Merge branch 'hapifhir:master' into master

checkstyle.xml

@@ -0,0 +1,27 @@
+<?xml version="1.0"?>
+<!DOCTYPE module PUBLIC
+        "-//Puppy Crawl//DTD Check Configuration 1.3//EN"
+        "http://www.puppycrawl.com/dtds/configuration_1_3.dtd">
+
+<module name="Checker">
+
+    <property name="severity" value="error"/>
+    <property name="charset" value="UTF-8"/>
+    <property name="fileExtensions" value="java, properties, xml, js, json"/>
+    <module name="TreeWalker">
+        <!--
+        <module name="TodoComment">-->
+            <!-- The (?i) below means Case Insensitive -->
+        <!--<property name="format" value="(?i)FIXME"/>
+-->
+  <module name="RegexpSinglelineJava">
+      <property name="format" value="org\.jetbrains\.annotations\.NotNull"/>
+  </module>
+  <module name="RegexpSinglelineJava">
+      <property name="format" value="org\.jetbrains\.annotations\.Nullable"/>
+  </module>
+  <module name="RegexpSinglelineJava">
+      <property name="format" value="org\.jetbrains\.annotations\.\*"/>
+  </module>
+</module>
+</module>

codecov.yml

@@ -0,0 +1,8 @@
+coverage:
+  status:
+    project:
+      default:
+        informational: true
+    patch:
+      default:
+        informational: true

org.hl7.fhir.convertors/checkstyle_suppressions.xml

@@ -0,0 +1,8 @@
+<?xml version="1.0"?>
+<!DOCTYPE suppressions PUBLIC
+        "-//Checkstyle//DTD SuppressionFilter Configuration 1.2//EN"
+        "https://checkstyle.org/dtds/suppressions_1_2.dtd">
+
+<suppressions>
+  
+</suppressions>

org.hl7.fhir.convertors/pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <groupId>ca.uhn.hapi.fhir</groupId>
         <artifactId>org.hl7.fhir.core</artifactId>
-        <version>5.6.99-SNAPSHOT</version>
+        <version>5.6.100-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 
@@ -87,7 +87,7 @@
         <dependency>
           <groupId>com.squareup.okhttp3</groupId>
           <artifactId>okhttp</artifactId>
-          <version>4.9.0</version>
+          <version>${okhttp.version}</version>
           <optional>true</optional>
         </dependency>
 

org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/loaders/loaderR5/BaseLoaderR5.java

@@ -3,8 +3,22 @@ package org.hl7.fhir.convertors.loaders.loaderR5;
 import java.io.IOException;
 
 import org.hl7.fhir.exceptions.FHIRException;
+import org.hl7.fhir.r5.conformance.profile.ProfileUtilities;
 import org.hl7.fhir.r5.context.IWorkerContext.IContextResourceLoader;
+import org.hl7.fhir.r5.model.CanonicalResource;
+import org.hl7.fhir.r5.model.CanonicalType;
+import org.hl7.fhir.r5.model.CapabilityStatement;
+import org.hl7.fhir.r5.model.CodeSystem;
+import org.hl7.fhir.r5.model.ElementDefinition;
+import org.hl7.fhir.r5.model.OperationDefinition;
+import org.hl7.fhir.r5.model.OperationDefinition.OperationDefinitionParameterComponent;
 import org.hl7.fhir.r5.model.Resource;
+import org.hl7.fhir.r5.model.StructureDefinition;
+import org.hl7.fhir.r5.model.UriType;
+import org.hl7.fhir.r5.model.ValueSet;
+import org.hl7.fhir.r5.model.ValueSet.ConceptSetComponent;
+import org.hl7.fhir.r5.model.ElementDefinition.TypeRefComponent;
+import org.hl7.fhir.utilities.Utilities;
 import org.hl7.fhir.utilities.VersionUtilities;
 import org.hl7.fhir.utilities.npm.NpmPackage;
 
@@ -18,12 +32,8 @@ import lombok.experimental.Accessors;
 public abstract class BaseLoaderR5 implements IContextResourceLoader {
 
   protected final String URL_BASE = "http://hl7.org/fhir/";
-  protected final String URL_DSTU2 = "http://hl7.org/fhir/1.0/";
-  protected final String URL_DSTU2016MAY = "http://hl7.org/fhir/1.4/";
-  protected final String URL_DSTU3 = "http://hl7.org/fhir/3.0/";
-  protected final String URL_R4 = "http://hl7.org/fhir/4.0/";
   protected final String URL_ELEMENT_DEF_NAMESPACE = "http://hl7.org/fhir/StructureDefinition/elementdefinition-namespace";
-  @Getter @Setter protected boolean patchUrls;
+  protected boolean patchUrls;
   @Getter @Setter protected boolean killPrimitives;
   @Getter protected String[] types;
   protected ILoaderKnowledgeProviderR5 lkp;
@@ -73,4 +83,87 @@ public abstract class BaseLoaderR5 implements IContextResourceLoader {
     }
   }
 
+  public boolean isPatchUrls() {
+    return patchUrls;
+  }
+
+  public void setPatchUrls(boolean patchUrls) {
+    this.patchUrls = patchUrls;
+  }
+
+  protected abstract String versionString();
+  
+
+  @Override
+  public String patchUrl(String url, String type) {
+    if (!patchUrls || url == null) {
+      return url;
+    } else if (url.startsWith("http://hl7.org/fhir/"+type+"/")) {
+      return "http://hl7.org/fhir/"+versionString()+"/"+url.substring(20);
+    } else if ("CodeSystem".equals(type) && url.startsWith("http://hl7.org/fhir/")) {      
+      return "http://hl7.org/fhir/"+versionString()+"/"+url.substring(20);
+    } else {
+      return url;
+    }
+  }
+
+  // we don't patch everything. It's quite hard work to do that,
+  // and we only patch URLs to support version transforms
+  // so we just patch sd/od -> vs -> cs
+  protected void doPatchUrls(Resource resource) {
+    if (resource instanceof CanonicalResource) {
+      CanonicalResource cr = (CanonicalResource) resource;
+      cr.setUrl(patchUrl(cr.getUrl(), cr.fhirType()));
+      if (cr instanceof StructureDefinition) {
+        StructureDefinition sd = (StructureDefinition) cr;
+        sd.setBaseDefinition(patchUrl(sd.getBaseDefinition(), sd.fhirType()));
+        new ProfileUtilities(null, null, null, null).setIds(sd, false);
+        sd.addExtension().setUrl(URL_ELEMENT_DEF_NAMESPACE).setValue(new UriType(URL_BASE));
+        for (ElementDefinition ed : sd.getSnapshot().getElement())
+          patchUrl(ed);
+        for (ElementDefinition ed : sd.getDifferential().getElement())
+          patchUrl(ed);
+      }
+
+      if (cr instanceof ValueSet) {
+        ValueSet vs = (ValueSet) cr;
+        for (ConceptSetComponent inc : vs.getCompose().getInclude()) {
+          inc.setSystem(patchUrl(inc.getSystem(), "CodeSystem"));
+        }
+        for (ConceptSetComponent inc : vs.getCompose().getExclude()) {
+          inc.setSystem(patchUrl(inc.getSystem(), "CodeSystem"));
+        }        
+      }
+      if (cr instanceof OperationDefinition) {
+        OperationDefinition od = (OperationDefinition) cr;
+        for (OperationDefinitionParameterComponent param : od.getParameter()) {
+          patchUrls(param);
+        }        
+      }
+    }
+  }
+  
+  private void patchUrls(OperationDefinitionParameterComponent param) {
+    if (param.hasBinding()) {
+      param.getBinding().setValueSet(patchUrl(param.getBinding().getValueSet(), "ValueSet"));      
+    }
+    for (OperationDefinitionParameterComponent p : param.getPart()) {
+      patchUrls(p);
+    }
+  }
+
+  private void patchUrl(ElementDefinition ed) {
+    for (TypeRefComponent tr : ed.getType()) {
+      if (!Utilities.isAbsoluteUrl(tr.getCode())) {
+        tr.setCode(URL_BASE+versionString()+"/StructureDefinition/"+tr.getCode());
+      }
+      for (CanonicalType s : tr.getTargetProfile()) {
+        s.setValue(patchUrl(s.getValue(), "StructureDefinitino"));
+      }
+    }
+    if (ed.hasBinding()) {
+      ed.getBinding().setValueSet(patchUrl(ed.getBinding().getValueSet(), "ValueSet"));
+    }
+  }
+
 }

org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/loaders/loaderR5/R2016MayToR5Loader.java

@@ -98,13 +98,10 @@ public class R2016MayToR5Loader extends BaseLoaderR5 {
       }
       b.getEntry().removeAll(remove);
     }
-    for (BundleEntryComponent be : b.getEntry()) {
-      if (be.hasResource() && be.getResource() instanceof StructureDefinition) {
-        StructureDefinition sd = (StructureDefinition) be.getResource();
-        new ProfileUtilities(null, null, null, null).setIds(sd, false);
     if (patchUrls) {
-          sd.setUrl(sd.getUrl().replace(URL_BASE, URL_DSTU2016MAY));
+      for (BundleEntryComponent be : b.getEntry()) {
-          sd.addExtension().setUrl(URL_ELEMENT_DEF_NAMESPACE).setValue(new UriType(URL_BASE));
+        if (be.hasResource()) {
+          doPatchUrls(be.getResource());
         }
       }
     }
@@ -128,33 +125,20 @@ public class R2016MayToR5Loader extends BaseLoaderR5 {
       throw new FHIRException("Cannot kill primitives when using deferred loading");
     }
     if (patchUrls) {
-      if (r5 instanceof StructureDefinition) {
+      doPatchUrls(r5);
-        StructureDefinition sd = (StructureDefinition) r5;
-        sd.setUrl(sd.getUrl().replace(URL_BASE, URL_R4));
-        sd.addExtension().setUrl(URL_ELEMENT_DEF_NAMESPACE).setValue(new UriType(URL_BASE));
-        for (ElementDefinition ed : sd.getSnapshot().getElement())
-          patchUrl(ed);
-        for (ElementDefinition ed : sd.getDifferential().getElement())
-          patchUrl(ed);
-      }
     }
     return r5;
   }
 
-  private void patchUrl(ElementDefinition ed) {
-    for (TypeRefComponent tr : ed.getType()) {
-      for (CanonicalType s : tr.getTargetProfile()) {
-        s.setValue(s.getValue().replace(URL_BASE, URL_DSTU2016MAY));
-      }
-      for (CanonicalType s : tr.getProfile()) {
-        s.setValue(s.getValue().replace(URL_BASE, URL_DSTU2016MAY));
-      }
-    }
-  }
 
   @Override
   public List<CodeSystem> getCodeSystems() {
     return new ArrayList<>();
   }
 
+  @Override
+  protected String versionString() {
+    return "4.3";
+  }
+
 }

org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/loaders/loaderR5/R2ToR5Loader.java

@@ -102,10 +102,8 @@ public class R2ToR5Loader extends BaseLoaderR5 implements IContextResourceLoader
     }
     if (patchUrls) {
       for (BundleEntryComponent be : b.getEntry()) {
-        if (be.hasResource() && be.getResource() instanceof StructureDefinition) {
+        if (be.hasResource()) {
-          StructureDefinition sd = (StructureDefinition) be.getResource();
+          doPatchUrls(be.getResource());
-          sd.setUrl(sd.getUrl().replace(URL_BASE, URL_DSTU2));
-          sd.addExtension().setUrl(URL_ELEMENT_DEF_NAMESPACE).setValue(new UriType(URL_BASE));
         }
       }
     }
@@ -126,30 +124,11 @@ public class R2ToR5Loader extends BaseLoaderR5 implements IContextResourceLoader
       throw new FHIRException("Cannot kill primitives when using deferred loading");
     }
     if (patchUrls) {
-      if (r5 instanceof StructureDefinition) {
+      doPatchUrls(r5);
-        StructureDefinition sd = (StructureDefinition) r5;
-        sd.setUrl(sd.getUrl().replace(URL_BASE, URL_R4));
-        sd.addExtension().setUrl(URL_ELEMENT_DEF_NAMESPACE).setValue(new UriType(URL_BASE));
-        for (ElementDefinition ed : sd.getSnapshot().getElement())
-          patchUrl(ed);
-        for (ElementDefinition ed : sd.getDifferential().getElement())
-          patchUrl(ed);
-      }
     }
     return r5;
   }
 
-  private void patchUrl(ElementDefinition ed) {
-    for (TypeRefComponent tr : ed.getType()) {
-      for (CanonicalType s : tr.getTargetProfile()) {
-        s.setValue(s.getValue().replace(URL_BASE, URL_DSTU2));
-      }
-      for (CanonicalType s : tr.getProfile()) {
-        s.setValue(s.getValue().replace(URL_BASE, URL_DSTU2));
-      }
-    }
-  }
-  
   @Override
   public List<CodeSystem> getCodeSystems() {
     List<CodeSystem> list = new ArrayList<>();
@@ -160,4 +139,9 @@ public class R2ToR5Loader extends BaseLoaderR5 implements IContextResourceLoader
     return list;
   }
 
+  @Override
+  protected String versionString() {
+    return "1.0";
+  }
+
 }

org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/loaders/loaderR5/R3ToR5Loader.java

@@ -99,14 +99,8 @@ public class R3ToR5Loader extends BaseLoaderR5 implements IContextResourceLoader
     }
     if (patchUrls) {
       for (BundleEntryComponent be : b.getEntry()) {
-        if (be.hasResource() && be.getResource() instanceof StructureDefinition) {
+        if (be.hasResource()) {
-          StructureDefinition sd = (StructureDefinition) be.getResource();
+          doPatchUrls(be.getResource());
-          sd.setUrl(sd.getUrl().replace(URL_BASE, URL_DSTU3));
-          sd.addExtension().setUrl(URL_ELEMENT_DEF_NAMESPACE).setValue(new UriType(URL_BASE));
-          for (ElementDefinition ed : sd.getSnapshot().getElement())
-            patchUrl(ed);
-          for (ElementDefinition ed : sd.getDifferential().getElement())
-            patchUrl(ed);
         }          
       }
     }
@@ -130,33 +124,19 @@ public class R3ToR5Loader extends BaseLoaderR5 implements IContextResourceLoader
       throw new FHIRException("Cannot kill primitives when using deferred loading");
     }
     if (patchUrls) {
-      if (r5 instanceof StructureDefinition) {
+      doPatchUrls(r5);
-        StructureDefinition sd = (StructureDefinition) r5;
-        sd.setUrl(sd.getUrl().replace(URL_BASE, URL_R4));
-        sd.addExtension().setUrl(URL_ELEMENT_DEF_NAMESPACE).setValue(new UriType(URL_BASE));
-        for (ElementDefinition ed : sd.getSnapshot().getElement())
-          patchUrl(ed);
-        for (ElementDefinition ed : sd.getDifferential().getElement())
-          patchUrl(ed);
-      }
     }
     return r5;
   }
 
-  private void patchUrl(ElementDefinition ed) {
-    for (TypeRefComponent tr : ed.getType()) {
-      for (CanonicalType s : tr.getTargetProfile()) {
-        s.setValue(s.getValue().replace(URL_BASE, URL_DSTU3));
-      }
-      for (CanonicalType s : tr.getProfile()) {
-        s.setValue(s.getValue().replace(URL_BASE, URL_DSTU3));
-      }
-    }
-  }
-  
   @Override
   public List<CodeSystem> getCodeSystems() {
     return new ArrayList<>();
   }
 
+  @Override
+  protected String versionString() {
+    return "3.0";
+  }
+
 }

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

@@ -103,14 +103,8 @@ public class R4BToR5Loader extends BaseLoaderR5 implements IContextResourceLoade
     }
     if (patchUrls) {
       for (BundleEntryComponent be : b.getEntry()) {
-        if (be.hasResource() && be.getResource() instanceof StructureDefinition) {
+        if (be.hasResource()) {
-          StructureDefinition sd = (StructureDefinition) be.getResource();
+          doPatchUrls(be.getResource());
-          sd.setUrl(sd.getUrl().replace(URL_BASE, URL_R4));
-          sd.addExtension().setUrl(URL_ELEMENT_DEF_NAMESPACE).setValue(new UriType(URL_BASE));
-          for (ElementDefinition ed : sd.getSnapshot().getElement())
-            patchUrl(ed);
-          for (ElementDefinition ed : sd.getDifferential().getElement())
-            patchUrl(ed);
         }
       }
     }
@@ -137,34 +131,20 @@ public class R4BToR5Loader extends BaseLoaderR5 implements IContextResourceLoade
       r5 = new StructureDefinitionHacker(version).fixSD((StructureDefinition) r5);
     }
     if (patchUrls) {
-      if (r5 instanceof StructureDefinition) {
+      doPatchUrls(r5);
-        StructureDefinition sd = (StructureDefinition) r5;
-        sd.setUrl(sd.getUrl().replace(URL_BASE, "http://hl7.org/fhir/4.0/"));
-        sd.addExtension().setUrl(URL_ELEMENT_DEF_NAMESPACE).setValue(new UriType("http://hl7.org/fhir"));
-        for (ElementDefinition ed : sd.getSnapshot().getElement())
-          patchUrl(ed);
-        for (ElementDefinition ed : sd.getDifferential().getElement())
-          patchUrl(ed);
-      }
     }
     return r5;
   }
   
-  private void patchUrl(ElementDefinition ed) {
-    for (TypeRefComponent tr : ed.getType()) {
-      for (CanonicalType s : tr.getTargetProfile()) {
-        s.setValue(s.getValue().replace(URL_BASE, "http://hl7.org/fhir/4.0/"));
-      }
-      for (CanonicalType s : tr.getProfile()) {
-        s.setValue(s.getValue().replace(URL_BASE, "http://hl7.org/fhir/4.0/"));
-      }
-    }
-  }
-  
   @Override
   public List<CodeSystem> getCodeSystems() {
     return new ArrayList<>();
   }
 
+  @Override
+  protected String versionString() {
+    return "4.3";
+  }
+
 
 }

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

@@ -103,14 +103,8 @@ public class R4ToR5Loader extends BaseLoaderR5 implements IContextResourceLoader
     }
     if (patchUrls) {
       for (BundleEntryComponent be : b.getEntry()) {
-        if (be.hasResource() && be.getResource() instanceof StructureDefinition) {
+        if (be.hasResource()) {
-          StructureDefinition sd = (StructureDefinition) be.getResource();
+          doPatchUrls(be.getResource());
-          sd.setUrl(sd.getUrl().replace(URL_BASE, URL_R4));
-          sd.addExtension().setUrl(URL_ELEMENT_DEF_NAMESPACE).setValue(new UriType(URL_BASE));
-          for (ElementDefinition ed : sd.getSnapshot().getElement())
-            patchUrl(ed);
-          for (ElementDefinition ed : sd.getDifferential().getElement())
-            patchUrl(ed);
         }
       }
     }
@@ -137,34 +131,21 @@ public class R4ToR5Loader extends BaseLoaderR5 implements IContextResourceLoader
       r5 = new StructureDefinitionHacker(version).fixSD((StructureDefinition) r5);
     }
     if (patchUrls) {
-      if (r5 instanceof StructureDefinition) {
+      doPatchUrls(r5);
-        StructureDefinition sd = (StructureDefinition) r5;
-        sd.setUrl(sd.getUrl().replace(URL_BASE, "http://hl7.org/fhir/4.0/"));
-        sd.addExtension().setUrl(URL_ELEMENT_DEF_NAMESPACE).setValue(new UriType("http://hl7.org/fhir"));
-        for (ElementDefinition ed : sd.getSnapshot().getElement())
-          patchUrl(ed);
-        for (ElementDefinition ed : sd.getDifferential().getElement())
-          patchUrl(ed);
-      }
     }
     return r5;
   }
 
-  private void patchUrl(ElementDefinition ed) {
-    for (TypeRefComponent tr : ed.getType()) {
-      for (CanonicalType s : tr.getTargetProfile()) {
-        s.setValue(s.getValue().replace(URL_BASE, "http://hl7.org/fhir/4.0/"));
-      }
-      for (CanonicalType s : tr.getProfile()) {
-        s.setValue(s.getValue().replace(URL_BASE, "http://hl7.org/fhir/4.0/"));
-      }
-    }
-  }
   
   @Override
   public List<CodeSystem> getCodeSystems() {
     return new ArrayList<>();
   }
 
+  @Override
+  protected String versionString() {
+    return "4.0";
+  }
+
 
 }

org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/loaders/loaderR5/R5ToR5Loader.java

@@ -96,14 +96,8 @@ public class R5ToR5Loader extends BaseLoaderR5 {
     }
     if (patchUrls) {
       for (BundleEntryComponent be : b.getEntry()) {
-        if (be.hasResource() && be.getResource() instanceof StructureDefinition) {
+        if (be.hasResource()) {
-          StructureDefinition sd = (StructureDefinition) be.getResource();
+          doPatchUrls(be.getResource());
-          sd.setUrl(sd.getUrl().replace(URL_BASE, URL_R4));
-          sd.addExtension().setUrl(URL_ELEMENT_DEF_NAMESPACE).setValue(new UriType(URL_BASE));
-          for (ElementDefinition ed : sd.getSnapshot().getElement())
-            patchUrl(ed);
-          for (ElementDefinition ed : sd.getDifferential().getElement())
-            patchUrl(ed);
         }
       }
     }
@@ -126,34 +120,20 @@ public class R5ToR5Loader extends BaseLoaderR5 {
       throw new FHIRException("Cannot kill primitives when using deferred loading");
     }
     if (patchUrls) {
-      if (r5 instanceof StructureDefinition) {
+      doPatchUrls(r5);
-        StructureDefinition sd = (StructureDefinition) r5;
-        sd.setUrl(sd.getUrl().replace(URL_BASE, URL_R4));
-        sd.addExtension().setUrl(URL_ELEMENT_DEF_NAMESPACE).setValue(new UriType(URL_BASE));
-        for (ElementDefinition ed : sd.getSnapshot().getElement())
-          patchUrl(ed);
-        for (ElementDefinition ed : sd.getDifferential().getElement())
-          patchUrl(ed);
-      }
     }
     return r5;
   }
   
-  private void patchUrl(ElementDefinition ed) {
-    for (TypeRefComponent tr : ed.getType()) {
-      for (CanonicalType s : tr.getTargetProfile()) {
-        s.setValue(s.getValue().replace(URL_BASE, URL_R4));
-      }
-      for (CanonicalType s : tr.getProfile()) {
-        s.setValue(s.getValue().replace(URL_BASE, URL_R4));
-      }
-    }
-  }
-  
   @Override
   public List<CodeSystem> getCodeSystems() {
     return new ArrayList<>();
   }
 
+  @Override
+  protected String versionString() {
+    return "5.0";
+  }
+
 
 }

org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/txClient/TerminologyClientFactory.java

@@ -60,7 +60,7 @@ public class TerminologyClientFactory {
   private static String checkEndsWith(String term, String url) {
     if (url.endsWith(term))
       return url;
-    if (url.startsWith("http://tx.fhir.org"))
+    if (url.startsWith("http://tx.fhir.org") || url.startsWith("https://tx.fhir.org"))
       return Utilities.pathURL(url, term);
     if (url.equals("http://local.fhir.org:8080"))
       return Utilities.pathURL(url, term);

org.hl7.fhir.convertors/src/test/java/org/hl7/fhir/convertors/txClient/TerminologyClientFactoryTest.java

@@ -0,0 +1,74 @@
+package org.hl7.fhir.convertors.txClient;
+
+import org.hl7.fhir.r5.terminologies.TerminologyClient;
+import org.hl7.fhir.utilities.FhirPublication;
+import org.junit.jupiter.api.Test;
+import org.junit.jupiter.params.ParameterizedTest;
+import org.junit.jupiter.params.provider.Arguments;
+import org.junit.jupiter.params.provider.MethodSource;
+import org.xml.sax.SAXException;
+
+import javax.xml.parsers.ParserConfigurationException;
+import java.io.IOException;
+import java.net.URISyntaxException;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.stream.Stream;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertThrows;
+
+public class TerminologyClientFactoryTest {
+
+  public static Stream<Arguments> data() throws ParserConfigurationException, SAXException, IOException {
+    List<Arguments> objects = new ArrayList<>();
+    objects.addAll(getDefaultServerArgs("tx.fhir.org/r4", "tx.fhir.org", FhirPublication.R4));
+    objects.addAll(getHttpAndHttpsArgs("tx.fhir.org", null, "tx.fhir.org/r4"));
+    objects.addAll(getHttpAndHttpsArgs("tx.fhir.org/r4", null, "tx.fhir.org/r4"));
+    objects.addAll(getDefaultServerArgs("tx.fhir.org/r2", "tx.fhir.org", FhirPublication.DSTU2));
+    objects.addAll(getDefaultServerArgs("tx.fhir.org/r3", "tx.fhir.org", FhirPublication.DSTU2016May));
+    objects.addAll(getDefaultServerArgs("tx.fhir.org/r4", "tx.fhir.org", FhirPublication.R4B));
+    objects.addAll(getDefaultServerArgs("tx.fhir.org/r4", "tx.fhir.org", FhirPublication.R5));
+    objects.addAll(getDefaultServerArgs("tx.fhir.org/r3", "tx.fhir.org", FhirPublication.STU3));
+    objects.addAll(getHttpAndHttpsArgs("someserver.org", FhirPublication.R4, "someserver.org"));
+    objects.addAll(getHttpAndHttpsArgs("someserver.org", null, "someserver.org"));
+    return objects.stream();
+  }
+
+  private static List<Arguments> getDefaultServerArgs(String explicitUrl, String baseUrl, FhirPublication fhirPublication) {
+    List<Arguments> objects = new ArrayList<>();
+    objects.addAll(getHttpAndHttpsArgs(baseUrl, fhirPublication, explicitUrl));
+    objects.addAll(getHttpAndHttpsArgs(explicitUrl, fhirPublication, explicitUrl));
+    return objects;
+  }
+
+  private static List<Arguments> getHttpAndHttpsArgs(String baseUrl, FhirPublication fhirPublication, String baseExpectedAddress) {
+    return List.of(
+      Arguments.of("https://" + baseUrl, fhirPublication, "https://" + baseExpectedAddress),
+      Arguments.of("http://" + baseUrl, fhirPublication, "http://" + baseExpectedAddress)
+    );
+  }
+
+  @ParameterizedTest
+  @MethodSource("data")
+  public void testMakeClient(String url, FhirPublication fhirPublication, String expectedAddress) throws URISyntaxException {
+    TerminologyClient terminologyClient = TerminologyClientFactory.makeClient(url, "dummyUserAgent", fhirPublication);
+    assertEquals(expectedAddress, terminologyClient.getAddress());
+  }
+
+  @Test
+  public void testMakeClientDstu1Fails() throws URISyntaxException {
+    assertThrows(Error.class, () -> {
+        TerminologyClient terminologyClient = TerminologyClientFactory.makeClient("urldoesnotmatter", "dummyUserAgent", FhirPublication.DSTU1);
+      }
+    );
+  }
+
+  @Test
+  public void testMakeClientNullFails() throws URISyntaxException {
+    assertThrows(Error.class, () -> {
+        TerminologyClient terminologyClient = TerminologyClientFactory.makeClient("urldoesnotmatter", "dummyUserAgent", FhirPublication.NULL);
+      }
+    );
+  }
+}

org.hl7.fhir.core.generator/configuration/RdfParser.java

@@ -29,8 +29,8 @@ public class RdfParser extends RdfParserBase {
   private void composeEnum(Complex parent, String parentType, String name, Enumeration<? extends Enum> value, int index) {
     if (value == null)
       return;
-    Complex t = parent.predicate("fhir:"+parentType+"."+name);
+    Complex t = parent.predicate("fhir:"+name, index > -1);
-    t.predicate("fhir:value", ttlLiteral(value.asStringValue()));
+    t.predicate("fhir:v", ttlLiteral(value.asStringValue()), false);
     composeElement(t, parentType, name, value, index);
     decorateCode(t, value);
   }
@@ -39,24 +39,24 @@ public class RdfParser extends RdfParserBase {
   protected void composeDate(Complex parent, String parentType, String name, DateType value, int index) {
     if (value == null)
       return;
-    Complex t = parent.predicate("fhir:"+parentType+"."+name);
+    Complex t = parent.predicate("fhir:"+name, index > -1);
-    t.predicate("fhir:value", ttlLiteral(value.asStringValue()));
+    t.predicate("fhir:v", ttlLiteral(value.asStringValue()), false);
     composeElement(t, parentType, name, value, index);
   }
 
   protected void composeDateTime(Complex parent, String parentType, String name, DateTimeType value, int index) {
     if (value == null)
       return;
-    Complex t = parent.predicate("fhir:"+parentType+"."+name);
+    Complex t = parent.predicate("fhir:"+name, index > -1);
-    t.predicate("fhir:value", ttlLiteral(value.asStringValue()));
+    t.predicate("fhir:v", ttlLiteral(value.asStringValue()), false);
     composeElement(t, parentType, name, value, index);
   }
 
   protected void composeCode(Complex parent, String parentType, String name, CodeType value, int index) {
     if (value == null)
       return;
-    Complex t = parent.predicate("fhir:"+parentType+"."+name);
+    Complex t = parent.predicate("fhir:"+name, index > -1);
-    t.predicate("fhir:value", ttlLiteral(value.asStringValue()));
+    t.predicate("fhir:v", ttlLiteral(value.asStringValue()), false);
     composeElement(t, parentType, name, value, index);
     decorateCode(t, value);
   }
@@ -64,136 +64,136 @@ public class RdfParser extends RdfParserBase {
   protected void composeString(Complex parent, String parentType, String name, StringType value, int index) {
     if (value == null)
       return;
-    Complex t = parent.predicate("fhir:"+parentType+"."+name);
+    Complex t = parent.predicate("fhir:"+name, index > -1);
-    t.predicate("fhir:value", ttlLiteral(value.asStringValue()));
+    t.predicate("fhir:v", ttlLiteral(value.asStringValue()), false);
     composeElement(t, parentType, name, value, index);
   }
 
   protected void composeInteger(Complex parent, String parentType, String name, IntegerType value, int index) {
     if (value == null)
       return;
-    Complex t = parent.predicate("fhir:"+parentType+"."+name);
+    Complex t = parent.predicate("fhir:"+name, index > -1);
-    t.predicate("fhir:value", ttlLiteral(value.asStringValue()));
+    t.predicate("fhir:v", ttlLiteral(value.asStringValue()), false);
     composeElement(t, parentType, name, value, index);
   }
 
   protected void composeInteger64(Complex parent, String parentType, String name, Integer64Type value, int index) {
     if (value == null)
       return;
-    Complex t = parent.predicate("fhir:"+parentType+"."+name);
+    Complex t = parent.predicate("fhir:"+name, index > -1);
-    t.predicate("fhir:value", ttlLiteral(value.asStringValue()));
+    t.predicate("fhir:v", ttlLiteral(value.asStringValue()), false);
     composeElement(t, parentType, name, value, index);
   }
 
   protected void composeOid(Complex parent, String parentType, String name, OidType value, int index) {
     if (value == null)
       return;
-    Complex t = parent.predicate("fhir:"+parentType+"."+name);
+    Complex t = parent.predicate("fhir:"+name, index > -1);
-    t.predicate("fhir:value", ttlLiteral(value.asStringValue()));
+    t.predicate("fhir:v", ttlLiteral(value.asStringValue()), false);
     composeElement(t, parentType, name, value, index);
   }
 
   protected void composeCanonical(Complex parent, String parentType, String name, CanonicalType value, int index) {
     if (value == null)
       return;
-    Complex t = parent.predicate("fhir:"+parentType+"."+name);
+    Complex t = parent.predicate("fhir:"+name, index > -1);
-    t.predicate("fhir:value", ttlLiteral(value.asStringValue()));
+    t.predicate("fhir:v", ttlLiteral(value.asStringValue()), false);
     composeElement(t, parentType, name, value, index);
   }
 
   protected void composeUri(Complex parent, String parentType, String name, UriType value, int index) {
     if (value == null)
       return;
-    Complex t = parent.predicate("fhir:"+parentType+"."+name);
+    Complex t = parent.predicate("fhir:"+name, index > -1);
-    t.predicate("fhir:value", ttlLiteral(value.asStringValue()));
+    t.predicate("fhir:v", ttlLiteral(value.asStringValue()), false);
     composeElement(t, parentType, name, value, index);
   }
 
   protected void composeUuid(Complex parent, String parentType, String name, UuidType value, int index) {
     if (value == null)
       return;
-    Complex t = parent.predicate("fhir:"+parentType+"."+name);
+    Complex t = parent.predicate("fhir:"+name, index > -1);
-    t.predicate("fhir:value", ttlLiteral(value.asStringValue()));
+    t.predicate("fhir:v", ttlLiteral(value.asStringValue()), false);
     composeElement(t, parentType, name, value, index);
   }
 
   protected void composeUrl(Complex parent, String parentType, String name, UrlType value, int index) {
     if (value == null)
       return;
-    Complex t = parent.predicate("fhir:"+parentType+"."+name);
+    Complex t = parent.predicate("fhir:"+name, index > -1);
-    t.predicate("fhir:value", ttlLiteral(value.asStringValue()));
+    t.predicate("fhir:v", ttlLiteral(value.asStringValue()), false);
     composeElement(t, parentType, name, value, index);
   }
 
   protected void composeInstant(Complex parent, String parentType, String name, InstantType value, int index) {
     if (value == null)
       return;
-    Complex t = parent.predicate("fhir:"+parentType+"."+name);
+    Complex t = parent.predicate("fhir:"+name, index > -1);
-    t.predicate("fhir:value", ttlLiteral(value.asStringValue()));
+    t.predicate("fhir:v", ttlLiteral(value.asStringValue()), false);
     composeElement(t, parentType, name, value, index);
   }
 
   protected void composeBoolean(Complex parent, String parentType, String name, BooleanType value, int index) {
     if (value == null)
       return;
-    Complex t = parent.predicate("fhir:"+parentType+"."+name);
+    Complex t = parent.predicate("fhir:"+name, index > -1);
-    t.predicate("fhir:value", ttlLiteral(value.asStringValue()));
+    t.predicate("fhir:v", ttlLiteral(value.asStringValue()), false);
     composeElement(t, parentType, name, value, index);
   }
 
   protected void composeBase64Binary(Complex parent, String parentType, String name, Base64BinaryType value, int index) {
     if (value == null)
       return;
-    Complex t = parent.predicate("fhir:"+parentType+"."+name);
+    Complex t = parent.predicate("fhir:"+name, index > -1);
-    t.predicate("fhir:value", ttlLiteral(value.asStringValue()));
+    t.predicate("fhir:v", ttlLiteral(value.asStringValue()), false);
     composeElement(t, parentType, name, value, index);
   }
 
   protected void composeUnsignedInt(Complex parent, String parentType, String name, UnsignedIntType value, int index) {
     if (value == null)
       return;
-    Complex t = parent.predicate("fhir:"+parentType+"."+name);
+    Complex t = parent.predicate("fhir:"+name, index > -1);
-    t.predicate("fhir:value", ttlLiteral(value.asStringValue()));
+    t.predicate("fhir:v", ttlLiteral(value.asStringValue()), false);
     composeElement(t, parentType, name, value, index);
   }
 
   protected void composeMarkdown(Complex parent, String parentType, String name, MarkdownType value, int index) {
     if (value == null)
       return;
-    Complex t = parent.predicate("fhir:"+parentType+"."+name);
+    Complex t = parent.predicate("fhir:"+name, index > -1);
-    t.predicate("fhir:value", ttlLiteral(value.asStringValue()));
+    t.predicate("fhir:v", ttlLiteral(value.asStringValue()), false);
     composeElement(t, parentType, name, value, index);
   }
 
   protected void composeTime(Complex parent, String parentType, String name, TimeType value, int index) {
     if (value == null)
       return;
-    Complex t = parent.predicate("fhir:"+parentType+"."+name);
+    Complex t = parent.predicate("fhir:"+name, index > -1);
-    t.predicate("fhir:value", ttlLiteral(value.asStringValue()));
+    t.predicate("fhir:v", ttlLiteral(value.asStringValue()), false);
     composeElement(t, parentType, name, value, index);
   }
 
   protected void composeId(Complex parent, String parentType, String name, IdType value, int index) {
     if (value == null)
       return;
-    Complex t = parent.predicate("fhir:"+parentType+"."+name);
+    Complex t = parent.predicate("fhir:"+name, index > -1);
-    t.predicate("fhir:value", ttlLiteral(value.asStringValue()));
+    t.predicate("fhir:v", ttlLiteral(value.asStringValue()), false);
     composeElement(t, parentType, name, value, index);
   }
 
   protected void composePositiveInt(Complex parent, String parentType, String name, PositiveIntType value, int index) {
     if (value == null)
       return;
-    Complex t = parent.predicate("fhir:"+parentType+"."+name);
+    Complex t = parent.predicate("fhir:"+name, index > -1);
-    t.predicate("fhir:value", ttlLiteral(value.asStringValue()));
+    t.predicate("fhir:v", ttlLiteral(value.asStringValue()), false);
     composeElement(t, parentType, name, value, index);
   }
 
   protected void composeDecimal(Complex parent, String parentType, String name, DecimalType value, int index) {
     if (value == null)
       return;
-    Complex t = parent.predicate("fhir:"+parentType+"."+name);
+    Complex t = parent.predicate("fhir:"+name, index > -1);
-    t.predicate("fhir:value", ttlLiteral(value.asStringValue()));
+    t.predicate("fhir:v", ttlLiteral(value.asStringValue()), false);
     composeElement(t, parentType, name, value, index);
   }
 

org.hl7.fhir.core.generator/src/org/hl7/fhir/core/generator/codegen/JavaParserRdfGenerator.java

