Ongoing wrk

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/dstu3/BaseDstu3Config.java

@@ -81,7 +81,7 @@ public FhirContext fhirContextDstu3() {
 	@Bean(name = GRAPHQL_PROVIDER_NAME)
 	@Lazy
 	public GraphQLProvider graphQLProvider(ISearchParamRegistry theSearchParamRegistry) {
-		return new GraphQLProviderWithIntrospection(fhirContextDstu3(), validationSupportChain(), graphqlStorageServices(), theSearchParamRegistry);
+		return new GraphQLProviderWithIntrospection(fhirContextDstu3(), validationSupportChain(), graphqlStorageServices(), theSearchParamRegistry, daoRegistry());
 	}
 
 	@Bean

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/r4/BaseR4Config.java

@@ -87,7 +87,7 @@ public ITransactionProcessorVersionAdapter transactionProcessorVersionFacade() {
 	@Bean(name = GRAPHQL_PROVIDER_NAME)
 	@Lazy
 	public GraphQLProvider graphQLProvider(ISearchParamRegistry theSearchParamRegistry) {
-		return new GraphQLProviderWithIntrospection(fhirContextR4(), validationSupportChain(), graphqlStorageServices(), theSearchParamRegistry);
+		return new GraphQLProviderWithIntrospection(fhirContextR4(), validationSupportChain(), graphqlStorageServices(), theSearchParamRegistry, daoRegistry());
 	}
 
 	@Bean(name = "myResourceCountsCache")

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/r5/BaseR5Config.java

@@ -85,7 +85,7 @@ public ITransactionProcessorVersionAdapter transactionProcessorVersionFacade() {
 	@Bean(name = GRAPHQL_PROVIDER_NAME)
 	@Lazy
 	public GraphQLProvider graphQLProvider(ISearchParamRegistry theSearchParamRegistry) {
-		return new GraphQLProviderWithIntrospection(fhirContextR5(), validationSupportChain(), graphqlStorageServices(), theSearchParamRegistry);
+		return new GraphQLProviderWithIntrospection(fhirContextR5(), validationSupportChain(), graphqlStorageServices(), theSearchParamRegistry, daoRegistry());
 	}
 
 	@Bean(name = "myResourceCountsCache")

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/graphql/GraphQLProviderWithIntrospection.java

@@ -23,8 +23,10 @@
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.context.RuntimeSearchParam;
 import ca.uhn.fhir.context.support.IValidationSupport;
+import ca.uhn.fhir.jpa.api.IDaoRegistry;
 import ca.uhn.fhir.rest.api.server.RequestDetails;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
+import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
 import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
 import ca.uhn.fhir.rest.server.util.ISearchParamRegistry;
 import ca.uhn.fhir.util.StringUtil;
@@ -58,9 +60,12 @@
 import java.io.Writer;
 import java.util.ArrayList;
 import java.util.Collection;
+import java.util.Collections;
 import java.util.EnumSet;
+import java.util.HashSet;
 import java.util.List;
 import java.util.Map;
+import java.util.stream.Collectors;
 
 import static ca.uhn.fhir.util.MessageSupplier.msg;
 
@@ -71,15 +76,17 @@ public class GraphQLProviderWithIntrospection extends GraphQLProvider {
 	private final IValidationSupport myValidationSupport;
 	private final ISearchParamRegistry mySearchParamRegistry;
 	private final VersionSpecificWorkerContextWrapper myContext;
+	private final IDaoRegistry myDaoRegistry;
 
 	/**
 	 * Constructor
 	 */
-	public GraphQLProviderWithIntrospection(FhirContext theFhirContext, IValidationSupport theValidationSupport, IGraphQLStorageServices theIGraphQLStorageServices, ISearchParamRegistry theSearchParamRegistry) {
+	public GraphQLProviderWithIntrospection(FhirContext theFhirContext, IValidationSupport theValidationSupport, IGraphQLStorageServices theIGraphQLStorageServices, ISearchParamRegistry theSearchParamRegistry, IDaoRegistry theDaoRegistry) {
 		super(theFhirContext, theValidationSupport, theIGraphQLStorageServices);
 
 		myValidationSupport = theValidationSupport;
 		mySearchParamRegistry = theSearchParamRegistry;
+		myDaoRegistry = theDaoRegistry;
 
