Add a few tests and remove some dead code

hapi-fhir-base/src/main/java/ca/uhn/fhir/model/api/BaseBundle.java

@@ -1,64 +0,0 @@
-package ca.uhn.fhir.model.api;
-
-/*
- * #%L
- * HAPI FHIR - Core Library
- * %%
- * Copyright (C) 2014 - 2019 University Health Network
- * %%
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- *      http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- * #L%
- */
-
-import ca.uhn.fhir.model.primitive.IdDt;
-import ca.uhn.fhir.model.primitive.StringDt;
-import ca.uhn.fhir.util.ElementUtil;
-
-public class BaseBundle extends BaseElement /*implements IElement*/ {
-
-	private static final long serialVersionUID = 3349586533271409727L;
-	private StringDt myAuthorName;
-	private StringDt myAuthorUri;
-	private IdDt myId;
-
-	public StringDt getAuthorName() {
-		if (myAuthorName == null) {
-			myAuthorName = new StringDt();
-		}
-		return myAuthorName;
-	}
-
-	public StringDt getAuthorUri() {
-		if (myAuthorUri == null) {
-			myAuthorUri = new StringDt();
-		}
-		return myAuthorUri;
-	}
-
-	public IdDt getId() {
-		if (myId==null) {
-			myId=new IdDt();
-		}
-		return myId;
-	}
-
-	@Override
-	public boolean isEmpty() {
-		return ElementUtil.isEmpty(myAuthorName, myAuthorUri);
-	}
-
-	public void setId(IdDt theId) {
-		myId = theId;
-	}
-
-}

hapi-fhir-base/src/main/java/ca/uhn/fhir/model/primitive/IdrefDt.java

@@ -1,38 +0,0 @@
-package ca.uhn.fhir.model.primitive;
-
-/*
- * #%L
- * HAPI FHIR - Core Library
- * %%
- * Copyright (C) 2014 - 2019 University Health Network
- * %%
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- *      http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- * #L%
- */
-
-import ca.uhn.fhir.model.api.IElement;
-import ca.uhn.fhir.model.api.annotation.DatatypeDef;
-
-@DatatypeDef(name = "idref")
-public class IdrefDt extends StringDt {
-
-	private IElement myTarget;
-
-	public IElement getTarget() {
-		return myTarget;
-	}
-
-	public void setTarget(IElement theTarget) {
-		myTarget = theTarget;
-	}
-}

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoValueSetR4.java

@@ -145,14 +145,6 @@ public class FhirResourceDaoValueSetR4 extends FhirResourceDaoR4<ValueSet> imple
 		return retVal;
 	}
 
-	private void validateIncludes(String name, List<ConceptSetComponent> listToValidate) {
-		for (ConceptSetComponent nextExclude : listToValidate) {
-			if (isBlank(nextExclude.getSystem()) && !ElementUtil.isEmpty(nextExclude.getConcept(), nextExclude.getFilter())) {
-				throw new InvalidRequestException("ValueSet contains " + name + " criteria with no system defined");
-			}
-		}
-	}
-
 	@Override
 	public ValueSet expandByIdentifier(String theUri, String theFilter) {
 		if (isBlank(theUri)) {

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r5/FhirResourceDaoValueSetR5.java

@@ -151,14 +151,6 @@ public class FhirResourceDaoValueSetR5 extends FhirResourceDaoR5<ValueSet> imple
 		return retVal;
 	}
 
-	private void validateIncludes(String name, List<ConceptSetComponent> listToValidate) {
-		for (ConceptSetComponent nextExclude : listToValidate) {
-			if (isBlank(nextExclude.getSystem()) && !ElementUtil.isEmpty(nextExclude.getConcept(), nextExclude.getFilter())) {
-				throw new InvalidRequestException("ValueSet contains " + name + " criteria with no system defined");
-			}
-		}
-	}
-
 	@Override
 	public ValueSet expandByIdentifier(String theUri, String theFilter) {
 		if (isBlank(theUri)) {

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/r5/JpaConformanceProviderR5.java

@@ -58,7 +58,6 @@ public class JpaConformanceProviderR5 extends org.hl7.fhir.r5.hapi.rest.server.S
 	@CoverageIgnore
 	public JpaConformanceProviderR5(){
 		super();
-		super.setCache(false);
 		setIncludeResourceCounts(true);
 	}
 	
