Extensions in generated profiles working again

hapi-tinder-plugin/src/main/java/ca/uhn/fhir/tinder/BaseStructureParser.java

@@ -330,12 +330,12 @@ public abstract class BaseStructureParser {
 		String base = "/home/t3903uhn/workspace/uhn-fhir-service/";
 		TinderStructuresMojo m = new TinderStructuresMojo();
 		m.setPackageName("ca.uhn.sailfhirmodel");
-		m.setResourceProfileFiles(new ArrayList<String>());
+//		m.setResourceProfileFiles(new ArrayList<String>());
-		m.getResourceProfileFiles().add(base + "src/main/resources/profile/patient.xml");
+//		m.getResourceProfileFiles().add(base + "src/main/resources/profile/patient.xml");
-		m.getResourceProfileFiles().add(base + "src/main/resources/profile/organization.xml");
+//		m.getResourceProfileFiles().add(base + "src/main/resources/profile/organization.xml");
-		m.setResourceValueSetFiles(new ArrayList<String>());
+//		m.setResourceValueSetFiles(new ArrayList<String>());
-		m.getResourceValueSetFiles().add(base + "src/main/resources/valueset/valueset-cgta-patientidpool.xml");
+//		m.getResourceValueSetFiles().add(base + "src/main/resources/valueset/valueset-cgta-patientidpool.xml");
-		m.getResourceValueSetFiles().add(base + "src/main/resources/valueset/valueset-cgta-provideridpool.xml");
+//		m.getResourceValueSetFiles().add(base + "src/main/resources/valueset/valueset-cgta-provideridpool.xml");
 		m.setTargetDirectory(base + "target/generated-sources/tinder");
 		m.setBuildDatatypes(true);
 		m.execute();

