Fix for issues/766 - reverse references with _history in GraphQL (#790)

* Create and use getIdPart

* Add tests and changes for dstu3, r4, r4b, and r5

* Update get/set Id javadoc

Co-authored-by: dotasek <david.otasek@smilecdr.com>

RELEASE_NOTES.md

@@ -4,4 +4,5 @@
 
 ## Other code changes
 
-* no changes
+* Fix reverse references in GraphQL searches
+

org.hl7.fhir.dstu3/src/main/java/org/hl7/fhir/dstu3/model/Resource.java

@@ -111,16 +111,25 @@ public abstract class Resource extends BaseResource implements IAnyResource {
       return this;
     }
 
-    /**
+  /**
-     * @return The logical id of the resource, as used in the URL for the resource. Once assigned, this value never changes.
+   * @return The id value of the resource. Once assigned, this value never
-     */
+   * changes.
+   *
+   * @see IdType
+   * @see IdType#getValue()
+   */
     public String getId() { 
       return this.id == null ? null : this.id.getValue();
     }
 
-    /**
+  /**
-     * @param value The logical id of the resource, as used in the URL for the resource. Once assigned, this value never changes.
+   * @return The most complete id value of the resource, containing all
-     */
+   * available context and history. Once assigned this value never changes.
+   * NOTE: this value is NOT limited to just the logical id property of a
+   * resource id.
+   * @see IdType
+   * @see IdType#getValue()
+   */
     public Resource setId(String value) { 
       if (Utilities.noString(value))
         this.id = null;
@@ -132,6 +141,14 @@ public abstract class Resource extends BaseResource implements IAnyResource {
       return this;
     }
 
+  /**
+   * @return  the logical ID part of this resource's id
+   * @see IdType#getIdPart()
+   */
+  public String getIdPart() {
+    return getIdElement().getIdPart();
+  }
+
     /**
      * @return {@link #meta} (The metadata about the resource. This is content that is maintained by the infrastructure. Changes to the content may not always be associated with version changes to the resource.)
      */

org.hl7.fhir.dstu3/src/main/java/org/hl7/fhir/dstu3/utils/GraphQLEngine.java

@@ -643,7 +643,7 @@ public class GraphQLEngine implements IGraphQLEngine {
     Argument arg = new Argument();
     params.add(arg);
     arg.setName(getSingleValue(parg));
-    arg.addValue(new StringValue(source.fhirType()+"/"+source.getId()));
+    arg.addValue(new StringValue(source.fhirType()+"/"+source.getIdPart()));
     services.listResources(appInfo, field.getName().substring(0, field.getName().length() - 4), params, list);
     arg = null;
     ObjectValue obj = null;

org.hl7.fhir.r4/src/main/java/org/hl7/fhir/r4/model/Resource.java

@@ -117,16 +117,25 @@ public abstract class Resource extends BaseResource implements IAnyResource {
       return this;
     }
 
-    /**
+  /**
-     * @return The logical id of the resource, as used in the URL for the resource. Once assigned, this value never changes.
+   * @return The most complete id value of the resource, containing all
-     */
+   * available context and history. Once assigned this value never changes.
+   * NOTE: this value is NOT limited to just the logical id property of a
+   * resource id.
+   * @see IdType
+   * @see IdType#getValue()
+   */
     public String getId() { 
       return this.id == null ? null : this.id.getValue();
     }
 
-    /**
+  /**
-     * @param value The logical id of the resource, as used in the URL for the resource. Once assigned, this value never changes.
+   * @param value The id value of the resource. Once assigned, this value
-     */
+   *              never changes.
+   *
+   * @see IdType
+   * @see IdType#setValue(String)
+   */
     public Resource setId(String value) { 
       if (Utilities.noString(value))
         this.id = null;
@@ -138,6 +147,14 @@ public abstract class Resource extends BaseResource implements IAnyResource {
       return this;
     }
 