@@ -66,11 +65,10 @@ public class JpaConformanceProviderR5 extends org.hl7.fhir.r5.hapi.rest.server.S
 	 * Constructor
 	 */
 	public JpaConformanceProviderR5(RestfulServer theRestfulServer, IFhirSystemDao<Bundle, Meta> theSystemDao, DaoConfig theDaoConfig) {
-		super(theRestfulServer);
+		super();
 		myRestfulServer = theRestfulServer;
 		mySystemDao = theSystemDao;
 		myDaoConfig = theDaoConfig;
-		super.setCache(false);
 		setIncludeResourceCounts(true);
 		setSearchParamRegistry(theSystemDao.getSearchParamRegistry());
 	}

hapi-fhir-structures-r4/src/main/java/org/hl7/fhir/r4/hapi/rest/server/ServerCapabilityStatementProvider.java

@@ -573,15 +573,6 @@ public class ServerCapabilityStatementProvider extends BaseServerCapabilityState
     // ignore
   }
 
-  private void sortRuntimeSearchParameters(List<RuntimeSearchParam> searchParameters) {
-    Collections.sort(searchParameters, new Comparator<RuntimeSearchParam>() {
-      @Override
-      public int compare(RuntimeSearchParam theO1, RuntimeSearchParam theO2) {
-        return theO1.getName().compareTo(theO2.getName());
-      }
-    });
-  }
-
   private void sortSearchParameters(List<SearchParameter> searchParameters) {
     Collections.sort(searchParameters, new Comparator<SearchParameter>() {
       @Override

hapi-fhir-structures-r5/src/main/java/org/hl7/fhir/r5/hapi/ctx/FhirServerR5.java

@@ -9,7 +9,7 @@ import org.hl7.fhir.r5.hapi.rest.server.ServerProfileProvider;
 public class FhirServerR5 implements IFhirVersionServer {
   @Override
   public ServerCapabilityStatementProvider createServerConformanceProvider(RestfulServer theServer) {
-    return new ServerCapabilityStatementProvider(theServer);
+    return new ServerCapabilityStatementProvider();
   }
 
   @Override

hapi-fhir-structures-r5/src/main/java/org/hl7/fhir/r5/hapi/rest/server/ServerCapabilityStatementProvider.java

@@ -15,8 +15,8 @@ import ca.uhn.fhir.rest.server.RestfulServer;
 import ca.uhn.fhir.rest.server.RestfulServerConfiguration;
 import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
 import ca.uhn.fhir.rest.server.method.*;
-import ca.uhn.fhir.rest.server.method.OperationMethodBinding.ReturnType;
 import ca.uhn.fhir.rest.server.method.SearchParameter;
+import ca.uhn.fhir.rest.server.method.OperationMethodBinding.ReturnType;
 import ca.uhn.fhir.rest.server.util.BaseServerCapabilityStatementProvider;
 import org.apache.commons.lang3.StringUtils;
 import org.hl7.fhir.exceptions.FHIRException;
@@ -77,16 +77,6 @@ public class ServerCapabilityStatementProvider extends BaseServerCapabilityState
     super();
   }
 
-  /**
-   * Constructor
-   *
-   * @deprecated Use no-args constructor instead. Deprecated in 4.0.0
-   */
-  @Deprecated
-  public ServerCapabilityStatementProvider(RestfulServer theRestfulServer) {
-    this();
-  }
-
   /**
    * Constructor - This is intended only for JAX-RS server
    */
@@ -558,33 +548,11 @@ public class ServerCapabilityStatementProvider extends BaseServerCapabilityState
     return op;
   }
 
-  /**
-   * Sets the cache property (default is true). If set to true, the same response will be returned for each invocation.
-   * <p>
-   * See the class documentation for an important note if you are extending this class
-   * </p>
-   *
-   * @deprecated Since 4.0.0 - This method no longer does anything
-   */
-  @Deprecated
-  public ServerCapabilityStatementProvider setCache(boolean theCache) {
-    return this;
-  }
-
   @Override
   public void setRestfulServer(RestfulServer theRestfulServer) {
     // ignore
   }
 
-  private void sortRuntimeSearchParameters(List<RuntimeSearchParam> searchParameters) {
-    Collections.sort(searchParameters, new Comparator<RuntimeSearchParam>() {
-      @Override
-      public int compare(RuntimeSearchParam theO1, RuntimeSearchParam theO2) {
-        return theO1.getName().compareTo(theO2.getName());
-      }
-    });
-  }
-
 	private void sortSearchParameters(List<SearchParameter> searchParameters) {
     Collections.sort(searchParameters, new Comparator<SearchParameter>() {
       @Override

hapi-fhir-structures-r5/src/test/java/ca/uhn/fhir/rest/server/PatientResourceProvider.java