hapi-tinder-plugin/src/main/java/ca/uhn/fhir/tinder/CopyOfProfileParser.java

@@ -0,0 +1,312 @@
+
+package ca.uhn.fhir.tinder;
+
+import static org.apache.commons.lang.StringUtils.capitalize;
+import static org.apache.commons.lang.StringUtils.isBlank;
+
+import java.io.File;
+import java.io.FileReader;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import org.apache.commons.io.IOUtils;
+import org.apache.commons.lang3.StringUtils;
+import org.apache.maven.plugin.MojoFailureException;
+
+import ca.uhn.fhir.context.ConfigurationException;
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.model.dstu.resource.Profile;
+import ca.uhn.fhir.model.dstu.resource.Profile.ExtensionDefn;
+import ca.uhn.fhir.model.dstu.resource.Profile.Structure;
+import ca.uhn.fhir.model.dstu.resource.Profile.StructureElement;
+import ca.uhn.fhir.model.dstu.resource.Profile.StructureElementDefinition;
+import ca.uhn.fhir.model.dstu.resource.Profile.StructureElementDefinitionType;
+import ca.uhn.fhir.model.dstu.resource.Profile.StructureSearchParam;
+import ca.uhn.fhir.model.dstu.valueset.DataTypeEnum;
+import ca.uhn.fhir.model.dstu.valueset.SlicingRulesEnum;
+import ca.uhn.fhir.tinder.model.AnyChild;
+import ca.uhn.fhir.tinder.model.BaseElement;
+import ca.uhn.fhir.tinder.model.BaseRootType;
+import ca.uhn.fhir.tinder.model.Child;
+import ca.uhn.fhir.tinder.model.Extension;
+import ca.uhn.fhir.tinder.model.Resource;
+import ca.uhn.fhir.tinder.model.ResourceBlock;
+import ca.uhn.fhir.tinder.model.SearchParameter;
+import ca.uhn.fhir.tinder.model.SimpleChild;
+import ca.uhn.fhir.tinder.model.Slicing;
+
+public class CopyOfProfileParser extends BaseStructureParser {
+
+	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(CopyOfProfileParser.class);
+
+	private ExtensionDefn findExtension(Profile theProfile, String theCode) {
+		for (ExtensionDefn next : theProfile.getExtensionDefn()) {
+			if (theCode.equals(next.getCode().getValue())) {
+				return next;
+			}
+		}
+		return null;
+	}
+
+	@Override
+	protected String getFilenameSuffix() {
+		return "";
+	}
+
+	@Override
+	protected String getTemplate() {
+		return "/vm/resource.vm";
+	}
+
+	public void parseBaseResources(List<String> theBaseResourceNames) throws MojoFailureException {
+		FhirContext fhirContext = new FhirContext(Profile.class);
+
+		for (String nextFileName : theBaseResourceNames) {
+			ourLog.info("Parsing file: {}", nextFileName);
+
+			Profile profile;
+			try {
+				profile = (Profile) fhirContext.newXmlParser().parseResource(IOUtils.toString(new FileReader(nextFileName)));
+			} catch (Exception e) {
+				throw new MojoFailureException("Failed to load or parse file: " + nextFileName, e);
+			}
+
+			try {
+				parseSingleProfile(profile, "");
+			} catch (Exception e) {
+				throw new MojoFailureException("Failed to process file: " + nextFileName, e);
+			}
+		}
+
+		// for (int i = 0; i < theBaseResourceNames.size(); i++) {
+		// theBaseResourceNames.set(i,
+		// theBaseResourceNames.get(i).toLowerCase());
+		// }
+		//
+		// try {
+		//
+		// Bundle bundle =
+		// fhirContext.newXmlParser().parseBundle(IOUtils.toString(getClass().getResourceAsStream("/prof/allprofiles.xml")));
+		// TreeSet<String> allProfiles = new TreeSet<String>();
+		// for (BundleEntry nextResource : bundle.getEntries() ) {
+		// Profile nextProfile = (Profile) nextResource.getResource();
+		// allProfiles.add(nextProfile.getName().getValue());
+		// if
+		// (theBaseResourceNames.contains(nextProfile.getName().getValue().toLowerCase())){
+		// parseSingleProfile(nextProfile,
+		// bundle.getLinkBase().getValueNotNull());
+		// }
+		// }
+		//
+		// ourLog.info("Base profiles found: {}", allProfiles);
+		//
+		// } catch (Exception e) {
+		// throw new MojoFailureException("Failed to load base resources", e);
+		// }
+	}
+
+	public BaseRootType parseSingleProfile(Profile theProfile, String theUrlTOThisProfile) throws Exception {
+		BaseRootType retVal = null;
+		for (Structure nextStructure : theProfile.getStructure()) {
+
+			int elemIdx = 0;
+			boolean extensionsSliced = false;
+			SlicingRulesEnum extensionsSlicingIsOpen = SlicingRulesEnum.OPEN;
+
+			Map<String, BaseElement> elements = new HashMap<String, BaseElement>();
+			for (StructureElement next : nextStructure.getElement()) {
+
+				BaseElement elem;
+				if (elemIdx == 0) {
+					retVal = new Resource();
+					retVal.setProfile(theProfile.getIdentifier().getValue());
+					if (retVal.getProfile() == null) {
+						retVal.setProfile(theUrlTOThisProfile);
+					}
+
+					for (StructureSearchParam nextParam : nextStructure.getSearchParam()) {
+						SearchParameter param = new SearchParameter();
+						param.setName(nextParam.getName().getValue());
+						param.setPath(nextParam.getXpath().getValue());
+						param.setType(nextParam.getType().getValue());
+						param.setDescription(nextParam.getDocumentation().getValue());
+						retVal.getSearchParameters().add(param);
+					}
+
+					addResource(retVal);
+					elem = retVal;
+					// below StringUtils.isBlank(type) || type.startsWith("=")
+				} else {
+					if (next.getDefinition().getType().size() > 0 && next.getDefinition().getType().get(0).getCode().getValue().equals("Extension")) {
+						if (!next.getSlicing().isEmpty()) {
+							if (!"url".equals(next.getSlicing().getDiscriminator().getValue())) {
+								throw new ConfigurationException("Invalid extension slicing discriminator (must be 'url'): " + next.getSlicing().getDiscriminator().getValue());
+							}
+							extensionsSliced = true;
+							if (StringUtils.isNotBlank(next.getSlicing().getRules().getValueAsString())) {
+								extensionsSlicingIsOpen = next.getSlicing().getRules().getValueAsEnum();
+								if (extensionsSlicingIsOpen == null) {
+									throw new ConfigurationException("Invalid extension slicing rules: " + next.getSlicing().getRules().getValueAsString());
+								}
+							}
+							continue;
+						} else {
+							if (!extensionsSliced) {
+								continue;
+							}
+							
+							if (next.getDefinition().getType().size() != 1) {
+								throw new ConfigurationException("Extension definition '" + next.getName().getValue() + "' has multiple type blocks. This is not supported.");
+							}
+							String extUrl = next.getDefinition().getType().get(0).getProfile().getValueAsString();
