Minor FHIR API fixes

commons/com.b2international.index/src/com/b2international/index/es/query/Es8QueryBuilder.java

@@ -22,6 +22,7 @@
 import java.util.function.Function;
 import java.util.stream.Collectors;
 
+import org.elasticsearch.index.query.RegexpFlag;
 import org.elasticsearch.script.Script;
 import org.slf4j.Logger;
 
@@ -467,7 +468,7 @@
 	}
 
 	private void visit(RegexpPredicate regexp) {
-		deque.push(QueryBuilders.regexp(r -> r.boost(this.boost).field(toFieldPath(regexp)).value(regexp.getArgument()).caseInsensitive(regexp.isCaseInsensitive())));
+		deque.push(QueryBuilders.regexp(r -> r.boost(this.boost).field(toFieldPath(regexp)).value(regexp.getArgument()).caseInsensitive(regexp.isCaseInsensitive()).flags(RegexpFlag.NONE.name())));
 	}
 
 	private void visit(RangePredicate<?> range) {

commons/com.b2international.index/src/com/b2international/index/es/query/EsQueryBuilder.java

@@ -385,7 +385,7 @@ private void visit(PrefixPredicate predicate) {
 	}
 
 	private void visit(RegexpPredicate regexp) {
-		deque.push(QueryBuilders.regexpQuery(toFieldPath(regexp), regexp.getArgument()).caseInsensitive(regexp.isCaseInsensitive()));
+		deque.push(QueryBuilders.regexpQuery(toFieldPath(regexp), regexp.getArgument()).caseInsensitive(regexp.isCaseInsensitive()).flags(RegexpFlag.NONE));
 	}
 
 	private void visit(RangePredicate<?> range) {

core/com.b2international.snowowl.core.rest.tests/src/com/b2international/snowowl/core/rest/resource/ResourceApiTest.java

@@ -502,7 +502,7 @@ public void ensureUrlIsUniqueGlobally() throws Exception {
 		// create a resource with ID
 		var codeSystemId = IDs.base62UUID();
 		CodeSystemRestRequests.createCodeSystem(codeSystemId).statusCode(201);
-		var codeSystemUrlToUse = CodeSystemRestRequests.getCodeSystemUrl(codeSystemId);
+		var codeSystemUrlToUse = CodeSystemRestRequests.getSnomedIntUrl(codeSystemId);
 
 		// simulate that the user only has access to another resource
 		String token = RestExtensions.generateToken(Permission.requireAll(Permission.OPERATION_BROWSE, "another-resource"));

fhir/com.b2international.snowowl.fhir.core/src/com/b2international/snowowl/fhir/core/model/valueset/Compose.java

@@ -94,7 +94,7 @@ public Builder inactive(final boolean isInactive) {
 
 		@JsonProperty("include")
 		@JsonFormat(with = JsonFormat.Feature.ACCEPT_SINGLE_VALUE_AS_ARRAY)
-		public Builder profiles(Collection<Include> includes) {
+		public Builder includes(Collection<Include> includes) {
 			this.includes = includes;
 			return this;
 		}

fhir/com.b2international.snowowl.fhir.core/src/com/b2international/snowowl/fhir/core/request/codesystem/FhirRequest.java

@@ -1,5 +1,5 @@
 /*
- * Copyright 2021-2023 B2i Healthcare, https://b2ihealthcare.com
+ * Copyright 2021-2024 B2i Healthcare, https://b2ihealthcare.com
  * 
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
@@ -15,16 +15,21 @@
  */
 package com.b2international.snowowl.fhir.core.request.codesystem;
 
+import java.util.Optional;
+
 import com.b2international.commons.CompareUtils;
 import com.b2international.commons.exceptions.NotFoundException;
 import com.b2international.commons.http.AcceptLanguageHeader;
+import com.b2international.snowowl.core.RepositoryManager;
 import com.b2international.snowowl.core.ServiceProvider;
 import com.b2international.snowowl.core.events.Request;
+import com.b2international.snowowl.core.uri.ResourceURLSchemaSupport;
 import com.b2international.snowowl.fhir.core.model.ResourceResponseEntry;
 import com.b2international.snowowl.fhir.core.model.codesystem.CodeSystem;
 import com.b2international.snowowl.fhir.core.model.dt.Code;
 import com.b2international.snowowl.fhir.core.request.FhirRequests;
 import com.b2international.snowowl.fhir.core.search.Summary;
+import com.google.common.base.Strings;
 
