reorganise to test cross-version extensions

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

@@ -32,7 +32,7 @@ import org.hl7.fhir.dstu2016may.formats.XmlParser;
 import org.hl7.fhir.dstu2016may.model.Resource;
 import org.hl7.fhir.exceptions.FHIRException;
 import org.hl7.fhir.r5.conformance.ProfileUtilities;
-import org.hl7.fhir.r5.context.SimpleWorkerContext.IContextResourceLoader;
+import org.hl7.fhir.r5.context.IWorkerContext.IContextResourceLoader;
 import org.hl7.fhir.r5.model.Bundle;
 import org.hl7.fhir.r5.model.Bundle.BundleEntryComponent;
 import org.hl7.fhir.r5.model.Bundle.BundleType;

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

@@ -31,7 +31,7 @@ import org.hl7.fhir.dstu2.formats.JsonParser;
 import org.hl7.fhir.dstu2.formats.XmlParser;
 import org.hl7.fhir.dstu2.model.Resource;
 import org.hl7.fhir.exceptions.FHIRException;
-import org.hl7.fhir.r5.context.SimpleWorkerContext.IContextResourceLoader;
+import org.hl7.fhir.r5.context.IWorkerContext.IContextResourceLoader;
 import org.hl7.fhir.r5.model.Bundle;
 import org.hl7.fhir.r5.model.Bundle.BundleEntryComponent;
 import org.hl7.fhir.r5.model.Bundle.BundleType;

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

@@ -31,7 +31,7 @@ import org.hl7.fhir.dstu3.formats.JsonParser;
 import org.hl7.fhir.dstu3.formats.XmlParser;
 import org.hl7.fhir.dstu3.model.Resource;
 import org.hl7.fhir.exceptions.FHIRException;
-import org.hl7.fhir.r5.context.SimpleWorkerContext.IContextResourceLoader;
+import org.hl7.fhir.r5.context.IWorkerContext.IContextResourceLoader;
 import org.hl7.fhir.r5.model.Bundle;
 import org.hl7.fhir.r5.model.Bundle.BundleEntryComponent;
 import org.hl7.fhir.r5.model.Bundle.BundleType;

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

@@ -31,7 +31,7 @@ import org.hl7.fhir.exceptions.FHIRException;
 import org.hl7.fhir.r4.formats.JsonParser;
 import org.hl7.fhir.r4.formats.XmlParser;
 import org.hl7.fhir.r4.model.Resource;
-import org.hl7.fhir.r5.context.SimpleWorkerContext.IContextResourceLoader;
+import org.hl7.fhir.r5.context.IWorkerContext.IContextResourceLoader;
 import org.hl7.fhir.r5.model.Bundle;
 import org.hl7.fhir.r5.model.Bundle.BundleEntryComponent;
 import org.hl7.fhir.r5.model.Bundle.BundleType;

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

@@ -31,7 +31,7 @@ import org.hl7.fhir.exceptions.FHIRException;
 import org.hl7.fhir.r5.formats.JsonParser;
 import org.hl7.fhir.r5.formats.XmlParser;
 import org.hl7.fhir.r5.model.Resource;
-import org.hl7.fhir.r5.context.SimpleWorkerContext.IContextResourceLoader;
+import org.hl7.fhir.r5.context.IWorkerContext.IContextResourceLoader;
 import org.hl7.fhir.r5.model.Bundle;
 import org.hl7.fhir.r5.model.Bundle.BundleEntryComponent;
 import org.hl7.fhir.r5.model.Bundle.BundleType;

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

@@ -91,6 +91,8 @@ import org.hl7.fhir.r5.terminologies.ValueSetExpander.ValueSetExpansionOutcome;
 import org.hl7.fhir.r5.utils.NarrativeGenerator;
 import org.hl7.fhir.r5.utils.ToolingExtensions;
 import org.hl7.fhir.r5.utils.TranslatingUtilities;
+import org.hl7.fhir.r5.utils.XVerExtensionManager;
+import org.hl7.fhir.r5.utils.XVerExtensionManager.XVerExtensionStatus;
 import org.hl7.fhir.r5.utils.formats.CSVWriter;
 import org.hl7.fhir.r5.utils.formats.XLSXWriter;
 import org.hl7.fhir.utilities.CommaSeparatedStringBuilder;
@@ -265,6 +267,7 @@ public class ProfileUtilities extends TranslatingUtilities {
   private boolean newSlicingProcessing;
   private String defWebRoot;
   private boolean autoFixSliceNames;
+  private XVerExtensionManager xver;
 