+							elem = new Extension(next.getName().getValue(), extUrl, "CodeDt");
+						}
+					} else {
+						if (next.getDefinition().getType().isEmpty()) {
+							elem = new ResourceBlock();
+							// } else if (type.startsWith("@")) {
+							// elem = new ResourceBlockCopy();
+						} else if (next.getDefinition().getType().get(0).getCode().getValue().equals("*")) {
+							elem = new AnyChild();
+						} else {
+							elem = new SimpleChild();
+						}
+					}
+				}
+
+				elem.setName(next.getPath().getValue());
+				elem.setElementNameAndDeriveParentElementName(next.getPath().getValue());
+
+				boolean allResourceReferences = next.getDefinition().getType().size() > 0;
+				for (StructureElementDefinitionType nextType : next.getDefinition().getType()) {
+					if (nextType.getCode().getValueAsEnum() != DataTypeEnum.RESOURCEREFERENCE) {
+						allResourceReferences = false;
+					}
+				}
+				elem.setResourceRef(allResourceReferences);
+
+				StructureElementDefinition definition = next.getDefinition();
+
+				BaseElement parentElement = elements.get(elem.getElementParentName());
+				Slicing childIsSliced = parentElement != null ? parentElement.getChildElementNameToSlicing().get(elem.getName()) : null;
+
+				if (next.getSlicing().getDiscriminator().getValue() != null) {
+					Slicing slicing = new Slicing();
+					slicing.setDiscriminator(next.getSlicing().getDiscriminator().getValue());
+					if (parentElement.getChildElementNameToSlicing().get(elem.getName()) != null) {
+						throw new ConfigurationException("Found multiple slicing definitions for path: " + next.getPath().getValue());
+					}
+					parentElement.getChildElementNameToSlicing().put(elem.getName(), slicing);
+					continue;
+				}
+
+				/*
+				 * Profiles come with a number of standard elements which are generally ignored because they are boilerplate, unless the definition is somehow changing their behaviour (e.g. through
+				 * slices)
+				 */
+				if (next.getPath().getValue().endsWith(".contained")) {
+					continue;
+				}
+				if (next.getPath().getValue().endsWith(".text")) {
+					continue;
+				}
+				if (next.getPath().getValue().endsWith(".extension")) {
+					if (childIsSliced != null) {
+						if (!"url".equals(childIsSliced.getDiscriminator())) {
+							throw new ConfigurationException("Extensions must be sliced on 'url' discriminator. Found: " + next.getSlicing().getDiscriminator().getValue());
+						}
+						if (next.getDefinition().getType().size() != 1 || next.getDefinition().getType().get(0).getCode().getValueAsEnum() != DataTypeEnum.EXTENSION) {
+							throw new ConfigurationException("Extension slices must have a single type with a code of 'Extension'");
+						}
+						String name = next.getName().getValue();
+						if (StringUtils.isBlank(name)) {
+							throw new ConfigurationException("Extension slices must have a 'name' defined, none found at path: " + next.getPath());
+						}
+						elem.setName(name);
+						elem.setElementName(name);
+						String profile = next.getDefinition().getType().get(0).getProfile().getValueAsString();
+						if (isBlank(profile)) {
+							throw new ConfigurationException("Extension slice for " + next.getPath().getValue() + " has no profile specified in its type");
+						}
+						if (profile.startsWith("#")) {
+							Profile.ExtensionDefn extension = findExtension(theProfile, profile.substring(1));
+							if (extension == null) {
+								throw new ConfigurationException("Unknown local extension reference: " + profile);
+							}
+							ourLog.info("Element at path {} is using extension {}", next.getPath(), profile);
+							definition = extension.getDefinition();
+							String extensionUrl = theUrlTOThisProfile + profile;
+							elem.setExtensionUrl(extensionUrl);
+						} else {
+							// TODO: implement this
+							throw new ConfigurationException("Extensions specified outside of the given profile are not yet supported");
+						}
+					} else {
+						continue;
+					}
+				}
+				if (next.getPath().getValue().endsWith(".modifierExtension")) {
+					continue;
+				}
+
+				for (StructureElementDefinitionType nextType : definition.getType()) {
+					if (nextType.getCode().getValueAsEnum() == DataTypeEnum.RESOURCEREFERENCE) {
+						if (nextType.getProfile().getValueAsString().startsWith("http://hl7.org/fhir/profiles/")) {
+							elem.getType().add(capitalize(nextType.getProfile().getValueAsString().substring("http://hl7.org/fhir/profiles/".length())));
+						} else {
+							// TODO: implement this.. we need to be able to
+							// reference other profiles
+							throw new ConfigurationException("Profile type not yet supported");
+						}
+					} else {
+						elem.getType().add(capitalize(nextType.getCode().getValue()) + "Dt");
+					}
+
+				}
+
+				elem.setBinding(definition.getBinding().getName().getValue());
+				elem.setShortName(definition.getShort().getValue());
+				elem.setDefinition(definition.getFormal().getValue());
+				elem.setRequirement(definition.getRequirements().getValue());
+				elem.setCardMin(definition.getMin().getValueAsString());
+				elem.setCardMax(definition.getMax().getValue());
+
+				if (elem instanceof Child) {
+					Child child = (Child) elem;
+					elements.put(elem.getName(), elem);
+					if (parentElement == null) {
+						throw new Exception("Can't find element " + elem.getElementParentName() + "  -  Valid values are: " + elements.keySet());
+					}
+					parentElement.addChild(child);
+
+					/*
+					 * Find simple setters
+					 */
+					scanForSimpleSetters(child);
+				} else {
+					BaseRootType res = (BaseRootType) elem;
+					elements.put(res.getName(), res);
+				}
+
+				elemIdx++;
+			}
+
+		}
+
+		return retVal;
+	}
+
+	public static void main(String[] args) throws Exception {
+		String str = IOUtils.toString(Profile.class.getResourceAsStream("/tmp.txt"));
+		str = IOUtils.toString(new FileReader("../hapi-tinder-test/src/test/resources/profile/organization.xml"));
+		Profile prof = new FhirContext(Profile.class).newXmlParser().parseResource(Profile.class, str);
+
+		CopyOfProfileParser pp = new CopyOfProfileParser();
+		pp.parseSingleProfile(prof, "http://foo");
+		pp.markResourcesForImports();
+		pp.writeAll(new File("target/gen/test/resource"), "test");
+
+	}
+
+}