 /**
  * @since 8.0
@@ -45,7 +50,42 @@ public FhirRequest(String system, String version) {
 
 	@Override
 	public final R execute(ServiceProvider context) {
-		CodeSystem codeSystem = FhirRequests
+		// try as is via the URL + version (optional) config
+		CodeSystem codeSystem = fetchCodeSystemByUrlAndVersion(context)
+				.or(() -> fetchCodeSystemByIdAndVersion(context))
+				.or(() -> {
+					// perform the third step only if there is a version specified
+					if (Strings.isNullOrEmpty(version)) {
+						return Optional.empty();
+					} else {
+						return fetchCodeSystemByUrl(context, system)
+								// if there is a codesystem with the specified URL then construct a versioned form using its official URL schema from its tooling
+								.flatMap((cs) -> fetchCodeSystemByUrl(context, context.service(RepositoryManager.class).get(cs.getToolingId()).service(ResourceURLSchemaSupport.class).withVersion(system, version, null)));
+					}
+				})
+				.orElseThrow(() -> new NotFoundException("CodeSystem", system));
+
+		return doExecute(context, codeSystem);
+	}
+
+	private Optional<? extends CodeSystem> fetchCodeSystemByIdAndVersion(ServiceProvider context) {
+		return FhirRequests
+			.codeSystems().prepareSearch()
+			.one()
+			.filterById(system)
+			.filterByVersion(version)
+			.setSummary(configureSummary())
+			.buildAsync()
+			.getRequest()
+			.execute(context)
+			.first()
+			.map(ResourceResponseEntry.class::cast)
+			.map(ResourceResponseEntry::getResponseResource)
+			.map(CodeSystem.class::cast);
+	}
+
+	private Optional<CodeSystem> fetchCodeSystemByUrlAndVersion(ServiceProvider context) {
+		return FhirRequests
 				.codeSystems().prepareSearch()
 				.one()
 				.filterByUrl(system)
@@ -57,25 +97,22 @@ public final R execute(ServiceProvider context) {
 				.first()
 				.map(ResourceResponseEntry.class::cast)
 				.map(ResourceResponseEntry::getResponseResource)
-				.map(CodeSystem.class::cast)
-				.or(() -> {
-					return FhirRequests
-						.codeSystems().prepareSearch()
-						.one()
-						.filterById(system)
-						.filterByVersion(version)
-						.setSummary(configureSummary())
-						.buildAsync()
-						.getRequest()
-						.execute(context)
-						.first()
-						.map(ResourceResponseEntry.class::cast)
-						.map(ResourceResponseEntry::getResponseResource)
-						.map(CodeSystem.class::cast);
-				})
-				.orElseThrow(() -> new NotFoundException("CodeSystem", system));
-
-		return doExecute(context, codeSystem);
+				.map(CodeSystem.class::cast);
+	}
+
+	private Optional<CodeSystem> fetchCodeSystemByUrl(ServiceProvider context, String url) {
+		return FhirRequests
+				.codeSystems().prepareSearch()
+				.one()
+				.filterByUrl(url)
+				.setSummary(configureSummary())
+				.buildAsync()
+				.getRequest()
+				.execute(context)
+				.first()
+				.map(ResourceResponseEntry.class::cast)
+				.map(ResourceResponseEntry::getResponseResource)
+				.map(CodeSystem.class::cast);
 	}
 
 	protected String configureSummary() {

fhir/com.b2international.snowowl.fhir.rest.tests/.launch/fhir-api-tests.launch

@@ -107,6 +107,7 @@
         <setEntry value="org.apache.commons.cli@default:default"/>
         <setEntry value="org.apache.commons.commons-codec@default:default"/>
         <setEntry value="org.apache.commons.commons-collections4@default:default"/>
+        <setEntry value="org.apache.commons.commons-compress@default:default"/>
         <setEntry value="org.apache.commons.commons-io@default:default"/>
         <setEntry value="org.apache.commons.lang3@default:default"/>
         <setEntry value="org.apache.commons.logging@default:default"/>

fhir/com.b2international.snowowl.fhir.rest.tests/src/com/b2international/snowowl/fhir/rest/tests/codesystem/FhirCodeSystemLookupOperationTest.java

@@ -26,6 +26,7 @@
 import com.b2international.snowowl.fhir.core.model.codesystem.LookupRequest;
 import com.b2international.snowowl.fhir.core.model.dt.Coding;
 import com.b2international.snowowl.fhir.tests.FhirRestTest;
+import com.b2international.snowowl.snomed.common.SnomedTerminologyComponentConstants;
 import com.b2international.snowowl.snomed.common.SnomedConstants.Concepts;
 import com.b2international.snowowl.test.commons.codesystem.CodeSystemRestRequests;
 