@@ -108,7 +108,7 @@ public class JavaParserRdfGenerator extends JavaBaseGenerator {
     composer.append("    if (Utilities.noString(parentType))\r\n");
     composer.append("      t = parent;\r\n");
     composer.append("    else {\r\n");
-    composer.append("      t = parent.predicate(\"fhir:\"+parentType+'.'+name);\r\n");
+    composer.append("      t = parent.predicate(\"fhir:\"+name,index > -1);\r\n");
     composer.append("    }\r\n");
     composer.append("    compose"+ti.getAncestorName()+"(t, \""+ti.getDefn().getName()+"\", name, element, index);\r\n");
     if (tn.equals("Coding")) 

org.hl7.fhir.dstu2/checkstyle_suppressions.xml

@@ -0,0 +1,8 @@
+<?xml version="1.0"?>
+<!DOCTYPE suppressions PUBLIC
+        "-//Checkstyle//DTD SuppressionFilter Configuration 1.2//EN"
+        "https://checkstyle.org/dtds/suppressions_1_2.dtd">
+
+<suppressions>
+  
+</suppressions>

org.hl7.fhir.dstu2/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>org.hl7.fhir.core</artifactId>
-		<version>5.6.99-SNAPSHOT</version>
+		<version>5.6.100-SNAPSHOT</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 

org.hl7.fhir.dstu2/src/main/java/org/hl7/fhir/dstu2/utils/ProfileUtilities.java

@@ -79,6 +79,7 @@ import org.hl7.fhir.utilities.xhtml.HierarchicalTableGenerator;
 import org.hl7.fhir.utilities.xhtml.HierarchicalTableGenerator.Cell;
 import org.hl7.fhir.utilities.xhtml.HierarchicalTableGenerator.Piece;
 import org.hl7.fhir.utilities.xhtml.HierarchicalTableGenerator.Row;
+import org.hl7.fhir.utilities.xhtml.HierarchicalTableGenerator.TableGenerationMode;
 import org.hl7.fhir.utilities.xhtml.HierarchicalTableGenerator.TableModel;
 import org.hl7.fhir.utilities.xhtml.XhtmlNode;
 import org.hl7.fhir.utilities.xml.SchematronWriter;
@@ -1183,7 +1184,7 @@ public class ProfileUtilities {
 
   public XhtmlNode generateExtensionTable(String defFile, StructureDefinition ed, String imageFolder, boolean inlineGraphics, boolean full, String corePath, Set<String> outputTracker) throws IOException, FHIRException {
     HierarchicalTableGenerator gen = new HierarchicalTableGenerator(imageFolder, inlineGraphics);
-    TableModel model = gen.initNormalTable(corePath, false, true, ed.getId(), false);
+    TableModel model = gen.initNormalTable(corePath, false, true, ed.getId(), false, TableGenerationMode.XML);
 
     boolean deep = false;
     boolean vdeep = false;
@@ -1447,7 +1448,7 @@ public class ProfileUtilities {
   public XhtmlNode generateTable(String defFile, StructureDefinition profile, boolean diff, String imageFolder, boolean inlineGraphics, String profileBaseFileName, boolean snapshot, String corePath, Set<String> outputTracker) throws IOException, FHIRException {
     assert(diff != snapshot);// check it's ok to get rid of one of these
     HierarchicalTableGenerator gen = new HierarchicalTableGenerator(imageFolder, inlineGraphics);
-    TableModel model = gen.initNormalTable(corePath, false, true, profile.getId()+(diff ? "d" : "s"), false);
+    TableModel model = gen.initNormalTable(corePath, false, true, profile.getId()+(diff ? "d" : "s"), false, TableGenerationMode.XML);
     List<ElementDefinition> list = diff ? profile.getDifferential().getElement() : profile.getSnapshot().getElement();
     List<StructureDefinition> profiles = new ArrayList<StructureDefinition>();
     profiles.add(profile);

org.hl7.fhir.dstu2016may/checkstyle_suppressions.xml

@@ -0,0 +1,8 @@
+<?xml version="1.0"?>
+<!DOCTYPE suppressions PUBLIC
+        "-//Checkstyle//DTD SuppressionFilter Configuration 1.2//EN"
+        "https://checkstyle.org/dtds/suppressions_1_2.dtd">
+
+<suppressions>
+  
+</suppressions>

org.hl7.fhir.dstu2016may/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>org.hl7.fhir.core</artifactId>
-		<version>5.6.99-SNAPSHOT</version>
+		<version>5.6.100-SNAPSHOT</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 

org.hl7.fhir.dstu2016may/src/main/java/org/hl7/fhir/dstu2016may/utils/ProfileUtilities.java

@@ -80,6 +80,7 @@ import org.hl7.fhir.utilities.xhtml.HierarchicalTableGenerator;
 import org.hl7.fhir.utilities.xhtml.HierarchicalTableGenerator.Cell;
 import org.hl7.fhir.utilities.xhtml.HierarchicalTableGenerator.Piece;
 import org.hl7.fhir.utilities.xhtml.HierarchicalTableGenerator.Row;
+import org.hl7.fhir.utilities.xhtml.HierarchicalTableGenerator.TableGenerationMode;
 import org.hl7.fhir.utilities.xhtml.HierarchicalTableGenerator.TableModel;
 import org.hl7.fhir.utilities.xhtml.XhtmlNode;
 import org.hl7.fhir.utilities.xml.SchematronWriter;
@@ -1184,7 +1185,7 @@ public class ProfileUtilities {
 
   public XhtmlNode generateExtensionTable(String defFile, StructureDefinition ed, String imageFolder, boolean inlineGraphics, boolean full, String corePath, Set<String> outputTracker) throws IOException, FHIRException {
     HierarchicalTableGenerator gen = new HierarchicalTableGenerator(imageFolder, inlineGraphics);
-    TableModel model = gen.initNormalTable(corePath, false, true, ed.getId(), false);
+    TableModel model = gen.initNormalTable(corePath, false, true, ed.getId(), false, TableGenerationMode.XML);
 
     boolean deep = false;
     boolean vdeep = false;
@@ -1446,7 +1447,7 @@ public class ProfileUtilities {
   public XhtmlNode generateTable(String defFile, StructureDefinition profile, boolean diff, String imageFolder, boolean inlineGraphics, String profileBaseFileName, boolean snapshot, String corePath, boolean logicalModel, Set<String> outputTracker) throws IOException, FHIRException {
     assert(diff != snapshot);// check it's ok to get rid of one of these
     HierarchicalTableGenerator gen = new HierarchicalTableGenerator(imageFolder, inlineGraphics);
-    TableModel model = gen.initNormalTable(corePath, false, true, profile.getId()+(diff ? "d" : "s"), false);
+    TableModel model = gen.initNormalTable(corePath, false, true, profile.getId()+(diff ? "d" : "s"), false, TableGenerationMode.XML);
     List<ElementDefinition> list = diff ? profile.getDifferential().getElement() : profile.getSnapshot().getElement();
     List<StructureDefinition> profiles = new ArrayList<StructureDefinition>();
     profiles.add(profile);

org.hl7.fhir.dstu3/checkstyle_suppressions.xml

@@ -0,0 +1,8 @@
+<?xml version="1.0"?>
+<!DOCTYPE suppressions PUBLIC
+        "-//Checkstyle//DTD SuppressionFilter Configuration 1.2//EN"
+        "https://checkstyle.org/dtds/suppressions_1_2.dtd">
+
+<suppressions>
+  
+</suppressions>

org.hl7.fhir.dstu3/pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <groupId>ca.uhn.hapi.fhir</groupId>
         <artifactId>org.hl7.fhir.core</artifactId>
-        <version>5.6.99-SNAPSHOT</version>
+        <version>5.6.100-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 
@@ -55,7 +55,7 @@
         <dependency>
             <groupId>com.squareup.okhttp3</groupId>
             <artifactId>okhttp</artifactId>
-            <version>4.9.0</version>
+            <version>${okhttp.version}</version>
             <optional>true</optional>
         </dependency>
 

org.hl7.fhir.dstu3/src/main/java/org/hl7/fhir/dstu3/conformance/ProfileUtilities.java

@@ -102,6 +102,7 @@ import org.hl7.fhir.utilities.xhtml.HierarchicalTableGenerator;
 import org.hl7.fhir.utilities.xhtml.HierarchicalTableGenerator.Cell;
 import org.hl7.fhir.utilities.xhtml.HierarchicalTableGenerator.Piece;
 import org.hl7.fhir.utilities.xhtml.HierarchicalTableGenerator.Row;
+import org.hl7.fhir.utilities.xhtml.HierarchicalTableGenerator.TableGenerationMode;
 import org.hl7.fhir.utilities.xhtml.HierarchicalTableGenerator.TableModel;
 import org.hl7.fhir.utilities.xhtml.XhtmlNode;
 import org.hl7.fhir.utilities.xml.SchematronWriter;
@@ -1621,7 +1622,7 @@ public class ProfileUtilities extends TranslatingUtilities {
   public XhtmlNode generateExtensionTable(String defFile, StructureDefinition ed, String imageFolder, boolean inlineGraphics, boolean full, String corePath, String imagePath, Set<String> outputTracker) throws IOException, FHIRException {
     HierarchicalTableGenerator gen = new HierarchicalTableGenerator(imageFolder, inlineGraphics);
     gen.setTranslator(getTranslator());
-    TableModel model = gen.initNormalTable(corePath, false, true, ed.getId(), false);
+    TableModel model = gen.initNormalTable(corePath, false, true, ed.getId(), false, TableGenerationMode.XML);
 
     boolean deep = false;
     String m = "";
@@ -1990,7 +1991,7 @@ public class ProfileUtilities extends TranslatingUtilities {
     assert(diff != snapshot);// check it's ok to get rid of one of these
     HierarchicalTableGenerator gen = new HierarchicalTableGenerator(imageFolder, inlineGraphics);
     gen.setTranslator(getTranslator());
-    TableModel model = gen.initNormalTable(corePath, false, true, profile.getId()+(diff ? "d" : "s"), false);
+    TableModel model = gen.initNormalTable(corePath, false, true, profile.getId()+(diff ? "d" : "s"), false, TableGenerationMode.XML);
     List<ElementDefinition> list = diff ? profile.getDifferential().getElement() : profile.getSnapshot().getElement();
     List<StructureDefinition> profiles = new ArrayList<StructureDefinition>();
     profiles.add(profile);

org.hl7.fhir.r4/checkstyle_suppressions.xml

@@ -0,0 +1,8 @@
+<?xml version="1.0"?>
+<!DOCTYPE suppressions PUBLIC
+        "-//Checkstyle//DTD SuppressionFilter Configuration 1.2//EN"
+        "https://checkstyle.org/dtds/suppressions_1_2.dtd">
+
+<suppressions>
+  
+</suppressions>

org.hl7.fhir.r4/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>org.hl7.fhir.core</artifactId>
-		<version>5.6.99-SNAPSHOT</version>
+		<version>5.6.100-SNAPSHOT</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 
@@ -67,7 +67,7 @@
 		<dependency>
 			<groupId>com.squareup.okhttp3</groupId>
 			<artifactId>okhttp</artifactId>
-			<version>4.9.0</version>
+			<version>${okhttp.version}</version>
 			<optional>true</optional>
 		</dependency>
 		<dependency>

org.hl7.fhir.r4/src/main/java/org/hl7/fhir/r4/conformance/ProfileUtilities.java

@@ -110,6 +110,7 @@ import org.hl7.fhir.utilities.xhtml.HierarchicalTableGenerator;
 import org.hl7.fhir.utilities.xhtml.HierarchicalTableGenerator.Cell;
 import org.hl7.fhir.utilities.xhtml.HierarchicalTableGenerator.Piece;
 import org.hl7.fhir.utilities.xhtml.HierarchicalTableGenerator.Row;
+import org.hl7.fhir.utilities.xhtml.HierarchicalTableGenerator.TableGenerationMode;
 import org.hl7.fhir.utilities.xhtml.HierarchicalTableGenerator.TableModel;
 import org.hl7.fhir.utilities.xhtml.XhtmlNode;
 import org.hl7.fhir.utilities.xml.SchematronWriter;
@@ -2149,7 +2150,7 @@ public class ProfileUtilities extends TranslatingUtilities {
   public XhtmlNode generateExtensionTable(String defFile, StructureDefinition ed, String imageFolder, boolean inlineGraphics, boolean full, String corePath, String imagePath, Set<String> outputTracker) throws IOException, FHIRException {
     HierarchicalTableGenerator gen = new HierarchicalTableGenerator(imageFolder, inlineGraphics, true);
     gen.setTranslator(getTranslator());
-    TableModel model = gen.initNormalTable(corePath, false, true, ed.getId(), false);
+    TableModel model = gen.initNormalTable(corePath, false, true, ed.getId(), false, TableGenerationMode.XML);
 
     boolean deep = false;
     String m = "";
@@ -2519,7 +2520,7 @@ public class ProfileUtilities extends TranslatingUtilities {
     assert(diff != snapshot);// check it's ok to get rid of one of these
     HierarchicalTableGenerator gen = new HierarchicalTableGenerator(imageFolder, inlineGraphics, true);
     gen.setTranslator(getTranslator());
-    TableModel model = gen.initNormalTable(corePath, false, true, profile.getId()+(diff ? "d" : "s"), false);
+    TableModel model = gen.initNormalTable(corePath, false, true, profile.getId()+(diff ? "d" : "s"), false, TableGenerationMode.XML);
     List<ElementDefinition> list = diff ? profile.getDifferential().getElement() : profile.getSnapshot().getElement();
     List<StructureDefinition> profiles = new ArrayList<StructureDefinition>();
     profiles.add(profile);

org.hl7.fhir.r4/src/main/java/org/hl7/fhir/r4/utils/StructureMapUtilities.java

@@ -265,8 +265,10 @@ public class StructureMapUtilities {
   public StructureMapUtilities(IWorkerContext worker) {
     super();
     this.worker = worker;
+    if (worker != null) {
       fpe = new FHIRPathEngine(worker);
       fpe.setHostServices(new FFHIRPathHostServices());
+    }
   }
 
 	public static String render(StructureMap map) {

org.hl7.fhir.r4b/checkstyle_suppressions.xml

@@ -0,0 +1,8 @@
+<?xml version="1.0"?>
+<!DOCTYPE suppressions PUBLIC
+        "-//Checkstyle//DTD SuppressionFilter Configuration 1.2//EN"
+        "https://checkstyle.org/dtds/suppressions_1_2.dtd">
+
+<suppressions>
+  
+</suppressions>

org.hl7.fhir.r4b/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>org.hl7.fhir.core</artifactId>
-		<version>5.6.99-SNAPSHOT</version>
+		<version>5.6.100-SNAPSHOT</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 
@@ -61,19 +61,19 @@
 		<dependency>
 			<groupId>com.squareup.okhttp3</groupId>
 			<artifactId>okhttp</artifactId>
-			<version>4.9.0</version>
+			<version>${okhttp.version}</version>
 			<optional>true</optional>
 		</dependency>
 		<dependency>
 			<groupId>com.squareup.okhttp3</groupId>
 			<artifactId>logging-interceptor</artifactId>
-			<version>4.9.0</version>
+			<version>${okhttp.version}</version>
 			<optional>true</optional>
 		</dependency>
 		<dependency>
 			<groupId>com.squareup.okhttp3</groupId>
 			<artifactId>mockwebserver</artifactId>
-			<version>4.9.0</version>
+			<version>${okhttp.version}</version>
 			<optional>true</optional>
 			<scope>test</scope>
 		</dependency>

org.hl7.fhir.r4b/src/main/java/org/hl7/fhir/r4b/conformance/ProfileUtilities.java

@@ -130,6 +130,7 @@ import org.hl7.fhir.utilities.xhtml.HierarchicalTableGenerator;
 import org.hl7.fhir.utilities.xhtml.HierarchicalTableGenerator.Cell;
 import org.hl7.fhir.utilities.xhtml.HierarchicalTableGenerator.Piece;
 import org.hl7.fhir.utilities.xhtml.HierarchicalTableGenerator.Row;
+import org.hl7.fhir.utilities.xhtml.HierarchicalTableGenerator.TableGenerationMode;
 import org.hl7.fhir.utilities.xhtml.HierarchicalTableGenerator.TableModel;
 import org.hl7.fhir.utilities.xhtml.XhtmlNode;
 import org.hl7.fhir.utilities.xml.SchematronWriter;
@@ -3471,7 +3472,7 @@ public class ProfileUtilities extends TranslatingUtilities {
   public XhtmlNode generateExtensionTable(String defFile, StructureDefinition ed, String imageFolder, boolean inlineGraphics, boolean full, String corePath, String imagePath, Set<String> outputTracker, RenderingContext rc) throws IOException, FHIRException {
     HierarchicalTableGenerator gen = new HierarchicalTableGenerator(imageFolder, inlineGraphics, true);
     gen.setTranslator(getTranslator());
-    TableModel model = gen.initNormalTable(corePath, false, true, ed.getId()+(full ? "f" : "n"), true);
+    TableModel model = gen.initNormalTable(corePath, false, true, ed.getId()+(full ? "f" : "n"), true, TableGenerationMode.XHTML);
 
     boolean deep = false;
     String m = "";
@@ -3988,7 +3989,7 @@ public class ProfileUtilities extends TranslatingUtilities {
     assert(diff != snapshot);// check it's ok to get rid of one of these
     HierarchicalTableGenerator gen = new HierarchicalTableGenerator(imageFolder, inlineGraphics, true);
     gen.setTranslator(getTranslator());
-    TableModel model = gen.initNormalTable(corePath, false, true, profile.getId()+(diff ? "d" : "s"), active);
+    TableModel model = gen.initNormalTable(corePath, false, true, profile.getId()+(diff ? "d" : "s"), active, active ? TableGenerationMode.XHTML : TableGenerationMode.XML);
     List<ElementDefinition> list = new ArrayList<>();
     if (diff)
       list.addAll(profile.getDifferential().getElement());

org.hl7.fhir.r4b/src/main/java/org/hl7/fhir/r4b/model/BaseResource.java

@@ -58,7 +58,7 @@ public abstract class BaseResource extends Base implements IAnyResource, IElemen
 
 	@Override
 	public FhirVersionEnum getStructureFhirVersionEnum() {
-		return FhirVersionEnum.R5; // to: change to R5
+		return FhirVersionEnum.R4B;
 	}
 
   @Override

org.hl7.fhir.r5/checkstyle_suppressions.xml

@@ -0,0 +1,8 @@
+<?xml version="1.0"?>
+<!DOCTYPE suppressions PUBLIC
+        "-//Checkstyle//DTD SuppressionFilter Configuration 1.2//EN"
+        "https://checkstyle.org/dtds/suppressions_1_2.dtd">
+
+<suppressions>
+  
+</suppressions>

org.hl7.fhir.r5/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>org.hl7.fhir.core</artifactId>
-		<version>5.6.99-SNAPSHOT</version>
+		<version>5.6.100-SNAPSHOT</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 
@@ -111,13 +111,13 @@
 		<dependency>
 			<groupId>com.squareup.okhttp3</groupId>
 			<artifactId>okhttp</artifactId>
-			<version>4.9.0</version>
+			<version>${okhttp.version}</version>
 			<optional>true</optional>
 		</dependency>
 		<dependency>
 			<groupId>com.squareup.okhttp3</groupId>
 			<artifactId>logging-interceptor</artifactId>
-			<version>4.9.0</version>
+			<version>${okhttp.version}</version>
 			<optional>true</optional>
 		</dependency>
 
@@ -148,7 +148,7 @@
 		<dependency>
 			<groupId>com.squareup.okhttp3</groupId>
 			<artifactId>mockwebserver</artifactId>
-			<version>4.9.0</version>
+			<version>${okhttp.version}</version>
 			<optional>true</optional>
 			<scope>test</scope>
 		</dependency>

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

@@ -23,6 +23,7 @@ import org.hl7.fhir.r5.model.NamingSystem.NamingSystemIdentifierType;
 import org.hl7.fhir.r5.model.NamingSystem.NamingSystemUniqueIdComponent;
 import org.hl7.fhir.r5.model.StructureDefinition.StructureDefinitionKind;
 import org.hl7.fhir.r5.model.StructureDefinition.TypeDerivationRule;
+import org.hl7.fhir.r5.model.StructureMap;
 import org.hl7.fhir.r5.utils.ToolingExtensions;
 import org.hl7.fhir.r5.utils.XVerExtensionManager;
 import org.hl7.fhir.r5.model.Identifier;
@@ -42,6 +43,9 @@ public class ContextUtilities implements ProfileKnowledgeProvider {
   private boolean ignoreProfileErrors;
   private XVerExtensionManager xverManager;
   private Map<String, String> oidCache = new HashMap<>();
+  private List<StructureDefinition> allStructuresList = new ArrayList<StructureDefinition>();
+  private List<String> canonicalResourceNames;
+  private List<String> concreteResourceNames;
   
   public ContextUtilities(IWorkerContext context) {
     super();
@@ -196,20 +200,24 @@ public class ContextUtilities implements ProfileKnowledgeProvider {
    * @return a list of the resource names that are canonical resources defined for this version
    */
   public List<String> getCanonicalResourceNames() {
-    List<String> names = new ArrayList<>();
+    if (canonicalResourceNames == null) {
+      canonicalResourceNames =  new ArrayList<>();
+      Set<String> names = new HashSet<>();
       for (StructureDefinition sd : allStructures()) {
         if (sd.getKind() == StructureDefinitionKind.RESOURCE && !sd.getAbstract() && hasUrlProperty(sd)) {
           names.add(sd.getType());
         }
       }
-    return names;
+      canonicalResourceNames.addAll(Utilities.sorted(names));
+    }
+    return canonicalResourceNames;
   }
 
   /**
    * @return a list of all structure definitions, with snapshots generated (if possible)
    */
   public List<StructureDefinition> allStructures(){
-    List<StructureDefinition> result = new ArrayList<StructureDefinition>();
+    if (allStructuresList.isEmpty()) {
       Set<StructureDefinition> set = new HashSet<StructureDefinition>();
       for (StructureDefinition sd : getStructures()) {
         if (!set.contains(sd)) {
@@ -224,11 +232,12 @@ public class ContextUtilities implements ProfileKnowledgeProvider {
               }
             }
           }
-        result.add(sd);
+          allStructuresList.add(sd);
           set.add(sd);
         }
       }
-    return result;
+    }
+    return allStructuresList;
   }
 
   /**
@@ -368,5 +377,32 @@ public class ContextUtilities implements ProfileKnowledgeProvider {
     return null;
   }
 
+  public List<String>  getConcreteResources() {
+    if (concreteResourceNames == null) {
+      concreteResourceNames =  new ArrayList<>();
+      Set<String> names = new HashSet<>();
+      for (StructureDefinition sd : allStructures()) {
+        if (sd.getKind() == StructureDefinitionKind.RESOURCE && !sd.getAbstract()) {
+          names.add(sd.getType());
+        }
+      }
+      concreteResourceNames.addAll(Utilities.sorted(names));
+    }
+    return concreteResourceNames;
+  }
+
+  public List<StructureMap> listMaps(String url) {
+    List<StructureMap> res = new ArrayList<>();
+    String start = url.substring(0, url.indexOf("*"));
+    String end = url.substring(url.indexOf("*")+1);
+    for (StructureMap map : context.fetchResourcesByType(StructureMap.class)) {
+      String u = map.getUrl();
+      if (u.startsWith(start) && u.endsWith(end)) {
+        res.add(map);
+      }
+    }
+    return res;
+  }
+
 }
 

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

@@ -321,6 +321,22 @@ public interface IWorkerContext {
      * @return
      */
     List<CodeSystem> getCodeSystems();  
+    
+    /**
+     * if this is true, then the loader will patch canonical URLs and cross-links 
+     * to add /X.X/ into the URL so that different versions can be loaded safely 
+     * 
+     * default is false
+     */
+    void setPatchUrls(boolean value);
+
+    /**
+     * patch the URL if necessary
+     * 
+     * @param url
+     * @return
+     */
+    String patchUrl(String url, String resourceType);
   }
 
   /**

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

@@ -97,7 +97,7 @@ public class SimpleWorkerContext extends BaseWorkerContext implements IWorkerCon
     private final IContextResourceLoader loader;
 
     public PackageResourceLoader(PackageResourceInformation pri, IContextResourceLoader loader) {
-      super(pri.getResourceType(), pri.getId(), pri.getUrl(),pri.getVersion());
+      super(pri.getResourceType(), pri.getId(), loader == null ? pri.getUrl() :loader.patchUrl(pri.getUrl(), pri.getResourceType()), pri.getVersion());
       this.filename = pri.getFilename();
       this.loader = loader;
     }

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

@@ -129,6 +129,7 @@ public class Element extends Base {
   private int instanceId;
   private boolean isNull;
   private Base source;
+  private boolean ignorePropertyOrder;
 
 	public Element(String name) {
 		super();
@@ -148,6 +149,9 @@ public class Element extends Base {
 		super();
 		this.name = name;
 		this.property = property;
+		if (property.isResource()) {
+		  children = new ArrayList<>();
+		}
 	}
 
 	public Element(String name, Property property, String type, String value) {
@@ -211,8 +215,9 @@ public class Element extends Base {
 		this.value = value;
 	}
 
-	public void setType(String type) {
+	public Element setType(String type) {
 		this.type = type;
+		return this;
 
 	}
 
@@ -286,10 +291,22 @@ public class Element extends Base {
 		for (Element child : children) {
 			if (name.equals(child.getName()))
 				return child.getValue();
+		}
+		for (Element child : children) {
+      if (name.equals(child.getNameBase()))
+        return child.getValue();
     }
   	return null;
 	}
 
+  private String getNameBase() {
+    if (property.isChoice()) {
+      return property.getName().replace("[x]", "");
+    } else  {
+      return getName();
+    }
+  }
+
   public void setChildValue(String name, String value) {
     if (children == null)
       children = new ArrayList<Element>();
@@ -538,6 +555,16 @@ public class Element extends Base {
         Element ne = new Element(name, p);
         children.add(ne);
         return ne;
+      } else if (p.getDefinition().isChoice() && name.startsWith(p.getName().replace("[x]", ""))) {
+        String type = name.substring(p.getName().length()-3);
+        if (new ContextUtilities(property.getContext()).isPrimitiveDatatype(Utilities.uncapitalize(type))) {
+          type = Utilities.uncapitalize(type);
+        }
+        Element ne = new Element(name, p);
+        ne.setType(type);
+        children.add(ne);
+        return ne;
+        
       }
     }
       
@@ -598,7 +625,7 @@ public class Element extends Base {
 
 	@Override
 	public String primitiveValue() {
-		if (isPrimitive())
+		if (isPrimitive() || value != null)
 		  return value;
 		else {
 			if (hasPrimitiveValue() && children != null) {
@@ -1361,5 +1388,18 @@ public class Element extends Base {
     return this;
   }
 
+  public boolean isIgnorePropertyOrder() {
+    return ignorePropertyOrder;
+  }
+
+  public void setIgnorePropertyOrder(boolean ignorePropertyOrder) {
+    this.ignorePropertyOrder = ignorePropertyOrder;
+    if (children != null) {
+      for (Element e : children) {
+        e.setIgnorePropertyOrder(ignorePropertyOrder);
+      }
+    }
+  }
+  
   
