Merge remote-tracking branch 'origin/master'

RELEASE_NOTES.md

@@ -1,9 +1,7 @@
 ## Validator Changes
 
-* Fix FHIRPath type resolution for logical models
+* no changes
-* Update parsers to record the element format for logical model validation
-* fix profile matching for CDA logical models
 
 ## Other code changes
 
-* Upgrade PackageVisitor for XIG
+* no changes

org.hl7.fhir.convertors/pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <groupId>ca.uhn.hapi.fhir</groupId>
         <artifactId>org.hl7.fhir.core</artifactId>
-        <version>6.1.11-SNAPSHOT</version>
+        <version>6.1.13-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

org.hl7.fhir.dstu2/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>org.hl7.fhir.core</artifactId>
-		<version>6.1.11-SNAPSHOT</version>
+		<version>6.1.13-SNAPSHOT</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 

org.hl7.fhir.dstu2016may/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>org.hl7.fhir.core</artifactId>
-		<version>6.1.11-SNAPSHOT</version>
+		<version>6.1.13-SNAPSHOT</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 

org.hl7.fhir.dstu3/pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <groupId>ca.uhn.hapi.fhir</groupId>
         <artifactId>org.hl7.fhir.core</artifactId>
-        <version>6.1.11-SNAPSHOT</version>
+        <version>6.1.13-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

org.hl7.fhir.r4/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>org.hl7.fhir.core</artifactId>
-		<version>6.1.11-SNAPSHOT</version>
+		<version>6.1.13-SNAPSHOT</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 

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

@@ -10,22 +10,33 @@ import org.hl7.fhir.exceptions.FHIRException;
 import org.hl7.fhir.r4.context.SimpleWorkerContext;
 import org.hl7.fhir.r4.formats.IParser.OutputStyle;
 import org.hl7.fhir.r4.formats.JsonParser;
+<<<<<<< HEAD
 import org.hl7.fhir.r4.formats.XmlParser;
+=======
+>>>>>>> master
 import org.hl7.fhir.r4.model.Base;
 import org.hl7.fhir.r4.model.BooleanType;
 import org.hl7.fhir.r4.model.Bundle;
 import org.hl7.fhir.r4.model.Bundle.BundleEntryComponent;
 import org.hl7.fhir.r4.model.CapabilityStatement;
+<<<<<<< HEAD
 import org.hl7.fhir.r4.model.CodeSystem;
+=======
+>>>>>>> master
 import org.hl7.fhir.r4.model.CodeType;
 import org.hl7.fhir.r4.model.CodeableConcept;
 import org.hl7.fhir.r4.model.Coding;
 import org.hl7.fhir.r4.model.Condition;
+<<<<<<< HEAD
 import org.hl7.fhir.r4.model.DateType;
 import org.hl7.fhir.r4.model.HumanName;
 import org.hl7.fhir.r4.model.Immunization;
 import org.hl7.fhir.r4.model.Parameters;
 import org.hl7.fhir.r4.model.Parameters.ParametersParameterComponent;
+=======
+import org.hl7.fhir.r4.model.HumanName;
+import org.hl7.fhir.r4.model.Immunization;
+>>>>>>> master
 import org.hl7.fhir.r4.model.Patient;
 import org.hl7.fhir.r4.model.Period;
 import org.hl7.fhir.r4.model.Procedure;
@@ -68,8 +79,11 @@ public class CmdLineApp {
           finished = true;
         } else if (p.length == 1 && p[0].equals("?")) {
           genMenu();
+<<<<<<< HEAD
         } else if (p.length == 1 && p[0].equals("?tx")) {
           genMenuTx();
+=======
+>>>>>>> master
         } else if (p.length >= 1 && p[0].equals("c")) {
           if (p.length == 1) {
             connectToServer("http://hapi.fhir.org/baseR4");
@@ -115,10 +129,15 @@ public class CmdLineApp {
           select("Patient", p[1]);
         } else if (p.length == 3 && p[0].equals("e")) {
           edit(p[1], p[2]);
+<<<<<<< HEAD
         } else if (p.length > 3 && p[0].equals("tx")) {
           tx(p);
         } else {
           tx(p);
+=======
+        } else {
+          System.out.println("Command unknown or not understood: "+cmd);
+>>>>>>> master
         }
       } catch (Exception e) {
         System.out.println("Error executing command "+p[0]+": "+e.getMessage());
@@ -128,6 +147,7 @@ public class CmdLineApp {
     System.out.println("Finished!"); 
   }
 
