6 @@
 		<dependency>
 			<groupId>com.squareup.okhttp3</groupId>
 			<artifactId>okhttp</artifactId>
-			<version>${okhttp.version}</version>
 			<optional>true</optional>
 		</dependency>
 		<dependency>

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/conformance/R5ExtensionsLoader.java

@@ -123,16 +123,20 @@ public class R5ExtensionsLoader {
       if (Utilities.existsInList(lsd.info.getId(), types)) {
         StructureDefinition sd = lsd.getResource();
         count++;
+        List<ElementDefinition> rl = new ArrayList<>();
         for (ElementDefinition ed : sd.getDifferential().getElement()) {
           if (!stripTypes(ed, sd, types)) {
-            System.out.println("A problem...");
+            rl.add(ed);
           }
         }
+        sd.getDifferential().getElement().removeAll(rl);
+        rl.clear();
         for (ElementDefinition ed : sd.getSnapshot().getElement()) {
           if (!stripTypes(ed, sd, types)) {
-            System.out.println("A problem...");
+            rl.add(ed);
           }
         } 
+        sd.getSnapshot().getElement().removeAll(rl);
         sd.setWebPath(Utilities.pathURL(lsd.source.getWebLocation(), sd.getId().toLowerCase()+".html"));
         registerTerminologies(sd);
         context.cacheResourceFromPackage(sd, new PackageInformation(lsd.source));

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

@@ -157,8 +157,7 @@ public class ProfilePathProcessor {
    * @throws DefinitionException, FHIRException
    * @throws Exception
    */
-  private ElementDefinition processPaths(
+  private ElementDefinition processPaths(final ProfilePathProcessorState cursors) throws FHIRException {
-                                         final ProfilePathProcessorState cursors) throws FHIRException {
     debugProcessPathsEntry(cursors);
     ElementDefinition res = null;
     List<TypeSlice> typeList = new ArrayList<>();
@@ -170,7 +169,6 @@ public class ProfilePathProcessor {
       debugProcessPathsIteration(cursors, currentBasePath);
       List<ElementDefinition> diffMatches = profileUtilities.getDiffMatches(getDifferential(), currentBasePath, cursors.diffCursor, getDiffLimit(), getProfileName()); // get a list of matching elements in scope
 
-      
       // in the simple case, source is not sliced.
       if (!currentBase.hasSlicing() || currentBasePath.equals(getSlicing().getPath()))
       {
@@ -253,9 +251,8 @@ public class ProfilePathProcessor {
           .incrementDebugIndent()
           .withBaseLimit(newBaseLimit)
           .withDiffLimit(newDiffLimit)
-          .withProfileName(getProfileName() + profileUtilities.pathTail(diffMatches, 0)).withSlicing(new PathSlicingParams(true, null, null)).
+          .withProfileName(getProfileName() + profileUtilities.pathTail(diffMatches, 0)).withSlicing(new PathSlicingParams(true, null, null))
-      processPaths(new ProfilePathProcessorState(cursors.base, cursors.baseCursor, newDiffCursor,
+          .processPaths(new ProfilePathProcessorState(cursors.base, cursors.baseCursor, newDiffCursor, cursors.contextName, cursors.resultPathBase));
-          cursors.contextName, cursors.resultPathBase));
       if (e == null)
         throw new FHIRException(profileUtilities.getContext().formatMessage(I18nConstants.DID_NOT_FIND_SINGLE_SLICE_, diffMatches.get(0).getPath()));
       e.setSlicing(diffMatches.get(0).getSlicing());
@@ -267,9 +264,10 @@ public class ProfilePathProcessor {
       outcome.setPath(profileUtilities.fixedPathDest(getContextPathTarget(), outcome.getPath(), getRedirector(), getContextPathSource()));
       profileUtilities.updateFromBase(outcome, currentBase, getSourceStructureDefinition().getUrl());
 
-      if (!diffMatches.get(0).hasSlicing())
+      if (!diffMatches.get(0).hasSlicing()) {
         outcome.setSlicing(profileUtilities.makeExtensionSlicing());
-      else {
+        outcome.setUserData("auto-added-slicing", true);
+      } else {
         outcome.setSlicing(diffMatches.get(0).getSlicing().copy());
         for (int i = 1; i < diffMatches.size(); i++) {
           if (diffMatches.get(i).hasSlicing()) {
@@ -348,7 +346,8 @@ public class ProfilePathProcessor {
           .withBaseLimit(newBaseLimit)
           .withDiffLimit(newDiffLimit)
           .withProfileName(getProfileName() + profileUtilities.pathTail(diffMatches, i))
-          .withSlicing(new PathSlicingParams(true, slicerElement, null)).processPaths(new ProfilePathProcessorState(cursors.base, cursors.baseCursor, newDiffCursor, cursors.contextName, cursors.resultPathBase));
+          .withSlicing(new PathSlicingParams(true, slicerElement, null))
+          .processPaths(new ProfilePathProcessorState(cursors.base, cursors.baseCursor, newDiffCursor, cursors.contextName, cursors.resultPathBase));
     }
     // ok, done with that - next in the base list
     cursors.baseCursor = newBaseLimit + 1;