   public ProfileUtilities(IWorkerContext context, List<ValidationMessage> messages, ProfileKnowledgeProvider pkp) {
     super();
@@ -617,6 +620,11 @@ public class ProfileUtilities extends TranslatingUtilities {
         for (TypeRefComponent t : ed.getType()) {
           for (UriType u : t.getProfile()) {
             StructureDefinition sd = context.fetchResource(StructureDefinition.class, u.getValue());
+            if (sd == null) {
+              if (xver != null && xver.matchingUrl(u.getValue()) && xver.status(u.getValue()) == XVerExtensionStatus.Valid) {
+                sd = xver.makeDefinition(u.getValue());              
+              }
+            }
             if (sd == null) {
               if (messages != null) {
                 messages.add(new ValidationMessage(Source.ProfileValidator, ValidationMessage.IssueType.VALUE, url+"#"+ed.getId(), "The type of profile "+u.getValue()+" cannot be checked as the profile is not known", IssueSeverity.WARNING));
@@ -876,6 +884,16 @@ public class ProfileUtilities extends TranslatingUtilities {
           if (diffMatches.get(0).hasType() && diffMatches.get(0).getType().size() == 1 && diffMatches.get(0).getType().get(0).hasProfile() && !"Reference".equals(diffMatches.get(0).getType().get(0).getWorkingCode())) {
             CanonicalType p = diffMatches.get(0).getType().get(0).getProfile().get(0);
             StructureDefinition sd = context.fetchResource(StructureDefinition.class, p.getValue());
+            if (sd == null && xver != null && xver.matchingUrl(p.getValue())) {
+              switch (xver.status(p.getValue())) {
+              case BadVersion: throw new FHIRException("Reference to invalid version in extension url "+p.getValue());
+              case Invalid: throw new FHIRException("Reference to invalid extension "+p.getValue());
+              case Unknown: throw new FHIRException("Reference to unknown extension "+p.getValue()); 
+              case Valid: 
+                sd = xver.makeDefinition(p.getValue());
+                generateSnapshot(context.fetchTypeDefinition("Extension"), sd, sd.getUrl(), webUrl, sd.getName());
+              }
+            }
             if (sd != null) {
               checkNotGenerating(sd, "an extension definition");
               if (!sd.hasSnapshot()) {
@@ -5662,6 +5680,15 @@ public class ProfileUtilities extends TranslatingUtilities {
     return base;
   }
 
+  public XVerExtensionManager getXver() {
+    return xver;
+  }
+
+  public ProfileUtilities setXver(XVerExtensionManager xver) {
+    this.xver = xver;
+    return this;
+  }
+
 
 
   

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

@@ -1,5 +1,8 @@
 package org.hl7.fhir.r5.context;
 
+import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.io.InputStream;
 import java.util.EnumSet;
 
 /*-
@@ -41,6 +44,7 @@ import org.hl7.fhir.r5.model.CodeableConcept;
 import org.hl7.fhir.r5.model.Coding;
 import org.hl7.fhir.r5.model.ConceptMap;
 import org.hl7.fhir.r5.model.ElementDefinition.ElementDefinitionBindingComponent;
+import org.hl7.fhir.r5.model.Bundle;
 import org.hl7.fhir.r5.model.CanonicalResource;
 import org.hl7.fhir.r5.model.Parameters;
 import org.hl7.fhir.r5.model.Resource;
@@ -53,6 +57,7 @@ import org.hl7.fhir.r5.terminologies.ValueSetExpander.ValueSetExpansionOutcome;
 import org.hl7.fhir.r5.utils.INarrativeGenerator;
 import org.hl7.fhir.r5.utils.IResourceValidator;
 import org.hl7.fhir.utilities.TranslationServices;
+import org.hl7.fhir.utilities.cache.NpmPackage;
 import org.hl7.fhir.utilities.validation.ValidationOptions;
 import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity;
 