+<<<<<<< HEAD
   private boolean tx(String[] p) throws IOException {
     if (p[1].equals("l")) {
       if (p.length == 4) {
@@ -170,6 +190,9 @@ public class CmdLineApp {
   }
 
   private void getImmunizations() throws IOException {
+=======
+  private void getImmunizations() {
+>>>>>>> master
 
     Bundle bnd = client.search("Immunization", "?patient="+currentId);
     System.out.println(""+bnd.getTotal()+" Immunizations found. Printing "+bnd.getEntry().size());
@@ -180,7 +203,11 @@ public class CmdLineApp {
     } 
   }
 
+<<<<<<< HEAD
   private void getProcedures() throws IOException {
+=======
+  private void getProcedures() {
+>>>>>>> master
 
     Bundle bnd = client.search("Procedure", "?patient="+currentId);
     System.out.println(""+bnd.getTotal()+" Procedures found. Printing "+bnd.getEntry().size());
@@ -191,7 +218,11 @@ public class CmdLineApp {
     } 
   }
   
+<<<<<<< HEAD
   private void getConditions() throws IOException {
+=======
+  private void getConditions() {
+>>>>>>> master
 
     Bundle bnd = client.search("Condition", "?patient="+currentId);
     System.out.println(""+bnd.getTotal()+" Conditions found. Printing "+bnd.getEntry().size());
@@ -226,7 +257,10 @@ public class CmdLineApp {
     case "boolean" : return new BooleanType(value);
     case "code" :  return new CodeType(value);
     case "string" : return new StringType(value);
+<<<<<<< HEAD
     case "date" : return new DateType(value);
+=======
+>>>>>>> master
     }
     throw new FHIRException("Unhandled type "+p.getTypeCode());
   }
@@ -244,7 +278,11 @@ public class CmdLineApp {
     System.out.println(new JsonParser().setOutputStyle(OutputStyle.PRETTY).composeString(currentResource));
   }
 
+<<<<<<< HEAD
   private void select(String type, String id) throws IOException {
+=======
+  private void select(String type, String id) {
+>>>>>>> master
     if (type.equals("Patient")) {
       currentResource = client.fetchResource(Patient.class, id);
     } else if (type.equals("Immunization")) {
@@ -260,8 +298,12 @@ public class CmdLineApp {
     System.out.println("Resource = "+currentId+" "+summary(currentResource));
   }
 
+<<<<<<< HEAD
   private String summary(Resource r) throws IOException {
 //    return new XmlParser().composeString(r);
+=======
+  private String summary(Resource r) {
+>>>>>>> master
     if (r instanceof Patient) {
       Patient pat = (Patient) r;
       return pat.getIdBase()+" "+pat.getGender()+" "+pat.getBirthDateElement().asStringValue()+" "+name(pat);
@@ -324,7 +366,11 @@ public class CmdLineApp {
     return "";
   }
 
+<<<<<<< HEAD
   private void search(String[] p) throws IOException {
+=======
+  private void search(String[] p) {
+>>>>>>> master
     if (client == null) {
       throw new FHIRException("Not connected to to a server");
     }
@@ -332,7 +378,11 @@ public class CmdLineApp {
     if (p.length > 2) {
       search = search +"&gender="+p[2];
       if (p.length > 3) {
+<<<<<<< HEAD
         search = search +"&birthdate="+p[3];
+=======
+        search = search +"&dob="+p[3];
+>>>>>>> master
       }
     }
     Bundle bnd = client.search("Patient", search);
@@ -368,6 +418,7 @@ public class CmdLineApp {
   private void connectToServer(String url) throws URISyntaxException {
     client = new FHIRToolingClient(url, "FHIR-Command-Line-App");
     CapabilityStatement cs = client.getCapabilitiesStatementQuick();
+<<<<<<< HEAD
     System.out.println("Connected to "+url+": "+cs.getSoftware().getName()+", version "+cs.getFhirVersion().toCode());
   }
 
@@ -380,6 +431,11 @@ public class CmdLineApp {
     System.out.println(" x - exit");    
   }
   