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

@@ -777,17 +777,21 @@ public class ProfileUtilities extends TranslatingUtilities {
               int count = slice.checkMin();
               boolean repeats = !"1".equals(slice.getFocus().getBase().getMax()); // type slicing if repeats = 1
               if (count > -1 && repeats) {
-                String msg = "The slice definition for "+slice.getFocus().getId()+" has a minimum of "+slice.getFocus().getMin()+" but the slices add up to a minimum of "+count; 
+                if (slice.getFocus().hasUserData("auto-added-slicing")) {
-                messages.add(new ValidationMessage(Source.ProfileValidator, ValidationMessage.IssueType.VALUE, url+"#"+ed.getId(), msg, forPublication ? ValidationMessage.IssueSeverity.ERROR : ValidationMessage.IssueSeverity.INFORMATION));                            
+                  slice.getFocus().setMin(count);
+                } else {
+                  String msg = "The slice definition for "+slice.getFocus().getId()+" has a minimum of "+slice.getFocus().getMin()+" but the slices add up to a minimum of "+count; 
+                  messages.add(new ValidationMessage(Source.ProfileValidator, ValidationMessage.IssueType.VALUE, url+"#"+slice.getFocus().getId(), msg, forPublication ? ValidationMessage.IssueSeverity.ERROR : ValidationMessage.IssueSeverity.INFORMATION));
+                }
               }
               count = slice.checkMax();
               if (count > -1 && repeats) {
                 String msg = "The slice definition for "+slice.getFocus().getId()+" has a maximum of "+slice.getFocus().getMax()+" but the slices add up to a maximum of "+count+". Check that this is what is intended"; 
-                messages.add(new ValidationMessage(Source.ProfileValidator, ValidationMessage.IssueType.VALUE, url+"#"+ed.getId(), msg, ValidationMessage.IssueSeverity.INFORMATION));                                            
+                messages.add(new ValidationMessage(Source.ProfileValidator, ValidationMessage.IssueType.VALUE, url+"#"+slice.getFocus().getId(), msg, ValidationMessage.IssueSeverity.INFORMATION));                                            
               }
               if (!slice.checkMinMax()) {
                 String msg = "The slice definition for "+slice.getFocus().getId()+" has a maximum of "+slice.getFocus().getMax()+" which is less than the minimum of "+slice.getFocus().getMin(); 
-                messages.add(new ValidationMessage(Source.ProfileValidator, ValidationMessage.IssueType.VALUE, url+"#"+ed.getId(), msg, ValidationMessage.IssueSeverity.WARNING));                                                            
+                messages.add(new ValidationMessage(Source.ProfileValidator, ValidationMessage.IssueType.VALUE, url+"#"+slice.getFocus().getId(), msg, ValidationMessage.IssueSeverity.WARNING));                                                            
               }
               slices.remove(s);
             }            

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

@@ -12,6 +12,8 @@ import org.hl7.fhir.r5.context.IWorkerContext;
 import org.hl7.fhir.r5.model.CodeSystem;
 import org.hl7.fhir.r5.model.CodeSystem.ConceptDefinitionComponent;
 import org.hl7.fhir.r5.model.CodeSystem.ConceptDefinitionDesignationComponent;
+import org.hl7.fhir.r5.model.CodeSystem.ConceptPropertyComponent;
+import org.hl7.fhir.r5.model.DataType;
 import org.hl7.fhir.r5.model.Resource;
 import org.hl7.fhir.r5.terminologies.CodeSystemUtilities;
 import org.hl7.fhir.utilities.TextFile;
@@ -36,7 +38,7 @@ import org.hl7.fhir.utilities.i18n.LanguageFileProducer.TranslationUnit;
  */
 public class LanguageUtils {
 
-  public static final List<String> TRANSLATION_SUPPLEMENT_RESOURCE_TYPES = Arrays.asList("CodeSystem", "StructureDefinition");
+  public static final List<String> TRANSLATION_SUPPLEMENT_RESOURCE_TYPES = Arrays.asList("CodeSystem", "StructureDefinition", "Questionnaire");
 
   private static final String ORPHAN_TRANSLATIONS_NAME = "translations.orphans";
 
@@ -64,7 +66,7 @@ public class LanguageUtils {
         if (translation == null) {
           translation = element.getTranslation(langSession.getTargetLang());
         }
-        langSession.entry(new TextUnit(pathForElement(element), base, translation));
+        langSession.entry(new TextUnit(pathForElement(element), contextForElement(element), base, translation));
       }
     }
     for (Element c: element.getChildren()) {
@@ -75,6 +77,10 @@ public class LanguageUtils {
   }
   
 
+  private String contextForElement(Element element) {
+    throw new Error("Not done yet");
+  }
+
   private String getSpecialTranslation(Element parent, Element element, String targetLang) {
     if (parent == null) {
       return null;
@@ -188,7 +194,7 @@ public class LanguageUtils {
   private Set<TranslationUnit> findTranslations(String path, String src, Set<TranslationUnit> translations) {
     Set<TranslationUnit> res = new HashSet<>();
     for (TranslationUnit translation : translations) {
-      if (path.equals(translation.getContext()) && src.equals(translation.getSrcText())) {
+      if (path.equals(translation.getId()) && src.equals(translation.getSrcText())) {
         res.add(translation);
       }
     }
@@ -202,7 +208,7 @@ public class LanguageUtils {
   public static void fillSupplement(CodeSystem cs, List<TranslationUnit> list) {
     cs.setUserData(SUPPLEMENT_NAME, "true");
     for (TranslationUnit tu : list) {
-      ConceptDefinitionComponent cd = CodeSystemUtilities.getCode(cs, tu.getContext());
+      ConceptDefinitionComponent cd = CodeSystemUtilities.getCode(cs, tu.getId());
       if (cd != null && cd.hasDisplay() && cd.getDisplay().equals(tu.getSrcText())) {
         cd.addDesignation().setLanguage(tu.getLanguage()).setValue(tu.getTgtText());
       } else {
@@ -273,9 +279,18 @@ public class LanguageUtils {
         target = d.getValue();
       }
     }
-    list.add(new TranslationUnit(lang, code, display, target));
+    list.add(new TranslationUnit(lang, code, getDefinition(cd), display, target));
     for (ConceptDefinitionComponent cd1 : cd.getConcept()) {
       generateTranslations(list, cd1, lang);
     }
   }
+
+  private static String getDefinition(ConceptDefinitionComponent cd) {
+    ConceptPropertyComponent v = CodeSystemUtilities.getProperty(cd, "translation-context");
+    if (v != null && v.hasValue()) {
+      return v.getValue().primitiveValue();
+    } else {
+      return cd.getDefinition();
+    }
+  }
 }