+  /**
+   * @return  the logical ID part of this resource's id
+   * @see IdType#getIdPart()
+   */
+    public String getIdPart() {
+      return getIdElement().getIdPart();
+    }
+
     /**
      * @return {@link #meta} (The metadata about the resource. This is content that is maintained by the infrastructure. Changes to the content might not always be associated with version changes to the resource.)
      */

org.hl7.fhir.r4/src/main/java/org/hl7/fhir/r4/test/utils/TestingUtilities.java

@@ -65,7 +65,7 @@ import com.google.gson.JsonPrimitive;
 import com.google.gson.JsonSyntaxException;
 
 public class TestingUtilities {
-  private static final boolean SHOW_DIFF = true;
+  private static final boolean SHOW_DIFF = false;
   
 	static public IWorkerContext fcontext;
 	
@@ -74,7 +74,7 @@ public class TestingUtilities {
 	    FilesystemPackageCacheManager pcm;
 	    try {
 	      pcm = new FilesystemPackageCacheManager(true, ToolsVersion.TOOLS_VERSION);
-	      fcontext = SimpleWorkerContext.fromPackage(pcm.loadPackage("hl7.fhir.core", "4.0.0"));
+	      fcontext = SimpleWorkerContext.fromPackage(pcm.loadPackage("hl7.fhir.r4.core", "4.0.1"));
 	      fcontext.setUcumService(new UcumEssenceService(TestingUtilities.resourceNameToFile("ucum", "ucum-essence.xml")));
 	      fcontext.setExpansionProfile(new Parameters());
 	    } catch (Exception e) {

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

@@ -507,7 +507,7 @@ public class GraphQLEngine implements IGraphQLEngine {
     Argument arg = new Argument();
     params.add(arg);
     arg.setName(getSingleValue(parg));
-    arg.addValue(new StringValue(source.fhirType() + "/" + source.getId()));
+    arg.addValue(new StringValue(source.fhirType() + "/" + source.getIdPart()));
     services.listResources(appInfo, field.getName().substring(0, field.getName().length() - 4), params, list);
     arg = null;
     ObjectValue obj = null;

org.hl7.fhir.r4/src/test/java/org/hl7/fhir/r4/test/GraphQLEngineTests.java

@@ -14,13 +14,11 @@ import org.hl7.fhir.r4.test.utils.TestingUtilities;
 import org.hl7.fhir.r4.utils.GraphQLEngine;
 import org.hl7.fhir.utilities.TextFile;
 import org.hl7.fhir.utilities.Utilities;
-import org.hl7.fhir.utilities.graphql.Argument;
+import org.hl7.fhir.utilities.graphql.*;
-import org.hl7.fhir.utilities.graphql.IGraphQLStorageServices;
-import org.hl7.fhir.utilities.graphql.NameValue;
-import org.hl7.fhir.utilities.graphql.Parser;
 import org.hl7.fhir.utilities.xml.XMLUtil;
 import org.junit.jupiter.api.Assertions;
 import org.junit.jupiter.api.Disabled;
+import org.junit.jupiter.api.Test;
 import org.junit.jupiter.params.ParameterizedTest;
 import org.junit.jupiter.params.provider.Arguments;
 import org.junit.jupiter.params.provider.MethodSource;
@@ -37,7 +35,7 @@ import java.util.ArrayList;
 import java.util.List;
 import java.util.stream.Stream;
 
-@Disabled
+
 public class GraphQLEngineTests implements IGraphQLStorageServices {
 
   public static Stream<Arguments> data() throws FileNotFoundException, IOException, ParserConfigurationException, SAXException {
@@ -52,6 +50,7 @@ public class GraphQLEngineTests implements IGraphQLStorageServices {
     return objects.stream();
   }
 
+  @Disabled
   @ParameterizedTest(name = "{index}: {0}")
   @MethodSource("data")
   public void test(String name, String source, String output, String context, String resource, String operation) throws Exception {
@@ -66,12 +65,35 @@ public class GraphQLEngineTests implements IGraphQLStorageServices {
         filename = TestingUtilities.resourceNameToFile(parts[0].toLowerCase() + "-" + parts[1].toLowerCase() + ".xml");
     }
 
