WIP track derived content for ValidatedFragment

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

@@ -50,7 +50,7 @@ public class FmlParser extends ParserBase {
     ByteArrayInputStream stream = new ByteArrayInputStream(content);
     String text = TextFile.streamToString(stream);
     List<ValidatedFragment> result = new ArrayList<>();
-    ValidatedFragment focusFragment = new ValidatedFragment(ValidatedFragment.FOCUS_NAME, "fml", content);
+    ValidatedFragment focusFragment = new ValidatedFragment(ValidatedFragment.FOCUS_NAME, "fml", content, false);
     focusFragment.setElement(parse(focusFragment.getErrors(), text));
     result.add(focusFragment);
     return result;

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

@@ -122,7 +122,7 @@ public class JsonParser extends ParserBase {
   public List<ValidatedFragment> parse(InputStream inStream) throws IOException, FHIRException {
 //    long start = System.currentTimeMillis();
     byte[] content = TextFile.streamToBytes(inStream);
-    ValidatedFragment focusFragment = new ValidatedFragment(ValidatedFragment.FOCUS_NAME, "json", content);
+    ValidatedFragment focusFragment = new ValidatedFragment(ValidatedFragment.FOCUS_NAME, "json", content, false);
     
     ByteArrayInputStream stream = new ByteArrayInputStream(content);
     

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", "json", content);
+    ValidatedFragment shc = new ValidatedFragment("shc", "json", content, false);
     res.add(shc);
 
     String src = TextFile.streamToString(stream).trim();
@@ -165,7 +165,7 @@ public class SHCParser extends ParserBase {
         return res;
       }
       // ok. all checks passed, we can now validate the bundle
-      ValidatedFragment bnd = new ValidatedFragment(path, "json", org.hl7.fhir.utilities.json.parser.JsonParser.composeBytes(cs.getJsonObject("fhirBundle")));
+      ValidatedFragment bnd = new ValidatedFragment(path, "json", org.hl7.fhir.utilities.json.parser.JsonParser.composeBytes(cs.getJsonObject("fhirBundle")), true);
       res.add(bnd);
       bnd.setElement(jsonParser.parse(bnd.getErrors(), cs.getJsonObject("fhirBundle")));
     }  

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

@@ -82,7 +82,7 @@ public class TurtleParser extends ParserBase {
   @Override
   public List<ValidatedFragment> parse(InputStream inStream) throws IOException, FHIRException {
     byte[] content = TextFile.streamToBytes(inStream);
-    ValidatedFragment focusFragment = new ValidatedFragment(ValidatedFragment.FOCUS_NAME, "ttl", content);
+    ValidatedFragment focusFragment = new ValidatedFragment(ValidatedFragment.FOCUS_NAME, "ttl", content, false);
     ByteArrayInputStream stream = new ByteArrayInputStream(content);
 
     Turtle src = new Turtle();

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

@@ -3,57 +3,50 @@ 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
   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 getExtension() {
-    return extension;
-  }
 }

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

@@ -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(ValidatedFragment.FOCUS_NAME, "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

@@ -114,7 +114,7 @@ public class XmlParser extends ParserBase {
   public List<ValidatedFragment> parse(InputStream inStream) throws FHIRFormatError, DefinitionException, FHIRException, IOException {
     
     byte[] content = TextFile.streamToBytes(inStream);
-    ValidatedFragment focusFragment = new ValidatedFragment(ValidatedFragment.FOCUS_NAME, "xml", content);
+    ValidatedFragment focusFragment = new ValidatedFragment(ValidatedFragment.FOCUS_NAME, "xml", content, false);
     
     ByteArrayInputStream stream = new ByteArrayInputStream(content);
     Document doc = null;

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

@@ -127,27 +127,28 @@ public class ValidationService {
       List<ValidatedFragment> validatedFragments = validator.validateAsFragments(fileToValidate.getFileContent().getBytes(), Manager.FhirFormat.getFhirFormat(fileToValidate.getFileType()),
         request.getCliContext().getProfiles(), messages);
 
-      // TODO this chunk does not work for multi-file validation, as the fileName is overwritten
+      if (validatedFragments.size() == 1 && !validatedFragments.get(0).isDerivedContent()) {
-      for (ValidatedFragment validatedFragment : validatedFragments) {
+        ValidatedFragment validatedFragment = validatedFragments.get(0);
         ValidationOutcome outcome = new ValidationOutcome();
-        FileInfo fileInfo = new FileInfo(
+          FileInfo fileInfo = new FileInfo(
-          validatedFragment.getFilename(),
+          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);
+        }
       }
-
-      //TODO the code below works correctly for multi-file validation.
-      /*
-      validator.validate(fp.getFileContent().getBytes(), Manager.FhirFormat.getFhirFormat(fp.getFileType()),
-        request.getCliContext().getProfiles(), messages);
-
-      ValidationOutcome outcome = new ValidationOutcome().setFileInfo(fp);
-      messages.forEach(outcome::addMessage);
-      response.addOutcome(outcome);
-      */
     }
     System.out.println("  Max Memory: "+Runtime.getRuntime().maxMemory());
     return response;