 }

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

@@ -0,0 +1,585 @@
+package org.hl7.fhir.r5.elementmodel;
+
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.OutputStream;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import org.hl7.fhir.exceptions.DefinitionException;
+import org.hl7.fhir.exceptions.FHIRException;
+import org.hl7.fhir.exceptions.FHIRFormatError;
+import org.hl7.fhir.r5.context.IWorkerContext;
+import org.hl7.fhir.r5.formats.IParser.OutputStyle;
+import org.hl7.fhir.r5.model.ExpressionNode;
+import org.hl7.fhir.r5.model.ConceptMap.ConceptMapGroupUnmappedMode;
+import org.hl7.fhir.r5.model.Enumerations.ConceptMapRelationship;
+import org.hl7.fhir.r5.model.Enumerations.PublicationStatus;
+import org.hl7.fhir.r5.model.StructureMap.StructureMapGroupTypeMode;
+import org.hl7.fhir.r5.model.StructureMap.StructureMapTransform;
+import org.hl7.fhir.r5.utils.FHIRLexer;
+import org.hl7.fhir.r5.utils.FHIRLexer.FHIRLexerException;
+import org.hl7.fhir.r5.utils.FHIRPathEngine;
+import org.hl7.fhir.r5.utils.structuremap.StructureMapUtilities;
+import org.hl7.fhir.utilities.SourceLocation;
+import org.hl7.fhir.utilities.TextFile;
+import org.hl7.fhir.utilities.Utilities;
+import org.hl7.fhir.utilities.validation.ValidationMessage;
+import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity;
+import org.hl7.fhir.utilities.validation.ValidationMessage.IssueType;
+import org.hl7.fhir.utilities.validation.ValidationMessage.Source;
+
+public class FmlParser extends ParserBase {
+
+  private FHIRPathEngine fpe;
+
+  public FmlParser(IWorkerContext context) {
+    super(context);
+    fpe = new FHIRPathEngine(context);
+  }
+
+  @Override
+  public List<NamedElement> parse(InputStream stream) throws IOException, FHIRFormatError, DefinitionException, FHIRException {
+    String text = TextFile.streamToString(stream);
+    List<NamedElement> result = new ArrayList<>();
+    result.add(new NamedElement(null, parse(text)));
+    return result;
+  }
+
+  @Override
+  public void compose(Element e, OutputStream destination, OutputStyle style, String base)
+      throws FHIRException, IOException {
+    throw new Error("Not done yet");
+  }
+
+  public Element parse(String text) throws FHIRException {
+    FHIRLexer lexer = new FHIRLexer(text, "source", true);
+    if (lexer.done())
+      throw lexer.error("Map Input cannot be empty");
+    Element result = Manager.build(context, context.fetchTypeDefinition("StructureMap"));
+    try {
+      if (lexer.hasToken("map")) {
+        lexer.token("map");
+        result.makeElement("url").markLocation(lexer.getCurrentLocation()).setValue(lexer.readConstant("url"));
+        lexer.token("=");
+        result.makeElement("name").markLocation(lexer.getCurrentLocation()).setValue(lexer.readConstant("name"));
+        if (lexer.hasComments()) {
+          result.makeElement("description").markLocation(lexer.getCurrentLocation()).setValue(lexer.getAllComments());
+        }
+      } else {
+        while (lexer.hasToken("///")) {
+          lexer.next();
+          String fid = lexer.takeDottedToken();
+          Element e = result.makeElement(fid).markLocation(lexer.getCurrentLocation());
+          lexer.token("=");
+          e.setValue(lexer.readConstant("meta value"));
+        }
+      }
+      lexer.setMetadataFormat(false);
+      while (lexer.hasToken("conceptmap"))
+        parseConceptMap(result, lexer);
+
+      while (lexer.hasToken("uses"))
+        parseUses(result, lexer);
+      while (lexer.hasToken("imports"))
+        parseImports(result, lexer);
+
+      while (!lexer.done()) {
+        parseGroup(result, lexer);
+      }
+    } catch (FHIRLexerException e) {
+      logError("2023-02-24", e.getLocation().getLine(), e.getLocation().getColumn(), "??", IssueType.INVALID, e.getMessage(), IssueSeverity.FATAL);
+    } catch (Exception e) {
+      logError("2023-02-24", -1, -1, "?", IssueType.INVALID, e.getMessage(), IssueSeverity.FATAL);
+    }
+
+    if (!result.hasChild("status")) {
+      result.makeElement("status").setValue("draft");
+    }
+    result.setIgnorePropertyOrder(true);
+    return result;
+  }
+
+  private void parseConceptMap(Element result, FHIRLexer lexer) throws FHIRLexerException {
+    lexer.token("conceptmap");
+    Element map = Manager.build(context, context.fetchTypeDefinition("ConceptMap"));
+    Element eid = map.makeElement("id").markLocation(lexer.getCurrentLocation());
+    String id = lexer.readConstant("map id");
+    if (id.startsWith("#"))
+      throw lexer.error("Concept Map identifier must start with #");
+    eid.setValue(id);
+    map.makeElement("status").setValue(PublicationStatus.DRAFT.toCode()); // todo: how to add this to the text format
+    result.makeElement("contained").setElement("resource", map);
+    lexer.token("{");
+    //    lexer.token("source");
+    //    map.setSource(new UriType(lexer.readConstant("source")));
+    //    lexer.token("target");
+    //    map.setSource(new UriType(lexer.readConstant("target")));
+    Map<String, String> prefixes = new HashMap<String, String>();
+    while (lexer.hasToken("prefix")) {
+      lexer.token("prefix");
+      String n = lexer.take();
+      lexer.token("=");
+      String v = lexer.readConstant("prefix url");
+      prefixes.put(n, v);
+    }
+    while (lexer.hasToken("unmapped")) {
+      lexer.token("unmapped");
+      lexer.token("for");
+      String n = readPrefix(prefixes, lexer);
+      Element g = getGroupE(map, n, null);
+      lexer.token("=");
+      SourceLocation loc = lexer.getCurrentLocation();
+      String v = lexer.take();
+      if (v.equals("provided")) {
+        g.makeElement("unmapped").makeElement("mode").markLocation(loc).setValue(ConceptMapGroupUnmappedMode.USESOURCECODE.toCode());
+      } else
+        throw lexer.error("Only unmapped mode PROVIDED is supported at this time");
+    }
+    while (!lexer.hasToken("}")) {
+      String srcs = readPrefix(prefixes, lexer);
+      lexer.token(":");
+      SourceLocation scloc = lexer.getCurrentLocation();
+      String sc = lexer.getCurrent().startsWith("\"") ? lexer.readConstant("code") : lexer.take();
+      SourceLocation relLoc = lexer.getCurrentLocation();
+      ConceptMapRelationship rel = readRelationship(lexer);
+      String tgts = readPrefix(prefixes, lexer);
+      Element g = getGroupE(map, srcs, tgts);
+      Element e = g.addElement("element");
+      e.makeElement("code").markLocation(scloc).setValue(sc.startsWith("\"") ? lexer.processConstant(sc) : sc);
+      Element tgt = e.addElement("target");
+      tgt.makeElement("relationship").markLocation(relLoc).setValue(rel.toCode());
+      lexer.token(":");
+      tgt.makeElement("code").markLocation(lexer.getCurrentLocation()).setValue(lexer.getCurrent().startsWith("\"") ? lexer.readConstant("code") : lexer.take());
+      if (lexer.hasComments()) {
+        tgt.makeElement("comment").markLocation(lexer.getCommentLocation()).setValue(lexer.getFirstComment());
+      }
+    }
+    lexer.token("}");
+  }
+  
+  private Element getGroupE(Element map, String srcs, String tgts) {
+    for (Element grp : map.getChildrenByName("group")) {
+      if (grp.getChildValue("source").equals(srcs)) {
+        Element tgt = grp.getNamedChild("target");
+        if (tgt == null || tgts == null || tgts.equals(tgt.getValue())) {
+          if (tgt == null && tgts != null)
+            grp.makeElement("target").setValue(tgts);
+          return grp;
+        }
+      }
+    }
+    Element grp = map.addElement("group");
+    grp.makeElement("source").setValue(srcs);
+    grp.makeElement("target").setValue(tgts);
+    return grp;
+  }
+
+  private String readPrefix(Map<String, String> prefixes, FHIRLexer lexer) throws FHIRLexerException {
+    String prefix = lexer.take();
+    if (!prefixes.containsKey(prefix))
+      throw lexer.error("Unknown prefix '" + prefix + "'");
+    return prefixes.get(prefix);
+  }
+
+
+  private ConceptMapRelationship readRelationship(FHIRLexer lexer) throws FHIRLexerException {
+    String token = lexer.take();
+    if (token.equals("-"))
+      return ConceptMapRelationship.RELATEDTO;
+    if (token.equals("=="))
+      return ConceptMapRelationship.EQUIVALENT;
+    if (token.equals("!="))
+      return ConceptMapRelationship.NOTRELATEDTO;
+    if (token.equals("<="))
+      return ConceptMapRelationship.SOURCEISNARROWERTHANTARGET;
+    if (token.equals(">="))
+      return ConceptMapRelationship.SOURCEISBROADERTHANTARGET;
+    throw lexer.error("Unknown relationship token '" + token + "'");
+  }
+
+  private void parseUses(Element result, FHIRLexer lexer) throws FHIRException {
+    lexer.token("uses");
+    Element st = result.addElement("structure");
+    st.makeElement("url").markLocation(lexer.getCurrentLocation()).setValue(lexer.readConstant("url"));
+    if (lexer.hasToken("alias")) {
+      lexer.token("alias");
+      st.makeElement("alias").markLocation(lexer.getCurrentLocation()).setValue(lexer.take());
+    }
+    lexer.token("as");
+    st.makeElement("mode").markLocation(lexer.getCurrentLocation()).setValue(lexer.take());
+    lexer.skipToken(";");
+    if (lexer.hasComments()) {
+      st.makeElement("documentation").markLocation(lexer.getCommentLocation()).setValue(lexer.getFirstComment());
+    }
+  }
+  
+
+  private void parseImports(Element result, FHIRLexer lexer) throws FHIRException {
+    lexer.token("imports");
+    result.addElement("import").markLocation(lexer.getCurrentLocation()).setValue(lexer.readConstant("url"));
+    lexer.skipToken(";");
+  }
+
+  private void parseGroup(Element result, FHIRLexer lexer) throws FHIRException {
+    SourceLocation commLoc = lexer.getCommentLocation();
+    String comment = lexer.getAllComments();
+    lexer.token("group");
+    Element group = result.addElement("group").markLocation(lexer.getCurrentLocation());
+    if (!Utilities.noString(comment)) {
+      group.makeElement("documentation").markLocation(commLoc).setValue(comment);
+    }
+    boolean newFmt = false;
+    if (lexer.hasToken("for")) {
+      lexer.token("for");
+      SourceLocation loc = lexer.getCurrentLocation();
+      if ("type".equals(lexer.getCurrent())) {
+        lexer.token("type");
+        lexer.token("+");
+        lexer.token("types");
+        group.makeElement("typeMode").markLocation(loc).setValue(StructureMapGroupTypeMode.TYPEANDTYPES.toCode());
+      } else {
+        lexer.token("types");
+        group.makeElement("typeMode").markLocation(loc).setValue(StructureMapGroupTypeMode.TYPES.toCode());
+      }
+    }
+    group.makeElement("name").markLocation(lexer.getCurrentLocation()).setValue(lexer.take());
+    if (lexer.hasToken("(")) {
+      newFmt = true;
+      lexer.take();
+      while (!lexer.hasToken(")")) {
+        parseInput(group, lexer, true);
+        if (lexer.hasToken(","))
+          lexer.token(",");
+      }
+      lexer.take();
+    }
+    if (lexer.hasToken("extends")) {
+      lexer.next();
+      group.makeElement("extends").markLocation(lexer.getCurrentLocation()).setValue(lexer.take());
+    }
+    if (newFmt) {
+      if (lexer.hasToken("<")) {
+        lexer.token("<");
+        lexer.token("<");
+        if (lexer.hasToken("types")) {
+          group.makeElement("typeMode").markLocation(lexer.getCurrentLocation()).setValue(StructureMapGroupTypeMode.TYPES.toCode());
+        } else {
+          group.makeElement("typeMode").markLocation(lexer.getCurrentLocation()).setValue(StructureMapGroupTypeMode.TYPEANDTYPES.toCode());
+          lexer.token("type");
+          lexer.token("+");
+        }
+        lexer.token(">");
+        lexer.token(">");
+      }
+      lexer.token("{");
+    }
+    if (newFmt) {
+      while (!lexer.hasToken("}")) {
+        if (lexer.done())
+          throw lexer.error("premature termination expecting 'endgroup'");
+        parseRule(result, group, lexer, true);
+      }
+    } else {
+      while (lexer.hasToken("input"))
+        parseInput(group, lexer, false);
+      while (!lexer.hasToken("endgroup")) {
+        if (lexer.done())
+          throw lexer.error("premature termination expecting 'endgroup'");
+        parseRule(result, group, lexer, false);
+      }
+    }
+    lexer.next();
+    if (newFmt && lexer.hasToken(";"))
+      lexer.next();
+  }
+  
+
+  private void parseRule(Element map, Element context, FHIRLexer lexer, boolean newFmt) throws FHIRException {
+    Element rule = context.addElement("rule").markLocation(lexer.getCurrentLocation());
+    if (!newFmt) {
+      rule.makeElement("name").markLocation(lexer.getCurrentLocation()).setValue(lexer.takeDottedToken());
+      lexer.token(":");
+      lexer.token("for");
+    } else {
+      if (lexer.hasComments()) {
+        rule.makeElement("documentation").markLocation(lexer.getCommentLocation()).setValue(lexer.getFirstComment());
+      }
+    }
+
+    boolean done = false;
+    while (!done) {
+      parseSource(rule, lexer);
+      done = !lexer.hasToken(",");
+      if (!done)
+        lexer.next();
+    }
+    if ((newFmt && lexer.hasToken("->")) || (!newFmt && lexer.hasToken("make"))) {
+      lexer.token(newFmt ? "->" : "make");
+      done = false;
+      while (!done) {
+        parseTarget(rule, lexer);
+        done = !lexer.hasToken(",");
+        if (!done)
+          lexer.next();
+      }
+    }
+    if (lexer.hasToken("then")) {
+      lexer.token("then");
+      if (lexer.hasToken("{")) {
+        lexer.token("{");
+        while (!lexer.hasToken("}")) {
+          if (lexer.done())
+            throw lexer.error("premature termination expecting '}' in nested group");
+          parseRule(map, rule, lexer, newFmt);
+        }
+        lexer.token("}");
+      } else {
+        done = false;
+        while (!done) {
+          parseRuleReference(rule, lexer);
+          done = !lexer.hasToken(",");
+          if (!done)
+            lexer.next();
+        }
+      }
+    }
+    if (!rule.hasChild("documentation") && lexer.hasComments()) {
+      rule.makeElement("documentation").markLocation(lexer.getCommentLocation()).setValue(lexer.getFirstComment());
+    }
+
+    if (isSimpleSyntax(rule)) {
+      rule.forceElement("source").makeElement("variable").setValue(StructureMapUtilities.AUTO_VAR_NAME);
+      rule.forceElement("target").makeElement("variable").setValue(StructureMapUtilities.AUTO_VAR_NAME);
+      rule.forceElement("target").makeElement("transform").setValue(StructureMapTransform.CREATE.toCode());
+      Element dep = rule.forceElement("dependent");
+      dep.makeElement("name").setValue(StructureMapUtilities.DEF_GROUP_NAME);
+      dep.makeElement("parameter").makeElement("valueId").setValue(StructureMapUtilities.AUTO_VAR_NAME);
+      dep.makeElement("parameter").makeElement("valueId").setValue(StructureMapUtilities.AUTO_VAR_NAME);
+      // no dependencies - imply what is to be done based on types
+    }
+    if (newFmt) {
+      if (lexer.isConstant()) {
+        if (lexer.isStringConstant()) {
+          rule.makeElement("name").markLocation(lexer.getCurrentLocation()).setValue(lexer.readConstant("ruleName"));
+        } else {
+          rule.makeElement("name").markLocation(lexer.getCurrentLocation()).setValue(lexer.take());
+        }
+      } else {
+        if (rule.getChildrenByName("source").size() != 1 || !rule.getChildrenByName("source").get(0).hasChild("element"))
+          throw lexer.error("Complex rules must have an explicit name");
+        if (rule.getChildrenByName("source").get(0).hasChild("type"))
+          rule.makeElement("name").setValue(rule.getChildrenByName("source").get(0).getNamedChildValue("element") + rule.getChildrenByName("source").get(0).getNamedChildValue("type"));
+        else
+          rule.makeElement("name").setValue(rule.getChildrenByName("source").get(0).getNamedChildValue("element"));
+      }
+      lexer.token(";");
+    }
+  }
+
+  private void parseRuleReference(Element rule, FHIRLexer lexer) throws FHIRLexerException {
+    Element ref = rule.addElement("dependent");
+    ref.makeElement("name").markLocation(lexer.getCurrentLocation()).setValue(lexer.take());
+    lexer.token("(");
+    boolean done = false;
+    while (!done) {
+      parseParameter(ref, lexer);
+      done = !lexer.hasToken(",");
+      if (!done)
+        lexer.next();
+    }
+    lexer.token(")");
+  }
+
+  private void parseSource(Element rule, FHIRLexer lexer) throws FHIRException {
+    Element source = rule.addElement("source").markLocation(lexer.getCurrentLocation());
+    source.makeElement("context").markLocation(lexer.getCurrentLocation()).setValue(lexer.take());
+    if (source.getChildValue("context").equals("search") && lexer.hasToken("(")) {
+      source.makeElement("context").markLocation(lexer.getCurrentLocation()).setValue("@search");
+      lexer.take();
+      SourceLocation loc = lexer.getCurrentLocation();
+      ExpressionNode node = fpe.parse(lexer);
+      source.setUserData(StructureMapUtilities.MAP_SEARCH_EXPRESSION, node);
+      source.makeElement("element").markLocation(loc).setValue(node.toString());
+      lexer.token(")");
+    } else if (lexer.hasToken(".")) {
+      lexer.token(".");
+      source.makeElement("element").markLocation(lexer.getCurrentLocation()).setValue(lexer.take());
+    }
+    if (lexer.hasToken(":")) {
+      // type and cardinality
+      lexer.token(":");
+      source.makeElement("type").markLocation(lexer.getCurrentLocation()).setValue(lexer.takeDottedToken());
+    }
+    if (Utilities.isInteger(lexer.getCurrent())) {
+      source.makeElement("min").markLocation(lexer.getCurrentLocation()).setValue(lexer.take());
+      lexer.token("..");
+      source.makeElement("max").markLocation(lexer.getCurrentLocation()).setValue(lexer.take());
+    }
+    if (lexer.hasToken("default")) {
+      lexer.token("default");
+     source.makeElement("defaultValue").markLocation(lexer.getCurrentLocation()).setValue(lexer.readConstant("default value"));
+    }
+    if (Utilities.existsInList(lexer.getCurrent(), "first", "last", "not_first", "not_last", "only_one")) {
+      source.makeElement("listMode").markLocation(lexer.getCurrentLocation()).setValue(lexer.take());
+    }
+
+    if (lexer.hasToken("as")) {
+      lexer.take();
+      source.makeElement("variable").markLocation(lexer.getCurrentLocation()).setValue(lexer.take());
+    }
+    if (lexer.hasToken("where")) {
+      lexer.take();
+      SourceLocation loc = lexer.getCurrentLocation();
+      ExpressionNode node = fpe.parse(lexer);
+      source.setUserData(StructureMapUtilities.MAP_WHERE_EXPRESSION, node);
+      source.makeElement("condition").markLocation(loc).setValue(node.toString());
+    }
+    if (lexer.hasToken("check")) {
+      lexer.take();
+      SourceLocation loc = lexer.getCurrentLocation();
+      ExpressionNode node = fpe.parse(lexer);
+      source.setUserData(StructureMapUtilities.MAP_WHERE_CHECK, node);
+      source.makeElement("check").markLocation(loc).setValue(node.toString());
+    }
+    if (lexer.hasToken("log")) {
+      lexer.take();
+      SourceLocation loc = lexer.getCurrentLocation();
+      ExpressionNode node = fpe.parse(lexer);
+      source.setUserData(StructureMapUtilities.MAP_WHERE_CHECK, node);
+      source.makeElement("logMessage").markLocation(loc).setValue(lexer.take());
+    }
+  }
+  
+  private void parseTarget(Element rule, FHIRLexer lexer) throws FHIRException {
+    Element target = rule.addElement("target").markLocation(lexer.getCurrentLocation());
+    SourceLocation loc = lexer.getCurrentLocation();
+    String start = lexer.take();
+    if (lexer.hasToken(".")) {
+      target.makeElement("context").markLocation(loc).setValue(start);
+      start = null;
+      lexer.token(".");
+      target.makeElement("element").markLocation(lexer.getCurrentLocation()).setValue(lexer.take());
+    }
+    String name;
+    boolean isConstant = false;
+    if (lexer.hasToken("=")) {
+      if (start != null) {
+        target.makeElement("context").markLocation(loc).setValue(start);
+      }
+      lexer.token("=");
+      isConstant = lexer.isConstant();
+      loc = lexer.getCurrentLocation();
+      name = lexer.take();
+    } else {
+      loc = lexer.getCurrentLocation();
+      name = start;
+    }
+
+    if ("(".equals(name)) {
+      // inline fluentpath expression
+      target.makeElement("transform").markLocation(lexer.getCurrentLocation()).setValue(StructureMapTransform.EVALUATE.toCode());
+      loc = lexer.getCurrentLocation();
+      ExpressionNode node = fpe.parse(lexer);
+      target.setUserData(StructureMapUtilities.MAP_EXPRESSION, node);
+      target.addElement("parameter").markLocation(loc).makeElement("valueString").setValue(node.toString());
+      lexer.token(")");
+    } else if (lexer.hasToken("(")) {
+      target.makeElement("transform").markLocation(loc).setValue(name);
+      lexer.token("(");
+      if (target.getChildValue("transform").equals(StructureMapTransform.EVALUATE.toCode())) {
+        parseParameter(target, lexer);
+        lexer.token(",");
+        loc = lexer.getCurrentLocation();
+        ExpressionNode node = fpe.parse(lexer);
+        target.setUserData(StructureMapUtilities.MAP_EXPRESSION, node);
+        target.addElement("parameter").markLocation(loc).setValue(node.toString());
+      } else {
+        while (!lexer.hasToken(")")) {
+          parseParameter(target, lexer);
+          if (!lexer.hasToken(")"))
+            lexer.token(",");
+        }
+      }
+      lexer.token(")");
+    } else if (name != null) {
+      target.makeElement("transform").markLocation(loc).setValue(StructureMapTransform.COPY.toCode());
+      if (!isConstant) {
+        loc = lexer.getCurrentLocation();
+        String id = name;
+        while (lexer.hasToken(".")) {
+          id = id + lexer.take() + lexer.take();
+        }
+        target.addElement("parameter").markLocation(loc).setValue(id);
+      } else {
+        target.addElement("parameter").markLocation(lexer.getCurrentLocation()).setValue(readConstant(name, lexer));
+      }
+    }
+    if (lexer.hasToken("as")) {
+      lexer.take();
+      target.makeElement("variable").markLocation(lexer.getCurrentLocation()).setValue(lexer.take());
+    }
+    while (Utilities.existsInList(lexer.getCurrent(), "first", "last", "share", "collate")) {
+      if (lexer.getCurrent().equals("share")) {
+        target.makeElement("listMode").markLocation(lexer.getCurrentLocation()).setValue(lexer.take());
+        target.makeElement("listRuleId").markLocation(lexer.getCurrentLocation()).setValue(lexer.take());
+      } else {
+        target.makeElement("listMode").markLocation(lexer.getCurrentLocation()).setValue(lexer.take());
+      }
+    }
+  }
+
+  private void parseParameter(Element ref, FHIRLexer lexer) throws FHIRLexerException, FHIRFormatError {
+    if (!lexer.isConstant()) {
+      ref.addElement("parameter").markLocation(lexer.getCurrentLocation()).makeElement("valueId").setValue(lexer.take());
+    } else if (lexer.isStringConstant())
+      ref.addElement("parameter").markLocation(lexer.getCurrentLocation()).makeElement("valueString").setValue(lexer.readConstant("??"));
+    else {
+      ref.addElement("parameter").markLocation(lexer.getCurrentLocation()).makeElement("valueString").setValue(readConstant(lexer.take(), lexer));
+    }
+  }
+ 
+  private void parseInput(Element group, FHIRLexer lexer, boolean newFmt) throws FHIRException {
+    Element input = group.addElement("input");
+    if (newFmt) {
+      input.makeElement("mode").markLocation(lexer.getCurrentLocation()).setValue(lexer.take());
+    } else
+      lexer.token("input");
+    input.makeElement("name").markLocation(lexer.getCurrentLocation()).setValue(lexer.take());
+    if (lexer.hasToken(":")) {
+      lexer.token(":");
+      input.makeElement("type").markLocation(lexer.getCurrentLocation()).setValue(lexer.take());
+    }
+    if (!newFmt) {
+      lexer.token("as");
+      input.makeElement("mode").markLocation(lexer.getCurrentLocation()).setValue(lexer.take());
+      if (lexer.hasComments()) {
+        input.makeElement("documentation").markLocation(lexer.getCommentLocation()).setValue(lexer.getFirstComment());
+      }
+      lexer.skipToken(";");
+    }
+  }
+  
+  private boolean isSimpleSyntax(Element rule) {
+    return
+      (rule.getChildren("source").size() == 1 && rule.getChildren("source").get(0).hasChild("context") && rule.getChildren("source").get(0).hasChild("element") && !rule.getChildren("source").get(0).hasChild("variable")) &&
+        (rule.getChildren("target").size() == 1 && rule.getChildren("target").get(0).hasChild("context") && rule.getChildren("target").get(0).hasChild("element") && !rule.getChildren("target").get(0).hasChild("variable") && 
+           !rule.getChildren("target").get(0).hasChild("parameter")) &&
+        (rule.getChildren("dependent").size() == 0 && rule.getChildren("rule").size() == 0);
+  }
+
+  private String readConstant(String s, FHIRLexer lexer) throws FHIRLexerException {
+    if (Utilities.isInteger(s))
+      return s;
+    else if (Utilities.isDecimal(s, false))
+      return s;
+    else if (Utilities.existsInList(s, "true", "false"))
+      return s;
+    else
+      return lexer.processConstant(s);
+  }
+
+  
+}

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

@@ -48,7 +48,7 @@ import org.hl7.fhir.r5.model.StructureDefinition;
 public class Manager {
 
   //TODO use EnumMap
-  public enum FhirFormat { XML, JSON, TURTLE, TEXT, VBAR, SHC; 
+  public enum FhirFormat { XML, JSON, TURTLE, TEXT, VBAR, SHC, FML; 
     // SHC = smart health cards, including as text versions of QR codes
 
     public String getExtension() {
@@ -65,6 +65,8 @@ public class Manager {
           return "hl7";
         case SHC:
           return "shc";
+        case FML:
+          return "fml";
       }
       return null;
     }
@@ -81,6 +83,8 @@ public class Manager {
           return TEXT;
         case "hl7":
           return VBAR;
+        case "fml":
+          return FML;
       }
       return null;
     }
@@ -115,6 +119,7 @@ public class Manager {
     case TURTLE : return new TurtleParser(context);
     case VBAR : return new VerticalBarParser(context);
     case SHC : return new SHCParser(context);
+    case FML : return new FmlParser(context);
     case TEXT : throw new Error("Programming logic error: do not call makeParser for a text resource");
     }
     return null;
@@ -123,6 +128,7 @@ public class Manager {
   public static Element build(IWorkerContext context, StructureDefinition sd) {
     Property p = new Property(context, sd.getSnapshot().getElementFirstRep(), sd);
     Element e = new Element(p.getName(), p);
+    e.setPath(sd.getType());
     return e;
   }
 

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

@@ -270,9 +270,10 @@ public class Property {
       String tc = definition.getType().get(0).getCode();
       return definition.getType().size() == 1 && (("Resource".equals(tc) || "DomainResource".equals(tc)) ||  Utilities.existsInList(tc, context.getResourceNames()));
     }
-	  else
+	  else {
 	    return !definition.getPath().contains(".") && (structure.getKind() == StructureDefinitionKind.RESOURCE);
 	  }
+	}
 
   public boolean isList() {
     return !"1".equals(definition.getMax());

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

@@ -333,14 +333,12 @@ public class TurtleParser extends ParserBase {
     }
     String subjId = genSubjectId(e);
 
-    String ontologyId = subjId.replace(">", ".ttl>");
+    Subject subject;
-    Section ontology = ttl.section("ontology header");
+    if (hasModifierExtension(e)) 
-    ontology.triple(ontologyId, "a", "owl:Ontology");
+    	subject = section.triple(subjId, "a", "fhir:_" + e.getType());
-    ontology.triple(ontologyId, "owl:imports", "fhir:fhir.ttl");
+     else 
-    if(ontologyId.startsWith("<" + FHIR_URI_BASE))
+    	subject = section.triple(subjId, "a", "fhir:" + e.getType());
-      ontology.triple(ontologyId, "owl:versionIRI", ontologyId.replace(FHIR_URI_BASE, FHIR_VERSION_BASE));
      
-    Subject subject = section.triple(subjId, "a", "fhir:" + e.getType());
 	subject.linkedPredicate("fhir:nodeRole", "fhir:treeRoot", linkResolver == null ? null : linkResolver.resolvePage("rdf.html#tree-root"), null);
 
 	for (Element child : e.getChildren()) {
@@ -349,6 +347,10 @@ public class TurtleParser extends ParserBase {
 
   }
   
+  private boolean hasModifierExtension(Element e) {
+	  return e.getChildren().stream().anyMatch(p -> p.getName().equals("modifierExtension"));
+  }
+  
   protected String getURIType(String uri) {
     if(uri.startsWith("<" + FHIR_URI_BASE))
       if(uri.substring(FHIR_URI_BASE.length() + 1).contains("/"))
@@ -415,17 +417,18 @@ public class TurtleParser extends ParserBase {
 	  Complex t;
 	  if (element.getSpecial() == SpecialElement.BUNDLE_ENTRY && parent != null && parent.getNamedChildValue("fullUrl") != null) {
 	    String url = "<"+parent.getNamedChildValue("fullUrl")+">";
-	    ctxt.linkedPredicate("fhir:"+en, url, linkResolver == null ? null : linkResolver.resolveProperty(element.getProperty()), comment);
+	    ctxt.linkedPredicate("fhir:"+en, url, linkResolver == null ? null : linkResolver.resolveProperty(element.getProperty()), comment, element.getProperty().isList());
 	    t = section.subject(url);
 	  } else {
-	    t = ctxt.linkedPredicate("fhir:"+en, linkResolver == null ? null : linkResolver.resolveProperty(element.getProperty()), comment);
+	    t = ctxt.linkedPredicate("fhir:"+en, linkResolver == null ? null : linkResolver.resolveProperty(element.getProperty()), comment, element.getProperty().isList());
+	  }
+	if (element.getProperty().getName().endsWith("[x]") && !element.hasValue()) {
+	  t.linkedPredicate("a", "fhir:" + element.fhirType(), linkResolver == null ? null : linkResolver.resolveType(element.fhirType()), null);
 	}
     if (element.getSpecial() != null)
       t.linkedPredicate("a", "fhir:"+element.fhirType(), linkResolver == null ? null : linkResolver.resolveType(element.fhirType()), null);
 	  if (element.hasValue())
-	  	t.linkedPredicate("fhir:value", ttlLiteral(element.getValue(), element.getType()), linkResolver == null ? null : linkResolver.resolveType(element.getType()), null);
+	  	t.linkedPredicate("fhir:v", ttlLiteral(element.getValue(), element.getType()), linkResolver == null ? null : linkResolver.resolveType(element.getType()), null);
-	  if (element.getProperty().isList() && (!element.isResource() || element.getSpecial() == SpecialElement.CONTAINED))
-	  	t.linkedPredicate("fhir:index", Integer.toString(element.getIndex()), linkResolver == null ? null : linkResolver.resolvePage("rdf.html#index"), null);
 
 	  if ("Coding".equals(element.getType()))
 	  	decorateCoding(t, element, section);
@@ -463,37 +466,27 @@ public class TurtleParser extends ParserBase {
 
   private String getFormalName(Element element) {
     String en = null;
-    if (element.getSpecial() == null) {
+    if (element.getSpecial() == null) 
-      if (element.getProperty().getDefinition().hasBase())
+    	en = element.getProperty().getName();
-        en = element.getProperty().getDefinition().getBase().getPath();
-    }
     else if (element.getSpecial() == SpecialElement.BUNDLE_ENTRY)
-      en = "Bundle.entry.resource";
+      en = "resource";
     else if (element.getSpecial() == SpecialElement.BUNDLE_OUTCOME)
-      en = "Bundle.entry.response.outcome";
+      en = "outcome";
     else if (element.getSpecial() == SpecialElement.PARAMETER)
       en = element.getElementProperty().getDefinition().getPath();
     else // CONTAINED
-      en = "DomainResource.contained";
+      en = "contained";
 
     if (en == null) 
-      en = element.getProperty().getDefinition().getPath();
+      en = element.getProperty().getName();
-    boolean doType = false;
-      if (en.endsWith("[x]")) {
-        en = en.substring(0, en.length()-3);
-        doType = true;
-      }
-     if (doType || (element.getProperty().getDefinition().getType().size() > 1 && !allReference(element.getProperty().getDefinition().getType())))
-       en = en + Utilities.capitalize(element.getType());
-    return en;
-  }
     
-	private boolean allReference(List<TypeRefComponent> types) {
+    if (en.endsWith("[x]")) 
-	  for (TypeRefComponent t : types) {
+      en = en.substring(0, en.length()-3);
-	    if (!t.getCode().equals("Reference"))
+    
-	      return false;
+    if (hasModifierExtension(element))
-	  }
+    	return "_" + en;
-    return true;
+    else
+      return en;
   }
 
   static public String ttlLiteral(String value, String type) {
@@ -550,10 +543,14 @@ public class TurtleParser extends ParserBase {
       else
         t.linkedPredicate("a", "sct:" + urlescape(code), null, null);
     } else if ("http://loinc.org".equals(system)) {
-      t.prefix("loinc", "http://loinc.org/rdf#");
+      t.prefix("loinc", "https://loinc.org/rdf/");
       t.linkedPredicate("a", "loinc:"+urlescape(code).toUpperCase(), null, null);
+    } else if ("https://www.nlm.nih.gov/mesh".equals(system)) {
+    	t.prefix("mesh", "http://id.nlm.nih.gov/mesh/");
+    	t.linkedPredicate("a", "mesh:"+urlescape(code), null, null);
     }  
   }
+
   private void generateLinkedPredicate(Complex t, String code) throws FHIRException {
     Expression expression = SnomedExpressions.parse(code);
     

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/formats/FormatUtilities.java

@@ -81,6 +81,10 @@ public abstract class FormatUtilities {
   public static final String NS_XSI = "http://www.w3.org/2001/XMLSchema-instance";
   private static final int MAX_SCAN_LENGTH = 1000; // how many characters to scan into content when autodetermining format
   
+  public static final String MAP_ATTRIBUTE_NAME = "mapAttribute";
+  public static final String PROPERTY_NAME = "property";
+  public static String WORKING_CM_PROP_NAME = PROPERTY_NAME;
+  
   protected String toString(String value) {
     return value;
   }

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

@@ -9418,10 +9418,10 @@ public class JsonParser extends JsonParserBase {
 
   protected void parseConceptMapOtherElementComponentProperties(JsonObject json, ConceptMap.OtherElementComponent res) throws IOException, FHIRFormatError {
     parseBackboneElementProperties(json, res);
-    if (json.has("property"))
+    if (json.has(FormatUtilities.WORKING_CM_PROP_NAME))
-      res.setPropertyElement(parseUri(json.get("property").getAsString()));
+      res.setPropertyElement(parseUri(json.get(FormatUtilities.WORKING_CM_PROP_NAME).getAsString()));
-    if (json.has("_property"))
+    if (json.has("_"+FormatUtilities.WORKING_CM_PROP_NAME))
-      parseElementProperties(getJObject(json, "_property"), res.getPropertyElement());
+      parseElementProperties(getJObject(json, "_"+FormatUtilities.WORKING_CM_PROP_NAME), res.getPropertyElement());
     DataType value = parseType("value", json);
     if (value != null)
       res.setValue(value);
@@ -44920,8 +44920,8 @@ public class JsonParser extends JsonParserBase {
   protected void composeOtherElementComponentProperties(ConceptMap.OtherElementComponent element) throws IOException {
     composeBackboneElementProperties(element);
       if (element.hasPropertyElement()) {
-        composeUriCore("property", element.getPropertyElement(), false);
+        composeUriCore(FormatUtilities.WORKING_CM_PROP_NAME, element.getPropertyElement(), false);
-        composeUriExtras("property", element.getPropertyElement(), false);
+        composeUriExtras(FormatUtilities.WORKING_CM_PROP_NAME, element.getPropertyElement(), false);
       }
       if (element.hasValue()) {
         composeType("value", element.getValue());

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/formats/RdfParserBase.java

@@ -122,10 +122,10 @@ public abstract class RdfParserBase extends ParserBase implements IParser  {
 			return;
 		if ("http://snomed.info/sct".equals(element.getSystem())) {
 			t.prefix("sct", "http://snomed.info/sct/");
-			t.predicate("a", "sct:"+element.getCode());
+			t.predicate("a", "sct:"+element.getCode(), false);
 		} else if ("http://snomed.info/sct".equals(element.getSystem())) {
 			t.prefix("loinc", "http://loinc.org/rdf#");
-			t.predicate("a", "loinc:"+element.getCode());
+			t.predicate("a", "loinc:"+element.getCode(), false);
 		}  
 	}
 

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/formats/XmlParser.java

@@ -8204,7 +8204,7 @@ public class XmlParser extends XmlParserBase {
   }
 
   protected boolean parseConceptMapOtherElementComponentContent(int eventType, XmlPullParser xpp, ConceptMap.OtherElementComponent res) throws XmlPullParserException, IOException, FHIRFormatError {
-    if (eventType == XmlPullParser.START_TAG && xpp.getName().equals("property")) {
+    if (eventType == XmlPullParser.START_TAG && xpp.getName().equals(FormatUtilities.WORKING_CM_PROP_NAME)) {
       res.setPropertyElement(parseUri(xpp));
     } else if (eventType == XmlPullParser.START_TAG && nameIsTypeName(xpp, "value")) {
       res.setValue(parseType("value", xpp));
@@ -38972,7 +38972,7 @@ public class XmlParser extends XmlParserBase {
   protected void composeConceptMapOtherElementComponentElements(ConceptMap.OtherElementComponent element) throws IOException {
     composeBackboneElementElements(element);
     if (element.hasPropertyElement()) {
-      composeUri("property", element.getPropertyElement());
+      composeUri(FormatUtilities.WORKING_CM_PROP_NAME, element.getPropertyElement());
     }
     if (element.hasValue()) {
       composeType("value", element.getValue());

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

@@ -34,7 +34,11 @@ package org.hl7.fhir.r5.model;
 import java.util.ArrayList;
 import java.util.Date;
 import java.util.List;
+import java.util.Set;
+
 import org.hl7.fhir.r5.model.Enumerations.*;
+import org.hl7.fhir.r5.utils.ToolingExtensions;
+import org.hl7.fhir.utilities.StandardsStatus;
 import org.hl7.fhir.instance.model.api.IBaseBackboneElement;
 import org.hl7.fhir.exceptions.FHIRException;
 import org.hl7.fhir.instance.model.api.ICompositeType;
@@ -509,6 +513,15 @@ public void checkNoModifiers(String noun, String verb) throws FHIRException {
       }
       return Collections.unmodifiableList(retVal);
     }
+    
+    public StandardsStatus getStandardsStatus() {
+      return ToolingExtensions.getStandardsStatus(this);
+    }
+    
+    public void setStandardsStatus(StandardsStatus status) {
+      ToolingExtensions.setStandardsStatus(this, status, null);
+    }
+
 // end addition
 