hapi-tinder-plugin/src/main/java/ca/uhn/fhir/tinder/ProfileParser.java

@@ -4,6 +4,7 @@ import static org.apache.commons.lang.StringUtils.capitalize;
 import static org.apache.commons.lang.StringUtils.isBlank;
 
 import java.io.File;
+import java.io.FileNotFoundException;
 import java.io.FileReader;
 import java.io.IOException;
 import java.util.HashMap;
@@ -24,16 +25,16 @@ import ca.uhn.fhir.model.dstu.resource.Profile.StructureElementDefinition;
 import ca.uhn.fhir.model.dstu.resource.Profile.StructureElementDefinitionType;
 import ca.uhn.fhir.model.dstu.resource.Profile.StructureSearchParam;
 import ca.uhn.fhir.model.dstu.valueset.DataTypeEnum;
+import ca.uhn.fhir.parser.IParser;
 import ca.uhn.fhir.tinder.model.AnyChild;
 import ca.uhn.fhir.tinder.model.BaseElement;
-import ca.uhn.fhir.tinder.model.Child;
 import ca.uhn.fhir.tinder.model.BaseRootType;
+import ca.uhn.fhir.tinder.model.Child;
 import ca.uhn.fhir.tinder.model.Resource;
 import ca.uhn.fhir.tinder.model.ResourceBlock;
 import ca.uhn.fhir.tinder.model.SearchParameter;
 import ca.uhn.fhir.tinder.model.SimpleChild;
 import ca.uhn.fhir.tinder.model.Slicing;
-import ca.uhn.fhir.tinder.model.UndeclaredExtensionChild;
 
 public class ProfileParser extends BaseStructureParser {
 
@@ -58,7 +59,25 @@ public class ProfileParser extends BaseStructureParser {
 		return "/vm/resource.vm";
 	}
 
-	public void parseBaseResources(List<String> theBaseResourceNames) throws MojoFailureException {
+	public void parseSingleProfile(File theProfile, String theHttpUrl) throws MojoFailureException {
+		String profileString;
+		try {
+			profileString = IOUtils.toString(new FileReader(theProfile));
+		} catch (IOException e) {
+			throw new MojoFailureException("Failed to load: " + theProfile, e);
+		}
+		
+		FhirContext ctx = new FhirContext(Profile.class);
+		Profile profile = ctx.newXmlParser().parseResource(Profile.class, profileString);
+		try {
+			parseSingleProfile(profile, theHttpUrl);
+		} catch (Exception e) {
+			throw new MojoFailureException("Failed to parse profile", e);
+		}
+	}
+	
+	
+	public void parseBaseResources(List<String> theBaseResourceNames, String theHttpUrl) throws MojoFailureException {
 		FhirContext fhirContext = new FhirContext(Profile.class);
 