 		myContext = VersionSpecificWorkerContextWrapper.newVersionSpecificWorkerContextWrapper(theValidationSupport);
 		myGenerator = new GraphQLSchemaGenerator(myContext, VersionUtil.getVersion());
@@ -95,27 +102,39 @@ public String processGraphQlPostRequest(ServletRequestDetails theServletRequestD
 		if (theQueryBody.contains("__schema")) {
 			EnumSet<GraphQLSchemaGenerator.FHIROperationType> operations;
 			if (theId != null) {
-				operations = EnumSet.of(GraphQLSchemaGenerator.FHIROperationType.READ);
+				throw new InvalidRequestException("GraphQL introspection not supported at instance level. Please try at server- or instance- level.");
+			}
+
+			operations = EnumSet.of(GraphQLSchemaGenerator.FHIROperationType.READ, GraphQLSchemaGenerator.FHIROperationType.SEARCH);
+
+			Collection<String> resourceTypes;
+			if (theRequestDetails.getResourceName() != null) {
+				resourceTypes = Collections.singleton(theRequestDetails.getResourceName());
 			} else {
-				operations = EnumSet.of(GraphQLSchemaGenerator.FHIROperationType.SEARCH);
+				resourceTypes = new HashSet<>();
+				for (String next : myContext.getResourceNames()) {
+					if (myDaoRegistry.isResourceTypeSupported(next)) {
+						resourceTypes.add(next);
+					}
+				}
+				resourceTypes = resourceTypes
+					.stream()
+					.sorted()
+					.collect(Collectors.toList());
 			}
-			return generateSchema(theQueryBody, theRequestDetails.getResourceName(), operations);
+
+			return generateSchema(theQueryBody, resourceTypes, operations);
 		} else {
 			return super.processGraphQlPostRequest(theServletRequestDetails, theRequestDetails, theId, theQueryBody);
 		}
 	}
 
-	private String generateSchema(String theQueryBody, String theResourceName, EnumSet<GraphQLSchemaGenerator.FHIROperationType> theOperations) {
+	private String generateSchema(String theQueryBody, Collection<String> theResourceTypes, EnumSet<GraphQLSchemaGenerator.FHIROperationType> theOperations) {
 
 		final StringBuilder schemaBuilder = new StringBuilder();
 		try (Writer writer = new StringBuilderWriter(schemaBuilder)) {
 			// Generate FHIR base types schemas
-			myGenerator.generateTypes(writer);
-
-			// Generate schemas for the resource type
-			StructureDefinition sd = fetchStructureDefinition(theResourceName);
-			List<SearchParameter> parameters = toR5SearchParams(mySearchParamRegistry.getActiveSearchParams(theResourceName).values());
-			myGenerator.generateResource(writer, sd, parameters, theOperations);
+			myGenerator.generateTypes(writer, theOperations);
 
 			// Fix up a few things that are missing from the generated schema
 			writer
@@ -127,17 +146,29 @@ private String generateSchema(String theQueryBody, String theResourceName, EnumS
 				.append("\n  id: [token]" + "\n}")
 				.append("\n");
 
-			writer.append("\ntype Query {");
-			if (theOperations.contains(GraphQLSchemaGenerator.FHIROperationType.READ)) {
-				writer
-					.append("\n  ")
-					.append(theResourceName)
-					.append("(id: String): ")
-					.append(theResourceName);
+			// Generate schemas for the resource types
+			for (String nextResourceType : theResourceTypes) {
+				StructureDefinition sd = fetchStructureDefinition(nextResourceType);
+				List<SearchParameter> parameters = toR5SearchParams(mySearchParamRegistry.getActiveSearchParams(nextResourceType).values());
+				myGenerator.generateResource(writer, sd, parameters, theOperations);
 			}
-			if (theOperations.contains(GraphQLSchemaGenerator.FHIROperationType.SEARCH)) {
-				myGenerator.generateListAccessQuery(writer, parameters, theResourceName);
-				myGenerator.generateConnectionAccessQuery(writer, parameters, theResourceName);
+
+			// Generate queries
+			writer.append("\ntype Query {");
+			for (String nextResourceType : theResourceTypes) {
+				if (theOperations.contains(GraphQLSchemaGenerator.FHIROperationType.READ)) {
+					writer
+						.append("\n  ")
+						.append(nextResourceType)
+						.append("(id: String): ")
+						.append(nextResourceType)
+						.append("\n");
+				}
+				if (theOperations.contains(GraphQLSchemaGenerator.FHIROperationType.SEARCH)) {
+					List<SearchParameter> parameters = toR5SearchParams(mySearchParamRegistry.getActiveSearchParams(nextResourceType).values());
+					myGenerator.generateListAccessQuery(writer, parameters, nextResourceType);
+					myGenerator.generateConnectionAccessQuery(writer, parameters, nextResourceType);
+				}
 			}
 			writer.append("\n}");
 