 }

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

@@ -34,8 +34,11 @@ package org.hl7.fhir.r5.model;
 import java.util.ArrayList;
 import java.util.Date;
 import java.util.List;
+
+import org.hl7.fhir.utilities.StandardsStatus;
 import org.hl7.fhir.utilities.Utilities;
 import org.hl7.fhir.r5.model.Enumerations.*;
+import org.hl7.fhir.r5.utils.ToolingExtensions;
 import org.hl7.fhir.instance.model.api.IBaseDatatypeElement;
 import org.hl7.fhir.exceptions.FHIRException;
 import org.hl7.fhir.instance.model.api.ICompositeType;
@@ -430,6 +433,15 @@ public abstract class Element extends Base implements IBaseHasExtensions, IBaseE
     return ext.get(0).getValue().primitiveValue();
   }
 
+  public StandardsStatus getStandardsStatus() {
+    return ToolingExtensions.getStandardsStatus(this);
+  }
+  
+  public void setStandardsStatus(StandardsStatus status) {
+    ToolingExtensions.setStandardsStatus(this, status, null);
+  }
+
+
 // end addition
 
 }

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

@@ -13521,6 +13521,9 @@ If a pattern[x] is declared on a repeating element, the pattern applies to all r
     return hasPath() ? getPath().contains(".") ? getPath().substring(getPath().lastIndexOf(".")+1) : getPath() : null;
   }
 
+  public String getNameBase() {
+    return getName().replace("[x]", "");
+  }
   public boolean unbounded() {
     return getMax().equals("*") || Integer.parseInt(getMax()) > 1;
   }
@@ -13554,6 +13557,8 @@ If a pattern[x] is declared on a repeating element, the pattern applies to all r
     return getMin() == 1; 
   }
 
+
+
 // end addition
 
 }

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

@@ -115,10 +115,13 @@ public class TypeDetails {
     public boolean isSystemType() {
       return uri.startsWith(FP_NS);
     }
+    
   }
   
   private List<ProfiledType> types = new ArrayList<ProfiledType>();
   private CollectionStatus collectionStatus;
+  private Set<String> targets; // or, not and, canonical urls
+
   public TypeDetails(CollectionStatus collectionStatus, String... names) {
     super();
     this.collectionStatus = collectionStatus;
@@ -151,6 +154,7 @@ public class TypeDetails {
     addType(pt);
     return res;
   }
+  
   public void addType(ProfiledType pt) {
     for (ProfiledType et : types) {
       if (et.uri.equals(pt.uri)) {
@@ -176,6 +180,28 @@ public class TypeDetails {
     types.add(pt); 
   }
 
+  public void addType(CollectionStatus status, ProfiledType pt) {
+    addType(pt);
+    if (collectionStatus == null) {
+      collectionStatus = status;      
+    } else {
+      switch (status) {
+      case ORDERED:
+        if (collectionStatus == CollectionStatus.SINGLETON) {
+          collectionStatus = status;
+        }
+        break;
+      case SINGLETON:
+        break;
+      case UNORDERED:
+        collectionStatus = status;
+        break;
+      default:
+        break;    
+      }
+    }
+  }
+
   public void addTypes(Collection<String> names) {
     for (String n : names) 
       addType(new ProfiledType(n));
@@ -245,7 +271,14 @@ public class TypeDetails {
       collectionStatus = source.collectionStatus;
     else
       collectionStatus = CollectionStatus.ORDERED;
+    if (source.targets != null) {
+      if (targets == null) {
+        targets = new HashSet<>();
       }
+      targets.addAll(source.targets);
+    }
+  }
+  
   public TypeDetails union(TypeDetails right) {
     TypeDetails result = new TypeDetails(null);
     if (right.collectionStatus == CollectionStatus.UNORDERED || collectionStatus == CollectionStatus.UNORDERED)
@@ -256,6 +289,16 @@ public class TypeDetails {
       result.addType(pt);
     for (ProfiledType pt : right.types)
       result.addType(pt);
+    if (targets != null || right.targets != null) {
+      result.targets = new HashSet<>();
+      if (targets != null) {
+        result.targets.addAll(targets);
+      }
+      if (right.targets != null) {
+        result.targets.addAll(right.targets);
+      }
+    }
+
     return result;
   }
   
@@ -274,6 +317,15 @@ public class TypeDetails {
     }
     for (ProfiledType pt : right.types)
       result.addType(pt);
+    if (targets != null && right.targets != null) {
+      result.targets = new HashSet<>();
+      for (String s : targets) {
+        if (right.targets.contains(s)) {
+          result.targets.add(s);
+        }
+      }
+    }
+
     return result;
   }
   
@@ -360,4 +412,30 @@ public class TypeDetails {
   }
  
 
+  public void addTarget(String url) {
+    if (targets == null) {
+      targets = new HashSet<>();
+    }
+    targets.add(url);
+  }
+  public Set<String> getTargets() {
+    return targets;
+  }
+  public boolean typesHaveTargets() {
+    for (ProfiledType pt : types) {
+      if (Utilities.existsInList(pt.getUri(), "Reference", "CodeableReference", "canonical",  "http://hl7.org/fhir/StructureDefinition/Reference", "http://hl7.org/fhir/StructureDefinition/CodeableReference", "http://hl7.org/fhir/StructureDefinition/canonical")) {
+        return true;
+      }
+    }
+    return false;
+  }
+  public void addTargets(Set<String> src) {
+    if (src != null) {
+      for (String s : src) {
+        addTarget(s);
+      }
+    }
+    
+  }
+  
 }

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

@@ -212,7 +212,7 @@ public class ConceptMapRenderer extends TerminologyRenderer {
         } else
           tr.td().b().tx("Code");
         for (String s : sources.keySet()) {
-          if (!s.equals("code")) {
+          if (s != null && !s.equals("code")) {
             if (sources.get(s).size() == 1) {
               String url = sources.get(s).iterator().next();
               renderCSDetailsLink(tr, url, false);           
@@ -229,7 +229,7 @@ public class ConceptMapRenderer extends TerminologyRenderer {
         } else
           tr.td().b().tx("Code");
         for (String s : targets.keySet()) {
-          if (!s.equals("code")) {
+          if (s != null && !s.equals("code")) {
             if (targets.get(s).size() == 1) {
               String url = targets.get(s).iterator().next();
               renderCSDetailsLink(tr, url, false);           
@@ -291,7 +291,7 @@ public class ConceptMapRenderer extends TerminologyRenderer {
                   td.style("border-top-style: none; border-left-width: 0px");
               }
               for (String s : sources.keySet()) {
-                if (!s.equals("code")) {
+                if (s != null && !s.equals("code")) {
                   td = tr.td();
                   if (first) {
                     td.addText(getValue(ccm.getDependsOn(), s, sources.get(s).size() != 1));
@@ -323,7 +323,7 @@ public class ConceptMapRenderer extends TerminologyRenderer {
               tr.td().style("border-left-width: 0px").tx(display == null ? "" : display);
 
               for (String s : targets.keySet()) {
-                if (!s.equals("code")) {
+                if (s != null && !s.equals("code")) {
                   td = tr.td();
                   td.addText(getValue(ccm.getProduct(), s, targets.get(s).size() != 1));
                   display = getDisplay(ccm.getProduct(), s);

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

@@ -125,8 +125,12 @@ public class DiagnosticReportRenderer extends ResourceRenderer {
 
     pw = getProperty(dr, "conclusion");
     if (valued(pw)) {
+      if (pw.fhirType().equals("markdown")) {        
+        render(x, pw.value());        
+      } else {
         render(x.para(), pw.value());
       }
+    }
 
     pw = getProperty(dr, "conclusionCode");
     if (!valued(pw)) {

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

@@ -223,12 +223,15 @@ public abstract class ResourceRenderer extends DataRenderer {
       tr = resolveReference(rw, r.getReference());
 
       if (!r.getReference().startsWith("#")) {
-        if (tr != null && tr.getReference() != null)
+        if (tr != null && tr.getReference() != null) {
           c = x.ah(tr.getReference());
-        else
+        } else if (r.getReference().contains("?")) {
-          c = x.ah(r.getReference());
+          x.tx("Conditional Reference: ");
+          c = x.code("");
+        } else {
+          c = x.ah(r.getReference());
+        }
       } else {
-        
         c = x.ah(r.getReference());
       }
     } else {

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

@@ -77,6 +77,7 @@ import org.hl7.fhir.utilities.xhtml.HierarchicalTableGenerator;
 import org.hl7.fhir.utilities.xhtml.HierarchicalTableGenerator.Cell;
 import org.hl7.fhir.utilities.xhtml.HierarchicalTableGenerator.Piece;
 import org.hl7.fhir.utilities.xhtml.HierarchicalTableGenerator.Row;
+import org.hl7.fhir.utilities.xhtml.HierarchicalTableGenerator.TableGenerationMode;
 import org.hl7.fhir.utilities.xhtml.HierarchicalTableGenerator.TableModel;
 import org.hl7.fhir.utilities.xhtml.HierarchicalTableGenerator.Title;
 import org.hl7.fhir.utilities.xhtml.NodeType;
@@ -324,7 +325,7 @@ public class StructureDefinitionRenderer extends ResourceRenderer {
       model = initCustomTable(gen, corePath, false, true, profile.getId()+(diff ? "d" : "s"), rc.getRules() == GenerationRules.IG_PUBLISHER, columns);    
       break;
     case SUMMARY:
-      model = gen.initNormalTable(corePath, false, true, profile.getId()+(diff ? "d" : "s"), rc.getRules() == GenerationRules.IG_PUBLISHER);
+      model = gen.initNormalTable(corePath, false, true, profile.getId()+(diff ? "d" : "s"), rc.getRules() == GenerationRules.IG_PUBLISHER, rc.getRules() == GenerationRules.IG_PUBLISHER ? TableGenerationMode.XHTML : TableGenerationMode.XML);
       break;
     default:
       throw new Error("Unknown structure mode");
@@ -2052,7 +2053,7 @@ public class StructureDefinitionRenderer extends ResourceRenderer {
           } else if (definition.hasExample()) {
             for (ElementDefinitionExampleComponent ex : definition.getExample()) {
               if (!c.getPieces().isEmpty()) { c.addPiece(gen.new Piece("br")); }
-              c.getPieces().add(checkForNoChange(ex, gen.new Piece(null, "Example'"+("".equals("General")? "" : " "+ex.getLabel()+"'")+": ", null).addStyle("font-weight:bold")));
+              c.getPieces().add(checkForNoChange(ex, gen.new Piece(null, "Example'"+("".equals("General")? "": " "+ex.getLabel()+"'")+": ", "").addStyle("font-weight:bold")));
               c.getPieces().add(checkForNoChange(ex, gen.new Piece(null, buildJson(ex.getValue()), null).addStyle("color: darkgreen")));
             }
           }
@@ -2667,7 +2668,7 @@ public class StructureDefinitionRenderer extends ResourceRenderer {
   public XhtmlNode generateExtensionTable(String defFile, StructureDefinition ed, String imageFolder, boolean inlineGraphics, boolean full, String corePath, String imagePath, Set<String> outputTracker, RenderingContext rc) throws IOException, FHIRException {
     HierarchicalTableGenerator gen = new HierarchicalTableGenerator(imageFolder, inlineGraphics, true);
     gen.setTranslator(getTranslator());
-    TableModel model = gen.initNormalTable(corePath, false, true, ed.getId()+(full ? "f" : "n"), true);
+    TableModel model = gen.initNormalTable(corePath, false, true, ed.getId()+(full ? "f" : "n"), true, TableGenerationMode.XHTML);
 
     boolean deep = false;
     String m = "";

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/test/utils/TestPackageLoader.java

@@ -52,4 +52,14 @@ public class TestPackageLoader implements IContextResourceLoader {
     return new ArrayList<>();
   }
 
+  @Override
+  public void setPatchUrls(boolean value) {
+    
+  }
+
+  @Override
+  public String patchUrl(String url, String resourceType) {
+    return url;
+  }
+
 }

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

@@ -89,6 +89,7 @@ public class FHIRLexer {
   private String name;
   private boolean liquidMode; // in liquid mode, || terminates the expression and hands the parser back to the host
   private SourceLocation commentLocation;
+  private boolean metadataFormat;
 
   public FHIRLexer(String source, String name) throws FHIRLexerException {
     this.source = source == null ? "" : source;
@@ -102,6 +103,13 @@ public class FHIRLexer {
     currentLocation = new SourceLocation(1, 1);
     next();
   }
+  public FHIRLexer(String source, String name, boolean metadataFormat) throws FHIRLexerException {
+    this.source = source == null ? "" : source;
+    this.name = name == null ? "??" : name;
+    this.metadataFormat = metadataFormat;
+    currentLocation = new SourceLocation(1, 1);
+    next();
+  }
   public String getCurrent() {
     return current;
   }
@@ -211,10 +219,13 @@ public class FHIRLexer {
       } else if (ch == '/') {
         cursor++;
         if (cursor < source.length() && (source.charAt(cursor) == '/')) {
-          // this is en error - should already have been skipped
+          // we've run into metadata
-          error("This shouldn't happen?");
+          cursor++;
-        }
+          cursor++;
           current = source.substring(currentStart, cursor);
+        } else {
+          current = source.substring(currentStart, cursor);
+        }
       } else if (ch == '$') {
         cursor++;
         while (cursor < source.length() && (source.charAt(cursor) >= 'a' && source.charAt(cursor) <= 'z'))
@@ -309,7 +320,7 @@ public class FHIRLexer {
     boolean last13 = false;
     boolean done = false;
     while (cursor < source.length() && !done) {
-      if (cursor < source.length() -1 && "//".equals(source.substring(cursor, cursor+2))) {
+      if (cursor < source.length() -1 && "//".equals(source.substring(cursor, cursor+2)) && !isMetadataStart()) {
         commentLocation = currentLocation;
         int start = cursor+2;
         while (cursor < source.length() && !((source.charAt(cursor) == '\r') || source.charAt(cursor) == '\n')) { 
@@ -338,6 +349,10 @@ public class FHIRLexer {
     }
   }
   
+  private boolean isMetadataStart() {
+    return metadataFormat && cursor < source.length() - 2 && "///".equals(source.substring(cursor, cursor+3));
+  }
+  
   private boolean isDateChar(char ch,int start) {
     int eot = source.charAt(start+1) == 'T' ? 10 : 20;
     
@@ -550,5 +565,11 @@ public class FHIRLexer {
   public SourceLocation getCommentLocation() {
     return this.commentLocation;
   }
+  public boolean isMetadataFormat() {
+    return metadataFormat;
+  }
+  public void setMetadataFormat(boolean metadataFormat) {
+    this.metadataFormat = metadataFormat;
+  }
 
 }

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

@@ -30,6 +30,7 @@ import org.hl7.fhir.r5.context.IWorkerContext.ValidationResult;
 import org.hl7.fhir.r5.model.Base;
 import org.hl7.fhir.r5.model.BaseDateTimeType;
 import org.hl7.fhir.r5.model.BooleanType;
+import org.hl7.fhir.r5.model.CanonicalType;
 import org.hl7.fhir.r5.model.CodeableConcept;
 import org.hl7.fhir.r5.model.Constants;
 import org.hl7.fhir.r5.model.DateTimeType;
@@ -386,6 +387,7 @@ public class FHIRPathEngine {
       }
     }
     initFlags();
+    cu = new ContextUtilities(worker);
   }
 
   private void initFlags() {
@@ -578,6 +580,23 @@ public class FHIRPathEngine {
    * @if the path is not valid
    */
   public TypeDetails check(Object appContext, String resourceType, String context, ExpressionNode expr) throws FHIRLexerException, PathEngineException, DefinitionException {
+    return check(appContext, resourceType, context, expr, null);
+  }
+
+  /**
+   * check that paths referred to in the ExpressionNode are valid
+   * 
+   * xPathStartsWithValueRef is a hack work around for the fact that FHIR Path sometimes needs a different starting point than the xpath
+   * 
+   * returns a list of the possible types that might be returned by executing the ExpressionNode against a particular context
+   * 
+   * @param context - the logical type against which this path is applied
+   * @throws DefinitionException
+   * @throws PathEngineException 
+   * @if the path is not valid
+   */
+  public TypeDetails check(Object appContext, String resourceType, String context, ExpressionNode expr, Set<ElementDefinition> elementDependencies) throws FHIRLexerException, PathEngineException, DefinitionException {
+
     // if context is a path that refers to a type, do that conversion now 
     TypeDetails types; 
     if (context == null) {
@@ -610,7 +629,33 @@ public class FHIRPathEngine {
       }
     }
 
-    return executeType(new ExecutionTypeContext(appContext, resourceType, types, types), types, expr, true);
+    return executeType(new ExecutionTypeContext(appContext, resourceType, types, types), types, expr, elementDependencies, true);
+  }
+  
+  /**
+   * check that paths referred to in the ExpressionNode are valid
+   * 
+   * xPathStartsWithValueRef is a hack work around for the fact that FHIR Path sometimes needs a different starting point than the xpath
+   * 
+   * returns a list of the possible types that might be returned by executing the ExpressionNode against a particular context
+   * 
+   * @throws DefinitionException
+   * @throws PathEngineException 
+   * @if the path is not valid
+   */
+  public TypeDetails check(Object appContext, String resourceType, List<String> resourceTypes, ExpressionNode expr, Set<ElementDefinition> elementDependencies) throws FHIRLexerException, PathEngineException, DefinitionException {
+
+    // if context is a path that refers to a type, do that conversion now 
+    TypeDetails types = null;
+    for (String rt : resourceTypes) {
+      if (types == null) {
+        types = new TypeDetails(CollectionStatus.SINGLETON, rt);
+      } else {
+        types.addType(rt);
+      }
+    }
+
+    return executeType(new ExecutionTypeContext(appContext, resourceType, types, types), types, expr, elementDependencies, true);
   }
 
   private FHIRException makeExceptionPlural(Integer num, ExpressionNode holder, String constName, Object... args) {
@@ -659,13 +704,13 @@ public class FHIRPathEngine {
       }
     }
 
-    return executeType(new ExecutionTypeContext(appContext, sd.getUrl(), types, types), types, expr, true);
+    return executeType(new ExecutionTypeContext(appContext, sd.getUrl(), types, types), types, expr, null, true);
   }
 
   public TypeDetails check(Object appContext, StructureDefinition sd, ExpressionNode expr) throws FHIRLexerException, PathEngineException, DefinitionException {
     // if context is a path that refers to a type, do that conversion now 
     TypeDetails types = null; // this is a special case; the first path reference will have to resolve to something in the context
-    return executeType(new ExecutionTypeContext(appContext, sd == null ? null : sd.getUrl(), null, types), types, expr, true);
+    return executeType(new ExecutionTypeContext(appContext, sd == null ? null : sd.getUrl(), null, types), types, expr, null, true);
   }
 
   public TypeDetails check(Object appContext, String resourceType, String context, String expr) throws FHIRLexerException, PathEngineException, DefinitionException {
@@ -1557,7 +1602,7 @@ public class FHIRPathEngine {
     return new TypeDetails(CollectionStatus.SINGLETON, exp.getName());
   }
 
-  private TypeDetails executeType(ExecutionTypeContext context, TypeDetails focus, ExpressionNode exp, boolean atEntry) throws PathEngineException, DefinitionException {
+  private TypeDetails executeType(ExecutionTypeContext context, TypeDetails focus, ExpressionNode exp, Set<ElementDefinition> elementDependencies, boolean atEntry) throws PathEngineException, DefinitionException {
     TypeDetails result = new TypeDetails(null);
     switch (exp.getKind()) {
     case Name:
@@ -1571,7 +1616,7 @@ public class FHIRPathEngine {
         result.update(executeContextType(context, exp.getName(), exp));
       } else {
         for (String s : focus.getTypes()) {
-          result.update(executeType(s, exp, atEntry));
+          result.update(executeType(s, exp, atEntry, focus, elementDependencies));
         }
         if (result.hasNoTypes()) { 
           throw makeException(exp, I18nConstants.FHIRPATH_UNKNOWN_NAME, exp.getName(), focus.describe());
@@ -1579,7 +1624,7 @@ public class FHIRPathEngine {
       }
       break;
     case Function:
-      result.update(evaluateFunctionType(context, focus, exp));
+      result.update(evaluateFunctionType(context, focus, exp, elementDependencies));
       break;
     case Unary:
       result.addType(TypeDetails.FP_Integer);
@@ -1590,12 +1635,12 @@ public class FHIRPathEngine {
       result.update(resolveConstantType(context, exp.getConstant(), exp));
       break;
     case Group:
-      result.update(executeType(context, focus, exp.getGroup(), atEntry));
+      result.update(executeType(context, focus, exp.getGroup(), elementDependencies, atEntry));
     }
     exp.setTypes(result);
 
     if (exp.getInner() != null) {
-      result = executeType(context, result, exp.getInner(), false);
+      result = executeType(context, result, exp.getInner(), elementDependencies, false);
     }
 
     if (exp.isProximal() && exp.getOperation() != null) {
@@ -1606,7 +1651,7 @@ public class FHIRPathEngine {
         if (last.getOperation() == Operation.Is || last.getOperation() == Operation.As) {
           work = executeTypeName(context, focus, next, atEntry);
         } else {
-          work = executeType(context, focus, next, atEntry);
+          work = executeType(context, focus, next, elementDependencies, atEntry);
         }
         result = operateTypes(result, last.getOperation(), work, last);
         last = next;
@@ -1917,7 +1962,12 @@ public class FHIRPathEngine {
     case LessOrEqual: return new TypeDetails(CollectionStatus.SINGLETON, TypeDetails.FP_Boolean);
     case GreaterOrEqual: return new TypeDetails(CollectionStatus.SINGLETON, TypeDetails.FP_Boolean);
     case Is: return new TypeDetails(CollectionStatus.SINGLETON, TypeDetails.FP_Boolean);
-    case As: return new TypeDetails(CollectionStatus.SINGLETON, right.getTypes());
+    case As: 
+      TypeDetails td = new TypeDetails(CollectionStatus.SINGLETON, right.getTypes());
+      if (td.typesHaveTargets()) {
+        td.addTargets(left.getTargets());
+      }
+      return td;
     case Union: return left.union(right);
     case Or: return new TypeDetails(CollectionStatus.SINGLETON, TypeDetails.FP_Boolean);
     case And: return new TypeDetails(CollectionStatus.SINGLETON, TypeDetails.FP_Boolean);
@@ -3102,12 +3152,12 @@ public class FHIRPathEngine {
     return hostServices.resolveConstantType(context.appInfo, name);
   }
 
-  private TypeDetails executeType(String type, ExpressionNode exp, boolean atEntry) throws PathEngineException, DefinitionException {
+  private TypeDetails executeType(String type, ExpressionNode exp, boolean atEntry, TypeDetails focus, Set<ElementDefinition> elementDependencies) throws PathEngineException, DefinitionException {
     if (atEntry && Character.isUpperCase(exp.getName().charAt(0)) && hashTail(type).equals(exp.getName())) { // special case for start up
       return new TypeDetails(CollectionStatus.SINGLETON, type);
     }
     TypeDetails result = new TypeDetails(null);
-    getChildTypesByName(type, exp.getName(), result, exp);
+    getChildTypesByName(type, exp.getName(), result, exp, focus, elementDependencies);
     return result;
   }
 
@@ -3118,7 +3168,7 @@ public class FHIRPathEngine {
 
 
   @SuppressWarnings("unchecked")
-  private TypeDetails evaluateFunctionType(ExecutionTypeContext context, TypeDetails focus, ExpressionNode exp) throws PathEngineException, DefinitionException {
+  private TypeDetails evaluateFunctionType(ExecutionTypeContext context, TypeDetails focus, ExpressionNode exp, Set<ElementDefinition> elementDependencies) throws PathEngineException, DefinitionException {
     List<TypeDetails> paramTypes = new ArrayList<TypeDetails>();
     if (exp.getFunction() == Function.Is || exp.getFunction() == Function.As || exp.getFunction() == Function.OfType) {
       paramTypes.add(new TypeDetails(CollectionStatus.SINGLETON, TypeDetails.FP_String));
@@ -3126,9 +3176,9 @@ public class FHIRPathEngine {
       int i = 0;
       for (ExpressionNode expr : exp.getParameters()) {
         if (isExpressionParameter(exp, i)) {
-          paramTypes.add(executeType(changeThis(context, focus), focus, expr, true));
+          paramTypes.add(executeType(changeThis(context, focus), focus, expr, elementDependencies, true));
         } else {
-          paramTypes.add(executeType(context, context.thisItem, expr, true));
+          paramTypes.add(executeType(context, context.thisItem, expr, elementDependencies, true));
         }
         i++;
       }
@@ -3159,11 +3209,11 @@ public class FHIRPathEngine {
     case Where : 
       return focus;
     case Select : 
-      return anything(focus.getCollectionStatus());
+      return paramTypes.get(0);
     case All : 
       return new TypeDetails(CollectionStatus.SINGLETON, TypeDetails.FP_Boolean);
     case Repeat : 
-      return anything(focus.getCollectionStatus());
+      return paramTypes.get(0); // this might be a little more complicated...
     case Aggregate : 
       return anything(focus.getCollectionStatus());
     case Item : {
@@ -3173,11 +3223,19 @@ public class FHIRPathEngine {
     }
     case As : {
       checkParamTypes(exp, exp.getFunction().toCode(), paramTypes, new TypeDetails(CollectionStatus.SINGLETON, TypeDetails.FP_String));
-      return new TypeDetails(CollectionStatus.SINGLETON, exp.getParameters().get(0).getName());
+      TypeDetails td = new TypeDetails(CollectionStatus.SINGLETON, exp.getParameters().get(0).getName());
+      if (td.typesHaveTargets()) {
+        td.addTargets(focus.getTargets());
+      }
+      return td;
     }
     case OfType : { 
       checkParamTypes(exp, exp.getFunction().toCode(), paramTypes, new TypeDetails(CollectionStatus.SINGLETON, TypeDetails.FP_String)); 
-      return new TypeDetails(CollectionStatus.SINGLETON, exp.getParameters().get(0).getName());
+      TypeDetails td = new TypeDetails(CollectionStatus.SINGLETON, exp.getParameters().get(0).getName());
+      if (td.typesHaveTargets()) {
+        td.addTargets(focus.getTargets());
+      }
+      return td;
     }
     case Type : { 
       boolean s = false;
@@ -3326,12 +3384,20 @@ public class FHIRPathEngine {
       return new TypeDetails(CollectionStatus.SINGLETON, TypeDetails.FP_DateTime);
     case Resolve : {
       checkContextReference(focus, "resolve", exp);
-      return new TypeDetails(CollectionStatus.SINGLETON, "DomainResource"); 
+      return new TypeDetails(CollectionStatus.ORDERED, "DomainResource"); 
     }
     case Extension : {
       checkParamTypes(exp, exp.getFunction().toCode(), paramTypes, new TypeDetails(CollectionStatus.SINGLETON, TypeDetails.FP_String));
+      ExpressionNode p = exp.getParameters().get(0);
+      if (p.getKind() == Kind.Constant && p.getConstant() != null) {
+        String url = exp.getParameters().get(0).getConstant().primitiveValue();
+        StructureDefinition sd = worker.fetchResource(StructureDefinition.class, url);
+        if (sd != null) {
+          return new TypeDetails(CollectionStatus.ORDERED, new ProfiledType(url));
+        } 
         return new TypeDetails(CollectionStatus.SINGLETON, "Extension");
       }
+    }
     case AnyTrue: 
       return new TypeDetails(CollectionStatus.SINGLETON, TypeDetails.FP_Boolean);
     case AllTrue: 
@@ -3572,7 +3638,7 @@ public class FHIRPathEngine {
   private TypeDetails childTypes(TypeDetails focus, String mask, ExpressionNode expr) throws PathEngineException, DefinitionException {
     TypeDetails result = new TypeDetails(CollectionStatus.UNORDERED);
     for (String f : focus.getTypes()) {
-      getChildTypesByName(f, mask, result, expr);
+      getChildTypesByName(f, mask, result, expr, null, null);
     }
     return result;
   }
@@ -4011,6 +4077,7 @@ public class FHIRPathEngine {
   }
 
   private static final char[] HEX_ARRAY = "0123456789ABCDEF".toCharArray();
+  private ContextUtilities cu;
   public static String bytesToHex(byte[] bytes) {
     char[] hexChars = new char[bytes.length * 2];
     for (int j = 0; j < bytes.length; j++) {
@@ -5693,7 +5760,7 @@ public class FHIRPathEngine {
 
   }
 
-  private void getChildTypesByName(String type, String name, TypeDetails result, ExpressionNode expr) throws PathEngineException, DefinitionException {
+  private void getChildTypesByName(String type, String name, TypeDetails result, ExpressionNode expr, TypeDetails focus, Set<ElementDefinition> elementDependencies) throws PathEngineException, DefinitionException {
     if (Utilities.noString(type)) {
       throw makeException(expr, I18nConstants.FHIRPATH_NO_TYPE, "", "getChildTypesByName");
     } 
@@ -5737,11 +5804,11 @@ public class FHIRPathEngine {
             if (dt == null) {
               throw makeException(expr, I18nConstants.FHIRPATH_NO_TYPE, ProfileUtilities.sdNs(t.getCode(), null), "getChildTypesByName");
             }
-            addTypeAndDescendents(sdl, dt, new ContextUtilities(worker).allStructures());
+            addTypeAndDescendents(sdl, dt, cu.allStructures());
             // also add any descendant types
           }
       } else {
-        addTypeAndDescendents(sdl, sd, new ContextUtilities(worker).allStructures());
+        addTypeAndDescendents(sdl, sd, cu.allStructures());
         if (type.contains("#")) {
           tail = type.substring(type.indexOf("#")+1);
           tail = tail.substring(tail.indexOf("."));
@@ -5753,7 +5820,17 @@ public class FHIRPathEngine {
         if (name.equals("**")) {
           assert(result.getCollectionStatus() == CollectionStatus.UNORDERED);
           for (ElementDefinition ed : sdi.getSnapshot().getElement()) {
-            if (ed.getPath().startsWith(path))
+            if (ed.getPath().startsWith(path)) {
+              if (ed.hasContentReference()) {
+                String cpath = ed.getContentReference();
+                String tn = sdi.getType()+cpath;
+                if (!result.hasType(worker, tn)) {
+                  if (elementDependencies != null) {
+                    elementDependencies.add(ed);
+                  }
+                  getChildTypesByName(result.addType(tn), "**", result, expr, null, elementDependencies);
+                }
+              } else {
                 for (TypeRefComponent t : ed.getType()) {
                   if (t.hasCode() && t.getCodeElement().hasValue()) {
                     String tn = null;
@@ -5765,11 +5842,19 @@ public class FHIRPathEngine {
                     if (t.getCode().equals("Resource")) {
                       for (String rn : worker.getResourceNames()) {
                         if (!result.hasType(worker, rn)) {
-                        getChildTypesByName(result.addType(rn), "**", result, expr);
+                          if (elementDependencies != null) {
+                            elementDependencies.add(ed);
+                          }
+                          getChildTypesByName(result.addType(rn), "**", result, expr, null, elementDependencies);
                         }                  
                       }
                     } else if (!result.hasType(worker, tn)) {
-                    getChildTypesByName(result.addType(tn), "**", result, expr);
+                      if (elementDependencies != null) {
+                        elementDependencies.add(ed);
+                      }
+                      getChildTypesByName(result.addType(tn), "**", result, expr, null, elementDependencies);
+                    }
+                  }
                 }
               }
             }
@@ -5780,13 +5865,26 @@ public class FHIRPathEngine {
             if (ed.getPath().startsWith(path) && !ed.getPath().substring(path.length()).contains("."))
               for (TypeRefComponent t : ed.getType()) {
                 if (Utilities.noString(t.getCode())) { // Element.id or Extension.url
+                  if (elementDependencies != null) {
+                    elementDependencies.add(ed);
+                  }
                   result.addType("System.string");
                 } else if (t.getCode().equals("Element") || t.getCode().equals("BackboneElement")) {
+                  if (elementDependencies != null) {
+                    elementDependencies.add(ed);
+                  }
                   result.addType(sdi.getType()+"#"+ed.getPath());
                 } else if (t.getCode().equals("Resource")) {
+                  if (elementDependencies != null) {
+                    elementDependencies.add(ed);
+                  }
                   result.addTypes(worker.getResourceNames());
                 } else {
+                  if (elementDependencies != null) {
+                    elementDependencies.add(ed);
+                  }
                   result.addType(t.getCode());
+                  copyTargetProfiles(ed, t, focus, result);
                 }
               }
           }
@@ -5795,12 +5893,18 @@ public class FHIRPathEngine {
 
           ElementDefinitionMatch ed = getElementDefinition(sdi, path, isAllowPolymorphicNames(), expr);
           if (ed != null) {
-            if (!Utilities.noString(ed.getFixedType()))
+            if (!Utilities.noString(ed.getFixedType())) {
+              if (elementDependencies != null) {
+                elementDependencies.add(ed.definition);
+              }
               result.addType(ed.getFixedType());
-            else {
+            } else {
               for (TypeRefComponent t : ed.getDefinition().getType()) {
                 if (Utilities.noString(t.getCode())) {
                   if (Utilities.existsInList(ed.getDefinition().getId(), "Element.id", "Extension.url") || Utilities.existsInList(ed.getDefinition().getBase().getPath(), "Resource.id", "Element.id", "Extension.url")) { 
+                    if (elementDependencies != null) {
+                      elementDependencies.add(ed.definition);
+                    }
                     result.addType(TypeDetails.FP_NS, "string");
                   }
                   break; // throw new PathEngineException("Illegal reference to primitive value attribute @ "+path);
@@ -5810,6 +5914,9 @@ public class FHIRPathEngine {
                 if (t.getCode().equals("Element") || t.getCode().equals("BackboneElement")) {
                   pt = new ProfiledType(sdi.getUrl()+"#"+path);
                 } else if (t.getCode().equals("Resource")) {
+                  if (elementDependencies != null) {
+                    elementDependencies.add(ed.definition);
+                  }
                   result.addTypes(worker.getResourceNames());
                 } else {
                   pt = new ProfiledType(t.getCode());
@@ -5821,7 +5928,11 @@ public class FHIRPathEngine {
                   if (ed.getDefinition().hasBinding()) {
                     pt.addBinding(ed.getDefinition().getBinding());
                   }
-                  result.addType(pt);
+                  if (elementDependencies != null) {
+                    elementDependencies.add(ed.definition);
+                  }
+                  result.addType(ed.definition.unbounded() ? CollectionStatus.ORDERED : CollectionStatus.SINGLETON, pt);
+                  copyTargetProfiles(ed.getDefinition(), t, focus, result);
                 }
               }
             }
@@ -5831,6 +5942,18 @@ public class FHIRPathEngine {
     }
   }
 