 		for (String nextFileName : theBaseResourceNames) {
@@ -72,7 +91,7 @@ public class ProfileParser extends BaseStructureParser {
 			}
 
 			try {
-				parseSingleProfile(profile, "");
+				parseSingleProfile(profile, theHttpUrl);
 			} catch (Exception e) {
 				throw new MojoFailureException("Failed to process file: " + nextFileName, e);
 			}
@@ -133,20 +152,20 @@ public class ProfileParser extends BaseStructureParser {
 					addResource(retVal);
 					elem = retVal;
 					// below StringUtils.isBlank(type) || type.startsWith("=")
-				} else if (next.getDefinition().getType().isEmpty()) {
-					elem = new ResourceBlock();
-					// } else if (type.startsWith("@")) {
-					// elem = new ResourceBlockCopy();
-				} else if (next.getDefinition().getType().get(0).getCode().getValue().equals("*")) {
-					elem = new AnyChild();
-				} else if (next.getDefinition().getType().get(0).getCode().getValue().equals("Extension")) {
-					elem = new UndeclaredExtensionChild();
 				} else {
-					elem = new SimpleChild();
+					if (next.getDefinition().getType().isEmpty()) {
-				}
+						elem = new ResourceBlock();
+						// } else if (type.startsWith("@")) {
+						// elem = new ResourceBlockCopy();
+					} else if (next.getDefinition().getType().get(0).getCode().getValue().equals("*")) {
+						elem = new AnyChild();
+//					} else if (next.getDefinition().getType().get(0).getCode().getValue().equals("Extension")) {
+//						elem = new UndeclaredExtensionChild();
+					} else {
+						elem = new SimpleChild();
+					}
 
-				elem.setName(next.getPath().getValue());
+				}
-				elem.setElementNameAndDeriveParentElementName(next.getPath().getValue());
 
 				boolean allResourceReferences = next.getDefinition().getType().size() > 0;
 				for (StructureElementDefinitionType nextType : next.getDefinition().getType()) {
@@ -154,13 +173,12 @@ public class ProfileParser extends BaseStructureParser {
 						allResourceReferences = false;
 					}
 				}
-				elem.setResourceRef(allResourceReferences);
+
+				populateNewElement(next, elem, allResourceReferences);
 
 				StructureElementDefinition definition = next.getDefinition();
 
 				BaseElement parentElement = elements.get(elem.getElementParentName());
-				Slicing childIsSliced = parentElement != null ? parentElement.getChildElementNameToSlicing().get(elem.getName()) : null;
-
 				if (next.getSlicing().getDiscriminator().getValue() != null) {
 					Slicing slicing = new Slicing();
 					slicing.setDiscriminator(next.getSlicing().getDiscriminator().getValue());
@@ -171,6 +189,8 @@ public class ProfileParser extends BaseStructureParser {
 					continue;
 				}
 
+				Slicing childIsSliced = parentElement != null ? parentElement.getChildElementNameToSlicing().get(elem.getName()) : null;
+
 				/*
 				 * Profiles come with a number of standard elements which are generally ignored because they are boilerplate, unless the definition is somehow changing their behaviour (e.g. through
 				 * slices)
@@ -189,12 +209,17 @@ public class ProfileParser extends BaseStructureParser {
 						if (next.getDefinition().getType().size() != 1 || next.getDefinition().getType().get(0).getCode().getValueAsEnum() != DataTypeEnum.EXTENSION) {
 							throw new ConfigurationException("Extension slices must have a single type with a code of 'Extension'");
 						}
+
 						String name = next.getName().getValue();
 						if (StringUtils.isBlank(name)) {
 							throw new ConfigurationException("Extension slices must have a 'name' defined, none found at path: " + next.getPath());
 						}
 						elem.setName(name);
 						elem.setElementName(name);
+						
+//						elem = new Extension();
+//						populateNewElement(next, elem, allResourceReferences);
+						
 						String profile = next.getDefinition().getType().get(0).getProfile().getValueAsString();
 						if (isBlank(profile)) {
 							throw new ConfigurationException("Extension slice for " + next.getPath().getValue() + " has no profile specified in its type");
@@ -267,15 +292,27 @@ public class ProfileParser extends BaseStructureParser {
 		return retVal;
 	}
 