@@ -105,6 +110,13 @@ public interface IWorkerContext {
     }
   }
 
+  public interface IContextResourceLoader {
+    Bundle loadBundle(InputStream stream, boolean isJson) throws FHIRException, IOException;
+
+    String[] getTypes();
+  }
+
+
   /**
    * Get the versions of the definitions loaded in context
    * @return
@@ -618,5 +630,9 @@ public interface IWorkerContext {
   public String getLinkForUrl(String corePath, String s);
   public Map<String, byte[]> getBinaries();
 
+  void loadFromPackage(NpmPackage pi, IContextResourceLoader loader, String[] types) throws FileNotFoundException, IOException, FHIRException;
+
+  public boolean hasPackage(String id, String ver);
+
 
 }

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

@@ -90,12 +90,6 @@ public class SimpleWorkerContext extends BaseWorkerContext implements IWorkerCon
 
   }
 
-  public interface IContextResourceLoader {
-    Bundle loadBundle(InputStream stream, boolean isJson) throws FHIRException, IOException;
-
-    String[] getTypes();
-  }
-
   public interface IValidatorFactory {
     IResourceValidator makeValidator(IWorkerContext ctxts) throws FHIRException;
   }
@@ -106,6 +100,7 @@ public class SimpleWorkerContext extends BaseWorkerContext implements IWorkerCon
   private IValidatorFactory validatorFactory;
   private boolean ignoreProfileErrors;
   private boolean progress;
+  private List<String> loadedPackages = new ArrayList<String>();
   
   public SimpleWorkerContext() throws FileNotFoundException, IOException, FHIRException {
     super();
@@ -324,6 +319,7 @@ public class SimpleWorkerContext extends BaseWorkerContext implements IWorkerCon
     if (progress) {
       System.out.println("Load Package "+pi.name()+"#"+pi.version());
     }
+    loadedPackages.add(pi.id()+"#"+pi.version());
     for (String s : pi.listResources(loader.getTypes())) {
        try {
         loadDefinitionItem(s, pi.load("package", s), loader, filter, new PackageVersion(pi.id(), pi.version()));
@@ -339,10 +335,12 @@ public class SimpleWorkerContext extends BaseWorkerContext implements IWorkerCon
     }
   }
 
+  @Override
 	public void loadFromPackage(NpmPackage pi, IContextResourceLoader loader, String... types) throws FileNotFoundException, IOException, FHIRException {
 	  if (progress) {
 	    System.out.println("Load Package "+pi.name()+"#"+pi.version());
 	  }
+    loadedPackages.add(pi.id()+"#"+pi.version());
 	  if (types.length == 0)
 	    types = new String[] { "StructureDefinition", "ValueSet", "CodeSystem", "SearchParameter", "OperationDefinition", "Questionnaire", "ConceptMap", "StructureMap", "NamingSystem" };
 	  for (String s : pi.listResources(types)) {
@@ -699,6 +697,11 @@ public class SimpleWorkerContext extends BaseWorkerContext implements IWorkerCon
     this.progress = progress;
   }
 
+  @Override
+  public boolean hasPackage(String id, String ver) {
+    return loadedPackages.contains(id+"#"+ver);
+  }
+
 
 
 