@@ -87,7 +88,26 @@ public class FhirCodeSystemLookupOperationTest extends FhirRestTest {
 	@Test
 	public void GET_CodeSystem_$lookup_Existing_Versioned() throws Exception {
 		givenAuthenticatedRequest(FHIR_ROOT_CONTEXT)
-			.queryParam("system", CodeSystemRestRequests.getCodeSystemUrl("version/20020131"))
+			.queryParam("system", CodeSystemRestRequests.getSnomedIntUrl("version/20020131"))
+			.queryParam("code", Concepts.ROOT_CONCEPT)
+			.queryParam("_format", "json")
+			.when().get(CODESYSTEM_LOOKUP)
+			.then().assertThat()
+			.statusCode(200)
+			.body("resourceType", equalTo("Parameters"))
+			.body("parameter[0].name", equalTo("name"))
+			.body("parameter[0].valueString", equalTo("SNOMEDCT/2002-01-31"))
+			.body("parameter[1].name", equalTo("version"))
+			.body("parameter[1].valueString", equalTo("2002-01-31"))
+			.body("parameter[2].name", equalTo("display"))
+			.body("parameter[2].valueString", equalTo("SNOMED CT Concept"));
+	}
+
+	@Test
+	public void GET_CodeSystem_$lookup_Existing_Versioned_ViaVersionField() throws Exception {
+		givenAuthenticatedRequest(FHIR_ROOT_CONTEXT)
+			.queryParam("system", String.join("/", SnomedTerminologyComponentConstants.SNOMED_URI_SCT, Concepts.MODULE_SCT_CORE))
+			.queryParam("version", "20020131")
 			.queryParam("code", Concepts.ROOT_CONCEPT)
 			.queryParam("_format", "json")
 			.when().get(CODESYSTEM_LOOKUP)

fhir/com.b2international.snowowl.fhir.rest.tests/src/com/b2international/snowowl/fhir/tests/FhirRestTest.java

@@ -37,8 +37,6 @@ public class FhirRestTest extends FhirTest {
 
 	public static final String FHIR_ROOT_CONTEXT = "/fhir"; //$NON-NLS-N$
 
-	protected static final String SNOMED_VERSION = "2018-07-31";
-
 	public static final String SNOMEDCT_URL = SnomedTerminologyComponentConstants.SNOMED_URI_SCT + "/900000000000207008";
 
 	public static final class Endpoints {
@@ -74,7 +72,7 @@ public void after() {
 	}
 
 	protected final String getTestCodeSystemUrl() {
-		return CodeSystemRestRequests.getCodeSystemUrl(getTestCodeSystemId());
+		return CodeSystemRestRequests.getSnomedIntUrl(getTestCodeSystemId());
 	}
 
 }

fhir/com.b2international.snowowl.fhir.rest/src/com/b2international/snowowl/fhir/rest/FhirCodeSystemSubsumesController.java

@@ -142,7 +142,7 @@ public Promise<ResponseEntity<byte[]>> subsumes(
 	@ApiResponse(responseCode = "200", description = "OK")
 	@ApiResponse(responseCode = "400", description = "Bad request")
 	@ApiResponse(responseCode = "404", description = "Code system not found")
-	@GetMapping(value = "/{codeSystemId:**}/$subsumes", produces = {
+	@GetMapping(value = "/{id:**}/$subsumes", produces = {
 		APPLICATION_FHIR_JSON_VALUE,
 		APPLICATION_FHIR_XML_VALUE,
 		TEXT_JSON_VALUE,
@@ -153,7 +153,7 @@ public Promise<ResponseEntity<byte[]>> subsumes(
 	public Promise<ResponseEntity<byte[]>> subsumes(
 
 		@Parameter(description = "The id of the code system to invoke the operation on")
-		@PathVariable("codeSystemId") 
+		@PathVariable("id") 
 		String codeSystemId,
 
 		@Parameter(description = "The \"A\" code that is to be tested") 
@@ -293,7 +293,7 @@ public Promise<ResponseEntity<byte[]>> subsumes(
 	@ApiResponse(responseCode = "404", description = "Not found")
 	@ApiResponse(responseCode = "400", description = "Bad request")
 	@PostMapping(
-		value = "/{codeSystemId:**}/$subsumes", 
+		value = "/{id:**}/$subsumes", 
 		consumes = {
 			APPLICATION_FHIR_JSON_VALUE,
 			APPLICATION_FHIR_XML_VALUE,
@@ -314,7 +314,7 @@ public Promise<ResponseEntity<byte[]>> subsumes(
 	public Promise<ResponseEntity<byte[]>> subsumes(
 