+    Resource parsedResource = !Utilities.noString( filename ) ? new XmlParser().parse(new FileInputStream(filename)) : null;
+
+    testResource(parsedResource, output, source);
+  }
+
+  @Test
+  public void testReferenceReverseHistory() throws IOException, EGraphEngine, EGraphQLException {
+
+    String context = "Patient/example/$graphql";
+    String source = "reference-reverse.gql";
+    String output= "reference-reverse-history.json";
+
+    String[] parts = context.split("/");
+    String filename = TestingUtilities.resourceNameToFile(parts[0].toLowerCase() + "-" + parts[1].toLowerCase() + ".xml");
+
+    Resource parsedResource = new XmlParser().parse(new FileInputStream(filename));
+    parsedResource.setId("example/_history/1");
+
+    testResource(parsedResource, output, source);
+  }
+
+  private void testResource(Resource resource, String output, String source) throws IOException, EGraphEngine, EGraphQLException {
     GraphQLEngine gql = new GraphQLEngine(TestingUtilities.context());
     gql.setServices(this);
-    if (!Utilities.noString(filename))
+    if (resource != null) {
-      gql.setFocus(new XmlParser().parse(new FileInputStream(filename)));
+      gql.setFocus(resource);
+    }
     gql.setGraphQL(Parser.parseFile(TestingUtilities.resourceNameToFile("graphql", source)));
-    gql.getGraphQL().setOperationName(operation);
+    gql.getGraphQL().setOperationName(null);
     gql.getGraphQL().getVariables().add(new Argument("var", new NameValue("true")));
     boolean ok = false;
     String msg = null;
@@ -134,8 +156,9 @@ public class GraphQLEngineTests implements IGraphQLStorageServices {
 
   @Override
   public void listResources(Object appInfo, String type, List<Argument> searchParams, List<IBaseResource> matches) throws FHIRException {
+
     try {
-      if (type.equals("Condition"))
+      if (type.equals("Condition") && searchParams.get(0).hasValue("Patient/example"))
         matches.add(new XmlParser().parse(new FileInputStream(TestingUtilities.resourceNameToFile("condition-example.xml"))));
       else if (type.equals("Patient")) {
         matches.add(new XmlParser().parse(new FileInputStream(TestingUtilities.resourceNameToFile("patient-example.xml"))));

org.hl7.fhir.r4/src/test/resources/graphql/reference-reverse-history.json

@@ -0,0 +1,6 @@
+{
+  "id":"example/_history/1",
+  "ConditionList":[{
+    "id":"example"
+  }]
+}

org.hl7.fhir.r4b/src/main/java/org/hl7/fhir/r4b/model/Resource.java

@@ -119,15 +119,24 @@ public abstract class Resource extends BaseResource implements IAnyResource {
       return this;
     }
 
-    /**
+  /**
-     * @return The logical id of the resource, as used in the URL for the resource. Once assigned, this value never changes.
+   * @return The most complete id value of the resource, containing all
-     */
+   * available context and history. Once assigned this value never changes.
+   * NOTE: this value is NOT limited to just the logical id property of a
+   * resource id.
+   * @see IdType
+   * @see IdType#getValue()
+   */
     public String getId() { 
       return this.id == null ? null : this.id.getValue();
     }
 
     /**
-     * @param value The logical id of the resource, as used in the URL for the resource. Once assigned, this value never changes.
+     * @param value The id value of the resource. Once assigned, this value
+     *              never changes.
+     *
+     * @see IdType
+     * @see IdType#setValue(String)
      */
     public Resource setId(String value) { 
       if (Utilities.noString(value))
@@ -140,6 +149,14 @@ public abstract class Resource extends BaseResource implements IAnyResource {
       return this;
     }
 