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

@@ -129,7 +129,7 @@ public abstract class ParserBase {
     if (res == null) {
       throw new FHIRException("Parsing FHIR content failed: "+errors.get(0).summary());      
     } else if (res.size() == 0) {
-      throw new FHIRException("Parsing FHIR content returned no elements in a context where one element is required");
+      throw new FHIRException("Parsing FHIR content returned no elements in a context where one element is required because: "+errors.get(0).summary());
     }
     if (res.size() != 1) {
       throw new FHIRException("Parsing FHIR content returned multiple elements in a context where only one element is allowed");

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

@@ -665,16 +665,16 @@ public class ValueSetValidator {
     if (code.getDisplay() == null) {
       return new ValidationResult(code.getSystem(), cs.getVersion(), cc, vc.getDisplay());
     }
-    CommaSeparatedStringBuilder b = new CommaSeparatedStringBuilder();
+    CommaSeparatedStringBuilder b = new CommaSeparatedStringBuilder(", ", " or ");
     if (cc.hasDisplay() && isOkLanguage(cs.getLanguage())) {
-      b.append(cc.getDisplay());
+      b.append("'"+cc.getDisplay()+"'");
       if (code.getDisplay().equalsIgnoreCase(cc.getDisplay())) {
         return new ValidationResult(code.getSystem(), cs.getVersion(), cc, getPreferredDisplay(cc, cs));
       }
     }
     for (ConceptDefinitionDesignationComponent ds : cc.getDesignation()) {
       if (isOkLanguage(ds.getLanguage())) {
-        b.append(ds.getValue());
+        b.append("'"+ds.getValue()+"'");
         if (code.getDisplay().equalsIgnoreCase(ds.getValue())) {
           return new ValidationResult(code.getSystem(),cs.getVersion(),  cc, getPreferredDisplay(cc, cs));
         }
@@ -685,14 +685,14 @@ public class ValueSetValidator {
       ConceptReferencePair vs = findValueSetRef(code.getSystem(), code.getCode());
       if (vs != null && (vs.getCc().hasDisplay() ||vs.getCc().hasDesignation())) {
         if (vs.getCc().hasDisplay() && isOkLanguage(vs.getValueset().getLanguage())) {
-          b.append(vs.getCc().getDisplay());
+          b.append("'"+vs.getCc().getDisplay()+"'");
           if (code.getDisplay().equalsIgnoreCase(vs.getCc().getDisplay())) {
             return new ValidationResult(code.getSystem(), cs.getVersion(), cc, getPreferredDisplay(cc, cs));
           }
         }
         for (ConceptReferenceDesignationComponent ds : vs.getCc().getDesignation()) {
           if (isOkLanguage(ds.getLanguage())) {
-            b.append(ds.getValue());
+            b.append("'"+ds.getValue()+"'");
             if (code.getDisplay().equalsIgnoreCase(ds.getValue())) {
               return new ValidationResult(code.getSystem(), cs.getVersion(), cc, getPreferredDisplay(cc, cs));
             }

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

@@ -0,0 +1,45 @@
+package org.hl7.fhir.r5.utils;
+
+import org.hl7.fhir.r5.model.Base;
+import org.hl7.fhir.r5.model.Element;
+import org.hl7.fhir.r5.model.Property;
+import org.hl7.fhir.r5.model.Resource;
+
+public class ElementVisitor {
+
+  public interface IElementVisitor {
+    public void visit(Resource resource);
+    public void visit(Element element);
+  }
+
+  private IElementVisitor visitor;
+  
+  public ElementVisitor(IElementVisitor visitor) {
+    this.visitor = visitor;
+  }
+
+  private void visitBase(Base base) {
+    for (Property p : base.children()) {
+      if (p.hasValues()) {
+        for (Base b : p.getValues()) {
+          if (b instanceof Resource) {
+            visit((Resource) b);
+          } else {
+            visit((Element) b);
+          }
+        }
+      }
+    }
+  }
+
+  public void visit(Resource res) {
+    visitor.visit(res);
+    visitBase(res);
+  }
+
+  public void visit(Element e) {
+    visitor.visit(e);
+    visitBase(e);
+  }
+
+}

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

@@ -77,7 +77,7 @@ public class ResourceLanguageFileBuilder {
         String ppath = path+"."+p.getName()+(p.isList() ? "["+i+"]" : "");
         i++;
         if (isTranslatable(p, b, pid)) {
-          sess.entry(new TextUnit(ppath, b.primitiveValue(), getTranslation(b, target)));
+          sess.entry(new TextUnit(ppath, getContext(), b.primitiveValue(), getTranslation(b, target)));
         }
         for (Property pp : b.children()) {
           process(sess, pp, pid, ppath);      
@@ -86,6 +86,11 @@ public class ResourceLanguageFileBuilder {
     }  
   }
 
+  private String getContext() {
+    throw new Error("not done yet"); 
+  }
+
+
   private boolean isTranslatable(Property p, Base b, String id) {
     if (new ContextUtilities(context).isPrimitiveDatatype(b.fhirType())) { // never any translations for non-primitives
       ElementDefinition ed = null;

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

@@ -32,7 +32,9 @@ import org.hl7.fhir.r5.model.OperationDefinition.OperationDefinitionParameterCom
 import org.hl7.fhir.r5.model.Questionnaire;
 import org.hl7.fhir.r5.model.Questionnaire.QuestionnaireItemComponent;
 import org.hl7.fhir.r5.model.Resource;
+import org.hl7.fhir.r5.model.SearchParameter;
 import org.hl7.fhir.r5.model.StructureDefinition;
+import org.hl7.fhir.r5.model.StructureDefinition.StructureDefinitionKind;
 import org.hl7.fhir.r5.model.ValueSet;
 import org.hl7.fhir.utilities.Utilities;
 
@@ -46,33 +48,32 @@ public class ResourceMinifier {
        "ConceptMap", "NamingSystem", "OperationDefinition", "SearchParameter", "Questionnaire");
   }
   