@@ -148,6 +179,7 @@ private String generateSchema(String theQueryBody, String theResourceName, EnumS
 
 		String schema = schemaBuilder.toString().replace("\r", "");
 
+		// Set these to INFO if you're testing, then set back before committing
 		ourLog.debug("Schema generated: {} chars", schema.length());
 		ourLog.debug("Schema generated: {}", msg(() -> StringUtil.prependLineNumbers(schema)));
 

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/GraphQLR4Test.java

@@ -1,5 +1,6 @@
 package ca.uhn.fhir.jpa.provider.r4;
 
+import ca.uhn.fhir.util.FileUtil;
 import ca.uhn.fhir.util.TestUtil;
 import ca.uhn.fhir.util.UrlUtil;
 import org.apache.commons.io.IOUtils;
@@ -10,7 +11,9 @@
 import org.apache.http.entity.StringEntity;
 import org.hl7.fhir.instance.model.api.IIdType;
 import org.hl7.fhir.r4.model.Patient;
+import org.junit.jupiter.api.MethodOrderer;
 import org.junit.jupiter.api.Test;
+import org.junit.jupiter.api.TestMethodOrder;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -24,16 +27,39 @@
 import static org.hamcrest.Matchers.not;
 import static org.junit.jupiter.api.Assertions.assertEquals;
 
+@TestMethodOrder(MethodOrderer.MethodName.class)
 public class GraphQLR4Test extends BaseResourceProviderR4Test {
 	public static final String INTROSPECTION_QUERY = "{\"query\":\"\\n    query IntrospectionQuery {\\n      __schema {\\n        queryType { name }\\n        mutationType { name }\\n        subscriptionType { name }\\n        types {\\n          ...FullType\\n        }\\n        directives {\\n          name\\n          description\\n          locations\\n          args {\\n            ...InputValue\\n          }\\n        }\\n      }\\n    }\\n\\n    fragment FullType on __Type {\\n      kind\\n      name\\n      description\\n      fields(includeDeprecated: true) {\\n        name\\n        description\\n        args {\\n          ...InputValue\\n        }\\n        type {\\n          ...TypeRef\\n        }\\n        isDeprecated\\n        deprecationReason\\n      }\\n      inputFields {\\n        ...InputValue\\n      }\\n      interfaces {\\n        ...TypeRef\\n      }\\n      enumValues(includeDeprecated: true) {\\n        name\\n        description\\n        isDeprecated\\n        deprecationReason\\n      }\\n      possibleTypes {\\n        ...TypeRef\\n      }\\n    }\\n\\n    fragment InputValue on __InputValue {\\n      name\\n      description\\n      type { ...TypeRef }\\n      defaultValue\\n    }\\n\\n    fragment TypeRef on __Type {\\n      kind\\n      name\\n      ofType {\\n        kind\\n        name\\n        ofType {\\n          kind\\n          name\\n          ofType {\\n            kind\\n            name\\n            ofType {\\n              kind\\n              name\\n              ofType {\\n                kind\\n                name\\n                ofType {\\n                  kind\\n                  name\\n                  ofType {\\n                    kind\\n                    name\\n                  }\\n                }\\n              }\\n            }\\n          }\\n        }\\n      }\\n    }\\n  \",\"operationName\":\"IntrospectionQuery\"}";
 	private Logger ourLog = LoggerFactory.getLogger(GraphQLR4Test.class);
 	private IIdType myPatientId0;
 
 	@Test
-	public void testIntrospectRead_Patient() throws IOException {
+	public void testInstance_Read_Patient() throws IOException {
 		initTestPatients();
 
-		String uri = ourServerBase + "/Patient/1/$graphql";
+		String query = "{name{family,given}}";
+		HttpGet httpGet = new HttpGet(ourServerBase + "/Patient/" + myPatientId0.getIdPart() + "/$graphql?query=" + UrlUtil.escapeUrlParam(query));
+
+		try (CloseableHttpResponse response = ourHttpClient.execute(httpGet)) {
+			String resp = IOUtils.toString(response.getEntity().getContent(), StandardCharsets.UTF_8);
+			ourLog.info(resp);
+			assertEquals(TestUtil.stripWhitespace(DATA_PREFIX + "{\n" +
+				"  \"name\":[{\n" +
+				"    \"family\":\"FAM\",\n" +
+				"    \"given\":[\"GIVEN1\",\"GIVEN2\"]\n" +
+				"  },{\n" +
+				"    \"given\":[\"GivenOnly1\",\"GivenOnly2\"]\n" +
+				"  }]\n" +
+				"}" + DATA_SUFFIX), TestUtil.stripWhitespace(resp));
+		}
+
+	}
+
+	@Test
+	public void testType_Introspect_Patient() throws IOException {
+		initTestPatients();
+
+		String uri = ourServerBase + "/Patient/$graphql";
 		HttpPost httpGet = new HttpPost(uri);
 		httpGet.setEntity(new StringEntity(INTROSPECTION_QUERY, ContentType.APPLICATION_JSON));
 