+  /**
+   * @return the logical ID part of this resource's id
+   * @see IdType#getIdPart()
+   */
+  public String getIdPart() {
+      return getIdElement().getIdPart();
+    }
+
     /**
      * @return {@link #meta} (The metadata about the resource. This is content that is maintained by the infrastructure. Changes to the content might not always be associated with version changes to the resource.)
      */

org.hl7.fhir.r4b/src/main/java/org/hl7/fhir/r4b/utils/GraphQLEngine.java

@@ -674,7 +674,7 @@ public class GraphQLEngine implements IGraphQLEngine {
     Argument arg = new Argument();
     params.add(arg);
     arg.setName(getSingleValue(parg));
-    arg.addValue(new StringValue(source.fhirType()+"/"+source.getId()));
+    arg.addValue(new StringValue(source.fhirType()+"/"+source.getIdPart()));
     services.listResources(appInfo, field.getName().substring(0, field.getName().length() - 4), params, list);
     arg = null;
     ObjectValue obj = null;

org.hl7.fhir.r4b/src/test/java/org/hl7/fhir/r4b/test/GraphQLEngineTests.java

@@ -24,12 +24,11 @@ import org.hl7.fhir.r4b.test.utils.TestingUtilities;
 import org.hl7.fhir.r4b.utils.GraphQLEngine;
 import org.hl7.fhir.utilities.TextFile;
 import org.hl7.fhir.utilities.Utilities;
-import org.hl7.fhir.utilities.graphql.Argument;
+import org.hl7.fhir.utilities.graphql.*;
-import org.hl7.fhir.utilities.graphql.IGraphQLStorageServices;
-import org.hl7.fhir.utilities.graphql.NameValue;
-import org.hl7.fhir.utilities.graphql.Parser;
 import org.hl7.fhir.utilities.xml.XMLUtil;
 import org.junit.jupiter.api.Assertions;
+import org.junit.jupiter.api.Disabled;
+import org.junit.jupiter.api.Test;
 import org.junit.jupiter.params.ParameterizedTest;
 import org.junit.jupiter.params.provider.Arguments;
 import org.junit.jupiter.params.provider.MethodSource;
@@ -65,10 +64,17 @@ public class GraphQLEngineTests implements IGraphQLStorageServices {
         stream = TestingUtilities.loadTestResourceStream("r4b", parts[0].toLowerCase()+"-"+parts[1].toLowerCase()+".xml");
     }
 
+    Resource parsedResource =  stream != null ? new XmlParser().parse(stream) : null;
+
+    testResource(parsedResource, output, source, operation);
+  }
+
+  private void testResource(Resource resource, String output, String source, String operation) throws IOException, EGraphEngine, EGraphQLException {
     GraphQLEngine gql = new GraphQLEngine(TestingUtilities.context());
     gql.setServices(this);
-    if (stream != null)
+    if (resource != null) {
-      gql.setFocus(new XmlParser().parse(stream));
+      gql.setFocus(resource);
+    }
     gql.setGraphQL(Parser.parse(TestingUtilities.loadTestResource("r4b", "graphql", source)));
     gql.getGraphQL().setOperationName(operation);
     gql.getGraphQL().getVariables().add(new Argument("var", new NameValue("true")));
@@ -85,12 +91,12 @@ public class GraphQLEngineTests implements IGraphQLStorageServices {
     }
     if (ok) {
       Assertions.assertTrue(!output.equals("$error"), "Expected to fail, but didn't");
-      StringBuilder str = new StringBuilder();
+      StringBuilder actualStringBuilder = new StringBuilder();
       gql.getOutput().setWriteWrapper(false);
-      gql.getOutput().write(str, 0);
+      gql.getOutput().write(actualStringBuilder, 0);
       IOUtils.copy(TestingUtilities.loadTestResourceStream("r4b", "graphql", source), new FileOutputStream(TestingUtilities.tempFile("graphql", source)));
       IOUtils.copy(TestingUtilities.loadTestResourceStream("r4b", "graphql", output), new FileOutputStream(TestingUtilities.tempFile("graphql", output)));
-      TextFile.stringToFile(str.toString(), TestingUtilities.tempFile("graphql", output+".out"));
+      TextFile.stringToFile(actualStringBuilder.toString(), TestingUtilities.tempFile("graphql", output+".out"));
       msg = TestingUtilities.checkJsonIsSame(TestingUtilities.tempFile("graphql", output+".out"), TestingUtilities.tempFile("graphql", output));
       Assertions.assertTrue(Utilities.noString(msg), msg);
     }
@@ -98,6 +104,23 @@ public class GraphQLEngineTests implements IGraphQLStorageServices {
       Assertions.assertTrue(output.equals("$error"), "Error, but proper output was expected ("+msg+")");
   }
 