-  public void minify(Resource res) {
+  public boolean minify(Resource res) {
     if (res instanceof StructureDefinition) {
-      minifySD((StructureDefinition) res);
+      return minifySD((StructureDefinition) res);
-    }
+    } else if (res instanceof ValueSet) {
-    if (res instanceof ValueSet) {
       minifyVS((ValueSet) res);
-    }
+    } else if (res instanceof CodeSystem) {
-    if (res instanceof CodeSystem) {
       minifyCS((CodeSystem) res);
-    }
+    } else if (res instanceof CapabilityStatement) {
-    if (res instanceof CapabilityStatement) {
       minifyCS((CapabilityStatement) res);
-    }
+    } else if (res instanceof ConceptMap) {
-    if (res instanceof ConceptMap) {
       minifyCM((ConceptMap) res);
-    }
+    } else if (res instanceof NamingSystem) {
-    if (res instanceof NamingSystem) {
       minifyNS((NamingSystem) res);
-    }
+    } else if (res instanceof OperationDefinition) {
-
-    if (res instanceof OperationDefinition) {
       minifyOD((OperationDefinition) res);
-    }
+    } else if (res instanceof Questionnaire) {
-
-    if (res instanceof Questionnaire) {
       minifyQ((Questionnaire) res);
+    } else if (res instanceof SearchParameter) {
+      minifySP((SearchParameter) res);
     }
+    return true;
+  }
+
+  private void minifySP(SearchParameter sp) {
+    minCR(sp);
+    // nothing
   }
 
   private void minifyQ(Questionnaire q) {
@@ -242,14 +243,20 @@ public class ResourceMinifier {
     // can't remove anything else
   }
 
-  private void minifySD(StructureDefinition sd) {
+  private boolean minifySD(StructureDefinition sd) {
+    if (sd.getKind() == StructureDefinitionKind.LOGICAL) {
+      return false;
+    }
     minCR(sd);
     sd.setKeyword(null);
-    sd.setMapping(null); 
+    sd.setMapping(null);
-    sd.setSnapshot(null);
+    if (sd.hasDifferential()) {
+      sd.setSnapshot(null);
+    }
     for (ElementDefinition ed : sd.getDifferential().getElement()) {
       minifyED(ed);
     }
+    return true;
   }
 
   private void minifyED(ElementDefinition ed) {
@@ -272,6 +279,7 @@ public class ResourceMinifier {
       abn.setShortDoco(null);
     }
     ed.setMapping(null);
+    ed.setMustSupportElement(null);
   }
 
   private void minCR(CanonicalResource cr) {

org.hl7.fhir.report/pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <groupId>ca.uhn.hapi.fhir</groupId>
         <artifactId>org.hl7.fhir.core</artifactId>
-        <version>6.0.12-SNAPSHOT</version>
+        <version>6.0.16-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

org.hl7.fhir.utilities/pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <groupId>ca.uhn.hapi.fhir</groupId>
         <artifactId>org.hl7.fhir.core</artifactId>
-        <version>6.0.12-SNAPSHOT</version>
+        <version>6.0.16-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 
@@ -49,7 +49,6 @@
         <dependency>
             <groupId>com.squareup.okhttp3</groupId>
             <artifactId>okhttp</artifactId>
-            <version>${okhttp.version}</version>
             <optional>true</optional>
         </dependency>
 

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

@@ -74,7 +74,10 @@ public class JsonLangFileProducer extends LanguageFileProducer {
     public void entry(TextUnit unit) {
       JsonObject entry = new JsonObject();
       json.forceArray("entries").add(entry);
-      entry.add("context", unit.getContext());
+      entry.add("id", unit.getId());
+      if (unit.getContext1() != null) {
+        entry.add("context", unit.getContext1());
+      }
       entry.add("source", unit.getSrcText());
       entry.add("target", unit.getTgtText());
     }
@@ -88,7 +91,7 @@ public class JsonLangFileProducer extends LanguageFileProducer {
     JsonObject json = JsonParser.parseObject(source);
     for (JsonObject lang : json.forceArray("languages").asJsonObjects()) {
       for (JsonObject entry : lang.forceArray("entries").asJsonObjects()) {
-        list.add(new TranslationUnit(lang.asString("targetLang"), entry.asString("context"), entry.asString("source"), entry.asString("target")));
+        list.add(new TranslationUnit(lang.asString("targetLang"), entry.asString("id"), entry.asString("context"), entry.asString("source"), entry.asString("target")));
       }
     }
     return list;
@@ -118,7 +121,10 @@ public class JsonLangFileProducer extends LanguageFileProducer {
     for (TranslationUnit tu : translations) {
       JsonObject entry = new JsonObject();
       lj.forceArray("entries").add(entry);
-      entry.add("context", tu.getContext());
+      entry.add("id", tu.getId());
+      if (tu.getContext1() != null) { 
+        entry.add("context", tu.getContext1());
+      }
       entry.add("source", tu.getSrcText());
       entry.add("target", tu.getTgtText());
     }

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

@@ -18,35 +18,59 @@ import java.util.HashMap;
 public abstract class LanguageFileProducer {
 
   public static class TextUnit {
+    protected String id;
     protected String context;
     protected String srcText;
     protected String tgtText;
-    public TextUnit(String context, String srcText, String tgtText) {
+    public TextUnit(String id, String context, String srcText, String tgtText) {
       super();
+      this.id = id;
       this.context = context;
       this.srcText = srcText;
       this.tgtText = tgtText;
     }
 
-    public String getContext() {
+    /**
+     * The identity of the item being translated
+     * 
+     * @return
+     */
+    public String getId() {
+      return id;
+    }
+    
+    /**
+     * Additional language that helps establish the context
+     * @return
+     */
+    public String getContext1() {
       return context;
     }
 
+    /**
+     * The language that's being translated from
+     * 
+     * @return
+     */
     public String getSrcText() {
       return srcText;
     }
+    
+    /** 
+     * The language that's being translated to
+     * 
+     * @return
+     */
     public String getTgtText() {
       return tgtText;
     }
-
-    
   }
   
   public static class TranslationUnit extends TextUnit {
     private String language;
 