+  private void copyTargetProfiles(ElementDefinition ed, TypeRefComponent t, TypeDetails focus, TypeDetails result) {
+    if (t.hasTargetProfile()) {
+      for (CanonicalType u : t.getTargetProfile()) {
+        result.addTarget(u.primitiveValue());
+      }
+    } else if (focus != null && focus.hasType("CodeableReference") && ed.getPath().endsWith(".reference") && focus.getTargets() != null) { // special case, targets are on parent
+      for (String s : focus.getTargets()) {
+        result.addTarget(s);
+      }
+    }
+  }
+
   private void addTypeAndDescendents(List<StructureDefinition> sdl, StructureDefinition dt, List<StructureDefinition> types) {
     sdl.add(dt);
     for (StructureDefinition sd : types) {
@@ -5860,7 +5983,7 @@ public class FHIRPathEngine {
   }
 
 
-  private ElementDefinitionMatch getElementDefinition(StructureDefinition sd, String path, boolean allowTypedName, ExpressionNode expr) throws PathEngineException {
+  public ElementDefinitionMatch getElementDefinition(StructureDefinition sd, String path, boolean allowTypedName, ExpressionNode expr) throws PathEngineException {
     for (ElementDefinition ed : sd.getSnapshot().getElement()) {
       if (ed.getPath().equals(path)) {
         if (ed.hasContentReference()) {
@@ -6229,5 +6352,8 @@ public class FHIRPathEngine {
     this.liquidMode = liquidMode;
   }
 
+  public ProfileUtilities getProfileUtilities() {
+    return profileUtilities;
+  }
 
 }

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/utils/structuremap/StructureMapUtilities.java

@@ -103,7 +103,8 @@ public class StructureMapUtilities {
   public static final String MAP_SEARCH_EXPRESSION = "map.search.expression";
   public static final String MAP_EXPRESSION = "map.transform.expression";
   private static final boolean RENDER_MULTIPLE_TARGETS_ONELINE = true;
-  private static final String AUTO_VAR_NAME = "vvv";
+  public static final String AUTO_VAR_NAME = "vvv";
+  public static final String DEF_GROUP_NAME = "DefaultMappingGroupAnonymousAlias";
 
   private final IWorkerContext worker;
   private final FHIRPathEngine fpe;
@@ -619,15 +620,38 @@ public class StructureMapUtilities {
   }
 
   public StructureMap parse(String text, String srcName) throws FHIRException {
-    FHIRLexer lexer = new FHIRLexer(text, srcName);
+    FHIRLexer lexer = new FHIRLexer(Utilities.stripBOM(text), srcName, true);
     if (lexer.done())
       throw lexer.error("Map Input cannot be empty");
-    lexer.token("map");
     StructureMap result = new StructureMap();
+    if (lexer.hasToken("map")) { 
+      lexer.token("map");
       result.setUrl(lexer.readConstant("url"));
       lexer.token("=");
       result.setName(lexer.readConstant("name"));
       result.setDescription(lexer.getAllComments());
+      result.setStatus(PublicationStatus.DRAFT);
+    } else {
+      while (lexer.hasToken("///")) {
+        lexer.next();
+        String fid = lexer.takeDottedToken();
+        lexer.token("=");
+        switch (fid) {
+        case "url" :
+          result.setUrl(lexer.readConstant("url"));
+          break;
+        case "name" :
+          result.setName(lexer.readConstant("name"));
+          break;
+        case "title" : 
+          result.setTitle(lexer.readConstant("title"));
+          break;
+        default:
+          lexer.readConstant("nothing");
+          // nothing
+        }
+      }
+    }
     while (lexer.hasToken("conceptmap"))
       parseConceptMap(result, lexer);
 
@@ -643,36 +667,6 @@ public class StructureMapUtilities {
     return result;
   }
 
-  public Element parseEM(String text, String srcName, List<ValidationMessage> list) throws FHIRException {
-    FHIRLexer lexer = new FHIRLexer(text, srcName);
-    if (lexer.done())
-      throw lexer.error("Map Input cannot be empty");
-    lexer.token("map");
-    Element result = Manager.build(worker, worker.fetchTypeDefinition("StructureMap"));
-    try {
-      result.makeElement("url").markLocation(lexer.getCurrentLocation()).setValue(lexer.readConstant("url"));
-      lexer.token("=");
-      result.makeElement("name").markLocation(lexer.getCurrentLocation()).setValue(lexer.readConstant("name"));
-      result.makeElement("description").markLocation(lexer.getCurrentLocation()).setValue(lexer.getAllComments());
-      while (lexer.hasToken("conceptmap"))
-        parseConceptMapEM(result, lexer);
-
-      while (lexer.hasToken("uses"))
-        parseUsesEM(result, lexer);
-      while (lexer.hasToken("imports"))
-        parseImportsEM(result, lexer);
-
-      while (!lexer.done()) {
-        parseGroupEM(result, lexer);
-      }
-    } catch (FHIRLexerException e) {
-      list.add(new ValidationMessage(Source.InstanceValidator, IssueType.INVALID, e.getLocation().getLine(), e.getLocation().getColumn(), null, e.getMessage(), IssueSeverity.FATAL));
-    } catch (Exception e) {
-      list.add(new ValidationMessage(Source.InstanceValidator, IssueType.INVALID, null, e.getMessage(), IssueSeverity.FATAL));
-    }
-
-    return result;
-  }
   
   private void parseConceptMap(StructureMap result, FHIRLexer lexer) throws FHIRLexerException {
     lexer.token("conceptmap");
@@ -730,63 +724,7 @@ public class StructureMapUtilities {
     lexer.token("}");
   }
 
-  private void parseConceptMapEM(Element result, FHIRLexer lexer) throws FHIRLexerException {
+ 
-    lexer.token("conceptmap");
-    Element map = Manager.build(worker, worker.fetchTypeDefinition("ConceptMap"));
-    Element eid = map.makeElement("id").markLocation(lexer.getCurrentLocation());
-    String id = lexer.readConstant("map id");
-    if (id.startsWith("#"))
-      throw lexer.error("Concept Map identifier must start with #");
-    eid.setValue(id);
-    map.makeElement("status").setValue(PublicationStatus.DRAFT.toCode()); // todo: how to add this to the text format
-    result.makeElement("contained").setElement("resource", map);
-    lexer.token("{");
-    //    lexer.token("source");
-    //    map.setSource(new UriType(lexer.readConstant("source")));
-    //    lexer.token("target");
-    //    map.setSource(new UriType(lexer.readConstant("target")));
-    Map<String, String> prefixes = new HashMap<String, String>();
-    while (lexer.hasToken("prefix")) {
-      lexer.token("prefix");
-      String n = lexer.take();
-      lexer.token("=");
-      String v = lexer.readConstant("prefix url");
-      prefixes.put(n, v);
-    }
-    while (lexer.hasToken("unmapped")) {
-      lexer.token("unmapped");
-      lexer.token("for");
-      String n = readPrefix(prefixes, lexer);
-      Element g = getGroupE(map, n, null);
-      lexer.token("=");
-      SourceLocation loc = lexer.getCurrentLocation();
-      String v = lexer.take();
-      if (v.equals("provided")) {
-        g.makeElement("unmapped").makeElement("mode").markLocation(loc).setValue(ConceptMapGroupUnmappedMode.USESOURCECODE.toCode());
-      } else
-        throw lexer.error("Only unmapped mode PROVIDED is supported at this time");
-    }
-    while (!lexer.hasToken("}")) {
-      String srcs = readPrefix(prefixes, lexer);
-      lexer.token(":");
-      SourceLocation scloc = lexer.getCurrentLocation();
-      String sc = lexer.getCurrent().startsWith("\"") ? lexer.readConstant("code") : lexer.take();
-      SourceLocation relLoc = lexer.getCurrentLocation();
-      ConceptMapRelationship rel = readRelationship(lexer);
-      String tgts = readPrefix(prefixes, lexer);
-      Element g = getGroupE(map, srcs, tgts);
-      Element e = g.addElement("element");
-      e.makeElement("code").markLocation(scloc).setValue(sc.startsWith("\"") ? lexer.processConstant(sc) : sc);
-      Element tgt = e.addElement("target");
-      tgt.makeElement("relationship").markLocation(relLoc).setValue(rel.toCode());
-      lexer.token(":");
-      tgt.makeElement("code").markLocation(lexer.getCurrentLocation()).setValue(lexer.getCurrent().startsWith("\"") ? lexer.readConstant("code") : lexer.take());
-      if (lexer.hasComments()) {
-        tgt.makeElement("comment").markLocation(lexer.getCommentLocation()).setValue(lexer.getFirstComment());
-      }
-    }
-    lexer.token("}");
-  }
 
   private ConceptMapGroupComponent getGroup(ConceptMap map, String srcs, String tgts) {
     for (ConceptMapGroupComponent grp : map.getGroup()) {
@@ -803,22 +741,6 @@ public class StructureMapUtilities {
     return grp;
   }
   
-  private Element getGroupE(Element map, String srcs, String tgts) {
-    for (Element grp : map.getChildrenByName("group")) {
-      if (grp.getChildValue("source").equals(srcs)) {
-        Element tgt = grp.getNamedChild("target");
-        if (tgt == null || tgts == null || tgts.equals(tgt.getValue())) {
-          if (tgt == null && tgts != null)
-            grp.makeElement("target").setValue(tgts);
-          return grp;
-        }
-      }
-    }
-    Element grp = map.addElement("group");
-    grp.makeElement("source").setValue(srcs);
-    grp.makeElement("target").setValue(tgts);
-    return grp;
-  }
  
 
   private String readPrefix(Map<String, String> prefixes, FHIRLexer lexer) throws FHIRLexerException {
@@ -859,21 +781,7 @@ public class StructureMapUtilities {
     st.setDocumentation(lexer.getFirstComment());
   }
   
-  private void parseUsesEM(Element result, FHIRLexer lexer) throws FHIRException {
+  
-    lexer.token("uses");
-    Element st = result.addElement("structure");
-    st.makeElement("url").markLocation(lexer.getCurrentLocation()).setValue(lexer.readConstant("url"));
-    if (lexer.hasToken("alias")) {
-      lexer.token("alias");
-      st.makeElement("alias").markLocation(lexer.getCurrentLocation()).setValue(lexer.take());
-    }
-    lexer.token("as");
-    st.makeElement("mode").markLocation(lexer.getCurrentLocation()).setValue(lexer.take());
-    lexer.skipToken(";");
-    if (lexer.hasComments()) {
-      st.makeElement("documentation").markLocation(lexer.getCommentLocation()).setValue(lexer.getFirstComment());
-    }
-  }
 
   private void parseImports(StructureMap result, FHIRLexer lexer) throws FHIRException {
     lexer.token("imports");
@@ -881,12 +789,6 @@ public class StructureMapUtilities {
     lexer.skipToken(";");
   }
   
-  private void parseImportsEM(Element result, FHIRLexer lexer) throws FHIRException {
-    lexer.token("imports");
-    result.addElement("import").markLocation(lexer.getCurrentLocation()).setValue(lexer.readConstant("url"));
-    lexer.skipToken(";");
-  }
-
   private void parseGroup(StructureMap result, FHIRLexer lexer) throws FHIRException {
     String comment = lexer.getAllComments();
     lexer.token("group");
@@ -959,78 +861,7 @@ public class StructureMapUtilities {
       lexer.next();
   }
 
-  private void parseGroupEM(Element result, FHIRLexer lexer) throws FHIRException {
+ 
-    SourceLocation commLoc = lexer.getCommentLocation();
-    String comment = lexer.getAllComments();
-    lexer.token("group");
-    Element group = result.addElement("group");
-    if (comment != null) {
-      group.makeElement("documentation").markLocation(commLoc).setValue(comment);
-    }
-    boolean newFmt = false;
-    if (lexer.hasToken("for")) {
-      lexer.token("for");
-      SourceLocation loc = lexer.getCurrentLocation();
-      if ("type".equals(lexer.getCurrent())) {
-        lexer.token("type");
-        lexer.token("+");
-        lexer.token("types");
-        group.makeElement("typeMode").markLocation(loc).setValue(StructureMapGroupTypeMode.TYPEANDTYPES.toCode());
-      } else {
-        lexer.token("types");
-        group.makeElement("typeMode").markLocation(loc).setValue(StructureMapGroupTypeMode.TYPES.toCode());
-      }
-    }
-    group.makeElement("name").markLocation(lexer.getCurrentLocation()).setValue(lexer.take());
-    if (lexer.hasToken("(")) {
-      newFmt = true;
-      lexer.take();
-      while (!lexer.hasToken(")")) {
-        parseInputEM(group, lexer, true);
-        if (lexer.hasToken(","))
-          lexer.token(",");
-      }
-      lexer.take();
-    }
-    if (lexer.hasToken("extends")) {
-      lexer.next();
-      group.makeElement("extends").markLocation(lexer.getCurrentLocation()).setValue(lexer.take());
-    }
-    if (newFmt) {
-      if (lexer.hasToken("<")) {
-        lexer.token("<");
-        lexer.token("<");
-        if (lexer.hasToken("types")) {
-          group.makeElement("typeMode").markLocation(lexer.getCurrentLocation()).setValue(StructureMapGroupTypeMode.TYPES.toCode());
-        } else {
-          group.makeElement("typeMode").markLocation(lexer.getCurrentLocation()).setValue(StructureMapGroupTypeMode.TYPEANDTYPES.toCode());
-          lexer.token("type");
-          lexer.token("+");
-        }
-        lexer.token(">");
-        lexer.token(">");
-      }
-      lexer.token("{");
-    }
-    if (newFmt) {
-      while (!lexer.hasToken("}")) {
-        if (lexer.done())
-          throw lexer.error("premature termination expecting 'endgroup'");
-        parseRuleEM(result, group, lexer, true);
-      }
-    } else {
-      while (lexer.hasToken("input"))
-        parseInputEM(group, lexer, false);
-      while (!lexer.hasToken("endgroup")) {
-        if (lexer.done())
-          throw lexer.error("premature termination expecting 'endgroup'");
-        parseRuleEM(result, group, lexer, false);
-      }
-    }
-    lexer.next();
-    if (newFmt && lexer.hasToken(";"))
-      lexer.next();
-  }
   
   private void parseInput(StructureMapGroupComponent group, FHIRLexer lexer, boolean newFmt) throws FHIRException {
     StructureMapGroupInputComponent input = group.addInput();
@@ -1051,26 +882,7 @@ public class StructureMapUtilities {
     }
   }
 
-  private void parseInputEM(Element group, FHIRLexer lexer, boolean newFmt) throws FHIRException {
+
-    Element input = group.addElement("input");
-    if (newFmt) {
-      input.makeElement("mode").markLocation(lexer.getCurrentLocation()).setValue(lexer.take());
-    } else
-      lexer.token("input");
-    input.makeElement("name").markLocation(lexer.getCurrentLocation()).setValue(lexer.take());
-    if (lexer.hasToken(":")) {
-      lexer.token(":");
-      input.makeElement("type").markLocation(lexer.getCurrentLocation()).setValue(lexer.take());
-    }
-    if (!newFmt) {
-      lexer.token("as");
-      input.makeElement("mode").markLocation(lexer.getCurrentLocation()).setValue(lexer.take());
-      if (lexer.hasComments()) {
-        input.makeElement("documentation").markLocation(lexer.getCommentLocation()).setValue(lexer.getFirstComment());
-      }
-      lexer.skipToken(";");
-    }
-  }
 
   private void parseRule(StructureMap map, List<StructureMapGroupRuleComponent> list, FHIRLexer lexer, boolean newFmt) throws FHIRException {
     StructureMapGroupRuleComponent rule = new StructureMapGroupRuleComponent();
@@ -1147,84 +959,6 @@ public class StructureMapUtilities {
     }
   }
 
-  private void parseRuleEM(Element map, Element context, FHIRLexer lexer, boolean newFmt) throws FHIRException {
-    Element rule = context.addElement("rule");
-    if (!newFmt) {
-      rule.makeElement("name").markLocation(lexer.getCurrentLocation()).setValue(lexer.takeDottedToken());
-      lexer.token(":");
-      lexer.token("for");
-    } else {
-      if (lexer.hasComments()) {
-        rule.makeElement("documentation").markLocation(lexer.getCommentLocation()).setValue(lexer.getFirstComment());
-      }
-    }
-
-    boolean done = false;
-    while (!done) {
-      parseSourceEM(rule, lexer);
-      done = !lexer.hasToken(",");
-      if (!done)
-        lexer.next();
-    }
-    if ((newFmt && lexer.hasToken("->")) || (!newFmt && lexer.hasToken("make"))) {
-      lexer.token(newFmt ? "->" : "make");
-      done = false;
-      while (!done) {
-        parseTargetEM(rule, lexer);
-        done = !lexer.hasToken(",");
-        if (!done)
-          lexer.next();
-      }
-    }
-    if (lexer.hasToken("then")) {
-      lexer.token("then");
-      if (lexer.hasToken("{")) {
-        lexer.token("{");
-        while (!lexer.hasToken("}")) {
-          if (lexer.done())
-            throw lexer.error("premature termination expecting '}' in nested group");
-          parseRuleEM(map, rule, lexer, newFmt);
-        }
-        lexer.token("}");
-      } else {
-        done = false;
-        while (!done) {
-          parseRuleReferenceEM(rule, lexer);
-          done = !lexer.hasToken(",");
-          if (!done)
-            lexer.next();
-        }
-      }
-    }
-    if (!rule.hasChild("documentation") && lexer.hasComments()) {
-      rule.makeElement("documentation").markLocation(lexer.getCommentLocation()).setValue(lexer.getFirstComment());
-    }
-
-    if (isSimpleSyntaxEM(rule)) {
-      rule.forceElement("source").makeElement("variable").setValue(AUTO_VAR_NAME);
-      rule.forceElement("target").makeElement("variable").setValue(AUTO_VAR_NAME);
-      rule.forceElement("target").makeElement("transform").setValue(StructureMapTransform.CREATE.toCode());
-      // no dependencies - imply what is to be done based on types
-    }
-    if (newFmt) {
-      if (lexer.isConstant()) {
-        if (lexer.isStringConstant()) {
-          rule.makeElement("name").markLocation(lexer.getCurrentLocation()).setValue(lexer.readConstant("ruleName"));
-        } else {
-          rule.makeElement("name").markLocation(lexer.getCurrentLocation()).setValue(lexer.take());
-        }
-      } else {
-        if (rule.getChildrenByName("source").size() != 1 || !rule.getChildrenByName("source").get(0).hasChild("element"))
-          throw lexer.error("Complex rules must have an explicit name");
-        if (rule.getChildrenByName("source").get(0).hasChild("type"))
-          rule.makeElement("name").setValue(rule.getChildrenByName("source").get(0).getNamedChildValue("element") + "-" + rule.getChildrenByName("source").get(0).getNamedChildValue("type"));
-        else
-          rule.makeElement("name").setValue(rule.getChildrenByName("source").get(0).getNamedChildValue("element"));
-      }
-      lexer.token(";");
-    }
-  }
-
   private boolean isSimpleSyntax(StructureMapGroupRuleComponent rule) {
     return
       (rule.getSource().size() == 1 && rule.getSourceFirstRep().hasContext() && rule.getSourceFirstRep().hasElement() && !rule.getSourceFirstRep().hasVariable()) &&
@@ -1233,13 +967,6 @@ public class StructureMapUtilities {
   }
 
 
-  private boolean isSimpleSyntaxEM(Element rule) {
-    return
-      (rule.getChildren("source").size() == 1 && rule.getChildren("source").get(0).hasChild("context") && rule.getChildren("source").get(0).hasChild("element") && !rule.getChildren("source").get(0).hasChild("variable")) &&
-        (rule.getChildren("target").size() == 1 && rule.getChildren("target").get(0).hasChild("context") && rule.getChildren("target").get(0).hasChild("element") && !rule.getChildren("target").get(0).hasChild("variable") && 
-           !rule.getChildren("target").get(0).hasChild("parameter")) &&
-        (rule.getChildren("dependent").size() == 0 && rule.getChildren("rule").size() == 0);
-  }
  
   private void parseRuleReference(StructureMapGroupRuleComponent rule, FHIRLexer lexer) throws FHIRLexerException {
     StructureMapGroupRuleDependentComponent ref = rule.addDependent();
@@ -1255,19 +982,6 @@ public class StructureMapUtilities {
     lexer.token(")");
   }
 
-  private void parseRuleReferenceEM(Element rule, FHIRLexer lexer) throws FHIRLexerException {
-    Element ref = rule.addElement("dependent");
-    rule.makeElement("name").markLocation(lexer.getCurrentLocation()).setValue(lexer.take());
-    lexer.token("(");
-    boolean done = false;
-    while (!done) {
-      parseParameterEM(ref, lexer);
-      done = !lexer.hasToken(",");
-      if (!done)
-        lexer.next();
-    }
-    lexer.token(")");
-  }
  
   private void parseSource(StructureMapGroupRuleComponent rule, FHIRLexer lexer) throws FHIRException {
     StructureMapGroupRuleSourceComponent source = rule.addSource();
@@ -1287,12 +1001,12 @@ public class StructureMapUtilities {
       // type and cardinality
       lexer.token(":");
       source.setType(lexer.takeDottedToken());
-      if (!lexer.hasToken("as", "first", "last", "not_first", "not_last", "only_one", "default")) {
+    }
+    if (Utilities.isInteger(lexer.getCurrent())) {
       source.setMin(lexer.takeInt());
       lexer.token("..");
       source.setMax(lexer.take());
     }
-    }
     if (lexer.hasToken("default")) {
       lexer.token("default");
       source.setDefaultValue(lexer.readConstant("default value"));
@@ -1324,65 +1038,6 @@ public class StructureMapUtilities {
     }
   }
 
-  private void parseSourceEM(Element rule, FHIRLexer lexer) throws FHIRException {
-    Element source = rule.addElement("source");
-    source.makeElement("context").markLocation(lexer.getCurrentLocation()).setValue(lexer.take());
-    if (source.getChildValue("context").equals("search") && lexer.hasToken("(")) {
-      source.makeElement("context").markLocation(lexer.getCurrentLocation()).setValue("@search");
-      lexer.take();
-      SourceLocation loc = lexer.getCurrentLocation();
-      ExpressionNode node = fpe.parse(lexer);
-      source.setUserData(MAP_SEARCH_EXPRESSION, node);
-      source.makeElement("element").markLocation(loc).setValue(node.toString());
-      lexer.token(")");
-    } else if (lexer.hasToken(".")) {
-      lexer.token(".");
-      source.makeElement("element").markLocation(lexer.getCurrentLocation()).setValue(lexer.take());
-    }
-    if (lexer.hasToken(":")) {
-      // type and cardinality
-      lexer.token(":");
-      source.setType(lexer.takeDottedToken());
-      if (!lexer.hasToken("as", "first", "last", "not_first", "not_last", "only_one", "default")) {
-        source.makeElement("min").markLocation(lexer.getCurrentLocation()).setValue(lexer.take());
-        lexer.token("..");
-        source.makeElement("max").markLocation(lexer.getCurrentLocation()).setValue(lexer.take());
-      }
-    }
-    if (lexer.hasToken("default")) {
-      lexer.token("default");
-     source.makeElement("defaultValue").markLocation(lexer.getCurrentLocation()).setValue(lexer.readConstant("default value"));
-    }
-    if (Utilities.existsInList(lexer.getCurrent(), "first", "last", "not_first", "not_last", "only_one")) {
-      source.makeElement("listMode").markLocation(lexer.getCurrentLocation()).setValue(lexer.take());
-    }
-
-    if (lexer.hasToken("as")) {
-      lexer.take();
-      source.makeElement("variable").markLocation(lexer.getCurrentLocation()).setValue(lexer.take());
-    }
-    if (lexer.hasToken("where")) {
-      lexer.take();
-      SourceLocation loc = lexer.getCurrentLocation();
-      ExpressionNode node = fpe.parse(lexer);
-      source.setUserData(MAP_WHERE_EXPRESSION, node);
-      source.makeElement("condition").markLocation(loc).setValue(node.toString());
-    }
-    if (lexer.hasToken("check")) {
-      lexer.take();
-      SourceLocation loc = lexer.getCurrentLocation();
-      ExpressionNode node = fpe.parse(lexer);
-      source.setUserData(MAP_WHERE_CHECK, node);
-      source.makeElement("check").markLocation(loc).setValue(node.toString());
-    }
-    if (lexer.hasToken("log")) {
-      lexer.take();
-      SourceLocation loc = lexer.getCurrentLocation();
-      ExpressionNode node = fpe.parse(lexer);
-      source.setUserData(MAP_WHERE_CHECK, node);
-      source.makeElement("logMessage").markLocation(loc).setValue(lexer.take());
-    }
-  }
  
   private void parseTarget(StructureMapGroupRuleComponent rule, FHIRLexer lexer) throws FHIRException {
     StructureMapGroupRuleTargetComponent target = rule.addTarget();
@@ -1458,84 +1113,6 @@ public class StructureMapUtilities {
     }
   }
 
-  private void parseTargetEM(Element rule, FHIRLexer lexer) throws FHIRException {
-    Element target = rule.addElement("target");
-    SourceLocation loc = lexer.getCurrentLocation();
-    String start = lexer.take();
-    if (lexer.hasToken(".")) {
-      target.makeElement("context").markLocation(loc).setValue(start);
-      start = null;
-      lexer.token(".");
-      target.makeElement("element").markLocation(lexer.getCurrentLocation()).setValue(lexer.take());
-    }
-    String name;
-    boolean isConstant = false;
-    if (lexer.hasToken("=")) {
-      if (start != null) {
-        target.makeElement("context").markLocation(loc).setValue(start);
-      }
-      lexer.token("=");
-      isConstant = lexer.isConstant();
-      loc = lexer.getCurrentLocation();
-      name = lexer.take();
-    } else {
-      loc = lexer.getCurrentLocation();
-      name = start;
-    }
-
-    if ("(".equals(name)) {
-      // inline fluentpath expression
-      target.makeElement("transform").markLocation(lexer.getCurrentLocation()).setValue(StructureMapTransform.EVALUATE.toCode());
-      loc = lexer.getCurrentLocation();
-      ExpressionNode node = fpe.parse(lexer);
-      target.setUserData(MAP_EXPRESSION, node);
-      target.addElement("parameter").markLocation(loc).setValue(node.toString());
-      lexer.token(")");
-    } else if (lexer.hasToken("(")) {
-      target.makeElement("transform").markLocation(loc).setValue(name);
-      lexer.token("(");
-      if (target.getChildValue("transform").equals(StructureMapTransform.EVALUATE.toCode())) {
-        parseParameterEM(target, lexer);
-        lexer.token(",");
-        loc = lexer.getCurrentLocation();
-        ExpressionNode node = fpe.parse(lexer);
-        target.setUserData(MAP_EXPRESSION, node);
-        target.addElement("parameter").markLocation(loc).setValue(node.toString());
-      } else {
-        while (!lexer.hasToken(")")) {
-          parseParameterEM(target, lexer);
-          if (!lexer.hasToken(")"))
-            lexer.token(",");
-        }
-      }
-      lexer.token(")");
-    } else if (name != null) {
-      target.makeElement("transform").markLocation(loc).setValue(StructureMapTransform.COPY.toCode());
-      if (!isConstant) {
-        loc = lexer.getCurrentLocation();
-        String id = name;
-        while (lexer.hasToken(".")) {
-          id = id + lexer.take() + lexer.take();
-        }
-        target.addElement("parameter").markLocation(loc).setValue(id);
-      } else {
-        target.addElement("parameter").markLocation(lexer.getCurrentLocation()).setValue(readConstantEM(name, lexer));
-      }
-    }
-    if (lexer.hasToken("as")) {
-      lexer.take();
-      target.makeElement("variable").markLocation(lexer.getCurrentLocation()).setValue(lexer.take());
-    }
-    while (Utilities.existsInList(lexer.getCurrent(), "first", "last", "share", "collate")) {
-      if (lexer.getCurrent().equals("share")) {
-        target.makeElement("listMode").markLocation(lexer.getCurrentLocation()).setValue(lexer.take());
-        target.makeElement("listRuleId").markLocation(lexer.getCurrentLocation()).setValue(lexer.take());
-      } else {
-        target.makeElement("listMode").markLocation(lexer.getCurrentLocation()).setValue(lexer.take());
-      }
-    }
-  }
-
  
   private void parseParameter(StructureMapGroupRuleDependentComponent ref, FHIRLexer lexer) throws FHIRLexerException, FHIRFormatError {
     if (!lexer.isConstant()) {
@@ -1557,15 +1134,6 @@ public class StructureMapUtilities {
     }
   }
 
-  private void parseParameterEM(Element ref, FHIRLexer lexer) throws FHIRLexerException, FHIRFormatError {
-    if (!lexer.isConstant()) {
-      ref.addElement("parameter").markLocation(lexer.getCurrentLocation()).setValue(lexer.take());
-    } else if (lexer.isStringConstant())
-      ref.addElement("parameter").markLocation(lexer.getCurrentLocation()).setValue(lexer.readConstant("??"));
-    else {
-      ref.addElement("parameter").markLocation(lexer.getCurrentLocation()).setValue(readConstantEM(lexer.take(), lexer));
-    }
-  }
  
   private DataType readConstant(String s, FHIRLexer lexer) throws FHIRLexerException {
     if (Utilities.isInteger(s))
@@ -1578,16 +1146,6 @@ public class StructureMapUtilities {
       return new StringType(lexer.processConstant(s));
   }
 
-  private String readConstantEM(String s, FHIRLexer lexer) throws FHIRLexerException {
-    if (Utilities.isInteger(s))
-      return s;
-    else if (Utilities.isDecimal(s, false))
-      return s;
-    else if (Utilities.existsInList(s, "true", "false"))
-      return s;
-    else
-      return lexer.processConstant(s);
-  }
 
   public StructureDefinition getTargetType(StructureMap map) throws FHIRException {
     boolean found = false;

org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/StructureMapUtilitiesTest.java

@@ -91,24 +91,6 @@ public class StructureMapUtilitiesTest implements ITransformerServices {
     assertSerializeDeserialize(map);
   }
 
-
-  @Test
-  public void testSyntaxEM() throws IOException, FHIRException {
-    StructureMapUtilities scu = new StructureMapUtilities(context, this);
-    String fileMap = TestingUtilities.loadTestResource("r5", "structure-mapping", "syntax.map");
-    System.out.println(fileMap);
-
-    Element structureMap = scu.parseEM(fileMap, "Syntax", null);
-//    assertSerializeDeserialize(structureMap);
-//
-//    String renderedMap = StructureMapUtilities.render(structureMap);
-//    StructureMap map = scu.parse(renderedMap, "Syntax");
-//    System.out.println(map);
-//    assertSerializeDeserialize(map);
-  }
-
-
-
   @Override
   public void log(String message) {
   }

org.hl7.fhir.report/checkstyle_suppressions.xml

@@ -0,0 +1,8 @@
+<?xml version="1.0"?>
+<!DOCTYPE suppressions PUBLIC
+        "-//Checkstyle//DTD SuppressionFilter Configuration 1.2//EN"
+        "https://checkstyle.org/dtds/suppressions_1_2.dtd">
+
+<suppressions>
+  
+</suppressions>

org.hl7.fhir.report/pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <groupId>ca.uhn.hapi.fhir</groupId>
         <artifactId>org.hl7.fhir.core</artifactId>
-        <version>5.6.99-SNAPSHOT</version>
+        <version>5.6.100-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 
@@ -90,7 +90,7 @@
                     <groupId>org.sonatype.plugins</groupId>
                     <artifactId>nexus-staging-maven-plugin</artifactId>
                     <configuration>
-                        <skip>true</skip>
+                        <skipStaging>true</skipStaging>
                     </configuration>
                 </plugin>
                 <plugin>

org.hl7.fhir.utilities/checkstyle_suppressions.xml

@@ -0,0 +1,8 @@
+<?xml version="1.0"?>
+<!DOCTYPE suppressions PUBLIC
+        "-//Checkstyle//DTD SuppressionFilter Configuration 1.2//EN"
+        "https://checkstyle.org/dtds/suppressions_1_2.dtd">
+
+<suppressions>
+
+</suppressions>

org.hl7.fhir.utilities/pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <groupId>ca.uhn.hapi.fhir</groupId>
         <artifactId>org.hl7.fhir.core</artifactId>
-        <version>5.6.99-SNAPSHOT</version>
+        <version>5.6.100-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 
@@ -45,7 +45,7 @@
         <dependency>
             <groupId>com.squareup.okhttp3</groupId>
             <artifactId>okhttp</artifactId>
-            <version>4.9.0</version>
+            <version>${okhttp.version}</version>
             <optional>true</optional>
         </dependency>
 