+	private void populateNewElement(StructureElement next, BaseElement elem, boolean allResourceReferences) {
+		elem.setName(next.getPath().getValue());
+		elem.setElementNameAndDeriveParentElementName(next.getPath().getValue());
+		elem.setResourceRef(allResourceReferences);
+	}
+
 	public static void main(String[] args) throws Exception {
-		String str = IOUtils.toString(Profile.class.getResourceAsStream("/tmp.txt"));
+		IParser parser = new FhirContext(Profile.class).newXmlParser();
-		Profile prof = new FhirContext(Profile.class).newXmlParser().parseResource(Profile.class, str);
-		
 		ProfileParser pp = new ProfileParser();
-		pp.parseSingleProfile(prof, "http://foo");
-		pp.markResourcesForImports();
-		pp.writeAll(new File("target/gen"), "test");
 		
+		String str = IOUtils.toString(new FileReader("../hapi-tinder-test/src/test/resources/profile/organization.xml"));
+		Profile prof = parser.parseResource(Profile.class, str);
+		pp.parseSingleProfile(prof, "http://foo");
+
+		str = IOUtils.toString(new FileReader("../hapi-tinder-test/src/test/resources/profile/patient.xml"));
+		prof = parser.parseResource(Profile.class, str);
+		pp.parseSingleProfile(prof, "http://foo");
+
+		pp.markResourcesForImports();
+		pp.writeAll(new File("target/gen/test/resource"), "test");
+
 	}
 
 }

hapi-tinder-plugin/src/main/java/ca/uhn/fhir/tinder/TinderStructuresMojo.java

@@ -34,14 +34,37 @@ public class TinderStructuresMojo extends AbstractMojo {
 	private String packageName;
 
 	@Parameter(required = false)
-	private List<String> resourceProfileFiles;
+	private List<ProfileFileDefinition> resourceProfileFiles;
 
 	@Parameter(required = false)
-	private List<String> resourceValueSetFiles;
+	private List<ValueSetFileDefinition> resourceValueSetFiles;
 
 	@Parameter(required = true, defaultValue = "${project.build.directory}/generated-sources/tinder")
 	private String targetDirectory;
 
+	public static class ProfileFileDefinition
+	{
+		@Parameter(required = true)
+		private String profileFile;
+		
+		@Parameter(required = true)
+		private String profileSourceUrl;
+	}
+
+	public static class ValueSetFileDefinition
+	{
+		@Parameter(required = true)
+		private String valueSetFile;
+
+		public String getValueSetFile() {
+			return valueSetFile;
+		}
+
+		public void setValueSetFile(String theValueSetFile) {
+			valueSetFile = theValueSetFile;
+		}
+	}
+
 	@Override
 	public void execute() throws MojoExecutionException, MojoFailureException {
 		if (StringUtils.isBlank(packageName)) {
@@ -105,7 +128,9 @@ public class TinderStructuresMojo extends AbstractMojo {
 		if (resourceProfileFiles != null) {
 			ourLog.info("Loading profiles...");
 			ProfileParser pp = new ProfileParser();
-			pp.parseBaseResources(resourceProfileFiles);
+			for (ProfileFileDefinition next : resourceProfileFiles) {
+				pp.parseSingleProfile(new File(next.profileFile), next.profileSourceUrl);
+			}
 			
 			pp.bindValueSets(vsp);
 			pp.markResourcesForImports();
@@ -134,11 +159,11 @@ public class TinderStructuresMojo extends AbstractMojo {
 		return packageName;
 	}
 
-	public List<String> getResourceProfileFiles() {
+	public List<ProfileFileDefinition> getResourceProfileFiles() {
 		return resourceProfileFiles;
 	}
 
-	public List<String> getResourceValueSetFiles() {
+	public List<ValueSetFileDefinition> getResourceValueSetFiles() {
 		return resourceValueSetFiles;
 	}
 
@@ -162,11 +187,11 @@ public class TinderStructuresMojo extends AbstractMojo {
 		packageName = thePackageName;
 	}
 
-	public void setResourceProfileFiles(List<String> theResourceProfileFiles) {
+	public void setResourceProfileFiles(List<ProfileFileDefinition> theResourceProfileFiles) {
 		resourceProfileFiles = theResourceProfileFiles;
 	}
 