+=======
+    System.out.println("Connected to "+url+": "+cs.getSoftware().getName()+".");
+  }
+
+>>>>>>> master
   private void genMenu() {
     System.out.println("Simple Client. Commands you can run:");
     System.out.println(" c {url} - connect to a server");

org.hl7.fhir.r4b/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>org.hl7.fhir.core</artifactId>
-		<version>6.1.11-SNAPSHOT</version>
+		<version>6.1.13-SNAPSHOT</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 

org.hl7.fhir.r5/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>ca.uhn.hapi.fhir</groupId>
 		<artifactId>org.hl7.fhir.core</artifactId>
-		<version>6.1.11-SNAPSHOT</version>
+		<version>6.1.13-SNAPSHOT</version>
 		<relativePath>../pom.xml</relativePath>
 	</parent>
 

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

@@ -50,9 +50,9 @@ public class FmlParser extends ParserBase {
     ByteArrayInputStream stream = new ByteArrayInputStream(content);
     String text = TextFile.streamToString(stream);
     List<ValidatedFragment> result = new ArrayList<>();
-    ValidatedFragment ctxt = new ValidatedFragment("focus", "fml", content);
+    ValidatedFragment focusFragment = new ValidatedFragment(ValidatedFragment.FOCUS_NAME, "fml", content, false);
-    ctxt.setElement(parse(ctxt.getErrors(), text));
+    focusFragment.setElement(parse(focusFragment.getErrors(), text));
-    result.add(ctxt);
+    result.add(focusFragment);
     return result;
   }
 

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

@@ -123,7 +123,7 @@ public class JsonParser extends ParserBase {
   public List<ValidatedFragment> parse(InputStream inStream) throws IOException, FHIRException {
 //    long start = System.currentTimeMillis();
     byte[] content = TextFile.streamToBytes(inStream);
-    ValidatedFragment ctxt = new ValidatedFragment("focus", "json", content);
+    ValidatedFragment focusFragment = new ValidatedFragment(ValidatedFragment.FOCUS_NAME, "json", content, false);
     
     ByteArrayInputStream stream = new ByteArrayInputStream(content);
     
@@ -135,17 +135,17 @@ public class JsonParser extends ParserBase {
       try {
         obj = org.hl7.fhir.utilities.json.parser.JsonParser.parseObject(source, true, true); 
       } catch (Exception e) {
-        logError(ctxt.getErrors(), ValidationMessage.NO_RULE_DATE, -1, -1,context.formatMessage(I18nConstants.DOCUMENT), IssueType.INVALID, context.formatMessage(I18nConstants.ERROR_PARSING_JSON_, e.getMessage()), IssueSeverity.FATAL);
+        logError(focusFragment.getErrors(), ValidationMessage.NO_RULE_DATE, -1, -1,context.formatMessage(I18nConstants.DOCUMENT), IssueType.INVALID, context.formatMessage(I18nConstants.ERROR_PARSING_JSON_, e.getMessage()), IssueSeverity.FATAL);
       }
     } else {
       obj = org.hl7.fhir.utilities.json.parser.JsonParser.parseObject(source, true, true); 
     }
     
     if (obj != null) {
-      ctxt.setElement(parse(ctxt.getErrors(), obj));
+      focusFragment.setElement(parse(focusFragment.getErrors(), obj));
     }
     List<ValidatedFragment> res = new ArrayList<>();
-    res.add(ctxt);
+    res.add(focusFragment);
 
 //    long  t =System.currentTimeMillis()-start;
 //    System.out.println("json parser: "+(t)+"ms, "+(content.length/1024)+"kb "+(t == 0 ? "" : " @ "+(content.length / t)+"kb/s"));

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

@@ -83,7 +83,7 @@ public class SHCParser extends ParserBase {
     byte[] content = TextFile.streamToBytes(inStream);
     ByteArrayInputStream stream = new ByteArrayInputStream(content);
     List<ValidatedFragment> res = new ArrayList<>();
-    ValidatedFragment shc = new ValidatedFragment("shc", "txt", content);
+    ValidatedFragment shc = new ValidatedFragment("shc", "txt", content, false);
     res.add(shc);
 
     String src = TextFile.streamToString(stream).trim();
@@ -121,7 +121,7 @@ public class SHCParser extends ParserBase {
         return res;      
       }
 