@@ -159,7 +159,7 @@
         <dependency>
             <groupId>com.squareup.okhttp3</groupId>
             <artifactId>logging-interceptor</artifactId>
-            <version>4.9.0</version>
+            <version>${okhttp.version}</version>
             <scope>compile</scope>
         </dependency>
         -->

org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/MarkDownProcessor.java

@@ -69,6 +69,125 @@ public class MarkDownProcessor {
     }
   }
 
+  /**
+   * Returns true if this is intended to be processed as markdown
+   * 
+   * this is guess, based on textual analysis of the content. 
+   * 
+   * Uses of this routine:
+   *   In general, the main use of this is to decide to escape the string so erroneous markdown processing doesn't munge characters
+   *   If it's a plain string, and it's being put into something that's markdown, then you should escape the content
+   *   If it's markdown, but you're not sure whether to process it as markdown
+   *   
+   * The underlying problem is that markdown processing plain strings is problematic because some technical characters might 
+   * get lost. So it's good to escape them... but if it's meant to be markdown, then it'll get trashed. 
+   * 
+   * This method works by looking for character patterns that are unlikely to occur outside markdown - but it's still only unlikely
+   *  
+   * @param content
+   * @return
+   */
+  // todo: dialect dependency?
+  public boolean isProbablyMarkdown(String content, boolean mdIfParagrapghs) {
+    if (mdIfParagrapghs && content.contains("\n")) {
+      return true;
+    }
+    String[] lines = content.split("\\r?\\n");
+    for (String s : lines) {
+      if (s.startsWith("* ") || isHeading(s) || s.startsWith("1. ") || s.startsWith("    ")) {
+        return true;
+      }
+      if (s.contains("```") || s.contains("~~~") || s.contains("[[[")) {
+        return true;
+      }
+      if (hasLink(s)) {
+        return true;
+      }
+      if (hasTextSpecial(s, '*') || hasTextSpecial(s, '_') ) {
+        return true;
+      }
+    }
+      
+    return false;
+  }
+  
+  private boolean isHeading(String s) {
+    if (s.length() > 7 && s.startsWith("###### ") && !Character.isWhitespace(s.charAt(7))) {
+      return true;
+    }
+    if (s.length() > 6 && s.startsWith("##### ") && !Character.isWhitespace(s.charAt(6))) {
+      return true;
+    }
+    if (s.length() > 5 && s.startsWith("#### ") && !Character.isWhitespace(s.charAt(5))) {
+      return true;
+    }
+    if (s.length() > 4 && s.startsWith("### ") && !Character.isWhitespace(s.charAt(4))) {
+      return true;
+    }
+    if (s.length() > 3 && s.startsWith("## ") && !Character.isWhitespace(s.charAt(3))) {
+      return true;
+    }
+    //
+    // not sure about this one. # [string] is something that could easily arise in non-markdown, 
+    // so this appearing isn't enough to call it markdown
+    //
+//    if (s.length() > 2 && s.startsWith("# ") && !Character.isWhitespace(s.charAt(2))) {
+//      return true;
+//    }
+    return false;
+  }
+
+
+  private boolean hasLink(String s) {
+    int left = -1;
+    int mid = -1;
+    for (int i = 0; i < s.length(); i++) {
+      char c = s.charAt(i);
+      if (c == '[') {
+        mid = -1;
+        left = i;
+      } else if (left > -1 && i < s.length()-1 && c == ']' && s.charAt(i+1) == '(') {
+        mid = i;
+      } else if (left > -1 && c == ']') {
+        left = -1;
+      } else if (left > -1 && mid > -1 && c == ')') {
+        return true;
+      } else if (mid > -1 && c == '[' || c == ']' || (c == '(' && i > mid+1)) {
+        left = -1;
+        mid = -1;
+      }
+    }
+    return false;
+  }
+
+
+  private boolean hasTextSpecial(String s, char c) {
+    boolean second = false;
+    for (int i = 0; i < s.length(); i++) {
+      char prev = i == 0 ? ' ' : s.charAt(i-1);
+      char next = i < s.length() - 1 ? s.charAt(i+1) : ' ';
+      if (s.charAt(i) != c) {
+        // nothing
+      } else if (second) {
+        if (Character.isWhitespace(next) && (isPunctation(prev) || Character.isLetterOrDigit(prev))) {
+          return true;
+        }
+        second = false;        
+      } else {
+        if (Character.isWhitespace(prev) && (isPunctation(next) || Character.isLetterOrDigit(next))) {
+          second = true;
+        }            
+      }
+    }
+    return false;
+  }
+
+
+  private boolean isPunctation(char ch) {
+    return Utilities.existsInList(ch, '.', ',', '!', '?');
+  }
+
+
   /**
    * This deals with a painful problem created by the intersection of previous publishing processes 
    * and the way commonmark specifies that < is handled in content. For control reasons, the FHIR specification does 

org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/VersionUtilities.java

@@ -214,10 +214,18 @@ public class VersionUtilities {
     } else if (Utilities.charCount(version, '.') == 2) {
       String[] p = version.split("\\.");
       return p[0]+"."+p[1];
-    } else {
+    } else if (Utilities.existsInList(version, "R2", "R2B", "R3", "R4", "R4B", "R5")) {
-      return null;
+      switch (version) {
+      case "R2": return "1.0";
+      case "R2B": return "1.4";
+      case "R3": return "3.0";
+      case "R4": return "4.0";
+      case "R4B": return "4.3";
+      case "R5": return "5.0";
       }
     }  
+    return null;
+  }
 
   public static String getPatch(String version) {
     if (version == null)

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

@@ -774,6 +774,44 @@ public class I18nConstants {
   public static final String EXT_VER_URL_REVERSION = "EXT_VER_URL_REVERSION";
   public static final String ILLEGAL_COMMENT_TYPE = "ILLEGAL_COMMENT_TYPE";
   public static final String SD_NO_SLICING_ON_ROOT = "SD_NO_SLICING_ON_ROOT";
+  public static final String REFERENCE_REF_QUERY_INVALID = "REFERENCE_REF_QUERY_INVALID";
+  public static final String SM_RULEGROUP_NOT_FOUND = "SM_RULEGROUP_NOT_FOUND";
+  public static final String SM_NAME_INVALID = "SM_NAME_INVALID";
+  public static final String SM_GROUP_INPUT_DUPLICATE = "SM_GROUP_INPUT_DUPLICATE";
+  public static final String SM_GROUP_INPUT_MODE_INVALID = "SM_GROUP_INPUT_MODE_INVALID";
+  public static final String SM_GROUP_INPUT_NO_TYPE = "SM_GROUP_INPUT_NO_TYPE";
+  public static final String SM_GROUP_INPUT_TYPE_NOT_DECLARED = "SM_GROUP_INPUT_TYPE_NOT_DECLARED";
+  public static final String SM_GROUP_INPUT_MODE_MISMATCH = "SM_GROUP_INPUT_MODE_MISMATCH";
+  public static final String SM_GROUP_INPUT_TYPE_UNKNOWN_STRUCTURE = "SM_GROUP_INPUT_TYPE_UNKNOWN_STRUCTURE";
+  public static final String SM_GROUP_INPUT_TYPE_UNKNOWN_TYPE = "SM_GROUP_INPUT_TYPE_UNKNOWN_TYPE";
+  public static final String SM_SOURCE_CONTEXT_UNKNOWN = "SM_SOURCE_CONTEXT_UNKNOWN";
+  public static final String SM_SOURCE_PATH_INVALID = "SM_SOURCE_PATH_INVALID";
+  public static final String SM_RULE_SOURCE_MIN_REDUNDANT = "SM_RULE_SOURCE_MIN_REDUNDANT";
+  public static final String SM_RULE_SOURCE_MAX_REDUNDANT = "SM_RULE_SOURCE_MAX_REDUNDANT";
+  public static final String SM_RULE_SOURCE_LISTMODE_REDUNDANT = "SM_RULE_SOURCE_LISTMODE_REDUNDANT";
+  public static final String SM_TARGET_CONTEXT_UNKNOWN = "SM_TARGET_CONTEXT_UNKNOWN";
+  public static final String SM_TARGET_PATH_INVALID = "SM_TARGET_PATH_INVALID";
+  public static final String SM_NO_LIST_MODE_NEEDED = "SM_NO_LIST_MODE_NEEDED";
+  public static final String SM_NO_LIST_RULE_ID_NEEDED = "SM_NO_LIST_RULE_ID_NEEDED";
+  public static final String SM_LIST_RULE_ID_ONLY_WHEN_SHARE = "SM_LIST_RULE_ID_ONLY_WHEN_SHARE";
+  public static final String SM_RULE_SOURCE_UNASSIGNED = "SM_RULE_SOURCE_UNASSIGNED";
+  public static final String SM_TARGET_PATH_MULTIPLE_MATCHES = "SM_TARGET_PATH_MULTIPLE_MATCHES";
+  public static final String SM_SOURCE_TYPE_INVALID = "SM_SOURCE_TYPE_INVALID";
+  public static final String SM_TARGET_TRANSFORM_PARAM_COUNT_SINGLE = "SM_TARGET_TRANSFORM_PARAM_COUNT_SINGLE";
+  public static final String SM_TARGET_TRANSFORM_PARAM_COUNT_RANGE = "SM_TARGET_TRANSFORM_PARAM_COUNT_RANGE";
+  public static final String SM_TARGET_TRANSFORM_NOT_CHECKED = "SM_TARGET_TRANSFORM_NOT_CHECKED";
+  public static final String SM_TARGET_NO_TRANSFORM_NO_CHECKED = "SM_TARGET_NO_TRANSFORM_NO_CHECKED";
+  public static final String SM_TARGET_TRANSFORM_TYPE_UNPROCESSIBLE = "SM_TARGET_TRANSFORM_TYPE_UNPROCESSIBLE";
+  public static final String SM_TARGET_TRANSFORM_PARAM_UNPROCESSIBLE = "SM_TARGET_TRANSFORM_PARAM_UNPROCESSIBLE";
+  public static final String SM_TARGET_TRANSFORM_EXPRESSION_ERROR = "SM_TARGET_TRANSFORM_EXPRESSION_ERROR";
+  public static final String SM_IMPORT_NOT_FOUND = "SM_IMPORT_NOT_FOUND";
+  public static final String SM_TARGET_TYPE_MULTIPLE_POSSIBLE = "SM_TARGET_TYPE_MULTIPLE_POSSIBLE";
+  public static final String SM_DEPENDENT_PARAM_MODE_MISMATCH = "SM_DEPENDENT_PARAM_MODE_MISMATCH";
+  public static final String SM_DEPENDENT_PARAM_TYPE_MISMATCH = "SM_DEPENDENT_PARAM_TYPE_MISMATCH";
+  public static final String SM_ORPHAN_GROUP = "SM_ORPHAN_GROUP";
+  public static final String SM_SOURCE_TYPE_NOT_FOUND = "SM_SOURCE_TYPE_NOT_FOUND";
+  public static final String SM_TARGET_TYPE_NOT_FOUND = "SM_TARGET_TYPE_NOT_FOUND";
+  public static final String SM_MATCHING_RULEGROUP_NOT_FOUND = "SM_MATCHING_RULEGROUP_NOT_FOUND";
 }
 
 

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

@@ -27,19 +27,13 @@ public class PackageClient {
 
 
   private PackageServer server;
-  private String cacheFolder;
   private String address;
 
 
   public PackageClient(PackageServer server) {
     super();
     this.server = server;
-    address = server.getUrl();
+    address = this.server.getUrl();
-    try {
-      cacheFolder = Utilities.path(System.getProperty("user.home"), ".fhir", "package-client");
-      Utilities.createDirectory(cacheFolder);
-    } catch (IOException e) {
-    }
   }
 
   public boolean exists(String id, String ver) throws IOException {

org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/turtle/Turtle.java

@@ -72,22 +72,35 @@ public class Turtle {
 		protected List<Predicate> predicates = new ArrayList<Predicate>();
 
 		public Complex predicate(String predicate, String object) {
+			return predicate(predicate, object, false);
+		}
+		
+		public Complex predicate(String predicate, String object, boolean asList) {
 			predicateSet.add(predicate);
 			objectSet.add(object);
-			return predicate(predicate, new StringType(object));
+			return predicate(predicate, new StringType(object), asList);
 		}
 
 	public Complex linkedPredicate(String predicate, String object, String link, String comment) {
+		return linkedPredicate(predicate, object, link, comment, false);
+	}
+		
+    public Complex linkedPredicate(String predicate, String object, String link, String comment, boolean asList) {
       predicateSet.add(predicate);
       objectSet.add(object);
-      return linkedPredicate(predicate, new StringType(object), link, comment);
+      return linkedPredicate(predicate, new StringType(object), link, comment, asList);
     }
     
     public Complex predicate(String predicate, Triple object) {
+    	return predicate(predicate, object, false);
+    }
+
+	public Complex predicate(String predicate, Triple object, boolean asList) {
       Predicate p = getPredicate(predicate);
       if (p == null) {
         p = new Predicate();
 			p.predicate = predicate;
+			p.asList = asList;
 			predicateSet.add(predicate);
         predicates.add(p);
       }
@@ -105,12 +118,17 @@ public class Turtle {
     }
     
     public Complex linkedPredicate(String predicate, Triple object, String link, String comment) {
+    	return linkedPredicate(predicate, object, link, comment, false);
+    }
+
+    public Complex linkedPredicate(String predicate, Triple object, String link, String comment, boolean asList) {
       Predicate p = getPredicate(predicate);
       if (p == null) {
         p = new Predicate();
       p.predicate = predicate;
       p.link = link;
       p.comment = comment;
+      p.asList = asList;
       predicateSet.add(predicate);
         predicates.add(p);
       }
@@ -121,16 +139,24 @@ public class Turtle {
     }
     
     public Complex predicate(String predicate) {
+		return predicate(predicate, false);
+	}
+
+	public Complex predicate(String predicate, boolean asList) {
 		predicateSet.add(predicate);
 		Complex c = complex();
-			predicate(predicate, c);
+		predicate(predicate, c, asList);
 		return c;
 	}
 
 	public Complex linkedPredicate(String predicate, String link, String comment) {
+		return linkedPredicate(predicate, link, comment, false);
+	}
+	
+    public Complex linkedPredicate(String predicate, String link, String comment, boolean asList) {
       predicateSet.add(predicate);
       Complex c = complex();
-      linkedPredicate(predicate, c, link, comment);
+      linkedPredicate(predicate, c, link, comment, asList);
       return c;
     }
 
@@ -144,6 +170,7 @@ public class Turtle {
 		protected String link;
     protected List<Triple> objects = new ArrayList<Turtle.Triple>();
 		protected String comment;
+		protected boolean asList = false;
 
 		public String getPredicate() {
 			return predicate;
@@ -183,15 +210,15 @@ public class Turtle {
 
 		public void comment(String comment) {
 			if (!Utilities.noString(comment)) {
-				predicate("rdfs:comment", literal(comment));
+				predicate("rdfs:comment", literal(comment), false);
-				predicate("dcterms:description", literal(comment));
+				predicate("dcterms:description", literal(comment), false);
 			}
 		}
 
 		public void label(String label) {
 			if (!Utilities.noString(label)) {
-				predicate("rdfs:label", literal(label));
+				predicate("rdfs:label", literal(label), false);
-				predicate("dc:title", literal(label));
+				predicate("dc:title", literal(label), false);
 			}
 		}
 
@@ -445,7 +472,7 @@ public class Turtle {
 	  writer.ln();
 	  if (!section.comments.isEmpty()) {
 	    for (String s : section.comments) {
-	      writer.ln("# "+s);		  
+	      writer.ln("# "+formatMultilineComment(s));
 	    }
 	    writer.ln();
 	  }
@@ -464,10 +491,13 @@ public class Turtle {
 				writer.write(" ");
         boolean first = true;
         for (Triple o : p.getObjects()) {
-          if (first)
+          if (first) {
             first = false;
-          else
+            if (p.asList) writer.write("( ");
-            writer.write(", ");
+          } else {
+        	  if (!p.asList) writer.write(", ");
+        	  else writer.write(" ");
+          }
           if (o instanceof StringType)
             writer.write(((StringType) o).value);
 				else {
@@ -478,10 +508,11 @@ public class Turtle {
 						writer.write("]");
 				}
         }
-				String comment = p.comment == null? "" : " # "+p.comment;
+				String comment = p.comment == null? "" : " # "+formatMultilineComment(p.comment);
+				if (p.asList) writer.write(" )");	
 				i++;
 				if (i < sbj.predicates.size())
-					writer.write(";"+comment+"\r\n  ");
+					writer.write(" ;"+comment+"\r\n  ");
         else {
           if (Utilities.noString(sbj.id)) 
             writer.write("]");
@@ -491,6 +522,11 @@ public class Turtle {
 	}
   }
 	
+  private String formatMultilineComment(String s) {
+	  return s.replace("\n", "\n#");
+  }
+
+
   private void commitSection(StringBuilder b, Section section) throws Exception {
     b.append("# - "+section.name+" "+Utilities.padLeft("", '-', 75-section.name.length())+"\r\n");
     b.append("\r\n");
@@ -511,10 +547,12 @@ public class Turtle {
         b.append(" ");
         boolean first = true;
         for (Triple o : p.getObjects()) {
-          if (first)
+        if (first) {
           first = false;
-          else
+          if (p.asList) b.append("( ");
-            b.append(", ");
+        } else
+        	if (!p.asList) b.append(", ");
+        	else b.append(" ");
           if (o instanceof StringType)
             b.append(Utilities.escapeXml(((StringType) o).value));
           else {
@@ -525,12 +563,13 @@ public class Turtle {
               b.append("]");
           }
         }
-        String comment = p.comment == null? "" : " # "+p.comment;
+        String comment = p.comment == null? "" : " # "+formatMultilineComment(p.comment);
+        if (p.asList) b.append(" )");
         i++;
         if (i < sbj.predicates.size())
-          b.append(";"+Utilities.escapeXml(comment)+"\r\n  ");
+          b.append(" ;"+Utilities.escapeXml(comment)+"\r\n  ");
         else
-          b.append("."+Utilities.escapeXml(comment)+"\r\n\r\n");
+          b.append(" ."+Utilities.escapeXml(comment)+"\r\n\r\n");
       }
     }
   }
@@ -566,8 +605,11 @@ public class Turtle {
         if (first) {
           first = false;
           writer.write(left+" "+po.getPredicate()+" ");
-        } else
+          if (po.asList) writer.write("( ");
-          writer.write(", ");
+        } else {
+        	  if (!po.asList) writer.write(", ");
+        	  else writer.write(" ");
+        }
         if (o instanceof StringType)
           writer.write(((StringType) o).value);
 			else {
@@ -578,9 +620,10 @@ public class Turtle {
 					writer.write(" ]");
 			}
       }
+      if (po.asList) writer.write(" )");
 			i++;
 			if (i < complex.predicates.size())
-				writer.write(";");
+				writer.write(" ;");
 			if (!Utilities.noString(po.comment)) 
 				writer.write(" # "+escape(po.comment, false));
 		}
@@ -602,9 +645,11 @@ public class Turtle {
       for (Triple o : po.getObjects()) {
         if (first) {
           first = false;
-          b.append(left+" "+po.makelink()+" ");
+          if (po.asList) b.append(left+"( ");
+          b.append(po.makelink()+" ");
         } else
-          b.append(", ");
+        	if (!po.asList) b.append(", ");
+        	else b.append(" ");
         if (o instanceof StringType)
           b.append(Utilities.escapeXml(((StringType) o).value));
       else {
@@ -615,9 +660,10 @@ public class Turtle {
           b.append(" ]");
       }
       }
+      if (po.asList) b.append(" )");
       i++;
       if (i < complex.predicates.size())
-        b.append(";");
+        b.append(" ;");
       if (!Utilities.noString(po.comment)) 
         b.append(" # "+Utilities.escapeXml(escape(po.comment, false)));
     }

org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/xhtml/HierarchicalTableGenerator.java

@@ -83,9 +83,14 @@ import org.commonmark.renderer.html.HtmlRenderer;
 import org.hl7.fhir.exceptions.FHIRException;
 import org.hl7.fhir.utilities.TranslatingUtilities;
 import org.hl7.fhir.utilities.Utilities;
+import org.hl7.fhir.utilities.xhtml.HierarchicalTableGenerator.TableGenerationMode;
 
 
 public class HierarchicalTableGenerator extends TranslatingUtilities {
+  public enum TableGenerationMode {
+    XML, XHTML
+  }
+
   public static final String TEXT_ICON_REFERENCE = "Reference to another Resource";
   public static final String TEXT_ICON_PRIMITIVE = "Primitive Data Type";
   public static final String TEXT_ICON_KEY = "JSON Key Value";
@@ -599,6 +604,8 @@ public class HierarchicalTableGenerator extends TranslatingUtilities {
    */
   private boolean inLineGraphics;  
   
+  private TableGenerationMode mode;
+  
   public HierarchicalTableGenerator() {
     super();
   }
@@ -626,7 +633,9 @@ public class HierarchicalTableGenerator extends TranslatingUtilities {
     checkSetup();
   }
 
-  public TableModel initNormalTable(String prefix, boolean isLogical, boolean alternating, String id, boolean isActive) {
+  public TableModel initNormalTable(String prefix, boolean isLogical, boolean alternating, String id, boolean isActive, TableGenerationMode mode) {
+    this.mode = mode;
+    
     TableModel model = new TableModel(id, isActive);
     
     model.setAlternating(alternating);
@@ -686,12 +695,16 @@ public class HierarchicalTableGenerator extends TranslatingUtilities {
     tr.setAttribute("style", "border: " + Integer.toString(1 + border) + "px #F0F0F0 solid; font-size: 11px; font-family: verdana; vertical-align: top");
     XhtmlNode tc = null;
     for (Title t : model.getTitles()) {
-      tc = renderCell(tr, t, "th", null, null, null, false, null, "white", 0, imagePath, border, outputTracker, model, null);
+      tc = renderCell(tr, t, "th", null, null, null, false, null, "white", 0, imagePath, border, outputTracker, model, null, true);
       if (t.width != 0)
         tc.setAttribute("style", "width: "+Integer.toString(t.width)+"px");
     }
     if (tc != null && model.getDocoRef() != null) {
-      XhtmlNode img = tc.addTag("span").setAttribute("style", "float: right").addTag("a").setAttribute("title", "Legend for this format").setAttribute("href", model.getDocoRef()).addTag("img");
+      XhtmlNode a = tc.addTag("span").setAttribute("style", "float: right").addTag("a").setAttribute("title", "Legend for this format").setAttribute("href", model.getDocoRef());
+      if (mode == TableGenerationMode.XHTML) {
+        a.setAttribute("no-external", "true");
+      }
+      XhtmlNode img = a.addTag("img");
       img.setAttribute("alt", "doco").setAttribute("style", "background-color: inherit").setAttribute("src", model.getDocoImg());
       if (model.isActive()) {
         img.setAttribute("onLoad", "fhirTableInit(this)");
@@ -732,7 +745,7 @@ public class HierarchicalTableGenerator extends TranslatingUtilities {
     }
     boolean first = true;
     for (Cell t : r.getCells()) {
-      renderCell(tr, t, "td", first ? r.getIcon() : null, first ? r.getHint() : null, first ? indents : null, !r.getSubRows().isEmpty(), first ? r.getAnchor() : null, color, r.getLineColor(), imagePath, border, outputTracker, model, r);
+      renderCell(tr, t, "td", first ? r.getIcon() : null, first ? r.getHint() : null, first ? indents : null, !r.getSubRows().isEmpty(), first ? r.getAnchor() : null, color, r.getLineColor(), imagePath, border, outputTracker, model, r, first);
       first = false;
     }
     table.addText("\r\n");
@@ -751,7 +764,7 @@ public class HierarchicalTableGenerator extends TranslatingUtilities {
   }
 
 
-  private XhtmlNode renderCell(XhtmlNode tr, Cell c, String name, String icon, String hint, List<Integer> indents, boolean hasChildren, String anchor, String color, int lineColor, String imagePath, int border, Set<String> outputTracker, TableModel table, Row row) throws IOException  {
+  private XhtmlNode renderCell(XhtmlNode tr, Cell c, String name, String icon, String hint, List<Integer> indents, boolean hasChildren, String anchor, String color, int lineColor, String imagePath, int border, Set<String> outputTracker, TableModel table, Row row, boolean suppressExternals) throws IOException  {
     XhtmlNode tc = tr.addTag(name);
     tc.setAttribute("class", "hierarchy");
     if (c.span > 1) {
@@ -837,6 +850,9 @@ public class HierarchicalTableGenerator extends TranslatingUtilities {
       } else if (!Utilities.noString(p.getReference())) {
         XhtmlNode a = addStyle(tc.addTag("a"), p);
         a.setAttribute("href", p.getReference());
+        if (mode == TableGenerationMode.XHTML && suppressExternals) {
+          a.setAttribute("no-external", "true");
+        }
         if (!Utilities.noString(p.getHint()))
           a.setAttribute("title", p.getHint());
         if (p.getText() != null) {

org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/xhtml/XhtmlFluent.java

@@ -150,7 +150,9 @@ public abstract class XhtmlFluent {
 
 
   public XhtmlNode code(String text) {
-    return addTag("code").tx(text);
+    XhtmlNode code = addTag("code");
+    code.tx(text);
+    return code;
   }
 
   public XhtmlNode code() {

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

@@ -824,5 +824,45 @@ EXT_VER_URL_NOT_ALLOWED = The extension URL must not contain a version
 EXT_VER_URL_REVERSION = The extension URL must not contain a version. The extension was validated against version {0} of the extension
 ILLEGAL_COMMENT_TYPE = The fhir_comments property must be an array of strings
 SD_NO_SLICING_ON_ROOT = Slicing is not allowed at the root of a profile
+REFERENCE_REF_QUERY_INVALID = The query part of the conditional reference is not a valid query string ({0})
+SM_RULEGROUP_NOT_FOUND = The group {0} could not be resolved
+SM_NAME_INVALID = The name {0} is not valid
+SM_GROUP_INPUT_DUPLICATE = The name {0} is already used      
+SM_GROUP_INPUT_MODE_INVALID = The group parameter {0} mode {1} isn''t valid
+SM_GROUP_INPUT_NO_TYPE = The group parameter {0} has no type, so the paths cannot be validated
+SM_GROUP_INPUT_TYPE_NOT_DECLARED = The type {0} is not declared and is unknown
+SM_GROUP_INPUT_MODE_MISMATCH = The type {0} has mode {1} which doesn''t match the structure definition {2}
+SM_GROUP_INPUT_TYPE_UNKNOWN_STRUCTURE = The type {0} which maps to the canonical URL {1} is not known, so the paths cannot be validated
+SM_GROUP_INPUT_TYPE_UNKNOWN_TYPE = The type {0} is not known, so the paths cannot be validated
+SM_SOURCE_CONTEXT_UNKNOWN = The source context {0} is not known at this point
+SM_SOURCE_PATH_INVALID = The source path {0}.{1} refers to the path {2} which is unknown
+SM_RULE_SOURCE_MIN_REDUNDANT = The min value of {0} is redundant since the valid min is {0}
+SM_RULE_SOURCE_MAX_REDUNDANT = The max value of {0} is redundant since the valid max is {0}
+SM_RULE_SOURCE_LISTMODE_REDUNDANT = The listMode value of {0} is redundant since the valid max is {0}
+SM_TARGET_CONTEXT_UNKNOWN = The target context {0} is not known at this point
+SM_TARGET_PATH_INVALID = The target path {0}.{1} refers to the path {2} which is unknown
+SM_NO_LIST_MODE_NEEDED =  A list mode should not be provided since this is a rule that can only be executed once
+SM_NO_LIST_RULE_ID_NEEDED = A list ruleId should not be provided since this is a rule that can only be executed once
+SM_LIST_RULE_ID_ONLY_WHEN_SHARE = A ruleId should only be provided when the rule mode is ''share''
+SM_RULE_SOURCE_UNASSIGNED = The source statement doesn''t assign a variable to the source - check that this is what is intended
+SM_TARGET_PATH_MULTIPLE_MATCHES = The target path {0}.{1} refers to the path {2} which is could be a reference to multiple elements ({3}). No further checking can be performed
+SM_SOURCE_TYPE_INVALID = The type {0} is not valid in this source context {1}. The possible types are [{2}]
+SM_TARGET_TRANSFORM_PARAM_COUNT_RANGE = Transform {0} takes {1}-{2} parameter(s) but {3} were found
+SM_TARGET_TRANSFORM_PARAM_COUNT_SINGLE = Transform {0} takes {1} parameter(s) but {2} were found
+SM_TARGET_TRANSFORM_NOT_CHECKED = Transform {0} not checked yet
+SM_TARGET_NO_TRANSFORM_NO_CHECKED = When there is no transform, parameters can''t be provided
+SM_TARGET_TRANSFORM_TYPE_UNPROCESSIBLE = The value of the type parameter could not be processed
+SM_TARGET_TRANSFORM_PARAM_UNPROCESSIBLE = The parameter at index {0} could not be processed (type = {1})
+SM_TARGET_TRANSFORM_EXPRESSION_ERROR = The FHIRPath expression passed as the evaluate parameter is invalid: {0}
+SM_IMPORT_NOT_FOUND = No maps were found to match {0} - validation may be wrong
+SM_TARGET_TYPE_MULTIPLE_POSSIBLE = Multiple types are possible here ({0}) so further type checking is not possible
+SM_DEPENDENT_PARAM_MODE_MISMATCH = The parameter {0} refers to the variable {1} but it''s mode is {2} which is not the same as the mode required for the group {3}
+SM_DEPENDENT_PARAM_TYPE_MISMATCH =  The parameter {0} refers to the variable {1} but it''s type is {2} which is not compatible with the type required for the group {3}
+SM_ORPHAN_GROUP = This group is not called from within this mapping script, and does not have types on it's inputs, so type verification is not possible
+SM_SOURCE_TYPE_NOT_FOUND = No source type was found, so the default group for this implied dependent rule could not be determined
+SM_TARGET_TYPE_NOT_FOUND = No target type was found, so the default group for this implied dependent rule could not be determined
+SM_MATCHING_RULEGROUP_NOT_FOUND = Unable to find a default rule for the type pair source={0} and target={1}
+ 
+
 
  

org.hl7.fhir.utilities/src/test/java/org/hl7/fhir/utilities/FTPClientTest.java

@@ -30,7 +30,7 @@ public class FTPClientTest implements ResourceLoaderTests {
   public static final String DUMMY_FILE_TO_DELETE = "dummyFileToDelete";
 
   public static final String DUMMY_FILE_TO_UPLOAD = "dummyFileToUpload";
-  public static final int FAKE_FTP_PORT = 8021;
+  public static final int FAKE_FTP_PORT = 8022;
   public static final String DUMMY_FILE_CONTENT = "Dummy file content\nMore content\n";
   public static final String LOCALHOST = "localhost";
 

org.hl7.fhir.utilities/src/test/java/org/hl7/fhir/utilities/MarkdownTests.java

@@ -2,15 +2,72 @@ package org.hl7.fhir.utilities;
 
 import static org.junit.jupiter.api.Assertions.*;
 
+import org.hl7.fhir.utilities.MarkDownProcessor.Dialect;
 import org.junit.jupiter.api.Assertions;
 import org.junit.jupiter.api.Test;
 
 class MarkdownTests {
 
+  @Test
+  void testMarkdownDetection() {
+    testMarkdown("this is a test string", false);
+    testMarkdown("this is a \r\ntest string", false);
+    testMarkdown("this is a \r\ntest string", true, true);
+    testMarkdown("this is a t*est strin*g", false);
+    testMarkdown("this is a *test strin*g", false);
+    testMarkdown("this is a *test string*", true);
+    testMarkdown("this is a *test *string", false);
+    testMarkdown("this is a *test* string", true);
+    testMarkdown("this [is] a test string", false);
+    testMarkdown("this [is](link) a test string", true);
+    testMarkdown("this [is](link a test string", false);
+    testMarkdown("this [is] (link) a test string", false);
+    testMarkdown("this [is(link)] a test string", false);
+    testMarkdown("this [is](link a test string", false);
+    testMarkdown("this [i]s] (link) a test string", false);
+    testMarkdown("## heading", true);
+    testMarkdown("# heading", false);
+    testMarkdown("##  heading", false);
+    testMarkdown("###", false);
+  }
+
+  private void testMarkdown(String content, boolean isMD) {
+    testMarkdown(content, isMD, false);
+  }
+
+  private void testMarkdown(String content, boolean isMD, boolean ifLines) {
+    boolean test = new MarkDownProcessor(Dialect.COMMON_MARK).isProbablyMarkdown(content, ifLines);
+    assertEquals(isMD, test);    
+  }
+
   @Test
   void testStringToMarkdown() {
+    // first, we test the need for replacing
+    Assertions.assertEquals("<p>This is a string</p>", new MarkDownProcessor(Dialect.COMMON_MARK).process("This is a string", null).trim());
+    Assertions.assertEquals("<p>This is *a string</p>", new MarkDownProcessor(Dialect.COMMON_MARK).process("This is *a string", null).trim());
+    Assertions.assertNotEquals("<p>This is *a* string</p>", new MarkDownProcessor(Dialect.COMMON_MARK).process("This is *a* string", null).trim());
+    Assertions.assertEquals("<p>This is *a *string</p>", new MarkDownProcessor(Dialect.COMMON_MARK).process("This is *a *string", null).trim());
+    
+    Assertions.assertNotEquals("<p>This genomic study analyzes CYP2D6*1 and CYP2D6*2</p>", new MarkDownProcessor(Dialect.COMMON_MARK).process("This genomic study analyzes CYP2D6*1 and CYP2D6*2", null).trim());
+    Assertions.assertEquals("<p>This genomic study analyzes CYP2D6*1 and CYP2D6*2</p>", new MarkDownProcessor(Dialect.COMMON_MARK).process("This genomic study analyzes CYP2D6*1 and CYP2D6\\*2", null).trim());
+    
+    
     Assertions.assertEquals("This is \\*a test\\*", MarkDownProcessor.makeStringSafeAsMarkdown("This is *a test*"));
     Assertions.assertEquals("This is *a test*", MarkDownProcessor.makeMarkdownForString("This is \\*a test\\*"));
   }
 
 }
+//
+//case '*':
+//case '&':
+//case '#':
+//case '[':
+//case '>':
+//case '<':
+//case '`':
+//  -
+//  |
+//  :
+//  ~
+//  ^
+//  =

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

@@ -0,0 +1,8 @@
+<?xml version="1.0"?>
+<!DOCTYPE suppressions PUBLIC
+        "-//Checkstyle//DTD SuppressionFilter Configuration 1.2//EN"
+        "https://checkstyle.org/dtds/suppressions_1_2.dtd">
+
+<suppressions>
+
+</suppressions>