-    public TranslationUnit(String language, String context, String srcText, String tgtText) {
+    public TranslationUnit(String language, String id, String context, String srcText, String tgtText) {
-      super(context, srcText, tgtText);
+      super(id, context, srcText, tgtText);
       this.language = language;
     }
 

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

@@ -81,10 +81,10 @@ public class PoGetTextProducer extends LanguageFileProducer {
 
     @Override
     public void entry(TextUnit unit) {
-      ln("#: "+unit.getContext());
+      ln("#: "+unit.getId());
-      //    if (context != null) {
+      if (unit.getContext1() != null) {
-      //      ln("#. "+context);
+        ln("#. "+unit.getContext1());
-      //    }
+      }
       ln("msgid \""+unit.getSrcText()+"\"");
       ln("msgstr \""+(unit.getTgtText() == null ? "" : unit.getTgtText())+"\"");
       ln("");
@@ -117,7 +117,11 @@ public class PoGetTextProducer extends LanguageFileProducer {
                lang = p[1].trim();
              }
            } else if (s.startsWith("#:")) {
-             tu = new TranslationUnit(lang, s.substring(2).trim(), null, null);
+             tu = new TranslationUnit(lang, s.substring(2).trim(), null, null, null);
+           } else if (s.startsWith("#.")) {
+             if (tu != null) {
+               tu.setContext(s.substring(2).trim());
+             }
            } else {
              throw new IOException("Encountered unexpected line '"+s+"'");             
            }
@@ -166,10 +170,10 @@ public class PoGetTextProducer extends LanguageFileProducer {
     ln(po, "# "+baseLang+" -> "+targetLang);
     ln(po, "");
     for (TranslationUnit tu : translations) {
-      ln(po, "#: "+tu.getContext());
+      ln(po, "#: "+tu.getId());
-      //    if (context != null) {
+      if (tu.getContext1() != null) {
-      //      ln("#. "+context);
+        ln(po, "#. "+tu.getContext1());
-      //    }
+      }
       ln(po, "msgid \""+tu.getSrcText()+"\"");
       ln(po, "msgstr \""+(tu.getTgtText() == null ? "" : tu.getTgtText())+"\"");
       ln(po, "");

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

@@ -50,12 +50,12 @@ public class XLIFFProducer extends LanguageFileProducer {
     @Override
     public void entry(TextUnit unit) {
       i++;
-      ln("      <trans-unit id=\""+id+"\" resname=\""+unit.getContext()+"\">");
+      ln("      <trans-unit id=\""+id+"\" resname=\""+unit.getId()+"\">");
-//      if (context != null) {
+      if (unit.getContext1() != null) {
-//        ln("        <notes>");
+        ln("        <notes>");
-//        ln("          <note id=\"n"+i+"\">"+Utilities.escapeXml(context)+"</note>");
+        ln("          <note id=\"n"+i+"\">"+Utilities.escapeXml(unit.getContext1())+"</note>");
-//        ln("        </notes>");
+        ln("        </notes>");
-//      }
+      }
       ln("        <source>"+Utilities.escapeXml(unit.getSrcText())+"</source>");
       ln("        <target>"+Utilities.escapeXml(unit.getTgtText())+"</target>");
       ln("      </trans-unit>");
@@ -114,7 +114,9 @@ public class XLIFFProducer extends LanguageFileProducer {
     for (Element file : XMLUtil.getNamedChildren(xliff, "file")) {
       Element body = XMLUtil.getNamedChild(file, "body");
       for (Element transUnit : XMLUtil.getNamedChildren(body, "trans-unit")) {
-        TranslationUnit tu = new TranslationUnit(file.getAttribute("target-language"), transUnit.getAttribute("id"), 
+        Element notes = XMLUtil.getNamedChild(transUnit, "notes");
+        TranslationUnit tu = new TranslationUnit(file.getAttribute("target-language"), transUnit.getAttribute("resname"),
+            notes == null ? null : XMLUtil.getNamedChildText(notes, "note"),
             XMLUtil.getNamedChildText(transUnit, "source"), XMLUtil.getNamedChildText(transUnit, "target"));
         if (!Utilities.noString(tu.getSrcText()) && !Utilities.noString(tu.getTgtText())) {
           list.add(tu);
@@ -149,7 +151,14 @@ public class XLIFFProducer extends LanguageFileProducer {
       ln(xml, "  <file source-language=\""+baseLang+"\" target-language=\""+targetLang+"\" id=\""+id+"\" original=\"Resource "+id+"\" datatype=\"KEYVALUEJSON\">");
       ln(xml, "    <body>");
       for (TranslationUnit tu : translations) {
-        ln(xml, "      <trans-unit id=\""+id+"\" resname=\""+tu.getContext()+"\">");
+        int i = 0;
+        ln(xml, "      <trans-unit id=\""+id+"\" resname=\""+tu.getId()+"\">");
+        if (tu.getContext1() != null) {
+          i++;
+          ln(xml, "             <notes>");
+          ln(xml, "               <note id=\"n"+i+"\">"+Utilities.escapeXml(tu.getContext1())+"</note>");
+          ln(xml, "             </notes>");
+        }
         ln(xml, "        <source>"+Utilities.escapeXml(tu.getSrcText())+"</source>");
         ln(xml, "        <target>"+Utilities.escapeXml(tu.getTgtText())+"</target>");
         ln(xml, "      </trans-unit>");

org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/json/model/JsonObject.java

@@ -389,5 +389,9 @@ public class JsonObject extends JsonElement {
     this.extraComma = extraComma;
   }
   
+  public void clear() {
+    properties.clear();
+    propMap.clear();
+  }
   
 }

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

@@ -52,6 +52,7 @@ import java.util.List;
 import java.util.Map;
 import java.util.Map.Entry;
 import java.util.Set;
+import java.util.zip.Deflater;
 import java.util.zip.ZipEntry;
 import java.util.zip.ZipInputStream;
 