+  @Test
+  public void testReferenceReverseHistory() throws Exception {
+    String context = "Patient/example/$graphql";
+    String source = "reference-reverse.gql";
+    String output="reference-reverse-history.json";
+
+    String[] parts = context.split("/");
+    InputStream stream  = TestingUtilities.loadTestResourceStream("r4b", parts[0].toLowerCase()+"-"+parts[1].toLowerCase()+".xml");
+
+    Resource parsedResource = new XmlParser().parse(stream);
+
+    //Rather than duplicate the entire resource we modify the ID with a _history path
+    parsedResource.setId("example/_history/1");
+
+    testResource(parsedResource, output, source, null);
+  }
+
   @Override
   public Resource lookup(Object appInfo, String type, String id) throws FHIRException  {
     try {
@@ -136,7 +159,7 @@ public class GraphQLEngineTests implements IGraphQLStorageServices {
   @Override
   public void listResources(Object appInfo, String type, List<Argument> searchParams, List<IBaseResource> matches) throws FHIRException {
     try {
-      if (type.equals("Condition")) 
+      if (type.equals("Condition") && searchParams.get(0).hasValue("Patient/example"))
         matches.add(new XmlParser().parse(TestingUtilities.loadTestResourceStream("r4b", "condition-example.xml")));
       else if (type.equals("Patient")) {
         matches.add(new XmlParser().parse(TestingUtilities.loadTestResourceStream("r4b", "patient-example.xml")));

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/model/Resource.java

@@ -119,16 +119,25 @@ public abstract class Resource extends BaseResource implements IAnyResource {
       return this;
     }
 
-    /**
+  /**
-     * @return The logical id of the resource, as used in the URL for the resource. Once assigned, this value never changes.
+   * @return The most complete id value of the resource, containing all
-     */
+   * available context and history. Once assigned this value never changes.
+   * NOTE: this value is NOT limited to just the logical id property of a
+   * resource id.
+   * @see IdType
+   * @see IdType#getValue()
+   */
     public String getId() { 
       return this.id == null ? null : this.id.getValue();
     }
 
-    /**
+  /**
-     * @param value The logical id of the resource, as used in the URL for the resource. Once assigned, this value never changes.
+   * @param value The id value of the resource. Once assigned, this value
-     */
+   *              never changes.
+   *
+   * @see IdType
+   * @see IdType#setValue(String)
+   */
     public Resource setId(String value) { 
       if (Utilities.noString(value))
         this.id = null;
@@ -140,6 +149,14 @@ public abstract class Resource extends BaseResource implements IAnyResource {
       return this;
     }
 
+  /**
+   * @return  the logical ID part of this resource's id
+   * @see IdType#getIdPart()
+   */
+  public String getIdPart() {
+    return getIdElement().getIdPart();
+  }
+
     /**
      * @return {@link #meta} (The metadata about the resource. This is content that is maintained by the infrastructure. Changes to the content might not always be associated with version changes to the resource.)
      */
@@ -414,8 +431,8 @@ public abstract class Resource extends BaseResource implements IAnyResource {
           , language);
       }
 
-// Manual code (from Configuration.txt):
+  // Manual code (from Configuration.txt):
-@Override
+  @Override
   public String getIdBase() {
     return getId();
   }

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/utils/GraphQLEngine.java

@@ -673,7 +673,7 @@ public class GraphQLEngine implements IGraphQLEngine {
     Argument arg = new Argument();
     params.add(arg);
     arg.setName(getSingleValue(parg));
-    arg.addValue(new StringValue(source.fhirType()+"/"+source.getId()));
+    arg.addValue(new StringValue(source.fhirType()+"/"+source.getIdPart()));
     services.listResources(appInfo, field.getName().substring(0, field.getName().length() - 4), params, list);
     arg = null;
     ObjectValue obj = null;