@@ -44,17 +70,22 @@ public void testIntrospectRead_Patient() throws IOException {
 				String resp = IOUtils.toString(response.getEntity().getContent(), StandardCharsets.UTF_8);
 				ourLog.info(resp);
 				assertEquals(200, response.getStatusLine().getStatusCode());
-				assertThat(resp, containsString("{\"kind\":\"OBJECT\",\"name\":\"Query\",\"fields\":[{\"name\":\"Patient\""));
-				assertThat(resp, not(containsString("\"PatientList\"")));
+				assertThat(resp, containsString("{\"kind\":\"OBJECT\",\"name\":\"Patient\","));
+				assertThat(resp, not(containsString("{\"kind\":\"OBJECT\",\"name\":\"Observation\",")));
+				assertThat(resp, not(containsString("\"name\":\"Observation\",\"args\":[{\"name\":\"id\"")));
+				assertThat(resp, not(containsString("\"name\":\"ObservationList\",\"args\":[{\"name\":\"_filter\"")));
+				assertThat(resp, not(containsString("\"name\":\"ObservationConnection\",\"fields\":[{\"name\":\"count\"")));
+				assertThat(resp, containsString("\"name\":\"Patient\",\"args\":[{\"name\":\"id\""));
+				assertThat(resp, containsString("\"name\":\"PatientList\",\"args\":[{\"name\":\"_filter\""));
 			}
 		}
 	}
 
 	@Test
-	public void testIntrospectSearch_Patient() throws IOException {
+	public void testType_Introspect_Observation() throws IOException {
 		initTestPatients();
 
-		String uri = ourServerBase + "/Patient/$graphql";
+		String uri = ourServerBase + "/Observation/$graphql";
 		HttpPost httpGet = new HttpPost(uri);
 		httpGet.setEntity(new StringEntity(INTROSPECTION_QUERY, ContentType.APPLICATION_JSON));
 
@@ -65,20 +96,23 @@ public void testIntrospectSearch_Patient() throws IOException {
 				String resp = IOUtils.toString(response.getEntity().getContent(), StandardCharsets.UTF_8);
 				ourLog.info(resp);
 				assertEquals(200, response.getStatusLine().getStatusCode());
-				assertThat(resp, containsString("{\"kind\":\"OBJECT\",\"name\":\"Patient\","));
-				assertThat(resp, not(containsString("{\"kind\":\"OBJECT\",\"name\":\"Observation\",")));
-				assertThat(resp, not(containsString("{\"kind\":\"OBJECT\",\"name\":\"Query\",\"fields\":[{\"name\":\"Patient\"")));
-				assertThat(resp, containsString("{\"kind\":\"OBJECT\",\"name\":\"Query\",\"fields\":[{\"name\":\"PatientList\""));
-				assertThat(resp, not(containsString("{\"kind\":\"OBJECT\",\"name\":\"Query\",\"fields\":[{\"name\":\"ObservationList\"")));
+				assertThat(resp, not(containsString("{\"kind\":\"OBJECT\",\"name\":\"Patient\",")));
+				assertThat(resp, containsString("{\"kind\":\"OBJECT\",\"name\":\"Observation\","));
+				assertThat(resp, not(containsString("{\"kind\":\"OBJECT\",\"name\":\"Query\",\"fields\":[{\"name\":\"PatientList\"")));
+				assertThat(resp, containsString("\"name\":\"Observation\",\"args\":[{\"name\":\"id\""));
+				assertThat(resp, containsString("\"name\":\"ObservationList\",\"args\":[{\"name\":\"_filter\""));
+				assertThat(resp, containsString("\"name\":\"ObservationConnection\",\"fields\":[{\"name\":\"count\""));
+				assertThat(resp, not(containsString("\"name\":\"Patient\",\"args\":[{\"name\":\"id\"")));
+				assertThat(resp, not(containsString("\"name\":\"PatientList\",\"args\":[{\"name\":\"_filter\"")));
 			}
 		}
 	}
 
 	@Test
-	public void testIntrospectSearch_Observation() throws IOException {
+	public void testRoot_Introspect() throws IOException {
 		initTestPatients();
 