-      ValidatedFragment bnd = new ValidatedFragment("payload", "json", jwt.payloadSrc);
+      ValidatedFragment bnd = new ValidatedFragment("payload", "json", jwt.payloadSrc, true);
       res.add(bnd);
       checkNamedProperties(shc.getErrors(), jwt.getPayload(), prefix+"payload", "iss", "nbf", "vc");
       checkProperty(shc.getErrors(), jwt.getPayload(), prefix+"payload", "iss", true, "String");

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

@@ -280,7 +280,7 @@ public class SHLParser extends ParserBase {
   }
 
   private ValidatedFragment addNamedElement(List<ValidatedFragment> res, String name, String type, byte[] content) {
-    ValidatedFragment result = new ValidatedFragment(name, type, content);
+    ValidatedFragment result = new ValidatedFragment(name, type, content, true);
     res.add(result);
     return result;
   }

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

@@ -2,34 +2,34 @@ package org.hl7.fhir.r5.elementmodel;
 
 import java.io.ByteArrayInputStream;
 
-/*
+/*
-  Copyright (c) 2011+, HL7, Inc.
+  Copyright (c) 2011+, HL7, Inc.
-  All rights reserved.
+  All rights reserved.
-  
+  
-  Redistribution and use in source and binary forms, with or without modification, 
+  Redistribution and use in source and binary forms, with or without modification, 
-  are permitted provided that the following conditions are met:
+  are permitted provided that the following conditions are met:
-    
+    
-   * Redistributions of source code must retain the above copyright notice, this 
+   * Redistributions of source code must retain the above copyright notice, this 
-     list of conditions and the following disclaimer.
+     list of conditions and the following disclaimer.
-   * Redistributions in binary form must reproduce the above copyright notice, 
+   * Redistributions in binary form must reproduce the above copyright notice, 
-     this list of conditions and the following disclaimer in the documentation 
+     this list of conditions and the following disclaimer in the documentation 
-     and/or other materials provided with the distribution.
+     and/or other materials provided with the distribution.
-   * Neither the name of HL7 nor the names of its contributors may be used to 
+   * Neither the name of HL7 nor the names of its contributors may be used to 
-     endorse or promote products derived from this software without specific 
+     endorse or promote products derived from this software without specific 
-     prior written permission.
+     prior written permission.
-  
+  
-  THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 
+  THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 
-  ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 
+  ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 
-  WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. 
+  WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. 
-  IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, 
+  IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, 
-  INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT 
+  INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT 
-  NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR 
+  NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR 
-  PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, 
+  PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, 
-  WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) 
+  WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) 
-  ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE 
+  ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE 
-  POSSIBILITY OF SUCH DAMAGE.
+  POSSIBILITY OF SUCH DAMAGE.
-  
+  
- */
+ */
 
 
 
@@ -83,7 +83,7 @@ public class TurtleParser extends ParserBase {
   @Override
   public List<ValidatedFragment> parse(InputStream inStream) throws IOException, FHIRException {
     byte[] content = TextFile.streamToBytes(inStream);
-    ValidatedFragment ctxt = new ValidatedFragment("focus", "ttl", content);
+    ValidatedFragment focusFragment = new ValidatedFragment(ValidatedFragment.FOCUS_NAME, "ttl", content, false);
     ByteArrayInputStream stream = new ByteArrayInputStream(content);
 
     Turtle src = new Turtle();
@@ -91,16 +91,16 @@ public class TurtleParser extends ParserBase {
       try {
         src.parse(TextFile.streamToString(stream));
       } catch (Exception e) {  
-        logError(ctxt.getErrors(), ValidationMessage.NO_RULE_DATE, -1, -1, "(document)", IssueType.INVALID, context.formatMessage(I18nConstants.ERROR_PARSING_TURTLE_, e.getMessage()), IssueSeverity.FATAL);
+        logError(focusFragment.getErrors(), ValidationMessage.NO_RULE_DATE, -1, -1, "(document)", IssueType.INVALID, context.formatMessage(I18nConstants.ERROR_PARSING_TURTLE_, e.getMessage()), IssueSeverity.FATAL);
         return null;
       }
-      ctxt.setElement(parse(ctxt.getErrors(), src));
+      focusFragment.setElement(parse(focusFragment.getErrors(), src));
     } else {
       src.parse(TextFile.streamToString(stream));
-      ctxt.setElement(parse(ctxt.getErrors(), src));
+      focusFragment.setElement(parse(focusFragment.getErrors(), src));
     }
     List<ValidatedFragment> res = new ArrayList<>();
-    res.add(ctxt);
+    res.add(focusFragment);
     return res;
   }
   