@@ -0,0 +1,183 @@
+
+package ca.uhn.fhir.rest.server;
+
+import ca.uhn.fhir.model.api.Include;
+import ca.uhn.fhir.model.api.annotation.Description;
+import ca.uhn.fhir.rest.annotation.*;
+import ca.uhn.fhir.rest.api.Constants;
+import ca.uhn.fhir.rest.api.SortSpec;
+import ca.uhn.fhir.rest.api.server.IBundleProvider;
+import ca.uhn.fhir.rest.param.*;
+import org.hl7.fhir.r5.model.Organization;
+import org.hl7.fhir.r5.model.Patient;
+import org.hl7.fhir.r5.model.Practitioner;
+
+import java.util.Set;
+
+// import ca.uhn.fhir.model.dstu.resource.Binary;
+// import ca.uhn.fhir.model.dstu2.resource.Bundle;
+// import ca.uhn.fhir.model.api.Bundle;
+
+
+public class PatientResourceProvider implements IResourceProvider
+	{
+
+	@Override
+	public Class<Patient> getResourceType() {
+		return Patient.class;
+	}
+
+	@Search()
+	public IBundleProvider search(
+			javax.servlet.http.HttpServletRequest theServletRequest,
+	
+			@Description(shortDefinition="The resource identity")
+			@OptionalParam(name="_id")
+			StringAndListParam theId, 
+
+			@Description(shortDefinition="The resource language")
+			@OptionalParam(name="_language")
+			StringAndListParam theResourceLanguage, 
+
+			@Description(shortDefinition="Search the contents of the resource's data using a fulltext search")
+			@OptionalParam(name=Constants.PARAM_CONTENT)
+			StringAndListParam theFtContent, 
+
+			@Description(shortDefinition="Search the contents of the resource's narrative using a fulltext search")
+			@OptionalParam(name=Constants.PARAM_TEXT)
+			StringAndListParam theFtText, 
+
+			@Description(shortDefinition="Search for resources which have the given tag")
+			@OptionalParam(name=Constants.PARAM_TAG)
+			TokenAndListParam theSearchForTag, 
+
+			@Description(shortDefinition="Search for resources which have the given security labels")
+			@OptionalParam(name=Constants.PARAM_SECURITY)
+			TokenAndListParam theSearchForSecurity, 
+  
+			@Description(shortDefinition="Search for resources which have the given profile")
+			@OptionalParam(name=Constants.PARAM_PROFILE)
+			UriAndListParam theSearchForProfile, 
+
+  
+			@Description(shortDefinition="A patient identifier")
+			@OptionalParam(name="identifier")
+			TokenAndListParam theIdentifier, 
+  
+			@Description(shortDefinition="A portion of either family or given name of the patient")
+			@OptionalParam(name="name")
+			StringAndListParam theName, 
+  
+			@Description(shortDefinition="A portion of the family name of the patient")
+			@OptionalParam(name="family")
+			StringAndListParam theFamily, 
+  
+			@Description(shortDefinition="A portion of the given name of the patient")
+			@OptionalParam(name="given")
+			StringAndListParam theGiven, 
+  
+			@Description(shortDefinition="A portion of either family or given name using some kind of phonetic matching algorithm")
+			@OptionalParam(name="phonetic")
+			StringAndListParam thePhonetic, 
+  
+			@Description(shortDefinition="The value in any kind of telecom details of the patient")
+			@OptionalParam(name="telecom")
+			TokenAndListParam theTelecom, 
+  
+			@Description(shortDefinition="A value in a phone contact")
+			@OptionalParam(name="phone")
+			TokenAndListParam thePhone, 
+  
+			@Description(shortDefinition="A value in an email contact")
+			@OptionalParam(name="email")
+			TokenAndListParam theEmail, 
+  
+			@Description(shortDefinition="An address in any kind of address/part of the patient")
+			@OptionalParam(name="address")
+			StringAndListParam theAddress, 
+  
+			@Description(shortDefinition="A city specified in an address")
+			@OptionalParam(name="address-city")
+			StringAndListParam theAddress_city, 
+  
+			@Description(shortDefinition="A state specified in an address")
+			@OptionalParam(name="address-state")
+			StringAndListParam theAddress_state, 
+  
+			@Description(shortDefinition="A postalCode specified in an address")
+			@OptionalParam(name="address-postalcode")
+			StringAndListParam theAddress_postalcode, 
+  
+			@Description(shortDefinition="A country specified in an address")
+			@OptionalParam(name="address-country")
+			StringAndListParam theAddress_country, 
+  
+			@Description(shortDefinition="A use code specified in an address")
+			@OptionalParam(name="address-use")
+			TokenAndListParam theAddress_use, 
+  
+			@Description(shortDefinition="Gender of the patient")
+			@OptionalParam(name="gender")
+			TokenAndListParam theGender, 
+  
+			@Description(shortDefinition="Language code (irrespective of use value)")
+			@OptionalParam(name="language")
+			TokenAndListParam theLanguage, 
+  
+			@Description(shortDefinition="The patient's date of birth")
+			@OptionalParam(name="birthdate")
+			DateRangeParam theBirthdate, 
+  
+			@Description(shortDefinition="The organization at which this person is a patient")
+			@OptionalParam(name="organization", targetTypes={  Organization.class   } )
+			ReferenceAndListParam theOrganization, 
+  
+			@Description(shortDefinition="Patient's nominated care provider, could be a care manager, not the organization that manages the record")
+			@OptionalParam(name="careprovider", targetTypes={  Organization.class ,   Practitioner.class   } )
+			ReferenceAndListParam theCareprovider, 
+  
+			@Description(shortDefinition="Whether the patient record is active")
+			@OptionalParam(name="active")
+			TokenAndListParam theActive, 
+  
+			@Description(shortDefinition="The species for animal patients")
+			@OptionalParam(name="animal-species")
+			TokenAndListParam theAnimal_species, 
+  
+			@Description(shortDefinition="The breed for animal patients")
+			@OptionalParam(name="animal-breed")
+			TokenAndListParam theAnimal_breed, 
+  
+			@Description(shortDefinition="All patients linked to the given patient")
+			@OptionalParam(name="link", targetTypes={  Patient.class   } )
+			ReferenceAndListParam theLink, 
+  
+			@Description(shortDefinition="This patient has been marked as deceased, or as a death date entered")
+			@OptionalParam(name="deceased")
+			TokenAndListParam theDeceased, 
+  
+			@Description(shortDefinition="The date of death has been provided and satisfies this search value")
+			@OptionalParam(name="deathdate")
+			DateRangeParam theDeathdate, 
+
+			@IncludeParam(reverse=true)
+			Set<Include> theRevIncludes,
+			@Description(shortDefinition="Only return resources which were last updated as specified by the given range")
+			@OptionalParam(name="_lastUpdated")
+			DateRangeParam theLastUpdated, 
+
+			@IncludeParam(allow= {
+					"Patient:careprovider" , 					"Patient:link" , 					"Patient:organization" , 						"Patient:careprovider" , 					"Patient:link" , 					"Patient:organization" , 						"Patient:careprovider" , 					"Patient:link" , 					"Patient:organization" 					, "*"
+			}) 
+			Set<Include> theIncludes,
+			
+			@Sort 
+			SortSpec theSort,
+			
+			@Count
+			Integer theCount
+	) {
+		return null;
+	}
+
+}