-	public void setResourceValueSetFiles(List<String> theResourceValueSetFiles) {
+	public void setResourceValueSetFiles(List<ValueSetFileDefinition> theResourceValueSetFiles) {
 		resourceValueSetFiles = theResourceValueSetFiles;
 	}
 

hapi-tinder-plugin/src/main/java/ca/uhn/fhir/tinder/ValueSetGenerator.java

@@ -30,12 +30,13 @@ import ca.uhn.fhir.model.dstu.resource.ValueSet.Define;
 import ca.uhn.fhir.model.dstu.resource.ValueSet.DefineConcept;
 import ca.uhn.fhir.model.primitive.CodeDt;
 import ca.uhn.fhir.parser.IParser;
+import ca.uhn.fhir.tinder.TinderStructuresMojo.ValueSetFileDefinition;
 import ca.uhn.fhir.tinder.model.ValueSetTm;
 
 public class ValueSetGenerator {
 
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ValueSetGenerator.class);
-	private List<String> myResourceValueSetFiles;
+	private List<ValueSetFileDefinition> myResourceValueSetFiles;
 	private Set<ValueSetTm> myMarkedValueSets = new HashSet<ValueSetTm>();
 
 	private Map<String, ValueSetTm> myValueSets = new HashMap<String, ValueSetTm>();
@@ -68,8 +69,8 @@ public class ValueSetGenerator {
 		}
 
 		if (myResourceValueSetFiles != null) {
-			for (String next : myResourceValueSetFiles) {
+			for (ValueSetFileDefinition next : myResourceValueSetFiles) {
-				File file = new File(next);
+				File file = new File(next.getValueSetFile());
 				ourLog.info("Parsing ValueSet file: {}" + file.getName());
 				vs = IOUtils.toString(new FileReader(file));
 				ValueSet nextVs = (ValueSet) newXmlParser.parseResource(vs);
@@ -138,8 +139,8 @@ public class ValueSetGenerator {
 		return vs;
 	}
 
-	public void setResourceValueSetFiles(List<String> theString) {
+	public void setResourceValueSetFiles(List<ValueSetFileDefinition> theResourceValueSetFiles) {
-		myResourceValueSetFiles = theString;
+		myResourceValueSetFiles = theResourceValueSetFiles;
 	}
 
 	public void write(Collection<ValueSetTm> theValueSets, File theOutputDirectory, String thePackageBase) throws IOException {

hapi-tinder-plugin/src/main/resources/vm/templates.vm

@@ -8,7 +8,7 @@
 	@Child(name="${child.elementNameSimplified}", order=${foreach.index}, min=${child.cardMin}, max=${child.cardMaxForChildAnnotation}, type={
 #foreach ($nextType in ${child.referenceTypesForMultiple})
 #if ( ${child.resourceRef} && ${nextType} != "IResource" )
-		${packageBase}.resource.${nextType}.class,
+		${nextType}.class,
 #else
 		${nextType}.class,
 #end

hapi-tinder-plugin/src/test/resources/prof/organization.xml

@@ -41,6 +41,16 @@
 				<ordered value="false"/>
 				<rules value="open"/>
 			</slicing>
+			<definition>
+				<short value="Extensions" />
+				<formal value="Extensions" />
+				<min value="0" />
+				<max value="*" />
+				<type>
+					<code value="Extension" />
+				</type>
+				<isModifier value="false" />
+			</definition>
 		</element>
 		<element>
 			<path value="Organization.extension" />

hapi-tinder-test/.classpath

@@ -2,6 +2,7 @@
 <classpath>
 	<classpathentry kind="src" path="target/generated-sources/tinder"/>
 	<classpathentry kind="src" path="src/test/resources"/>
+	<classpathentry kind="src" path="src/test/java"/>
 	<classpathentry combineaccessrules="false" kind="src" path="/hapi-fhir-base"/>
 	<classpathentry kind="var" path="M2_REPO/javax/xml/stream/stax-api/1.0-2/stax-api-1.0-2.jar" sourcepath="M2_REPO/javax/xml/stream/stax-api/1.0-2/stax-api-1.0-2-sources.jar"/>
 	<classpathentry kind="var" path="M2_REPO/javax/servlet/javax.servlet-api/3.1.0/javax.servlet-api-3.1.0.jar" sourcepath="M2_REPO/javax/servlet/javax.servlet-api/3.1.0/javax.servlet-api-3.1.0-sources.jar"/>
@@ -37,5 +38,10 @@
 		</attributes>
 	</classpathentry>
 	<classpathentry kind="var" path="M2_REPO/log4j/log4j/1.2.17/log4j-1.2.17.jar"/>
+	<classpathentry kind="var" path="M2_REPO/junit/junit/4.11/junit-4.11.jar" sourcepath="M2_REPO/junit/junit/4.11/junit-4.11-sources.jar">
+		<attributes>
+			<attribute name="javadoc_location" value="jar:file:/Users/james/.m2/repository/junit/junit/4.11/junit-4.11-javadoc.jar!/"/>
+		</attributes>
+	</classpathentry>
 	<classpathentry kind="output" path="target/classes"/>
 </classpath>

hapi-tinder-test/pom.xml

@@ -21,6 +21,14 @@
 			<artifactId>hapi-fhir-base</artifactId>
 			<version>1.0-SNAPSHOT</version>
 		</dependency>
+		
+		<dependency>
+			<groupId>junit</groupId>
+			<artifactId>junit</artifactId>
+			<version>4.11</version>
+			<scope>test</scope>
+		</dependency>
+		
 	</dependencies>
 