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

@@ -3,63 +3,55 @@ package org.hl7.fhir.r5.elementmodel;
 import java.util.ArrayList;
 import java.util.List;
 
+import lombok.Getter;
+import lombok.Setter;
 import org.hl7.fhir.utilities.validation.ValidationMessage;
 
 public class ValidatedFragment {
+
+  @Getter
   private String name;
+
+  @Getter @Setter
   private String elementPath;
+
+  @Getter
   private String extension;
+
+  @Getter @Setter
   private Element element;
+
+  @Getter @Setter
   private byte[] content;
+
+  @Getter
+  private final boolean isDerivedContent;
+  public final static String FOCUS_NAME = "focus";
+
+  @Getter
   private List<ValidationMessage> errors = new ArrayList<>();
-  
+
-  public ValidatedFragment(String name, String extension, Element element, byte[] content) {
+
+  public ValidatedFragment(String name, String extension, Element element, byte[] content, boolean isDerivedContent) {
     super();
     this.name = name;
     this.element = element; 
     this.content = content;
     this.extension = extension;
+    this.isDerivedContent = isDerivedContent;
   }
 
-  public ValidatedFragment(String name, String extension, byte[] content) {
+  public ValidatedFragment(String name, String extension, byte[] content, boolean isDerivedContent) {
     super();
     this.name = name;
     this.content = content;
     this.extension = extension;
+    this.isDerivedContent = isDerivedContent;
   }
-  
-  public String getName() {
-    return name;
-  }
-  
-  public Element getElement() {
-    return element;
-  }
-
-  public byte[] getContent() {
-    return content;
-  }
-
-  public List<ValidationMessage> getErrors() {
-    return errors;
-  }
-
-  public void setElement(Element element) {
-    this.element = element;
-  }
-
   public String getFilename() {
     return name+"."+extension;
   }
 
-  public String getElementPath() {
-    return elementPath;
-  }
-
-  public void setElementPath(String elementPath) {
-    this.elementPath = elementPath;
-  }
-  
   public String path() {
     return elementPath == null ? name : elementPath;
   }

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

@@ -1,33 +1,33 @@
 package org.hl7.fhir.r5.elementmodel;
 
-/*
+/*
-  Copyright (c) 2011+, HL7, Inc.
+  Copyright (c) 2011+, HL7, Inc.
-  All rights reserved.
+  All rights reserved.
-  
+  
-  Redistribution and use in source and binary forms, with or without modification, 
+  Redistribution and use in source and binary forms, with or without modification, 
-  are permitted provided that the following conditions are met:
+  are permitted provided that the following conditions are met:
-    
+    
-   * Redistributions of source code must retain the above copyright notice, this 
+   * Redistributions of source code must retain the above copyright notice, this 
-     list of conditions and the following disclaimer.
+     list of conditions and the following disclaimer.
-   * Redistributions in binary form must reproduce the above copyright notice, 
+   * Redistributions in binary form must reproduce the above copyright notice, 
-     this list of conditions and the following disclaimer in the documentation 
+     this list of conditions and the following disclaimer in the documentation 
-     and/or other materials provided with the distribution.
+     and/or other materials provided with the distribution.
-   * Neither the name of HL7 nor the names of its contributors may be used to 
+   * Neither the name of HL7 nor the names of its contributors may be used to 
-     endorse or promote products derived from this software without specific 
+     endorse or promote products derived from this software without specific 
-     prior written permission.
+     prior written permission.
-  
+  
-  THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 
+  THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 
-  ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 
+  ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 
-  WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. 
+  WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. 
-  IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, 
+  IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, 
-  INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT 
+  INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT 
-  NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR 
+  NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR 
-  PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, 
+  PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, 
-  WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) 
+  WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) 
-  ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE 
+  ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE 
-  POSSIBILITY OF SUCH DAMAGE.
+  POSSIBILITY OF SUCH DAMAGE.
-  
+  
- */
+ */
 
 
 
@@ -465,7 +465,7 @@ public class VerticalBarParser extends ParserBase {
     while (!reader.isFinished()) //  && (getOptions().getSegmentLimit() == 0 || getOptions().getSegmentLimit() > message.getSegments().size()))
       readSegment(message, reader);
     List<ValidatedFragment> res = new ArrayList<>();
-    res.add(new ValidatedFragment("focus", "hl7", message, content));
+    res.add(new ValidatedFragment(ValidatedFragment.FOCUS_NAME, "hl7", message, content, false));
     return res;
   }
 