hapi-tinder-plugin/dstu2/fhirversion.properties

@@ -151,7 +151,6 @@ datatype.date=ca.uhn.fhir.model.primitive.DateDt
 datatype.dateTime=ca.uhn.fhir.model.primitive.DateTimeDt
 datatype.decimal=ca.uhn.fhir.model.primitive.DecimalDt
 datatype.id=ca.uhn.fhir.model.primitive.IdDt
-datatype.idref=ca.uhn.fhir.model.primitive.IdrefDt
 datatype.instant=ca.uhn.fhir.model.primitive.InstantDt
 datatype.integer=ca.uhn.fhir.model.primitive.IntegerDt
 datatype.markdown=ca.uhn.fhir.model.primitive.MarkdownDt

hapi-tinder-plugin/src/main/resources/ca/uhn/fhir/model/dstu2/fhirversion.properties

@@ -146,7 +146,6 @@ datatype.date=ca.uhn.fhir.model.primitive.DateDt
 datatype.dateTime=ca.uhn.fhir.model.primitive.DateTimeDt
 datatype.decimal=ca.uhn.fhir.model.primitive.DecimalDt
 datatype.id=ca.uhn.fhir.model.primitive.IdDt
-datatype.idref=ca.uhn.fhir.model.primitive.IdrefDt
 datatype.instant=ca.uhn.fhir.model.primitive.InstantDt
 datatype.integer=ca.uhn.fhir.model.primitive.IntegerDt
 datatype.markdown=ca.uhn.fhir.model.primitive.MarkdownDt