@@ -60,6 +61,7 @@ import org.apache.commons.compress.archivers.tar.TarArchiveInputStream;
 import org.apache.commons.compress.archivers.tar.TarArchiveOutputStream;
 import org.apache.commons.compress.compressors.gzip.GzipCompressorInputStream;
 import org.apache.commons.compress.compressors.gzip.GzipCompressorOutputStream;
+import org.apache.commons.compress.compressors.gzip.GzipParameters;
 import org.hl7.fhir.exceptions.FHIRException;
 import org.hl7.fhir.utilities.CommaSeparatedStringBuilder;
 import org.hl7.fhir.utilities.SimpleHTTPClient;
@@ -946,7 +948,9 @@ public class NpmPackage {
 
     OutputStream = new ByteArrayOutputStream();
     bufferedOutputStream = new BufferedOutputStream(OutputStream);
-    gzipOutputStream = new GzipCompressorOutputStream(bufferedOutputStream);
+    GzipParameters gp = new GzipParameters();
+    gp.setCompressionLevel(Deflater.BEST_COMPRESSION);
+    gzipOutputStream = new GzipCompressorOutputStream(stream, gp);
     tar = new TarArchiveOutputStream(gzipOutputStream);
 
 

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

@@ -463,8 +463,8 @@ Version_mismatch_The_context_has_version__loaded_and_the_new_content_being_loade
 Error_reading__from_package__ = Error reading {0} from package {1}#{2}: {3}
 Error_parsing_ = Error parsing {0}:{1}
 Unable_to_connect_to_terminology_server_Use_parameter_tx_na_tun_run_without_using_terminology_services_to_validate_LOINC_SNOMED_ICDX_etc_Error__ = Unable to connect to terminology server. Use parameter ''-tx n/a'' to run without using terminology services to validate LOINC, SNOMED, ICD-X etc. Error = {0}
-Display_Name_for__should_be_one_of__instead_of_one = Wrong Display Name ''{4}'' for {1}#{2} - should be ''{3}'' (for the language(s) ''{5}'') 
+Display_Name_for__should_be_one_of__instead_of_one = Wrong Display Name ''{4}'' for {1}#{2} - should be {3} (for the language(s) ''{5}'') 
-Display_Name_for__should_be_one_of__instead_of_other = Wrong Display Name ''{4}'' for {1}#{2} - should be one of {0} choices: ''{3}'' for the language(s) ''{5}''
+Display_Name_for__should_be_one_of__instead_of_other = Wrong Display Name ''{4}'' for {1}#{2} - should be one of {0} choices: {3} (for the language(s) ''{5}'')
 Unknown_Code__in_ = Unknown Code ''{0}'' in the system ''{1}''
 UNKNOWN_CODE__IN_FRAGMENT = Unknown Code ''{0}'' in the system ''{1}'' - note that the code system is labeled as a fragment, so the code may be valid in some other fragment
 Code_found_in_expansion_however_ = Code found in expansion, however: {0}

org.hl7.fhir.validation.cli/pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <groupId>ca.uhn.hapi.fhir</groupId>
         <artifactId>org.hl7.fhir.core</artifactId>
-        <version>6.0.12-SNAPSHOT</version>
+        <version>6.0.16-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 
@@ -204,7 +204,6 @@
         <dependency>
             <groupId>org.apache.poi</groupId>
             <artifactId>poi</artifactId>
-            <version>${apache_poi_version}</version>
             <optional>false</optional>
             <scope>compile</scope>
         </dependency>
@@ -212,7 +211,13 @@
         <dependency>
             <groupId>org.apache.poi</groupId>
             <artifactId>poi-ooxml</artifactId>
-            <version>${apache_poi_version}</version>
+            <optional>false</optional>
+            <scope>compile</scope>
+        </dependency>
+
+        <dependency>
+            <groupId>org.apache.poi</groupId>
+            <artifactId>poi-ooxml-full</artifactId>
             <optional>false</optional>
             <scope>compile</scope>
         </dependency>
@@ -275,7 +280,6 @@
         <dependency>
             <groupId>com.squareup.okhttp3</groupId>
             <artifactId>okhttp</artifactId>
-            <version>${okhttp.version}</version>
       </dependency>
         <dependency>
             <groupId>com.atlassian.commonmark</groupId>

org.hl7.fhir.validation/pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <groupId>ca.uhn.hapi.fhir</groupId>
         <artifactId>org.hl7.fhir.core</artifactId>
-        <version>6.0.12-SNAPSHOT</version>
+        <version>6.0.16-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 
@@ -14,6 +14,7 @@
 
     <properties>
         <checkstyle_config_location>${project.parent.basedir}</checkstyle_config_location>
+        <info_cqframework_version>1.5.12</info_cqframework_version>
     </properties>
 
     <dependencies>
@@ -132,6 +133,13 @@
             <groupId>info.cqframework</groupId>
             <artifactId>model</artifactId>
             <version>${info_cqframework_version}</version>
+            <exclusions>
+                <!-- exclude this in favor of 1.9.4 for security reasons -->
+                <exclusion>
+                    <groupId>commons-beanutils</groupId>
+                    <artifactId>commons-beanutils</artifactId>
+                </exclusion>
+            </exclusions>
         </dependency>
         <dependency>
             <groupId>info.cqframework</groupId>
@@ -153,12 +161,15 @@
             <artifactId>qdm</artifactId>
             <version>${info_cqframework_version}</version>
         </dependency>
-
+        <dependency>
+            <groupId>commons-beanutils</groupId>
+            <artifactId>commons-beanutils</artifactId>
+            <version>1.9.4</version>
+        </dependency>
         <!-- OkHttpDependency -->
         <dependency>
             <groupId>com.squareup.okhttp3</groupId>
             <artifactId>okhttp</artifactId>
-            <version>${okhttp.version}</version>
             <optional>true</optional>
         </dependency>
 

org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/cli/tasks/TxTestsTask.java