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

@@ -118,7 +118,7 @@ public class XmlParser extends ParserBase {
   public List<ValidatedFragment> parse(InputStream inStream) throws FHIRFormatError, DefinitionException, FHIRException, IOException {
     
     byte[] content = TextFile.streamToBytes(inStream);
-    ValidatedFragment context = new ValidatedFragment("focus", "xml", content);
+    ValidatedFragment focusFragment = new ValidatedFragment(ValidatedFragment.FOCUS_NAME, "xml", content, false);
     
     ByteArrayInputStream stream = new ByteArrayInputStream(content);
     Document doc = null;
@@ -138,7 +138,7 @@ public class XmlParser extends ParserBase {
         // if we can, we'll inspect the header/encoding ourselves 
 
         stream.mark(1024);
-        version = checkHeader(context.getErrors(), stream);
+        version = checkHeader(focusFragment.getErrors(), stream);
         stream.reset();
 
         // use a slower parser that keeps location data
@@ -172,17 +172,17 @@ public class XmlParser extends ParserBase {
       if (e.getMessage().contains("lineNumber:") && e.getMessage().contains("columnNumber:")) {
         int line = Utilities.parseInt(extractVal(e.getMessage(), "lineNumber"), 0); 
         int col = Utilities.parseInt(extractVal(e.getMessage(), "columnNumber"), 0); 
-        logError(context.getErrors(), ValidationMessage.NO_RULE_DATE, line, col, "(xml)", IssueType.INVALID, e.getMessage().substring(e.getMessage().lastIndexOf(";")+1).trim(), IssueSeverity.FATAL);
+        logError(focusFragment.getErrors(), ValidationMessage.NO_RULE_DATE, line, col, "(xml)", IssueType.INVALID, e.getMessage().substring(e.getMessage().lastIndexOf(";")+1).trim(), IssueSeverity.FATAL);
       } else {
-        logError(context.getErrors(), ValidationMessage.NO_RULE_DATE, 0, 0, "(xml)", IssueType.INVALID, e.getMessage(), IssueSeverity.FATAL);
+        logError(focusFragment.getErrors(), ValidationMessage.NO_RULE_DATE, 0, 0, "(xml)", IssueType.INVALID, e.getMessage(), IssueSeverity.FATAL);
       }
       doc = null;
     }
     if (doc != null) {
-      context.setElement(parse(context.getErrors(), doc));
+      focusFragment.setElement(parse(focusFragment.getErrors(), doc));
     }
     List<ValidatedFragment> res = new ArrayList<>();
-    res.add(context);
+    res.add(focusFragment);
     return res;
   }
 

org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/sql/SQLOnFhirTests.java

@@ -14,10 +14,8 @@ import javax.xml.parsers.ParserConfigurationException;
 import org.fhir.ucum.UcumException;
 import org.hl7.fhir.exceptions.FHIRException;
 import org.hl7.fhir.r5.model.Base;
-import org.hl7.fhir.r5.model.Factory;
 import org.hl7.fhir.r5.model.Resource;
 import org.hl7.fhir.r5.model.ResourceFactory;
-import org.hl7.fhir.r5.sql.SQLOnFhirTestCases.RowSorter;
 import org.hl7.fhir.r5.test.utils.CompareUtilities;
 import org.hl7.fhir.r5.test.utils.TestingUtilities;
 import org.hl7.fhir.r5.utils.sql.Provider;
@@ -28,12 +26,13 @@ import org.hl7.fhir.utilities.json.model.JsonElement;
 import org.hl7.fhir.utilities.json.model.JsonObject;
 import org.hl7.fhir.utilities.json.parser.JsonParser;
 import org.junit.jupiter.api.Assertions;
+import org.junit.jupiter.api.Disabled;
 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;
 