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

@@ -5,6 +5,7 @@ import java.io.FileInputStream;
 import java.io.FileNotFoundException;
 import java.io.FileOutputStream;
 import java.io.IOException;
+import java.io.InputStream;
 import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.HashSet;
@@ -22,11 +23,13 @@ import org.hl7.fhir.exceptions.FHIRFormatError;
 import org.hl7.fhir.exceptions.PathEngineException;
 import org.hl7.fhir.r5.conformance.ProfileUtilities;
 import org.hl7.fhir.r5.conformance.ProfileUtilities.ProfileKnowledgeProvider;
+import org.hl7.fhir.r5.context.IWorkerContext.IContextResourceLoader;
 import org.hl7.fhir.r5.context.SimpleWorkerContext;
 import org.hl7.fhir.r5.formats.IParser.OutputStyle;
 import org.hl7.fhir.r5.formats.JsonParser;
 import org.hl7.fhir.r5.formats.XmlParser;
 import org.hl7.fhir.r5.model.Base;
+import org.hl7.fhir.r5.model.Bundle;
 import org.hl7.fhir.r5.model.Coding;
 import org.hl7.fhir.r5.model.ElementDefinition.ElementDefinitionBindingComponent;
 import org.hl7.fhir.r5.model.ExpressionNode.CollectionStatus;
@@ -43,6 +46,7 @@ import org.hl7.fhir.r5.model.TestScript.TestActionComponent;
 import org.hl7.fhir.r5.model.TestScript.TestScriptFixtureComponent;
 import org.hl7.fhir.r5.model.TestScript.TestScriptTestComponent;
 import org.hl7.fhir.r5.test.SnapShotGenerationTests.TestFetchMode;
+import org.hl7.fhir.r5.test.SnapShotGenerationTests.TestLoader;
 import org.hl7.fhir.r5.test.utils.TestingUtilities;
 import org.hl7.fhir.r5.model.TypeDetails;
 import org.hl7.fhir.r5.model.ValueSet;
@@ -52,8 +56,12 @@ import org.hl7.fhir.r5.utils.FHIRPathEngine;
 import org.hl7.fhir.r5.utils.FHIRPathEngine.IEvaluationContext;
 import org.hl7.fhir.r5.utils.IResourceValidator;
 import org.hl7.fhir.r5.utils.NarrativeGenerator;
+import org.hl7.fhir.r5.utils.XVerExtensionManager;
 import org.hl7.fhir.utilities.TextFile;
 import org.hl7.fhir.utilities.Utilities;
+import org.hl7.fhir.utilities.cache.NpmPackage;
+import org.hl7.fhir.utilities.cache.PackageCacheManager;
+import org.hl7.fhir.utilities.cache.ToolsVersion;
 import org.hl7.fhir.utilities.validation.ValidationMessage;
 import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity;
 import org.hl7.fhir.utilities.xml.XMLUtil;
@@ -70,6 +78,26 @@ import junit.framework.Assert;
 @RunWith(Parameterized.class)
 public class SnapShotGenerationTests {
 
+  public class TestLoader implements IContextResourceLoader {
+
+    private String[] types;
+
+    public TestLoader(String[] types) {
+      this.types = types;
+    }
+
+    @Override
+    public Bundle loadBundle(InputStream stream, boolean isJson) throws FHIRException, IOException {
+      return null;
+    }
+
+    @Override
+    public String[] getTypes() {
+      return types;
+    }
+
+  }
+
   public enum TestFetchMode {
     INPUT,
     OUTPUT, 
@@ -499,6 +527,11 @@ public class SnapShotGenerationTests {
     pu.setThrowException(false);
     pu.setDebug(test.isDebug());
     pu.setIds(test.getSource(), false);
+    if (!TestingUtilities.context().hasPackage("hl7.fhir.xver-extensions", "0.0.3")) {
+      NpmPackage npm = new PackageCacheManager(true, ToolsVersion.TOOLS_VERSION).loadPackage("hl7.fhir.xver-extensions", "0.0.3");
+      TestingUtilities.context().loadFromPackage(npm, new TestLoader(new String[] {"StructureDefinition"}), new String[] {"StructureDefinition"});
+    }
+    pu.setXver(new XVerExtensionManager(TestingUtilities.context()));
     if (test.isSort()) {
       List<String> errors = new ArrayList<String>();
       int lastCount = output.getDifferential().getElement().size();

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

@@ -5,9 +5,9 @@ import org.hl7.fhir.convertors.*;
 import org.hl7.fhir.exceptions.DefinitionException;
 import org.hl7.fhir.exceptions.FHIRException;
 import org.hl7.fhir.r5.conformance.ProfileUtilities;
+import org.hl7.fhir.r5.context.IWorkerContext.IContextResourceLoader;
 import org.hl7.fhir.r5.context.IWorkerContext.PackageVersion;
 import org.hl7.fhir.r5.context.SimpleWorkerContext;
-import org.hl7.fhir.r5.context.SimpleWorkerContext.IContextResourceLoader;
 import org.hl7.fhir.r5.elementmodel.Element;
 import org.hl7.fhir.r5.elementmodel.Manager;
 import org.hl7.fhir.r5.elementmodel.Manager.FhirFormat;