@@ -42,7 +42,7 @@ public class TxTestsTask extends StandaloneTask{
       final String version = Params.getParam(args, Params.VERSION);
       final String tx = Params.getParam(args, Params.TERMINOLOGY);
       final String filter = Params.getParam(args, Params.FILTER);
-      boolean ok = new TxTester(new TxTester.InternalTxLoader(source, output), tx).setOutput(output).execute(version, filter);
+      boolean ok = new TxTester(new TxTester.InternalTxLoader(source, output), tx, false).setOutput(output).execute(version, filter);
       System.exit(ok ? 1 : 0);
   }
 }

org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/special/TxTester.java

@@ -58,16 +58,18 @@ public class TxTester {
   private String error;
   private String output;
   private ITerminologyClient tx;
+  private boolean tight;
   
 
-  public TxTester(ITxTesterLoader loader, String server) {
+  public TxTester(ITxTesterLoader loader, String server, boolean tight) {
     super();
     this.server = server;
     this.loader = loader;
+    this.tight = tight;
   }
 
   public static void main(String[] args) throws Exception {
-    new TxTester(new InternalTxLoader(args[0]), args[1]).execute(args[2], args[3]);
+    new TxTester(new InternalTxLoader(args[0]), args[1], "true".equals(args[2])).execute(args[2], args[3]);
   }
   
   public boolean execute(String version, String filter) throws IOException, URISyntaxException {
@@ -239,12 +241,12 @@ public class TxTester {
     String vsj;
     try {
       ValueSet vs = tx.expandValueset(null, p, null);
-      TxTesterScrubbers.scrub(vs);
+      TxTesterScrubbers.scrubVS(vs, tight);
       TxTesterSorters.sortValueSet(vs);
       vsj = new org.hl7.fhir.r5.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).composeString(vs);
     } catch (EFhirClientException e) {
       OperationOutcome oo = e.getServerErrors().get(0); 
-      TxTesterScrubbers.scrub(oo);
+      TxTesterScrubbers.scrubOO(oo, tight);
       vsj = new org.hl7.fhir.r5.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).composeString(oo);
     }
     String diff = CompareUtilities.checkJsonSrcIsSame(resp, vsj);
@@ -263,7 +265,7 @@ public class TxTester {
     String pj;
     try {
       Parameters po = tx.validateVS(p);
-      TxTesterScrubbers.scrub(po);
+      TxTesterScrubbers.scrubParams(po);
       TxTesterSorters.sortParameters(po);
       pj = new org.hl7.fhir.r5.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).composeString(po);
     } catch (EFhirClientException e) {

org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/special/TxTesterScrubbers.java

@@ -1,20 +1,85 @@
 package org.hl7.fhir.validation.special;
 
 import org.hl7.fhir.r5.model.DomainResource;
+import org.hl7.fhir.r5.model.Element;
+import org.hl7.fhir.r5.model.Extension;
+import org.hl7.fhir.r5.model.OperationOutcome;
 import org.hl7.fhir.r5.model.Parameters;
+import org.hl7.fhir.r5.model.Resource;
 import org.hl7.fhir.r5.model.ValueSet;
+import org.hl7.fhir.r5.utils.ElementVisitor;
+import org.hl7.fhir.r5.utils.ElementVisitor.IElementVisitor;
+import org.hl7.fhir.utilities.Utilities;
 
 public class TxTesterScrubbers {
 
-  public static void scrub(DomainResource dr) {
+
-    dr.setText(null);
+  public static class TxTesterScrubberVisitor implements IElementVisitor {
-    dr.setMeta(null);
+
+    private boolean tight;
     
+    protected TxTesterScrubberVisitor(boolean tight) {
+      super();
+      this.tight = tight;
+    }
+
+    private boolean isManagedExtension(Extension extension) {
+      return !tight || !Utilities.isAbsoluteUrl(extension.getUrl()) || Utilities.existsInList(extension.getUrl(), 
+          "http://hl7.org/fhir/StructureDefinition/codesystem-alternate", 
+          "http://hl7.org/fhir/StructureDefinition/codesystem-conceptOrder",
+          "http://hl7.org/fhir/StructureDefinition/codesystem-label", 
+          "http://hl7.org/fhir/StructureDefinition/coding-sctdescid",
+          "http://hl7.org/fhir/StructureDefinition/itemWeight", 
+          "http://hl7.org/fhir/StructureDefinition/rendering-style", 
+          "http://hl7.org/fhir/StructureDefinition/rendering-xhtml", 
+          "http://hl7.org/fhir/StructureDefinition/translation",
+          "http://hl7.org/fhir/StructureDefinition/valueset-concept-definition", 
+          "http://hl7.org/fhir/StructureDefinition/valueset-conceptOrder", 
+          "http://hl7.org/fhir/StructureDefinition/valueset-deprecated", 
+          "http://hl7.org/fhir/StructureDefinition/valueset-label", 
+          "http://hl7.org/fhir/StructureDefinition/valueset-supplement", 
+          "http://hl7.org/fhir/test/CodeSystem/de-multi", 
+          "http://hl7.org/fhir/test/CodeSystem/en-multi", 
+          "http://hl7.org/fhir/test/StructureDefinition/unknown-extension-1", 
+          "http://hl7.org/fhir/test/StructureDefinition/unknown-extension-3", 
+          "http://hl7.org/fhir/test/StructureDefinition/unknown-extension-4", 
+          "http://hl7.org/fhir/test/StructureDefinition/unknown-extension-5", 
+          "http://hl7.org/fhir/test/ValueSet/extensions-bad-supplement", 
+          "http://hl7.org/fhir/test/ValueSet/simple-all", 
+          "http://hl7.org/fhir/test/ValueSet/simple-enumerated", 
+          "http://hl7.org/fhir/test/ValueSet/simple-filter-isa");
+    }
+    
+    @Override
+    public void visit(Resource resource) {
+      if (resource instanceof DomainResource) {
+        DomainResource dr = (DomainResource) resource;
+        dr.getExtension().removeIf(ext -> !isManagedExtension(ext));
+      } 
+    }
+
+    @Override
+    public void visit(Element element) {
+      element.getExtension().removeIf(ext -> !isManagedExtension(ext));
+    }
+  }
+  
+  public static void scrubDR(DomainResource dr, boolean tight) {
+    dr.setText(null);
+    dr.setMeta(null);  
+    new ElementVisitor(new TxTesterScrubberVisitor(tight)).visit(dr);
   }
 