-public class SQLOnFhirTestCases {
+public class SQLOnFhirTests {
 
   public class TestProvider implements Provider {
 
@@ -110,6 +109,7 @@ public class SQLOnFhirTestCases {
   @SuppressWarnings("deprecation")
   @ParameterizedTest(name = "{index}: file {0}")
   @MethodSource("data")
+  @Disabled
   public void test(String name, TestDetails test) throws FileNotFoundException, IOException, FHIRException, org.hl7.fhir.exceptions.FHIRException, UcumException {
     this.details = test;
     Runner runner = new Runner();

org.hl7.fhir.report/pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <groupId>ca.uhn.hapi.fhir</groupId>
         <artifactId>org.hl7.fhir.core</artifactId>
-        <version>6.1.11-SNAPSHOT</version>
+        <version>6.1.13-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

org.hl7.fhir.utilities/pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <groupId>ca.uhn.hapi.fhir</groupId>
         <artifactId>org.hl7.fhir.core</artifactId>
-        <version>6.1.11-SNAPSHOT</version>
+        <version>6.1.13-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

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

@@ -249,7 +249,7 @@ Validation_VAL_Profile_MultipleMatches_other = Found multiple matching profiles
 Validation_VAL_Profile_NoDefinition = No definition found for resource type ''{0}''
 Validation_VAL_Profile_NoMatch = Unable to find a match for the specified profile among choices: {0}
 Validation_VAL_Profile_NoSnapshot = StructureDefinition {0} has no snapshot - validation is against the snapshot, so it must be provided
-Validation_VAL_Profile_NoType = The type of element {0} is not known - it couild not be determined from the information available. Valid types at this point are {1}
+Validation_VAL_Profile_NoType = The type of element {0} is not known - it could not be determined from the information available. Valid types at this point are {1}
 Validation_VAL_Profile_NotAllowed = This element is not allowed by the profile {0}
 Validation_VAL_Profile_NotSlice = This element does not match any known slice {0} and slicing is CLOSED: {1}
 Validation_VAL_Profile_OutOfOrder = As specified by profile {0}, Element ''{1}'' is out of order (found after {2})

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

@@ -5,7 +5,7 @@
     <parent>
         <groupId>ca.uhn.hapi.fhir</groupId>
         <artifactId>org.hl7.fhir.core</artifactId>
-        <version>6.1.11-SNAPSHOT</version>
+        <version>6.1.13-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

org.hl7.fhir.validation/pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <groupId>ca.uhn.hapi.fhir</groupId>
         <artifactId>org.hl7.fhir.core</artifactId>
-        <version>6.1.11-SNAPSHOT</version>
+        <version>6.1.13-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

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

@@ -32,12 +32,8 @@ import org.hl7.fhir.r5.context.IWorkerContext;
 import org.hl7.fhir.r5.context.IWorkerContextManager;
 import org.hl7.fhir.r5.context.SimpleWorkerContext;
 import org.hl7.fhir.r5.context.SystemOutLoggingService;
-import org.hl7.fhir.r5.elementmodel.Element;
+import org.hl7.fhir.r5.elementmodel.*;
-import org.hl7.fhir.r5.elementmodel.Manager;
 import org.hl7.fhir.r5.elementmodel.Manager.FhirFormat;
-import org.hl7.fhir.r5.elementmodel.ObjectConverter;
-import org.hl7.fhir.r5.elementmodel.ParserBase;
-import org.hl7.fhir.r5.elementmodel.SHCParser;
 import org.hl7.fhir.r5.formats.FormatUtilities;
 import org.hl7.fhir.r5.formats.IParser.OutputStyle;
 import org.hl7.fhir.r5.formats.JsonParser;
@@ -635,6 +631,13 @@ public class ValidationEngine implements IValidatorResourceFetcher, IValidationP
       return results.getEntryFirstRep().getResource();
   }
 
+
+  public List<ValidatedFragment> validateAsFragments(byte[] source, FhirFormat cntType, List<String> profiles, List<ValidationMessage> messages) throws FHIRException, IOException, EOperationOutcome {
+    InstanceValidator validator = getValidator(cntType);
+    validator.validate(null, messages, new ByteArrayInputStream(source), cntType, asSdList(profiles));
+    return validator.validatedContent;
+  }
+
   public OperationOutcome validate(byte[] source, FhirFormat cntType, List<String> profiles, List<ValidationMessage> messages) throws FHIRException, IOException, EOperationOutcome {
     InstanceValidator validator = getValidator(cntType);
 