 		@Parameter(description = "The id of the code system to invoke the operation on")
-		@PathVariable("codeSystemId") 
+		@PathVariable("id") 
 		String codeSystemId,
 
 		@io.swagger.v3.oas.annotations.parameters.RequestBody(description = "The operation's input parameters", content = { 

fhir/com.b2international.snowowl.fhir.rest/src/com/b2international/snowowl/fhir/rest/FhirCodeSystemValidateCodeController.java

@@ -257,7 +257,7 @@ public Promise<ResponseEntity<byte[]>> validateCode(
 		@ApiResponse(responseCode = "400", description = "Bad request"),
 		@ApiResponse(responseCode = "404", description = "Code system not found")
 	})
-	@GetMapping(value = "/{codeSystemId:**}/$validate-code", produces = {
+	@GetMapping(value = "/{id:**}/$validate-code", produces = {
 		APPLICATION_FHIR_JSON_VALUE,
 		APPLICATION_FHIR_XML_VALUE,
 		TEXT_JSON_VALUE,
@@ -268,7 +268,7 @@ public Promise<ResponseEntity<byte[]>> validateCode(
 	public Promise<ResponseEntity<byte[]>> validateCodeInstance(
 
 		@Parameter(description = "The id of the code system to validate against") 
-		@PathVariable(value = "codeSystemId") 
+		@PathVariable(value = "id") 
 		String codeSystemId, 
 
 		@Parameter(description = "The code to be validated") 
@@ -330,7 +330,7 @@ public Promise<ResponseEntity<byte[]>> validateCodeInstance(
 	/**
 	 * <code><b>POST /CodeSystem/{id}/$validate-code</b></code>
 	 * <p>
-	 * All parameters are in the request body, except the codeSystemId.
+	 * All parameters are in the request body, except the id.
 	 * 
 	 * @param codeSystemId
 	 * @param requestBody - an {@link InputStream} whose contents can be deserialized to FHIR parameters
@@ -348,7 +348,7 @@ public Promise<ResponseEntity<byte[]>> validateCodeInstance(
 	@ApiResponse(responseCode = "404", description = "Not found")
 	@ApiResponse(responseCode = "400", description = "Bad request")
 	@PostMapping(
-		value = "/{codeSystemId:**}/$validate-code", 
+		value = "/{id:**}/$validate-code", 
 		consumes = {
 			APPLICATION_FHIR_JSON_VALUE,
 			APPLICATION_FHIR_XML_VALUE,
@@ -369,7 +369,7 @@ public Promise<ResponseEntity<byte[]>> validateCodeInstance(
 	public Promise<ResponseEntity<byte[]>> validateCode(
 
 		@Parameter(description = "The id of the code system to validate against") 
-		@PathVariable(value = "codeSystemId") 
+		@PathVariable(value = "id") 
 		String codeSystemId, 
 
 		@io.swagger.v3.oas.annotations.parameters.RequestBody(description = "The operation's input parameters", content = { 

fhir/com.b2international.snowowl.fhir.rest/src/com/b2international/snowowl/fhir/rest/FhirConceptMapTranslateController.java

@@ -256,7 +256,7 @@ public Promise<ResponseEntity<byte[]>> translate(
 	@ApiResponse(responseCode = "200", description = "OK")
 	@ApiResponse(responseCode = "400", description = "Bad request")
 	@ApiResponse(responseCode = "404", description = "Concept map not found")
-	@GetMapping(value = "/{conceptMapId:**}/$translate", produces = {
+	@GetMapping(value = "/{id:**}/$translate", produces = {
 		APPLICATION_FHIR_JSON_VALUE,
 		APPLICATION_FHIR_XML_VALUE,
 		TEXT_JSON_VALUE,
@@ -267,7 +267,7 @@ public Promise<ResponseEntity<byte[]>> translate(
 	public Promise<ResponseEntity<byte[]>> translateInstance(
 
 		@Parameter(description = "The id of the Concept Map to base the translation on") 
-		@PathVariable("conceptMapId") 
+		@PathVariable("id") 
 		String conceptMapId,
 
 		@Parameter(description = "The code to translate")