-  public static void scrub(Parameters po) {
+  public static void scrubVS(ValueSet vs, boolean tight) {
+    scrubDR(vs, tight);    
+  }
+
+  public static void scrubParams(Parameters po) {
     po.setMeta(null);
-    
+  }
+
+  public static void scrubOO(OperationOutcome po, boolean tight) {
+    scrubDR(po, tight);
   }
 
 }

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

@@ -93,7 +93,7 @@ public class ExternalTerminologyServiceTests implements ITxTesterLoader {
   public void test() throws Exception {
     if (SERVER != null) {
       if (tester == null) {
-        tester = new TxTester(this, SERVER);
+        tester = new TxTester(this, SERVER, true);
       }
       String err = tester.executeTest(setup.suite, setup.test);
       Assertions.assertTrue(err == null, err);

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

@@ -161,7 +161,7 @@ public class TerminologyServiceTests {
           removeParameter(vse.getValueset(), "excludeNested");
         }
         TxTesterSorters.sortValueSet(vse.getValueset());
-        TxTesterScrubbers.scrub(vse.getValueset());
+        TxTesterScrubbers.scrubVS(vse.getValueset(), false);
         String vsj = new JsonParser().setOutputStyle(OutputStyle.PRETTY).composeString(vse.getValueset());
         String diff = CompareUtilities.checkJsonSrcIsSame(resp, vsj);
         if (diff != null) {
@@ -205,7 +205,7 @@ public class TerminologyServiceTests {
       }
       e.getDetails().setText(vse.getError());
       oo.addIssue(e);
-      TxTesterScrubbers.scrub(oo);
+      TxTesterScrubbers.scrubOO(oo, false);
       
       String ooj = new JsonParser().setOutputStyle(OutputStyle.PRETTY).composeString(oo);
       String diff = CompareUtilities.checkJsonSrcIsSame(resp, ooj);
@@ -291,7 +291,7 @@ public class TerminologyServiceTests {
       res.addParameter().setName("issues").setResource(oo);
     }
     TxTesterSorters.sortParameters(res);
-    TxTesterScrubbers.scrub(res);
+    TxTesterScrubbers.scrubParams(res);
     
     String pj = new JsonParser().setOutputStyle(OutputStyle.PRETTY).composeString(res);
     String diff = CompareUtilities.checkJsonSrcIsSame(resp, pj);

pom.xml

@@ -14,23 +14,22 @@
     HAPI FHIR
     -->
     <artifactId>org.hl7.fhir.core</artifactId>
-    <version>6.0.12-SNAPSHOT</version>
+    <version>6.0.16-SNAPSHOT</version>
     <packaging>pom</packaging>
 
     <properties>
         <hapi_fhir_version>6.4.1</hapi_fhir_version>
-        <validator_test_case_version>1.3.8</validator_test_case_version>
+        <validator_test_case_version>1.3.10-SNAPSHOT</validator_test_case_version>
         <jackson_version>2.14.0</jackson_version>
         <junit_jupiter_version>5.9.2</junit_jupiter_version>
         <junit_platform_launcher_version>1.8.2</junit_platform_launcher_version>
         <maven_surefire_version>3.0.0-M5</maven_surefire_version>
         <maven_clean_version>3.1.0</maven_clean_version>
-        <okhttp.version>4.9.3</okhttp.version>
+        <okhttp.version>4.10.0</okhttp.version>
         <jacoco_version>0.8.9</jacoco_version>
-        <info_cqframework_version>1.5.12</info_cqframework_version>
         <lombok_version>1.18.22</lombok_version>
         <byte_buddy_version>1.12.14</byte_buddy_version>
-        <apache_poi_version>4.1.1</apache_poi_version>
+        <apache_poi_version>5.2.1</apache_poi_version>
         <saxon_he_version>9.8.0-15</saxon_he_version>
         <maven.compiler.release>11</maven.compiler.release>
         <maven.compiler.source>11</maven.compiler.source>
@@ -164,7 +163,51 @@
                 <groupId>net.sf.saxon</groupId>
                 <artifactId>Saxon-HE</artifactId>
                 <version>${saxon_he_version}</version>
+            </dependency>
 
+            <!-- Apache POI -->
+            <dependency>
+                <groupId>org.apache.poi</groupId>
+                <artifactId>poi</artifactId>
+                <version>${apache_poi_version}</version>
+            </dependency>
+            <dependency>
+                <groupId>org.apache.poi</groupId>
+                <artifactId>poi-ooxml</artifactId>
+                <version>${apache_poi_version}</version>
+                <exclusions>
+                    <!-- exclude this because it collides with the needed poi-ooxml-full-->
+                    <exclusion>
+                        <groupId>org.apache.poi</groupId>
+                        <artifactId>poi-ooxml-lite</artifactId>
+                    </exclusion>
+                </exclusions>
+            </dependency>
+
+            <!-- include this to replace poi-ooxml-lite in poi-ooxml -->
+            <dependency>
+                <groupId>org.apache.poi</groupId>
+                <artifactId>poi-ooxml-full</artifactId>
+                <version>${apache_poi_version}</version>
+            </dependency>
+            <dependency>
+                <groupId>com.squareup.okhttp3</groupId>
+                <artifactId>okhttp</artifactId>
+                <version>${okhttp.version}</version>
+                <exclusions>
+                    <!-- Exclude this because older jetbrains pom contains an insecure pom definition-->
+                    <exclusion>
+                        <groupId>org.jetbrains</groupId>
+                        <artifactId>annotations</artifactId>
+                    </exclusion>
+                </exclusions>
+            </dependency>
+
+            <!-- Included because okttp3 used a vulnerable version -->
+            <dependency>
+                <groupId>org.jetbrains</groupId>
+                <artifactId>annotations</artifactId>
+                <version>16.0.1</version>
             </dependency>
         </dependencies>
     </dependencyManagement>