 	<build>
@@ -75,13 +83,24 @@
 						</goals>
 						<configuration>
 							<package>ca.uhn.test.customstructs</package>
+							<profileHttpBase>http://foo</profileHttpBase>
 							<resourceProfileFiles>
-								<resourceProfileFile>src/test/resources/profile/patient.xml</resourceProfileFile>
+								<resourceProfileFile>
-								<resourceProfileFile>src/test/resources/profile/organization.xml</resourceProfileFile>
+									<profileFile>${project.basedir}/src/test/resources/profile/patient.xml</profileFile>
+									<profileSourceUrl>http://foo1</profileSourceUrl>
+								</resourceProfileFile>
+								<resourceProfileFile>
+									<profileFile>${project.basedir}/src/test/resources/profile/organization.xml</profileFile>
+									<profileSourceUrl>http://foo1</profileSourceUrl>
+								</resourceProfileFile>
 							</resourceProfileFiles>
 							<resourceValueSetFiles>
-								<resourceValueSetFile>src/test/resources/valueset/valueset-cgta-patientidpool.xml</resourceValueSetFile>
+								<resourceValueSetFile>
-								<resourceValueSetFile>src/test/resources/valueset/valueset-cgta-provideridpool.xml</resourceValueSetFile>
+									<valueSetFile>${project.basedir}/src/test/resources/valueset/valueset-cgta-patientidpool.xml</valueSetFile>
+								</resourceValueSetFile>
+								<resourceValueSetFile>
+									<valueSetFile>${project.basedir}/src/test/resources/valueset/valueset-cgta-provideridpool.xml</valueSetFile>
+								</resourceValueSetFile>
 							</resourceValueSetFiles>
 						</configuration>
 					</execution>

hapi-tinder-test/src/test/java/test/TestCustomStructures.java

@@ -0,0 +1,32 @@
+package test;
+
+import static org.junit.Assert.*;
+
+import java.io.IOException;
+
+import org.junit.Test;
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.parser.DataFormatException;
+import ca.uhn.test.customstructs.resource.Organization;
+import ca.uhn.test.customstructs.valueset.ConnectingGTAProviderIDNamespacesEnum;
+
+public class TestCustomStructures {
+	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(TestCustomStructures.class);
+	
+	@Test
+	public void testExtension() throws DataFormatException, IOException {
+		
+		Organization org = new Organization();
+		org.addProviderIdPool(ConnectingGTAProviderIDNamespacesEnum.UNIVERSITY_HEALTH_NETWORK_PROVIDER_IDS);
+		
+		FhirContext ctx = new FhirContext(Organization.class);
+		String str = ctx.newXmlParser().encodeResourceToString(org);
+		
+		ourLog.info(str);
+		
+		assertTrue(str.contains("<extension url=\"http://foo1#providerIdPool\"><valueCode value=\"urn:oid:1.3.6.1.4.1.12201.1\"/></extension>"));
+		
+	}
+	
+}

hapi-tinder-test/src/test/resources/profile/organization.xml

@@ -41,6 +41,16 @@
 				<ordered value="false"/>
 				<rules value="open"/>
 			</slicing>
+			<definition>
+				<short value="Extensions" />
+				<formal value="Extensions" />
+				<min value="0" />
+				<max value="*" />
+				<type>
+					<code value="Extension" />
+				</type>
+				<isModifier value="false" />
+			</definition>
 		</element>
 		<element>
 			<path value="Organization.extension" />

pom.xml

@@ -23,7 +23,8 @@
 	<modules>
 		<module>hapi-fhir-base</module>
 		<module>hapi-tinder-plugin</module>
-		<!-- <module>hapi-tinder-test</module> <module>hapi-fhir-structures-dstu</module> -->
+		<module>hapi-tinder-test</module> 
+		<!-- <module>hapi-fhir-structures-dstu</module> -->
 	</modules>
 
 	<properties>