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

@@ -29,6 +29,7 @@ import org.hl7.fhir.r5.elementmodel.Element;
 import org.hl7.fhir.r5.elementmodel.LanguageUtils;
 import org.hl7.fhir.r5.elementmodel.Manager;
 import org.hl7.fhir.r5.elementmodel.Manager.FhirFormat;
+import org.hl7.fhir.r5.elementmodel.ValidatedFragment;
 import org.hl7.fhir.r5.formats.IParser;
 import org.hl7.fhir.r5.formats.IParser.OutputStyle;
 import org.hl7.fhir.r5.model.Bundle;
@@ -61,10 +62,7 @@ import org.hl7.fhir.utilities.i18n.XLIFFProducer;
 import org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager;
 import org.hl7.fhir.utilities.npm.NpmPackage;
 import org.hl7.fhir.utilities.validation.ValidationMessage;
-import org.hl7.fhir.validation.IgLoader;
+import org.hl7.fhir.validation.*;
-import org.hl7.fhir.validation.ValidationEngine;
-import org.hl7.fhir.validation.ValidationRecord;
-import org.hl7.fhir.validation.ValidatorUtils;
 import org.hl7.fhir.validation.ValidatorUtils.SourceFile;
 import org.hl7.fhir.validation.cli.model.CliContext;
 import org.hl7.fhir.validation.cli.model.FileInfo;
@@ -114,13 +112,43 @@ public class ValidationService {
 
     ValidationResponse response = new ValidationResponse().setSessionId(sessionId);
 
-    for (FileInfo fp : request.getFilesToValidate()) {
+    for (FileInfo fileToValidate : request.getFilesToValidate()) {
+      if (fileToValidate.getFileType() == null) {
+        Manager.FhirFormat format = ResourceChecker.checkIsResource(validator.getContext(),
+          false,
+          fileToValidate.getFileContent().getBytes(),
+          fileToValidate.getFileName(),
+          false);
+        fileToValidate.setFileType(format.getExtension());
+      }
+
       List<ValidationMessage> messages = new ArrayList<>();
-      validator.validate(fp.getFileContent().getBytes(), Manager.FhirFormat.getFhirFormat(fp.getFileType()),
+
+      List<ValidatedFragment> validatedFragments = validator.validateAsFragments(fileToValidate.getFileContent().getBytes(), Manager.FhirFormat.getFhirFormat(fileToValidate.getFileType()),
         request.getCliContext().getProfiles(), messages);
-      ValidationOutcome outcome = new ValidationOutcome().setFileInfo(fp);
+
-      messages.forEach(outcome::addMessage);
+      if (validatedFragments.size() == 1 && !validatedFragments.get(0).isDerivedContent()) {
-      response.addOutcome(outcome);
+        ValidatedFragment validatedFragment = validatedFragments.get(0);
+        ValidationOutcome outcome = new ValidationOutcome();
+          FileInfo fileInfo = new FileInfo(
+          fileToValidate.getFileName(),
+          new String(validatedFragment.getContent()),
+          validatedFragment.getExtension());
+        outcome.setMessages(validatedFragment.getErrors());
+        outcome.setFileInfo(fileInfo);
+        response.addOutcome(outcome);
+      } else {
+        for (ValidatedFragment validatedFragment : validatedFragments) {
+          ValidationOutcome outcome = new ValidationOutcome();
+          FileInfo fileInfo = new FileInfo(
+            validatedFragment.getFilename(),
+            new String(validatedFragment.getContent()),
+            validatedFragment.getExtension());
+          outcome.setMessages(validatedFragment.getErrors());
+          outcome.setFileInfo(fileInfo);
+          response.addOutcome(outcome);
+        }
+      }
     }
     System.out.println("  Max Memory: "+Runtime.getRuntime().maxMemory());
     return response;

pom.xml

@@ -14,13 +14,13 @@
     HAPI FHIR
     -->
     <artifactId>org.hl7.fhir.core</artifactId>
-    <version>6.1.11-SNAPSHOT</version>
+    <version>6.1.13-SNAPSHOT</version>
     <packaging>pom</packaging>
 
     <properties>
         <guava_version>32.0.1-jre</guava_version>
         <hapi_fhir_version>6.4.1</hapi_fhir_version>
-        <validator_test_case_version>1.4.7</validator_test_case_version>
+        <validator_test_case_version>1.4.8</validator_test_case_version>
         <jackson_version>2.15.2</jackson_version>
         <junit_jupiter_version>5.9.2</junit_jupiter_version>
         <junit_platform_launcher_version>1.8.2</junit_platform_launcher_version>