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>5.6.99-SNAPSHOT</version>
+        <version>5.6.100-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 
@@ -225,7 +225,7 @@
         <dependency>
             <groupId>com.squareup.okhttp3</groupId>
             <artifactId>mockwebserver</artifactId>
-            <version>4.9.0</version>
+            <version>${okhttp.version}</version>
             <optional>false</optional>
             <scope>compile</scope>
         </dependency>
@@ -273,7 +273,7 @@
         <dependency>
             <groupId>com.squareup.okhttp3</groupId>
             <artifactId>okhttp</artifactId>
-            <version>4.9.0</version>
+            <version>${okhttp.version}</version>
       </dependency>
         <dependency>
             <groupId>com.atlassian.commonmark</groupId>
@@ -310,7 +310,7 @@
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-jar-plugin</artifactId>
-                <version>3.1.2</version>
+                <version>${maven-jar-plugin.version}</version>
                 <configuration>
                     <archive>
                         <manifest>

org.hl7.fhir.validation/checkstyle_suppressions.xml

@@ -0,0 +1,8 @@
+<?xml version="1.0"?>
+<!DOCTYPE suppressions PUBLIC
+        "-//Checkstyle//DTD SuppressionFilter Configuration 1.2//EN"
+        "https://checkstyle.org/dtds/suppressions_1_2.dtd">
+
+<suppressions>
+
+</suppressions>

org.hl7.fhir.validation/pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <groupId>ca.uhn.hapi.fhir</groupId>
         <artifactId>org.hl7.fhir.core</artifactId>
-        <version>5.6.99-SNAPSHOT</version>
+        <version>5.6.100-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 
@@ -154,7 +154,7 @@
         <dependency>
             <groupId>com.squareup.okhttp3</groupId>
             <artifactId>okhttp</artifactId>
-            <version>4.9.0</version>
+            <version>${okhttp.version}</version>
             <optional>true</optional>
         </dependency>
 

org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/BaseValidator.java

@@ -1065,7 +1065,7 @@ public class BaseValidator implements IValidationContextResourceLoader {
     if (!context.getResourceNames().contains(tn)) {
       return false;
     } else {
-      return q.matches("([_a-zA-Z][_a-zA-Z0-9]*=[^=&]+)(&([_a-zA-Z][_a-zA-Z0-9]*=[^=&]+))*");
+      return q.matches("([_a-zA-Z][_a-zA-Z0-9]*=[^=&]*)(&([_a-zA-Z][_a-zA-Z0-9]*=[^=&]*))*");
     }
   }
 

org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/IgLoader.java

@@ -20,6 +20,7 @@ import org.hl7.fhir.convertors.factory.VersionConvertorFactory_30_50;
 import org.hl7.fhir.convertors.factory.VersionConvertorFactory_40_50;
 import org.hl7.fhir.convertors.factory.VersionConvertorFactory_43_50;
 import org.hl7.fhir.exceptions.FHIRException;
+import org.hl7.fhir.r5.context.IWorkerContext.IContextResourceLoader;
 import org.hl7.fhir.r5.context.SimpleWorkerContext;
 import org.hl7.fhir.r5.elementmodel.Manager;
 import org.hl7.fhir.r5.formats.JsonParser;
@@ -112,7 +113,9 @@ public class IgLoader {
       if (!srcPackage.contains("#")) {
         System.out.print("#" + npm.version());
       }
-      int count = getContext().loadFromPackage(npm, ValidatorUtils.loaderForVersion(npm.fhirVersion()));
+      IContextResourceLoader loader = ValidatorUtils.loaderForVersion(npm.fhirVersion());
+      loader.setPatchUrls(VersionUtilities.isCorePackage(npm.id()));
+      int count = getContext().loadFromPackage(npm, loader);
       System.out.println(" - " + count + " resources (" + getContext().clock().milestone() + ")");
     } else {
       System.out.print("  Load " + srcPackage);
@@ -183,8 +186,10 @@ public class IgLoader {
         res.cntType = Manager.FhirFormat.TURTLE;
       else if (t.getKey().endsWith(".shc"))
         res.cntType = Manager.FhirFormat.SHC;
-      else if (t.getKey().endsWith(".txt") || t.getKey().endsWith(".map"))
+      else if (t.getKey().endsWith(".txt"))
         res.cntType = Manager.FhirFormat.TEXT;
+      else if (t.getKey().endsWith(".fml") || t.getKey().endsWith(".map"))
+        res.cntType = Manager.FhirFormat.FML;
       else
         throw new FHIRException("Todo: Determining resource type is not yet done");
     }
@@ -762,6 +767,7 @@ public class IgLoader {
       if (isDebug() || ((e.getMessage() != null && e.getMessage().contains("cannot be cast")))) {
         e.printStackTrace();
       }
+      e.printStackTrace();
     }
     return r;
   }
@@ -774,7 +780,7 @@ public class IgLoader {
         res = new org.hl7.fhir.dstu3.formats.XmlParser().parse(new ByteArrayInputStream(content));
       else if (fn.endsWith(".json") && !fn.endsWith("template.json"))
         res = new org.hl7.fhir.dstu3.formats.JsonParser().parse(new ByteArrayInputStream(content));
-      else if (fn.endsWith(".txt") || fn.endsWith(".map"))
+      else if (fn.endsWith(".txt") || fn.endsWith(".map")  || fn.endsWith(".fml"))
         res = new org.hl7.fhir.dstu3.utils.StructureMapUtilities(null).parse(new String(content));
       else
         throw new FHIRException("Unsupported format for " + fn);
@@ -785,7 +791,7 @@ public class IgLoader {
         res = new org.hl7.fhir.r4.formats.XmlParser().parse(new ByteArrayInputStream(content));
       else if (fn.endsWith(".json") && !fn.endsWith("template.json"))
         res = new org.hl7.fhir.r4.formats.JsonParser().parse(new ByteArrayInputStream(content));
-      else if (fn.endsWith(".txt") || fn.endsWith(".map"))
+      else if (fn.endsWith(".txt") || fn.endsWith(".map")  || fn.endsWith(".fml"))
         res = new org.hl7.fhir.r4.utils.StructureMapUtilities(null).parse(new String(content), fn);
       else
         throw new FHIRException("Unsupported format for " + fn);
@@ -796,7 +802,7 @@ public class IgLoader {
         res = new org.hl7.fhir.r4b.formats.XmlParser().parse(new ByteArrayInputStream(content));
       else if (fn.endsWith(".json") && !fn.endsWith("template.json"))
         res = new org.hl7.fhir.r4b.formats.JsonParser().parse(new ByteArrayInputStream(content));
-      else if (fn.endsWith(".txt") || fn.endsWith(".map"))
+      else if (fn.endsWith(".txt") || fn.endsWith(".map")  || fn.endsWith(".fml"))
         res = new org.hl7.fhir.r4b.utils.structuremap.StructureMapUtilities(null).parse(new String(content), fn);
       else
         throw new FHIRException("Unsupported format for " + fn);
@@ -819,15 +825,15 @@ public class IgLoader {
       else
         throw new FHIRException("Unsupported format for " + fn);
       r = VersionConvertorFactory_10_50.convertResource(res, new org.hl7.fhir.convertors.misc.IGR2ConvertorAdvisor5());
-    } else if (fhirVersion.startsWith("5.0")) {
+    } else if (fhirVersion.startsWith("5.0") || "current".equals(fhirVersion)) {
       if (fn.endsWith(".xml") && !fn.endsWith("template.xml"))
         r = new XmlParser().parse(new ByteArrayInputStream(content));
       else if (fn.endsWith(".json") && !fn.endsWith("template.json"))
         r = new JsonParser().parse(new ByteArrayInputStream(content));
       else if (fn.endsWith(".txt"))
         r = new StructureMapUtilities(getContext(), null, null).parse(TextFile.bytesToString(content), fn);
-      else if (fn.endsWith(".map"))
+      else if (fn.endsWith(".map") || fn.endsWith(".fml"))
-        r = new StructureMapUtilities(null).parse(new String(content), fn);
+        r = new StructureMapUtilities(context).parse(new String(content), fn);
       else
         throw new FHIRException("Unsupported format for " + fn);
     } else

org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/ResourceChecker.java

@@ -43,8 +43,8 @@ public class ResourceChecker {
       if (Utilities.existsInList(ext, "ttl")) {
         return FhirFormat.TURTLE;            
       }
-      if (Utilities.existsInList(ext, "map")) {
+      if (Utilities.existsInList(ext, "map", "fml")) {
-        return Manager.FhirFormat.TEXT;
+        return Manager.FhirFormat.FML;
       }
       if (Utilities.existsInList(ext, "jwt", "jws")) {
         return Manager.FhirFormat.SHC;

org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/ValidationEngine.java

@@ -219,6 +219,8 @@ public class ValidationEngine implements IValidatorResourceFetcher, IValidationP
   @Getter @Setter private Coding jurisdiction;
 
 
+  private ContextUtilities cu = null;
+  
   /**
    * Creating a validation engine is an expensive operation - takes seconds. 
    * Once you have a validation engine created, you can quickly clone it to 
@@ -842,7 +844,7 @@ public class ValidationEngine implements IValidatorResourceFetcher, IValidationP
         new org.hl7.fhir.dstu3.formats.XmlParser().setOutputStyle(org.hl7.fhir.dstu3.formats.IParser.OutputStyle.PRETTY).compose(s, res);
       else if (fn.endsWith(".json") && !fn.endsWith("template.json"))
         new org.hl7.fhir.dstu3.formats.JsonParser().setOutputStyle(org.hl7.fhir.dstu3.formats.IParser.OutputStyle.PRETTY).compose(s, res);
-      else if (fn.endsWith(".txt") || fn.endsWith(".map"))
+      else if (fn.endsWith(".txt") || fn.endsWith(".map")  || fn.endsWith(".fml"))
         TextFile.stringToStream(org.hl7.fhir.dstu3.utils.StructureMapUtilities.render((org.hl7.fhir.dstu3.model.StructureMap) res), s, false);
       else
         throw new FHIRException("Unsupported format for " + fn);
@@ -852,7 +854,7 @@ public class ValidationEngine implements IValidatorResourceFetcher, IValidationP
         new org.hl7.fhir.r4.formats.XmlParser().setOutputStyle(org.hl7.fhir.r4.formats.IParser.OutputStyle.PRETTY).compose(s, res);
       else if (fn.endsWith(".json") && !fn.endsWith("template.json"))
         new org.hl7.fhir.r4.formats.JsonParser().setOutputStyle(org.hl7.fhir.r4.formats.IParser.OutputStyle.PRETTY).compose(s, res);
-      else if (fn.endsWith(".txt") || fn.endsWith(".map"))
+      else if (fn.endsWith(".txt") || fn.endsWith(".map")  || fn.endsWith(".fml"))
         TextFile.stringToStream(org.hl7.fhir.r4.utils.StructureMapUtilities.render((org.hl7.fhir.r4.model.StructureMap) res), s, false);
       else
         throw new FHIRException("Unsupported format for " + fn);
@@ -877,7 +879,7 @@ public class ValidationEngine implements IValidatorResourceFetcher, IValidationP
         new XmlParser().setOutputStyle(org.hl7.fhir.r5.formats.IParser.OutputStyle.PRETTY).compose(s, r);
       else if (fn.endsWith(".json") && !fn.endsWith("template.json"))
         new JsonParser().setOutputStyle(org.hl7.fhir.r5.formats.IParser.OutputStyle.PRETTY).compose(s, r);
-      else if (fn.endsWith(".txt") || fn.endsWith(".map"))
+      else if (fn.endsWith(".txt") || fn.endsWith(".map")  || fn.endsWith(".fml"))
         TextFile.stringToStream(StructureMapUtilities.render((org.hl7.fhir.r5.model.StructureMap) r), s, false);
       else
         throw new FHIRException("Unsupported format for " + fn);
@@ -1061,6 +1063,16 @@ public class ValidationEngine implements IValidatorResourceFetcher, IValidationP
       resolvedUrls.put(type+"|"+url, false);
       return false; // todo... how to access settings from here?
     }
+    if (url.contains("*") && !url.contains("?")) {
+      if (cu == null) {
+        cu = new ContextUtilities(context);
+      }
+      List<StructureMap> maps = cu.listMaps(url);
+      if (!maps.isEmpty()) {
+        return true;
+      }
+      
+    }
     if (fetcher != null) {
       try {
         boolean ok = fetcher.resolveURL(validator, appContext, path, url, type);

org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/cli/services/StandAloneValidatorFetcher.java

@@ -105,6 +105,8 @@ public class StandAloneValidatorFetcher implements IValidatorResourceFetcher, IV
     }
     if (base.equals("http://terminology.hl7.org")) {
       pid = "hl7.terminology";
+    } else if (base.equals("http://hl7.org/fhir")) {
+      return false;
     } else if (url.startsWith("http://hl7.org/fhir")) {
       pid = pcm.getPackageId(base);
     } else {

org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/cli/utils/Params.java

@@ -14,6 +14,7 @@ import org.hl7.fhir.validation.cli.model.HtmlInMarkdownCheck;
 public class Params {
 
   public static final String VERSION = "-version";
+  public static final String ALT_VERSION = "-alt-version";
   public static final String OUTPUT = "-output";
 
   public static final String OUTPUT_SUFFIX = "-outputSuffix";
@@ -306,10 +307,30 @@ public class Params {
           String version = Common.getVersionFromIGName(null, s);
           if (version == null) {
             cliContext.addIg(s);
+          } else {
+            String v = getParam(args, VERSION);
+            if (v != null && !v.equals(version)) {
+              throw new Error("Parameters are inconsistent: specified version is "+v+" but -ig parameter "+s+" implies a different version");
+            } else if (cliContext.getSv() != null && !version.equals(cliContext.getSv())) {
+              throw new Error("Parameters are inconsistent: multiple -ig parameters implying differetion versions ("+cliContext.getSv()+","+version+")");
             } else {
               cliContext.setSv(version);
             }
           }
+        }
+      } else if (args[i].equals(ALT_VERSION)) {
+        if (i + 1 == args.length)
+          throw new Error("Specified " + args[i] + " without indicating version");
+        else {
+          String s = args[++i];
+          String v = VersionUtilities.getMajMin(s);
+          if (v == null) {
+            throw new Error("Unsupported FHIR Version "+s);
+          }
+          String pid = VersionUtilities.packageForVersion(v);
+          pid = pid + "#"+VersionUtilities.getCurrentPackageVersion(v);
+          cliContext.addIg(pid);
+        }
       } else if (args[i].equals(MAP)) {
         if (cliContext.getMap() == null) {
           if (i + 1 == args.length)
@@ -336,6 +357,7 @@ public class Params {
         cliContext.addSource(args[i]);
       }
     }
+    
     return cliContext;
   }
 

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

@@ -189,6 +189,7 @@ import org.hl7.fhir.validation.instance.type.MeasureValidator;
 import org.hl7.fhir.validation.instance.type.QuestionnaireValidator;
 import org.hl7.fhir.validation.instance.type.SearchParameterValidator;
 import org.hl7.fhir.validation.instance.type.StructureDefinitionValidator;
+import org.hl7.fhir.validation.instance.type.StructureMapValidator;
 import org.hl7.fhir.validation.instance.type.ValueSetValidator;
 import org.hl7.fhir.validation.instance.utils.ChildIterator;
 import org.hl7.fhir.validation.instance.utils.ElementInfo;
@@ -3262,6 +3263,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
         refType = "bundled";
       }
     }
+    boolean conditional = ref.contains("?") && Utilities.existsInList(ref.substring(0, ref.indexOf("?")), context.getResourceNames());
     ReferenceValidationPolicy pol;
     if (refType.equals("contained") || refType.equals("bundled")) {
       pol = ReferenceValidationPolicy.CHECK_VALID;
@@ -3273,7 +3275,13 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
       }
     }
 
-    if (pol.checkExists()) {
+    if (conditional) {
+      String query = ref.substring(ref.indexOf("?"));
+      boolean test = !Utilities.noString(query) && query.matches("\\?([_a-zA-Z][_a-zA-Z0-9]*=[^=&]*)(&([_a-zA-Z][_a-zA-Z0-9]*=[^=&]*))*");
+          //("^\\?([\\w-]+(=[\\w-]*)?(&[\\w-]+(=[\\w-]*)?)*)?$"),
+      ok = rule(errors, "2023-02-20", IssueType.INVALID, element.line(), element.col(), path, test, I18nConstants.REFERENCE_REF_QUERY_INVALID, ref) && ok;
+  
+    } else if (pol.checkExists()) {
       if (we == null) {
         if (!refType.equals("contained")) {
           if (fetcher == null) {
@@ -3766,7 +3774,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
     }
 
     TypedElementDefinition ted = null;
-    String fp = FHIRPathExpressionFixer.fixExpr(discriminator, null);
+    String fp = FHIRPathExpressionFixer.fixExpr(discriminator, null, context.getVersion());
     ExpressionNode expr = null;
     try {
       expr = fpe.parse(fp);
@@ -4384,7 +4392,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
       }
 
       try {
-        n = fpe.parse(FHIRPathExpressionFixer.fixExpr(expression.toString(), null));
+        n = fpe.parse(FHIRPathExpressionFixer.fixExpr(expression.toString(), null, context.getVersion()));
       } catch (FHIRLexerException e) {
         if (STACK_TRACE) e.printStackTrace();
         throw new FHIRException(context.formatMessage(I18nConstants.PROBLEM_PROCESSING_EXPRESSION__IN_PROFILE__PATH__, expression, profile.getVersionedUrl(), path, e.getMessage()));
@@ -4993,6 +5001,8 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
       return new SearchParameterValidator(context, timeTracker, fpe, xverManager, jurisdiction).validateSearchParameter(errors, element, stack);
     } else if (element.getType().equals("StructureDefinition")) {
       return new StructureDefinitionValidator(context, timeTracker, fpe, wantCheckSnapshotUnchanged, xverManager, jurisdiction).validateStructureDefinition(errors, element, stack);
+    } else if (element.getType().equals("StructureMap")) {
+      return new StructureMapValidator(context, timeTracker, fpe, xverManager,profileUtilities, jurisdiction).validateStructureMap(errors, element, stack);
     } else if (element.getType().equals("ValueSet")) {
       return new ValueSetValidator(context, timeTracker, this, xverManager, jurisdiction).validateValueSet(errors, element, stack);
     } else {
@@ -5849,7 +5859,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
       }
 
       if (!ToolingExtensions.readBoolExtension(profile, "http://hl7.org/fhir/StructureDefinition/structuredefinition-xml-no-order")) {
-        boolean ok = (ei.definition == null) || (ei.index >= last) || isXmlAttr;
+        boolean ok = (ei.definition == null) || (ei.index >= last) || isXmlAttr || ei.getElement().isIgnorePropertyOrder();
         rule(errors, NO_RULE_DATE, IssueType.INVALID, ei.line(), ei.col(), ei.getPath(), ok, I18nConstants.VALIDATION_VAL_PROFILE_OUTOFORDER, profile.getVersionedUrl(), ei.getName(), lastei == null ? "(null)" : lastei.getName());
       }
       if (ei.slice != null && ei.index == last && ei.slice.getSlicing().getOrdered()) {
@@ -6010,7 +6020,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
         }
         List<ValidationMessage> invErrors = null;
         // We key based on inv.expression rather than inv.key because expressions can change in derived profiles and aren't guaranteed to be consistent across profiles.
-        String key = FHIRPathExpressionFixer.fixExpr(inv.getExpression(), inv.getKey());
+        String key = FHIRPathExpressionFixer.fixExpr(inv.getExpression(), inv.getKey(), context.getVersion());
         if (!invMap.keySet().contains(key)) {
           invErrors = new ArrayList<ValidationMessage>();
           invMap.put(key, invErrors);
@@ -6064,7 +6074,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
     if (n == null) {
       long t = System.nanoTime();
       try {
-        String expr = FHIRPathExpressionFixer.fixExpr(inv.getExpression(), inv.getKey());
+        String expr = FHIRPathExpressionFixer.fixExpr(inv.getExpression(), inv.getKey(), context.getVersion());
         n = fpe.parse(expr);
       } catch (FHIRException e) {
         rule(errors, NO_RULE_DATE, IssueType.INVARIANT, element.line(), element.col(), path, false, I18nConstants.PROBLEM_PROCESSING_EXPRESSION__IN_PROFILE__PATH__, inv.getExpression(), profile.getVersionedUrl(), path, e.getMessage());
@@ -6275,7 +6285,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
               try {
                 ExpressionNode n = (ExpressionNode) inv.getUserData("validator.expression.cache");
                 if (n == null) {
-                  n = fpe.parse(FHIRPathExpressionFixer.fixExpr(inv.getExpression(), inv.getKey()));
+                  n = fpe.parse(FHIRPathExpressionFixer.fixExpr(inv.getExpression(), inv.getKey(), context.getVersion()));
                   inv.setUserData("validator.expression.cache", n);
                 }
                 fpe.check(null, sd.getKind() == StructureDefinitionKind.RESOURCE ? sd.getType() : "DomainResource", ed.getPath(), n);