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

@@ -25,12 +25,10 @@ import org.hl7.fhir.r5.test.utils.TestingUtilities;
 import org.hl7.fhir.r5.utils.GraphQLEngine;
 import org.hl7.fhir.utilities.TextFile;
 import org.hl7.fhir.utilities.Utilities;
-import org.hl7.fhir.utilities.graphql.Argument;
+import org.hl7.fhir.utilities.graphql.*;
-import org.hl7.fhir.utilities.graphql.IGraphQLStorageServices;
-import org.hl7.fhir.utilities.graphql.NameValue;
-import org.hl7.fhir.utilities.graphql.Parser;
 import org.hl7.fhir.utilities.xml.XMLUtil;
 import org.junit.jupiter.api.Assertions;
+import org.junit.jupiter.api.Test;
 import org.junit.jupiter.params.ParameterizedTest;
 import org.junit.jupiter.params.provider.Arguments;
 import org.junit.jupiter.params.provider.MethodSource;
@@ -66,10 +64,16 @@ public class GraphQLEngineTests implements IGraphQLStorageServices {
         stream = TestingUtilities.loadTestResourceStream("r5", parts[0].toLowerCase()+"-"+parts[1].toLowerCase()+".xml");
     }
 
+    Resource parsedResource =  stream != null ? new XmlParser().parse(stream) : null;
+
+    testResource(parsedResource, output, source, operation);
+  }
+
+  private void testResource(Resource resource, String output, String source, String operation) throws IOException, EGraphEngine, EGraphQLException {
     GraphQLEngine gql = new GraphQLEngine(TestingUtilities.getSharedWorkerContext());
     gql.setServices(this);
-    if (stream != null)
+    if (resource != null)
-      gql.setFocus(new XmlParser().parse(stream));
+      gql.setFocus(resource);
     gql.setGraphQL(Parser.parse(TestingUtilities.loadTestResource("r5", "graphql", source)));
     gql.getGraphQL().setOperationName(operation);
     gql.getGraphQL().getVariables().add(new Argument("var", new NameValue("true")));
@@ -97,6 +101,24 @@ public class GraphQLEngineTests implements IGraphQLStorageServices {
     }
     else
       Assertions.assertTrue(output.equals("$error"), "Error, but proper output was expected ("+msg+")");
+
+  }
+
+  @Test
+  public void testReferenceReverseHistory() throws Exception {
+    String context = "Patient/example/$graphql";
+    String source = "reference-reverse.gql";
+    String output="reference-reverse-history.json";
+
+    String[] parts = context.split("/");
+    InputStream stream  = TestingUtilities.loadTestResourceStream("r5", parts[0].toLowerCase()+"-"+parts[1].toLowerCase()+".xml");
+
+    Resource parsedResource = new XmlParser().parse(stream);
+
+    //Rather than duplicate the entire resource we modify the ID with a _history path
+    parsedResource.setId("example/_history/1");
+
+    testResource(parsedResource, output, source, null);
   }
 
   @Override
@@ -137,7 +159,7 @@ public class GraphQLEngineTests implements IGraphQLStorageServices {
   @Override
   public void listResources(Object appInfo, String type, List<Argument> searchParams, List<IBaseResource> matches) throws FHIRException {
     try {
-      if (type.equals("Condition")) 
+      if (type.equals("Condition") && searchParams.get(0).hasValue("Patient/example"))
         matches.add(new XmlParser().parse(TestingUtilities.loadTestResourceStream("r5", "condition-example.xml")));
       else if (type.equals("Patient")) {
         matches.add(new XmlParser().parse(TestingUtilities.loadTestResourceStream("r5", "patient-example.xml")));

pom.xml

@@ -19,7 +19,7 @@
 
     <properties>
         <hapi_fhir_version>5.4.0</hapi_fhir_version>
-        <validator_test_case_version>1.1.97</validator_test_case_version>
+        <validator_test_case_version>1.1.98-SNAPSHOT</validator_test_case_version>
         <junit_jupiter_version>5.7.1</junit_jupiter_version>
         <junit_platform_launcher_version>1.7.1</junit_platform_launcher_version>
         <maven_surefire_version>3.0.0-M5</maven_surefire_version>