-		String uri = ourServerBase + "/Observation/$graphql";
+		String uri = ourServerBase + "/$graphql";
 		HttpPost httpGet = new HttpPost(uri);
 		httpGet.setEntity(new StringEntity(INTROSPECTION_QUERY, ContentType.APPLICATION_JSON));
 
@@ -87,40 +121,49 @@ public void testIntrospectSearch_Observation() throws IOException {
 		for (int i = 0; i < 3; i++) {
 			try (CloseableHttpResponse response = ourHttpClient.execute(httpGet)) {
 				String resp = IOUtils.toString(response.getEntity().getContent(), StandardCharsets.UTF_8);
-				ourLog.info(resp);
+				ourLog.info("Response has size: {}", FileUtil.formatFileSize(resp.length()));
 				assertEquals(200, response.getStatusLine().getStatusCode());
-				assertThat(resp, not(containsString("{\"kind\":\"OBJECT\",\"name\":\"Patient\",")));
+				assertThat(resp, containsString("{\"kind\":\"OBJECT\",\"name\":\"Patient\","));
 				assertThat(resp, containsString("{\"kind\":\"OBJECT\",\"name\":\"Observation\","));
-				assertThat(resp, not(containsString("{\"kind\":\"OBJECT\",\"name\":\"Query\",\"fields\":[{\"name\":\"PatientList\"")));
-				assertThat(resp, containsString("{\"kind\":\"OBJECT\",\"name\":\"Query\",\"fields\":[{\"name\":\"ObservationList\""));
+				assertThat(resp, containsString("\"name\":\"Observation\",\"args\":[{\"name\":\"id\""));
+				assertThat(resp, containsString("\"name\":\"ObservationList\",\"args\":[{\"name\":\"_filter\""));
+				assertThat(resp, containsString("\"name\":\"ObservationConnection\",\"fields\":[{\"name\":\"count\""));
+				assertThat(resp, containsString("\"name\":\"Patient\",\"args\":[{\"name\":\"id\""));
+				assertThat(resp, containsString("\"name\":\"PatientList\",\"args\":[{\"name\":\"_filter\""));
 			}
 		}
 	}
 
 	@Test
-	public void testInstanceSimpleRead() throws IOException {
+	public void testRoot_Read_Patient() throws IOException {
 		initTestPatients();
 
-		String query = "{name{family,given}}";
-		HttpGet httpGet = new HttpGet(ourServerBase + "/Patient/" + myPatientId0.getIdPart() + "/$graphql?query=" + UrlUtil.escapeUrlParam(query));
+		String query = "{Patient(id:\"" + myPatientId0.getIdPart() + "\"){name{family,given}}}";
+		HttpGet httpGet = new HttpGet(ourServerBase + "/$graphql?query=" + UrlUtil.escapeUrlParam(query));
 
 		try (CloseableHttpResponse response = ourHttpClient.execute(httpGet)) {
 			String resp = IOUtils.toString(response.getEntity().getContent(), StandardCharsets.UTF_8);
 			ourLog.info(resp);
-			assertEquals(TestUtil.stripWhitespace(DATA_PREFIX + "{\n" +
-				"  \"name\":[{\n" +
-				"    \"family\":\"FAM\",\n" +
-				"    \"given\":[\"GIVEN1\",\"GIVEN2\"]\n" +
-				"  },{\n" +
-				"    \"given\":[\"GivenOnly1\",\"GivenOnly2\"]\n" +
-				"  }]\n" +
-				"}" + DATA_SUFFIX), TestUtil.stripWhitespace(resp));
+			assertEquals(TestUtil.stripWhitespace(DATA_PREFIX +
+				"{\n" +
+				"\"Patient\":{\n" +
+				"\"name\":[{\n" +
+				"\"family\":\"FAM\",\n" +
+				"\"given\":[\"GIVEN1\",\"GIVEN2\"]\n" +
+				"},{\n" +
+				"\"given\":[\"GivenOnly1\",\"GivenOnly2\"]\n" +
+				"}]\n" +
+				"}\n" +
+				"}" +
+				DATA_SUFFIX), TestUtil.stripWhitespace(resp));
 		}
 
 	}
 
+
+
 	@Test
-	public void testSearch_Patient() throws IOException {
+	public void testRoot_Search_Patient() throws IOException {
 		initTestPatients();
 
 		String query = "{PatientList(given:\"given\"){name{family,given}}}";
@@ -146,8 +189,9 @@ public void testSearch_Patient() throws IOException {
 		}
 
 	}
+
 	@Test
-	public void testSearch_Observation() throws IOException {
+	public void testRoot_Search_Observation() throws IOException {
 		initTestPatients();
 
 		String query = "{ObservationList(date: \"2022\") {id}}";