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

@@ -0,0 +1,958 @@
+package org.hl7.fhir.validation.instance.type;
+
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.List;
+
+import org.hl7.fhir.r5.conformance.profile.ProfileUtilities;
+import org.hl7.fhir.r5.context.ContextUtilities;
+import org.hl7.fhir.r5.context.IWorkerContext;
+import org.hl7.fhir.r5.elementmodel.Element;
+import org.hl7.fhir.r5.model.Coding;
+import org.hl7.fhir.r5.model.ElementDefinition;
+import org.hl7.fhir.r5.model.ElementDefinition.TypeRefComponent;
+import org.hl7.fhir.r5.model.StructureDefinition;
+import org.hl7.fhir.r5.model.StructureMap;
+import org.hl7.fhir.r5.model.StructureMap.StructureMapGroupComponent;
+import org.hl7.fhir.r5.model.StructureMap.StructureMapGroupInputComponent;
+import org.hl7.fhir.r5.model.StructureMap.StructureMapGroupTypeMode;
+import org.hl7.fhir.r5.model.StructureMap.StructureMapInputMode;
+import org.hl7.fhir.r5.model.StructureMap.StructureMapModelMode;
+import org.hl7.fhir.r5.model.StructureMap.StructureMapStructureComponent;
+import org.hl7.fhir.r5.model.TypeDetails;
+import org.hl7.fhir.r5.utils.FHIRPathEngine;
+import org.hl7.fhir.r5.utils.XVerExtensionManager;
+import org.hl7.fhir.r5.utils.structuremap.StructureMapUtilities;
+import org.hl7.fhir.utilities.CommaSeparatedStringBuilder;
+import org.hl7.fhir.utilities.Utilities;
+import org.hl7.fhir.utilities.i18n.I18nConstants;
+import org.hl7.fhir.utilities.validation.ValidationMessage;
+import org.hl7.fhir.utilities.validation.ValidationMessage.IssueType;
+import org.hl7.fhir.utilities.validation.ValidationMessage.Source;
+import org.hl7.fhir.validation.BaseValidator;
+import org.hl7.fhir.validation.TimeTracker;
+import org.hl7.fhir.validation.instance.utils.NodeStack;
+
+public class StructureMapValidator extends BaseValidator {
+
+  public class ElementDefinitionSource {
+    private StructureDefinition sd;
+    private ElementDefinition ed;
+    protected ElementDefinitionSource(StructureDefinition sd, ElementDefinition ed) {
+      super();
+      this.sd = sd;
+      this.ed = ed;
+    }
+    public StructureDefinition getSd() {
+      return sd;
+    }
+    public ElementDefinition getEd() {
+      return ed;
+    }
+    
+  }
+
+  public class RuleInformation {
+
+    int maxCount = 1;
+    String defVariable;
+    
+    public void seeCardinality(int max) {
+      if (max == Integer.MAX_VALUE || maxCount == Integer.MAX_VALUE) {
+        maxCount = Integer.MAX_VALUE;
+      } else {
+        maxCount = maxCount * max;
+      }      
+    }
+
+    public boolean isList() {
+      return maxCount > 1;
+    }
+
+    public int getMaxCount() {
+      return maxCount;
+    }
+
+    public String getDefVariable() {
+      return defVariable;
+    }
+
+    public void setDefVariable(String defVariable) {
+      this.defVariable = defVariable;
+    }
+  }
+
+  public class VariableDefn {
+
+    private String name;
+    private String mode;
+    private int max;
+    private StructureDefinition sd;
+    private ElementDefinition ed;
+    private String type;
+    
+    
+    protected VariableDefn(String name, String mode) {
+      super();
+      this.name = name;
+      this.mode = mode;
+    }
+
+    public VariableDefn setType(int max, StructureDefinition sd, ElementDefinition ed, String type) {
+      this.max = max;
+      this.sd = sd;
+      this.ed = ed;
+      this.type = type;
+      return this;
+    }
+
+    public String getName() {
+      return name;
+    }
+
+    public String getMode() {
+      return mode;
+    }
+
+    public VariableDefn copy() {
+      VariableDefn n = new VariableDefn(name, mode);
+      n.max = max;
+      n.sd = sd;
+      n.ed = ed;
+      n.type = type;
+      return n;
+    }
+
+    public boolean hasTypeInfo() {
+      return sd != null;
+    }
+
+    public int getMax() {
+      return max;
+    }
+
+    public StructureDefinition getSd() {
+      return sd;
+    }
+
+    public ElementDefinition getEd() {
+      return ed;
+    }
+
+    public String getType() {
+      return type;
+    }
+
+    public void setType(String type) {
+      this.type = type;
+    }
+
+    public String getWorkingType() {
+      if (type != null) {
+        return type;
+      }
+      if (ed != null && ed.getType().size() == 1) {
+        return ed.getType().get(0).getWorkingCode();
+      }
+      return null;
+    }
+
+  }
+
+  public class VariableSet {
+
+    private List<VariableDefn> list = new ArrayList<>();
+    
+    public boolean hasVariable(String name) {
+      for (VariableDefn v : list) {
+        if (name.equals(v.getName())) {
+          return true;
+        }
+      }
+      return false;
+    }
+
+    public boolean hasVariable(String name, boolean source) {
+      for (VariableDefn v : list) {
+        if (name.equals(v.getName()) && source == ("source".equals(v.getMode()))) {
+          return true;
+        }
+      }
+      return false;
+    }
+
+    public VariableDefn add(String name, String mode) {
+      list.removeIf(item -> item.getName().equals(name) && item.getMode().equals(mode));
+      VariableDefn v = new VariableDefn(name, mode);
+      list.add(v);
+      return v;
+    }
+//
+//    public void add(VariableDefn v) {
+//      list.removeIf(item -> item.getName().equals(v.getName()) && item.getMode().equals(v.getMode()));
+//      list.add(v);      
+//    }
+//    
+    public VariableSet copy() {
+      VariableSet set = new VariableSet();
+      for (VariableDefn v : list) {
+        set.list.add(v.copy());
+      }
+      return set;
+    }
+
+    public VariableDefn getVariable(String name, boolean source) {
+      for (VariableDefn v : list) {
+        if (name.equals(v.getName()) && source == ("source".equals(v.getMode()))) {
+          return v;
+        }
+      }
+      return null;
+    }
+
+    public void add(String pname, VariableDefn v) {
+      VariableDefn vn = v.copy();
+      vn.name = pname;
+      list.add(vn);
+    }
+  }
+
+  private static final boolean SOURCE = true;
+  private static final boolean TARGET = false;
+
+  private FHIRPathEngine fpe;
+  private ProfileUtilities profileUtilities;
+  private ContextUtilities cu;
+  private List<StructureMap> imports = new ArrayList<>();
+
+  public StructureMapValidator(IWorkerContext context, TimeTracker timeTracker, FHIRPathEngine fpe, XVerExtensionManager xverManager, ProfileUtilities profileUtilities, Coding jurisdiction) {
+    super(context, xverManager);
+    source = Source.InstanceValidator;
+    this.fpe = fpe;
+    this.timeTracker = timeTracker;
+    this.jurisdiction = jurisdiction;
+    this.profileUtilities = profileUtilities;
+    this.cu = new ContextUtilities(context);
+
+  }
+  
+  public boolean validateStructureMap(List<ValidationMessage> errors, Element src, NodeStack stack)  {
+    boolean ok = true;
+    List<Element> imports = src.getChildrenByName("import");
+    int cc = 0;
+    for (Element import_ : imports) {
+      ok = validateImport(errors, src, import_, stack.push(import_, cc, null, null)) && ok;
+      cc++;
+    }
+    
+    List<Element> groups = src.getChildrenByName("group");
+    // we iterate the groups repeatedly, validating them if they have stated types or found types, until nothing happens
+    boolean fired = false;
+    do {
+      fired = false;
+      cc = 0;
+      for (Element group : groups) {
+        if (!group.hasUserData("structuremap.validated")) {
+          if (hasInputTypes(group) || group.hasUserData("structuremap.parameters")) {
+            group.setUserData("structuremap.validated", true);
+            fired = true;
+            ok = validateGroup(errors, src, group, stack.push(group, cc, null, null)) && ok;
+          }
+        }
+        cc++;
+      }            
+    } while (fired);
+    
+    cc = 0;
+    for (Element group : groups) {
+      if (!group.hasUserData("structuremap.validated")) {
+        hint(errors, "2023-03-01", IssueType.INFORMATIONAL, group.line(), group.col(), stack.getLiteralPath(), ok, I18nConstants.SM_ORPHAN_GROUP);
+        ok = validateGroup(errors, src, group, stack.push(group, cc, null, null)) && ok;
+      }
+      cc++;
+    }            
+    return ok;
+  }
+
+  private boolean hasInputTypes(Element group) {
+    List<Element> inputs = group.getChildrenByName("input");
+    for (Element input : inputs) {
+      if (!input.hasChild("type")) {
+        return false;
+      }
+    }
+    return true;
+  }
+
+  private boolean validateImport(List<ValidationMessage> errors, Element src, Element import_, NodeStack stack) {
+    String url = import_.primitiveValue();
+    boolean ok = false;
+    StructureMap map = context.fetchResource(StructureMap.class, url);
+    if (map != null) {
+      imports.add(map);
+      ok = true;
+    } else if (url.contains("*")) {
+      List<StructureMap> maps = cu.listMaps(url);
+      ok = !maps.isEmpty();
+      imports.addAll(maps);
+    }
+    warning(errors, "2023-03-01", IssueType.INVALID, import_.line(), import_.col(), stack.getLiteralPath(), ok, I18nConstants.SM_IMPORT_NOT_FOUND, url);
+    return true;
+  }
+
+  private boolean validateGroup(List<ValidationMessage> errors, Element src, Element group, NodeStack stack) {
+    String name = group.getChildValue("name");
+    boolean ok = rule(errors, "2023-03-01", IssueType.INVALID, group.line(), group.col(), stack.getLiteralPath(), idIsValid(name), I18nConstants.SM_NAME_INVALID, name);
+    
+    Element extend = group.getNamedChild("extends");
+    if (extend != null) {
+      StructureMapGroupComponent grp = resolveGroup(extend.primitiveValue(), src);
+      if (rule(errors, "2023-03-01", IssueType.NOTSUPPORTED, extend.line(), extend.col(), stack.push(extend, -1, null, null).getLiteralPath(), grp != null, I18nConstants.SM_RULEGROUP_NOT_FOUND, extend.primitiveValue())) {
+        // check inputs 
+      } else {
+        ok = false;
+      }
+    }
+    
+    VariableSet variables = new VariableSet(); 
+    VariableSet pvars = (VariableSet) group.getUserData("structuremap.parameters");
+
+    // first, load all the inputs
+    List<Element> inputs = group.getChildrenByName("input");
+    List<Element> structures = src.getChildrenByName("structure");
+    int cc = 0;
+    for (Element input : inputs) {
+      ok = validateInput(errors, src, group, input, stack.push(input, cc, null, null), structures, variables, pvars) && ok;
+      cc++;
+    }      
+    
+    // now check the rules.  
+    List<Element> rules = group.getChildrenByName("rule");
+    cc = 0;
+    for (Element rule : rules) {
+      ok = validateRule(errors, src, group, rule, stack.push(rule, cc, null, null), variables) && ok;
+      cc++;
+    }              
+    
+    return ok;
+  }
+
+  private StructureMapGroupComponent resolveGroup(String grpName, Element src) {
+    if (grpName == null) {
+      return null;
+    }
+    List<Element> groups = src.getChildrenByName("group");
+    for (Element group : groups) {
+      String name = group.getChildValue("name");
+      if (grpName.equals(name)) {
+        return makeGroupComponent(group);
+      }
+    }  
+    for (StructureMap map : imports) {
+      for (StructureMapGroupComponent grp : map.getGroup()) {
+        if (grpName.equals(grp.getName())) {
+          return grp;
+        }
+      }
+    }
+    return null;
+  }
+
+  private StructureMapGroupComponent makeGroupComponent(Element group) {
+    StructureMapGroupComponent grp = new StructureMapGroupComponent();
+    grp.setUserData("element.source", group);
+    grp.setName(group.getChildValue("name"));
+    List<Element> inputs = group.getChildrenByName("input");
+    for (Element input : inputs) {
+      StructureMapGroupInputComponent inp = grp.addInput();
+      inp.setName(input.getChildValue("name"));
+      inp.setType(input.getChildValue("type"));
+      try {
+        inp.setMode(StructureMapInputMode.fromCode(input.getChildValue("mode")));
+      } catch (Exception e) {
+        // nothing; will be an error elsewhere
+      }
+    }
+    return grp;
+  }
+
+  private boolean validateInput(List<ValidationMessage> errors, Element src, Element group, Element input, NodeStack stack, List<Element> structures, VariableSet variables, VariableSet pvars) {
+    boolean ok = false;
+    String name = input.getChildValue("name"); 
+    String mode = input.getChildValue("mode"); 
+    String type = input.getChildValue("type");
+    VariableDefn pv = null;
+    if (type == null && pvars != null) {
+      pv = pvars.getVariable(name, mode.equals("source"));
+      if (pv != null) {
+        type = pv.getWorkingType();
+      }
+    }
+
+    if (rule(errors, "2023-03-01", IssueType.NOTSUPPORTED, input.line(), input.col(), stack.getLiteralPath(), idIsValid(name), I18nConstants.SM_NAME_INVALID, name) &&  // the name {0} is not valid)
+        rule(errors, "2023-03-01", IssueType.DUPLICATE, input.line(), input.col(), stack.getLiteralPath(), !variables.hasVariable(name), I18nConstants.SM_GROUP_INPUT_DUPLICATE, name)) {  // the name {0} is not valid)      
+      VariableDefn v = variables.add(name, mode);
+      if (rule(errors, "2023-03-01", IssueType.INVALID, input.line(), input.col(), stack.getLiteralPath(), Utilities.existsInList(mode, "source", "target"), I18nConstants.SM_GROUP_INPUT_MODE_INVALID, name, mode) && // the group parameter {0} mode {1} isn't valid
+          warning(errors, "2023-03-01", IssueType.NOTSUPPORTED, input.line(), input.col(), stack.getLiteralPath(), type != null, I18nConstants.SM_GROUP_INPUT_NO_TYPE, name)) { // the group parameter {0} has no type, so the paths cannot be validated
+        String smode = null;
+        StructureDefinition sd = null;
+        ElementDefinition ed = null;
+        if (pv != null) {
+          sd = pv.getSd();
+          ed = pv.getEd();
+        } else {
+          Element structure = findStructure(structures, type);
+          if (structure != null) {
+            smode = structure.getChildValue("mode");
+            String url = structure.getChildValue("url");
+            sd = context.fetchResource(StructureDefinition.class, url);
+            if (sd == null) {              
+              rule(errors, "2023-03-01", IssueType.INVALID, input.line(), input.col(), stack.getLiteralPath(), sd != null, I18nConstants.SM_GROUP_INPUT_TYPE_UNKNOWN_STRUCTURE, type, url);
+            }
+          } else if (type != null) {
+            sd = context.fetchTypeDefinition(type);
+            if (sd == null) {              
+              rule(errors, "2023-03-01", IssueType.INVALID, input.line(), input.col(), stack.getLiteralPath(), sd != null, I18nConstants.SM_GROUP_INPUT_TYPE_UNKNOWN_TYPE, type);
+            }
+          } else {
+            rule(errors, "2023-03-01", IssueType.NOTSUPPORTED, input.line(), input.col(), stack.getLiteralPath(), structure != null, I18nConstants.SM_GROUP_INPUT_TYPE_NOT_DECLARED, type);
+            ok = false;
+          }
+          if (sd != null) {
+            ed = sd.getSnapshot().getElementFirstRep();
+          }
+        }
+        if (rule(errors, "2023-03-01", IssueType.NOTSUPPORTED, input.line(), input.col(), stack.getLiteralPath(), smode == null || mode.equals(smode), I18nConstants.SM_GROUP_INPUT_MODE_MISMATCH, type, mode, smode)) { // the type {0} has mode {1} which doesn't match the structure definition {2}
+          v.setType(1, sd, ed, null);
+          ok = true;
+        }
+      }
+    }
+    return ok;
+  }
+
+  private Element findStructure(List<Element> structures, String type) {
+    for (Element structure : structures ) {
+      String t = structure.getChildValue("alias");
+      if (type.equals(t)) {
+        return structure;
+      }
+    }
+    return null;
+  }
+
+  private boolean idIsValid(String name) {
+    return name != null && name.matches("[a-zA-Z][a-zA-Z0-9]*");
+  }
+
+  private boolean validateRule(List<ValidationMessage> errors, Element src, Element group, Element rule, NodeStack stack, VariableSet variables) {
+    String name = rule.getChildValue("name");
+    boolean ok = rule(errors, "2023-03-01", IssueType.INVALID, rule.line(), rule.col(), stack.getLiteralPath(), idIsValid(name), I18nConstants.SM_NAME_INVALID, name);
+    
+    RuleInformation ruleInfo = new RuleInformation();
+    // process the sources
+    VariableSet lvars = variables.copy();
+    List<Element> sources = rule.getChildrenByName("source");
+    int cc = 0;
+    for (Element source : sources) {
+      ok = validateRuleSource(errors, src, group, rule, source, stack.push(source, cc, null, null), lvars, ruleInfo, cc) && ok;
+      cc++;
+    }
+    // process the targets
+    List<Element> targets = rule.getChildrenByName("target");
+    cc = 0;
+    for (Element target : targets) {
+      ok = validateRuleTarget(errors, src, group, rule, target, stack.push(target, cc, null, null), lvars, ruleInfo) && ok;
+      cc++;
+    }
+    
+    // process the targets
+    List<Element> rules = rule.getChildrenByName("rule");
+    cc = 0;
+    for (Element child : rules) {
+      ok = validateRule(errors, src, group, child, stack.push(child, cc, null, null), lvars) && ok;
+      cc++;
+    }
+    // todo: check dependents
+    List<Element> dependents = rule.getChildrenByName("dependent");
+    cc = 0;
+    for (Element dependent : dependents) {
+      ok = validateDependent(errors, src, group, dependent, stack.push(dependent, cc, null, null), lvars) && ok;
+      cc++;
+    }
+    return ok;
+  }
+
+  private boolean validateRuleSource(List<ValidationMessage> errors, Element src, Element group, Element rule, Element source, NodeStack stack, VariableSet variables, RuleInformation ruleInfo, int loopCounter) {
+    String context = source.getChildValue("context");
+    if (loopCounter > 0) {
+      ruleInfo.setDefVariable(null);
+    }
+    boolean ok = rule(errors, "2023-03-01", IssueType.INVALID, source.line(), source.col(), stack.getLiteralPath(), idIsValid(context), I18nConstants.SM_NAME_INVALID, context) &&
+        rule(errors, "2023-03-01", IssueType.UNKNOWN, source.line(), source.col(), stack.getLiteralPath(), variables.hasVariable(context, SOURCE), I18nConstants.SM_SOURCE_CONTEXT_UNKNOWN, context);
+    if (ok) {
+      VariableDefn v = variables.getVariable(context, SOURCE);
+      if (v.hasTypeInfo()) { // if it doesn't, that's already an issue elsewhere 
+        // check type
+        // check defaultValue
+        // check element
+        String element = source.getChildValue("element");
+        if (element != null) {
+          String path = v.getEd().getPath()+"."+element;
+          String variable = source.getChildValue("variable");
+          VariableDefn vn = null;
+          if (hint(errors, "2023-03-01", IssueType.INVALID, source.line(), source.col(), stack.getLiteralPath(), variable != null, I18nConstants.SM_RULE_SOURCE_UNASSIGNED)) {
+            if (rule(errors, "2023-03-01", IssueType.INVALID, source.line(), source.col(), stack.getLiteralPath(), idIsValid(variable), I18nConstants.SM_NAME_INVALID, variable)) {
+              vn = variables.add(variable, v.getMode()); // may overwrite
+              if (loopCounter == 0) {
+                ruleInfo.setDefVariable(variable);
+              }
+            } else {
+              ok = false;
+            }
+          }            
+          
+          List<ElementDefinitionSource> els = getElementDefinitions(v.getSd(), v.getEd(), v.getType(), element);
+          if (rule(errors, "2023-03-01", IssueType.INVALID, source.line(), source.col(), stack.getLiteralPath(), !els.isEmpty(), I18nConstants.SM_SOURCE_PATH_INVALID, context, element, path)) {
+            if (warning(errors, "2023-03-01", IssueType.INVALID, source.line(), source.col(), stack.getLiteralPath(), els.size() == 1, I18nConstants.SM_TARGET_PATH_MULTIPLE_MATCHES, context, element, v.getEd().getPath()+"."+element, render(els))) {
+              ElementDefinitionSource el = els.get(0);
+              String type = source.getChildValue("type"); 
+              if (type != null) {
+                ok = rule(errors, "2023-03-01", IssueType.INVALID, source.line(), source.col(), stack.getLiteralPath(), hasType(el.getEd(), type), I18nConstants.SM_SOURCE_TYPE_INVALID, type, path, el.getEd().typeSummary()) && ok;
+              }
+              String min = source.getChildValue("min");
+              hint(errors, "2023-03-01", IssueType.INVALID, source.line(), source.col(), stack.getLiteralPath(), min == null || isMoreOrEqual(min, v.getEd().getMin()), I18nConstants.SM_RULE_SOURCE_MIN_REDUNDANT, min, v.getEd().getMin());
+
+              int existingMax = multiplyCardinality(v.getMax(), el.getEd().getMax());
+              String max = source.getChildValue("max");
+              int iMax = readMax(max, existingMax);
+              warning(errors, "2023-03-01", IssueType.INVALID, source.line(), source.col(), stack.getLiteralPath(), iMax <= existingMax, I18nConstants.SM_RULE_SOURCE_MAX_REDUNDANT, max, v.getMax());
+              ruleInfo.seeCardinality(iMax);
+
+
+              if (vn != null) {
+                vn.setType(iMax, el.getSd(), el.getEd(), type); // may overwrite
+              }
+            }
+          } else {
+            ok = false;
+          }
+        }
+        // check condition
+        // check check
+      }
+    }
+    return ok;
+  }
+
+  private boolean hasType(ElementDefinition ed, String type) {
+    for (TypeRefComponent td : ed.getType()) {
+      if (type.equals(td.getWorkingCode())) {
+        return true;
+      }
+    }
+    return false;
+  }
+
+  private int readMax(String max, int existingMax) {
+    if (max == null || !Utilities.isInteger(max)) {
+      return existingMax;
+    } else {
+      return Integer.parseInt(max);
+    }
+  }
+
+  private int multiplyCardinality(int max, String max2) {
+    if (max == Integer.MAX_VALUE || "*".equals(max2)) {
+      return Integer.MAX_VALUE;
+    } else {
+      return max * Integer.parseInt(max2);
+    }
+  }
+
+  private boolean validateRuleTarget(List<ValidationMessage> errors, Element src, Element group, Element rule, Element target, NodeStack stack, VariableSet variables, RuleInformation ruleInfo) {
+    String context = target.getChildValue("context");
+    if (context == null) {
+      return true;
+    }
+    boolean ok = rule(errors, "2023-03-01", IssueType.INVALID, target.line(), target.col(), stack.getLiteralPath(), idIsValid(context), I18nConstants.SM_NAME_INVALID, context) &&
+        rule(errors, "2023-03-01", IssueType.UNKNOWN, target.line(), target.col(), stack.getLiteralPath(), variables.hasVariable(context, TARGET), I18nConstants.SM_TARGET_CONTEXT_UNKNOWN, context);
+    if (ok) {
+      VariableDefn v = variables.getVariable(context, TARGET);
+      if (v.hasTypeInfo()) {
+        String listMode = target.getChildValue("listMode");
+        String listRuleId = target.getChildValue("listRuleId");
+        warning(errors, "2023-03-01", IssueType.INVALID, target.line(), target.col(), stack.getLiteralPath(), listRuleId == null || "share".equals(listMode), I18nConstants.SM_LIST_RULE_ID_ONLY_WHEN_SHARE);
+        if (!ruleInfo.isList()) {
+          warning(errors, "2023-03-01", IssueType.INVALID, target.line(), target.col(), stack.getLiteralPath(), listMode == null, I18nConstants.SM_NO_LIST_MODE_NEEDED);
+          warning(errors, "2023-03-01", IssueType.INVALID, target.line(), target.col(), stack.getLiteralPath(), listRuleId == null, I18nConstants.SM_NO_LIST_RULE_ID_NEEDED);
+        }
+        VariableDefn vn = null;
+        String variable = target.getChildValue("variable");
+        if (variable != null) {
+          if (rule(errors, "2023-03-01", IssueType.INVALID, target.line(), target.col(), stack.getLiteralPath(), idIsValid(variable), I18nConstants.SM_NAME_INVALID, variable)) {
+            vn = variables.add(variable, v.getMode()); // may overwrite
+          } else {
+            ok = false;
+          }
+        }
+
+        String element = target.getChildValue("element");
+        if (element != null) {
+          List<ElementDefinitionSource> els = getElementDefinitions(v.getSd(), v.getEd(), v.getType(), element);
+          if (rule(errors, "2023-03-01", IssueType.INVALID, target.line(), target.col(), stack.getLiteralPath(), !els.isEmpty(), I18nConstants.SM_TARGET_PATH_INVALID, context, element, v.getEd().getPath()+"."+element)) {
+            if (warning(errors, "2023-03-01", IssueType.INVALID, target.line(), target.col(), stack.getLiteralPath(), els.size() == 1, I18nConstants.SM_TARGET_PATH_MULTIPLE_MATCHES, context, element, v.getEd().getPath()+"."+element, render(els))) {
+              ElementDefinitionSource el = els.get(0);
+              String transform = target.getChildValue("transform");
+              List<Element> params = target.getChildren("parameter");
+              if (transform == null) {
+                transform = "create"; // implied
+                rule(errors, "2023-03-01", IssueType.INVALID, target.line(), target.col(), stack.getLiteralPath(), params.size() == 0, I18nConstants.SM_TARGET_NO_TRANSFORM_NO_CHECKED, transform);
+              } 
+              // List<String> types = listTypes(el.getEd().getType());
+              String type = null;
+              if (el.getEd().getType().size() == 1) {
+                type = el.getEd().getTypeFirstRep().getWorkingCode();
+              } else {                  
+                type = inferType(ruleInfo, variables, rule, transform, params);
+              }
+
+              switch (transform) {
+              case "create":
+                if (rule(errors, "2023-03-01", IssueType.INVALID, target.line(), target.col(), stack.getLiteralPath(), params.size() < 2, I18nConstants.SM_TARGET_TRANSFORM_PARAM_COUNT_RANGE, "create", "0", "1", params.size())) {
+                  if (params.size() == 1) {
+                    type = params.get(0).getChildValue("value");
+                    warning(errors, "2023-03-01", IssueType.INVALID, target.line(), target.col(), stack.getLiteralPath(),type != null, I18nConstants.SM_TARGET_TRANSFORM_TYPE_UNPROCESSIBLE);
+                  } else {
+                    // maybe can guess? maybe not ... type = 
+                  }
+                } else {
+                  ok = false;
+                }
+                break;
+              case "copy": // logic is the same as create?
+                if (rule(errors, "2023-03-01", IssueType.INVALID, target.line(), target.col(), stack.getLiteralPath(), params.size() < 2, I18nConstants.SM_TARGET_TRANSFORM_PARAM_COUNT_RANGE, "create", "0", "1", params.size())) {
+                  if (params.size() == 1) {
+                    type = params.get(0).getChildValue("value");
+                    warning(errors, "2023-03-01", IssueType.INVALID, target.line(), target.col(), stack.getLiteralPath(),type != null, I18nConstants.SM_TARGET_TRANSFORM_TYPE_UNPROCESSIBLE);
+                  } else {
+                    // maybe can guess? maybe not ... type = 
+                  }
+                } else {
+                  ok = false;
+                }
+                break;
+              case "reference":
+                if (rule(errors, "2023-03-01", IssueType.INVALID, target.line(), target.col(), stack.getLiteralPath(), params.size() == 1, I18nConstants.SM_TARGET_TRANSFORM_PARAM_COUNT_RANGE, "reference", "0", "1", params.size())) {
+                  type = "string";
+                } else {
+                  ok = false;
+                }
+                break;
+              case "evaluate":
+                if (rule(errors, "2023-03-01", IssueType.INVALID, target.line(), target.col(), stack.getLiteralPath(), params.size() == 1, I18nConstants.SM_TARGET_TRANSFORM_PARAM_COUNT_SINGLE, "evaluate", "1", params.size())) {
+                  String exp = params.get(0).getChildValue("value");
+                  if (rule(errors, "2023-03-01", IssueType.INVALID, params.get(0).line(), params.get(0).col(), stack.getLiteralPath(), exp != null, I18nConstants.SM_TARGET_TRANSFORM_PARAM_UNPROCESSIBLE, "0", params.size())) {
+                    try {
+                      TypeDetails td = fpe.check(null, v.getSd().getType(), v.getEd().getPath(), fpe.parse(exp));
+                      if (td.getTypes().size() == 1) {
+                        type = td.getType();
+                      }
+                    } catch (Exception e) {
+                      rule(errors, "2023-03-01", IssueType.INVALID, params.get(0).line(), params.get(0).col(), stack.getLiteralPath(), false, I18nConstants.SM_TARGET_TRANSFORM_EXPRESSION_ERROR, e.getMessage());
+                    }
+                  } else {
+                    ok = false;
+                  }
+                } else {
+                  ok = false;
+                }
+                break;
+              default:
+                rule(errors, "2023-03-01", IssueType.INVALID, target.line(), target.col(), stack.getLiteralPath(), false, I18nConstants.SM_TARGET_TRANSFORM_NOT_CHECKED, transform);
+                ok = false;
+              }
+              if (vn != null) {
+                // it's just a warning: maybe this'll work out at run time?
+                warning(errors, "2023-03-01", IssueType.INVALID, target.line(), target.col(), stack.getLiteralPath(), type != null, I18nConstants.SM_TARGET_TYPE_MULTIPLE_POSSIBLE, el.getEd().typeSummary());
+
+                vn.setType(ruleInfo.getMaxCount(), el.getSd(), el.getEd(), type); // may overwrite
+              }
+
+            }
+          } else {
+            ok = false;
+          }
+        }
+        //      
+      }
+    }
+    return ok;
+  }
+
+  private String inferType(RuleInformation ruleInfo, VariableSet variables, Element rule, String transform, List<Element> params) {
+    // under some special conditions, we can infer what the type will be:
+    //  * there's a nominated default variable 
+    //  * that variable has as single type
+    //  * there's a create with no param
+    //  * there's a single dependent rule with name = StructureMapUtilities.DEF_GROUP_NAME
+    //  * there's a default type group for the type of the source type
+    // otherwise, we can't know the target type. 
+    
+    if (ruleInfo.getDefVariable() != null && "create".equals(transform) && params.isEmpty()) {
+      VariableDefn v = variables.getVariable(ruleInfo.getDefVariable(), SOURCE);
+      if (v != null && (v.getEd().getType().size() == 1 || v.getType() != null)) {
+        List<Element> dependents = rule.getChildrenByName("dependent");
+        if (dependents.size() == 1 && StructureMapUtilities.DEF_GROUP_NAME.equals(dependents.get(0).getChildValue("name"))) {
+          String type = v.getType() != null ? v.getType() : v.getEd().getTypeFirstRep().getWorkingCode();
+          // now, we look for a default group.
+          // todo: look in this source
+          // now look through the inputs
+          for (StructureMap map : imports) {
+            for (StructureMapGroupComponent grp : map.getGroup()) {
+              if (grp.getTypeMode() == StructureMapGroupTypeMode.TYPEANDTYPES && grp.getInput().size() == 2) {
+                String grpType = getTypeForGroupInput(map, grp, grp.getInput().get(0));
+                if (sameTypes(type, grpType)) {
+                  String tgtType = getTypeForGroupInput(map, grp, grp.getInput().get(1));
+                  if (tgtType != null) {
+                    return tgtType;
+                  }
+                }
+              }
+            }
+          }
+        }
+      }
+    }
+    return null;
+  }
+
+  private boolean sameTypes(String type1, String type2) {
+    if (type1 == null || type2 == null) {
+      return false;
+    }
+    if (!Utilities.isAbsoluteUrl(type1)) {
+      type1 = "http://hl7.org/fhir/StructureDefinition/"+type1;
+    }
+    if (!Utilities.isAbsoluteUrl(type2)) {
+      type2 = "http://hl7.org/fhir/StructureDefinition/"+type2;
+    }
+    return type1.equals(type2);
+  }
+
+  private String getTypeForGroupInput(StructureMap map, StructureMapGroupComponent grp,  StructureMapGroupInputComponent input) {
+    String type = input.getType();
+    StructureMapModelMode mode = input.getMode() == StructureMapInputMode.SOURCE ? StructureMapModelMode.SOURCE : StructureMapModelMode.TARGET;
+    if (input == null) {
+      return null;
+    }
+    for (StructureMapStructureComponent st : map.getStructure()) {
+      if (type.equals(st.getAlias()) && mode == st.getMode()) {
+        return st.getUrl();
+      }
+    }
+    return type;
+  }
+
+  private List<String> listTypes(List<TypeRefComponent> types) {
+    List<String> res = new ArrayList<>();
+    for (TypeRefComponent td : types) {
+      res.add(td.getWorkingCode());
+    }
+    Collections.sort(res);
+    return res;
+  }
+
+  private String render(List<ElementDefinitionSource> list) {
+    CommaSeparatedStringBuilder b = new CommaSeparatedStringBuilder();
+    for (ElementDefinitionSource t : list) {
+      b.append(t.getEd().getId());
+    }
+    return b.toString();
+  }
+
+  private List<ElementDefinitionSource> getElementDefinitions(StructureDefinition sd, ElementDefinition ed, String type, String element) {
+    List<ElementDefinitionSource> result = new ArrayList<>();
+    List<ElementDefinition> children = profileUtilities.getChildList(sd, ed);
+    if (children == null || children.isEmpty()) {
+      getElementDefinitionChildrenFromTypes(result, sd, ed, type, element);
+    } else {
+      for (ElementDefinition t : children) {
+        if (t.getNameBase().equals(element)) {
+          result.add(new ElementDefinitionSource(sd, t));
+        }
+      }
+    }
+    return result;
+  }
+
+  private void getElementDefinitionChildrenFromTypes(List<ElementDefinitionSource> result, StructureDefinition sd, ElementDefinition ed, String type, String element) {
+    for (TypeRefComponent td : ed.getType()) {
+      if (type == null | td.getWorkingCode().equals(type)) {
+        StructureDefinition tsd = context.fetchTypeDefinition(td.getWorkingCode());
+        if (tsd != null) {
+          for (ElementDefinition t : tsd.getSnapshot().getElement()) {
+            if (Utilities.charCount(t.getPath(), '.') == 1 && t.getNameBase().equals(element)) {
+              result.add(new ElementDefinitionSource(tsd, t));
+            }
+          }
+        } else {
+          System.out.println("Unable to find type "+type);
+        }
+      }
+    }    
+  }
+
+  private boolean isLessOrEqual(String value, String limit) {
+    if (Utilities.isInteger(value) || !Utilities.isInteger(limit)) {
+      int v = Integer.parseInt(value);
+      int l = Integer.parseInt(limit);
+      return v <= l;
+    }
+    return true; // no issue in this case
+  }
+
+  private boolean isMoreOrEqual(String value, int limit) {
+    if (Utilities.isInteger(value)) {
+      int v = Integer.parseInt(value);
+      return v >= limit;
+    }
+    return true; // no issue in this case
+  }
+
+
+  private boolean validateDependent(List<ValidationMessage> errors, Element src, Element group, Element dependent, NodeStack stack, VariableSet variables) {
+    boolean ok = true;
+    String name = dependent.getChildValue("name");
+    if (StructureMapUtilities.DEF_GROUP_NAME.equals(name)) {
+      VariableDefn srcVar = variables.getVariable(StructureMapUtilities.AUTO_VAR_NAME, true);
+      VariableDefn tgtVar = variables.getVariable(StructureMapUtilities.AUTO_VAR_NAME, false);
+      if (srcVar != null && srcVar.hasTypeInfo() && tgtVar != null && tgtVar.hasTypeInfo()) {
+        String srcType = srcVar.getWorkingType();
+        String tgtType = tgtVar.getWorkingType();
+        if (rule(errors, "2023-03-01", IssueType.NOTFOUND, dependent.line(), dependent.col(), stack.getLiteralPath(), srcType != null, I18nConstants.SM_SOURCE_TYPE_NOT_FOUND) &&
+            rule(errors, "2023-03-01", IssueType.NOTFOUND, dependent.line(), dependent.col(), stack.getLiteralPath(), tgtType != null, I18nConstants.SM_TARGET_TYPE_NOT_FOUND)) {
+          StructureMapGroupComponent grp = findDefaultGroup(src, srcType, tgtType);
+          ok = rule(errors, "2023-03-01", IssueType.NOTFOUND, dependent.line(), dependent.col(), stack.getLiteralPath(), grp != null, I18nConstants.SM_MATCHING_RULEGROUP_NOT_FOUND, srcType, tgtType) && ok;
+        } else {
+          ok = false;
+        }      
+      }
+    } else {
+      StructureMapGroupComponent grp = resolveGroup(name, src);
+      if (rule(errors, "2023-03-01", IssueType.NOTFOUND, dependent.line(), dependent.col(), stack.getLiteralPath(), grp != null, I18nConstants.SM_RULEGROUP_NOT_FOUND, name)) {
+        List<Element> params = dependent.getChildren("parameter");
+        if (rule(errors, "2023-03-01", IssueType.INVALID, dependent.line(), dependent.col(), stack.getLiteralPath(), params.size() == grp.getInput().size(), I18nConstants.SM_RULEGROUP_NOT_FOUND, params.size(), grp.getInput().size())) {
+          VariableSet lvars = new VariableSet();
+          int cc = 0;
+          for (Element param : params) {
+            NodeStack pstack = stack.push(param, cc, null, null);
+            StructureMapGroupInputComponent input = grp.getInput().get(cc);
+            String pname = input.getName();
+            VariableDefn v = getParameter(errors, param, pstack, variables, input.getMode());
+            if (v != null) {
+              if (rule(errors, "2023-03-01", IssueType.INVALID, param.line(), param.col(), pstack.getLiteralPath(), v.mode.equals(input.getMode().toCode()), I18nConstants.SM_DEPENDENT_PARAM_MODE_MISMATCH, param.getChildValue("name"), v.mode, input.getMode().toCode()) &&
+                rule(errors, "2023-03-01", IssueType.INVALID, param.line(), param.col(), pstack.getLiteralPath(), typesMatch(v, input.getType()), I18nConstants.SM_DEPENDENT_PARAM_TYPE_MISMATCH, param.getChildValue("name"), v, input.getType())) {
+                lvars.add(pname, v);  
+              } else {
+                ok = false;
+              }
+            } else {
+              ok = false;
+            }
+            cc++;
+          }
+          if (ok && grp.hasUserData("element.source")) {
+            Element g = (Element) grp.getUserData("element.source");
+            if (g.hasUserData("structuremap.parameters")) {
+              throw new Error("bang! - this situation is not handled");
+            } else {
+              g.setUserData("structuremap.parameters", lvars);
+            }
+          }
+        }
+      } else {
+        ok = false;
+      }
+    }
+    return ok;
+  }
+
+  private StructureMapGroupComponent findDefaultGroup(Element src, String srcType, String tgtType) {    
+    List<Element> groups = src.getChildrenByName("group");
+    for (Element group : groups) {
+      if (Utilities.existsInList(group.getChildValue("typeMode"), "types", "type-and-types")) {
+        List<Element> inputs = group.getChildrenByName("input");
+        if (inputs.size() == 2 && "source".equals(inputs.get(0).getChildValue("mode")) && "source".equals(inputs.get(0).getChildValue("mode"))) {
+          String srcT = resolveInputType(src, inputs.get(0));
+          String tgtT = resolveInputType(src, inputs.get(1));
+          if (sameTypes(srcT, srcType) && sameTypes(tgtT, tgtType)) {
+            return makeGroupComponent(group);
+          }
+        }
+      }
+    }
+    for (StructureMap map : imports) {
+      for (StructureMapGroupComponent grp : map.getGroup()) {
+        if ((grp.getTypeMode() == StructureMapGroupTypeMode.TYPES || grp.getTypeMode() == StructureMapGroupTypeMode.TYPEANDTYPES) &&
+            grp.getInput().size() == 2 && grp.getInput().get(0).getMode() == StructureMapInputMode.SOURCE && grp.getInput().get(1).getMode() == StructureMapInputMode.TARGET) {
+          String srcT = resolveInputType(map, grp.getInput().get(0));
+          String tgtT = resolveInputType(map, grp.getInput().get(1));
+          if (sameTypes(srcT, srcType) && sameTypes(tgtT, tgtType)) {
+            return grp;
+          }
+        }
+      }
+    }
+    return null;
+  }
+
+
+  private String resolveInputType(StructureMap map, StructureMapGroupInputComponent input) {
+    String type = input.getType();
+    if (type == null) {
+      return null;
+    }
+    for (StructureMapStructureComponent structure : map.getStructure()) {
+      if (type.equals(structure.getAlias())) {
+        return structure.getUrl();
+      }
+    }
+    StructureDefinition sd = context.fetchTypeDefinition(type);
+    return sd == null ? null : sd.getUrl();
+  }
+
+  private String resolveInputType(Element src, Element input) {
+    String type = input.getChildValue("type");
+    if (type == null) {
+      return null;
+    }
+    for (Element structure : input.getChildren("structure")) {
+      if (type.equals(structure.getChildValue("alias"))) {
+        return structure.getChildValue("url");
+      }
+    }
+    StructureDefinition sd = context.fetchTypeDefinition(type);
+    return sd == null ? null : sd.getUrl();
+  }
+
+  private boolean typesMatch(VariableDefn v, String type) {
+    if (type == null) {
+      return true;
+    } else {
+      return false;
+    }
+  }
+
+  private VariableDefn getParameter(List<ValidationMessage> errors, Element param, NodeStack pstack, VariableSet variables, StructureMapInputMode mode) {
+    Element v = param.getNamedChild("value");
+    if (v.fhirType().equals("id")) {
+      return variables.getVariable(v.primitiveValue(), mode == StructureMapInputMode.SOURCE);
+    } else {
+      String type = v.fhirType();
+      StructureDefinition sd = context.fetchTypeDefinition(type);
+      return new VariableDefn("$", "source").setType(1, sd, sd.getSnapshot().getElementFirstRep(), null);
+    }
+  }
+
+}

org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/utils/FHIRPathExpressionFixer.java

@@ -1,16 +1,22 @@
 package org.hl7.fhir.validation.instance.utils;
 
+import org.hl7.fhir.utilities.VersionUtilities;
+
 public class FHIRPathExpressionFixer {
 
 
-  public static String fixExpr(String expr, String key) {
+  public static String fixExpr(String expr, String key, String version) {
     // this is a hack work around for past publication of wrong FHIRPath expressions
-    // R4
+
-    // waiting for 4.0.2
+    boolean r5 = VersionUtilities.isR5Ver(version);
+//    if (r5) {
+//      return expr;
+//    }
+
     //TODO is this expression below correct? @grahamegrieve
-    if ("probability is decimal implies (probability as decimal) <= 100".equals(expr)) {
+//    if ("probability is decimal implies (probability as decimal) <= 100".equals(expr)) {
-      return "probability.empty() or ((probability is decimal) implies ((probability as decimal) <= 100))";
+//      return "probability.empty() or ((probability is decimal) implies ((probability as decimal) <= 100))";
-    }
+//    }
     if ("enableWhen.count() > 2 implies enableBehavior.exists()".equals(expr)) {
       return "enableWhen.count() >= 2 implies enableBehavior.exists()";
     }
@@ -52,10 +58,10 @@ public class FHIRPathExpressionFixer {
     }  
     
     // clarification in FHIRPath spec
-    if ("eld-19".equals(key)) {
+    if (!r5 && "eld-19".equals(key)) {
       return "path.matches('^[^\\\\s\\\\.,:;\\\\\\'\"\\\\/|?!@#$%&*()\\\\[\\\\]{}]{1,64}(\\\\.[^\\\\s\\\\.,:;\\\\\\'\"\\\\/|?!@#$%&*()\\\\[\\\\]{}]{1,64}(\\\\[x\\\\])?(\\\\:[^\\\\s\\\\.]+)?)*$')";
     }
-    if ("eld-20".equals(key)) {
+    if (!r5 && "eld-20".equals(key)) {
       return "path.matches('^[A-Za-z][A-Za-z0-9]*(\\\\.[a-z][A-Za-z0-9]*(\\\\[x])?)*$')";
     }
   

org.hl7.fhir.validation/src/test/resources/txCache/org.hl7.fhir.validation/5.0.0/ucum.cache

@@ -79,3 +79,13 @@ v: {
   "system" : "http://unitsofmeasure.org"
 }
 -------------------------------------------------------------------------------------
+{"code" : {
+  "system" : "http://unitsofmeasure.org",
+  "code" : "cm"
+}, "valueSet" :null, "lang":"null", "useServer":"true", "useClient":"true", "guessSystem":"false", "valueSetMode":"ALL_CHECKS", "versionFlexible":"false"}####
+v: {
+  "display" : "cm",
+  "code" : "cm",
+  "system" : "http://unitsofmeasure.org"
+}
+-------------------------------------------------------------------------------------

pom.xml

@@ -14,7 +14,7 @@
     HAPI FHIR
     -->
     <artifactId>org.hl7.fhir.core</artifactId>
-    <version>5.6.99-SNAPSHOT</version>
+    <version>5.6.100-SNAPSHOT</version>
     <packaging>pom</packaging>
 
     <properties>
@@ -24,6 +24,7 @@
         <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>
         <jacoco_version>0.8.8</jacoco_version>
         <info_cqframework_version>1.5.1</info_cqframework_version>
         <lombok_version>1.18.22</lombok_version>
@@ -36,6 +37,7 @@
         <maven.compiler.testRelease>11</maven.compiler.testRelease>
         <maven.compiler.testSource>11</maven.compiler.testSource>
         <maven.compiler.testTarget>11</maven.compiler.testTarget>
+        <maven-jar-plugin.version>3.2.2</maven-jar-plugin.version>
     </properties>
 
     <name>HL7 Core Artifacts</name>
@@ -182,9 +184,22 @@
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-checkstyle-plugin</artifactId>
+                <executions>
+                    <execution>
+                        <phase>process-sources</phase>
+                        <goals>
+                            <goal>checkstyle</goal>
+                        </goals>
                         <configuration>
-                    <skip>true</skip>
+                            <failsOnError>true</failsOnError>
+                            <suppressionsLocation>${project.basedir}/checkstyle_suppressions.xml</suppressionsLocation>
+                            <enableRulesSummary>true</enableRulesSummary>
+                            <enableSeveritySummary>true</enableSeveritySummary>
+                            <consoleOutput>true</consoleOutput>
+                            <configLocation>${project.basedir}/../checkstyle.xml</configLocation>
                         </configuration>
+                    </execution>
+                </executions>
             </plugin>
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
@@ -228,7 +243,7 @@
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-jar-plugin</artifactId>
-                <version>3.2.0</version>
+                <version>${maven-jar-plugin.version}</version>
                 <executions>
                     <execution>
                         <goals>
@@ -415,6 +430,7 @@
                 </executions>
             </plugin>
         </plugins>
+
     </build>
 
     <profiles>

pull-request-pipeline-parameterized.yml

@@ -1,7 +1,7 @@
 jobs:
   - ${{ each image in parameters.images }}:
       - job:
-
+        dependsOn: [ 'setup' ]
         displayName: ${{image.displayName}}
         
         pool:
@@ -9,15 +9,21 @@ jobs:
         
         variables:
           currentImage: ${{image.vmImage}}
+          currentName: ${{image.displayName}}
           codecov: $(CODECOV_TOKEN)
           VERSION:
           JAVA_TOOL_OPTIONS: ${{image.javaToolOptions}}
 
         steps:
-          # Runs 'mvn clean install'
+          - task: Cache@2
+            inputs:
+              key: maven | $(Build.BuildId)
+              path: $(MAVEN_CACHE_FOLDER)
+          # Runs 'mvn install'
           - task: Maven@3
             inputs:
               mavenPomFile: 'pom.xml'
+              options: '-Dmaven.repo.local=$(MAVEN_CACHE_FOLDER)'
               mavenOptions: '-Xmx3072m'
               javaHomeOption: 'JDKVersion'
               jdkVersionOption: '${{image.jdkVersion}}'
@@ -33,7 +39,7 @@ jobs:
               javaHomeOption: 'JDKVersion'
               jdkVersionOption: '${{image.jdkVersion}}'
               jdkArchitectureOption: 'x64'
-              options: '-pl org.hl7.fhir.validation.cli'
+              options: '-pl org.hl7.fhir.validation.cli -Dmaven.repo.local=$(MAVEN_CACHE_FOLDER)'
               publishJUnitResults: false
               testResultsFiles: '**/surefire-reports/TEST-*.xml'
               goals: 'exec:exec'
@@ -41,13 +47,14 @@ jobs:
           # Upload test results to codecov
           - script: bash <(curl https://codecov.io/bash) -t $(codecov)
             displayName: 'codecov Bash Uploader'
-            condition: eq(variables.currentImage, 'ubuntu-latest')
+            condition: eq(variables.currentName, 'ubuntu-latest-java-11')
 
           # Publishes the test results to build artifacts.
           - task: PublishCodeCoverageResults@1
             displayName: 'Publish JaCoCo test results'
-            condition: eq(variables.currentImage, 'ubuntu-latest')
+            condition: eq(variables.currentName, 'ubuntu-latest-java-11')
             inputs:
               codeCoverageTool: 'JaCoCo'
               summaryFileLocation: '$(System.DefaultWorkingDirectory)/org.hl7.fhir.report/target/site/jacoco-aggregate/jacoco.xml'
               reportDirectory: '$(System.DefaultWorkingDirectory)/org.hl7.fhir.report/target/site/jacoco-aggregate/'
+

pull-request-pipeline.yml

@@ -1,3 +1,6 @@
+variables:
+  MAVEN_CACHE_FOLDER: $(Pipeline.Workspace)/.m2/repository
+
 trigger: none
 
 pr:
@@ -7,6 +10,41 @@ pr:
 # Different users have different machine setups, we run the build three times, on ubuntu, osx, and windows.
 # Azure doesn't always have the same Java versions on each system, so they are enumerated for each system independently.
 jobs:
+  - job: setup
+    displayName: cache-maven-dependencies
+    pool:
+      vmImage: ubuntu-latest
+    steps:
+      - checkout: self
+        fetchDepth: 1
+      - task: Cache@2
+        inputs:
+          key: maven | $(Build.BuildId)
+          path: $(MAVEN_CACHE_FOLDER)
+      - task: Bash@3
+        inputs:
+          targetType: 'inline'
+          script: mkdir -p $(MAVEN_CACHE_FOLDER); pwd; ls -al $(MAVEN_CACHE_FOLDER)
+      - task: Maven@3
+        inputs:
+          mavenPomFile: 'pom.xml'
+          options: '-Dmaven.repo.local=$(MAVEN_CACHE_FOLDER)'
+          mavenOptions: '-Xmx3072m'
+          javaHomeOption: 'JDKVersion'
+          jdkVersionOption: '1.11'
+          jdkArchitectureOption: 'x64'
+          publishJUnitResults: false
+          goals: 'dependency:resolve'
+      - task: Maven@3
+        inputs:
+          mavenPomFile: 'pom.xml'
+          options: '-Dmaven.repo.local=$(MAVEN_CACHE_FOLDER)'
+          mavenOptions: '-Xmx3072m'
+          javaHomeOption: 'JDKVersion'
+          jdkVersionOption: '1.11'
+          jdkArchitectureOption: 'x64'
+          publishJUnitResults: false
+          goals: 'dependency:resolve-plugins'
   - template: pull-request-pipeline-parameterized.yml
     parameters:
       images: