Merge pull request #1323 from b2ihealthcare/improvement/migrate-to-fhir-core

Migrate FHIR modules to use official HL7 FHIR libraries

Author: cmark

commons/com.b2international.commons/src/com/b2international/commons/exceptions/ApiException.java

@@ -1,5 +1,5 @@
 /*
- * Copyright 2011-2023 B2i Healthcare, https://b2ihealthcare.com
+ * Copyright 2011-2024 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.

core/com.b2international.snowowl.core/src/com/b2international/snowowl/core/Resource.java

@@ -53,7 +53,7 @@ public static final class Settings {
 	/**
 	 * @since 8.0
 	 */
-	public static final class Fields {
+	public static class Fields {
 		public static final String ID = ResourceDocument.Fields.ID;
 		public static final String TITLE = ResourceDocument.Fields.TITLE;
 		public static final String URL = ResourceDocument.Fields.URL;

core/com.b2international.snowowl.core/src/com/b2international/snowowl/core/TerminologyResource.java

@@ -94,6 +94,13 @@ public static abstract class Expand extends Resource.Expand {
 
 	}
 
+	public static abstract class Fields extends Resource.Fields {
+		
+		public static final String TOOLING_ID = "toolingId";
+		public static final String RESOURCE_URI = "resourceURI";
+		
+	}
+	
 	/**
 	 * @since 9.0
 	 */

fhir/com.b2international.snowowl.fhir.core/META-INF/MANIFEST.MF

@@ -6,55 +6,23 @@ Bundle-Version: 9.3.1.qualifier
 Bundle-Vendor: B2i Healthcare
 Bundle-RequiredExecutionEnvironment: JavaSE-17
 Export-Package: com.b2international.snowowl.fhir.core,
- com.b2international.snowowl.fhir.core.codesystems,
  com.b2international.snowowl.fhir.core.exceptions,
- com.b2international.snowowl.fhir.core.model,
- com.b2international.snowowl.fhir.core.model.capabilitystatement,
- com.b2international.snowowl.fhir.core.model.codesystem,
- com.b2international.snowowl.fhir.core.model.conceptmap,
- com.b2international.snowowl.fhir.core.model.converter,
- com.b2international.snowowl.fhir.core.model.dt,
- com.b2international.snowowl.fhir.core.model.operationdefinition,
- com.b2international.snowowl.fhir.core.model.property,
- com.b2international.snowowl.fhir.core.model.serialization,
- com.b2international.snowowl.fhir.core.model.structuredefinition,
- com.b2international.snowowl.fhir.core.model.typedproperty,
- com.b2international.snowowl.fhir.core.model.usagecontext,
- com.b2international.snowowl.fhir.core.model.valueset,
- com.b2international.snowowl.fhir.core.model.valueset.expansion,
  com.b2international.snowowl.fhir.core.request,
  com.b2international.snowowl.fhir.core.request.bundle,
  com.b2international.snowowl.fhir.core.request.codesystem,
  com.b2international.snowowl.fhir.core.request.conceptmap,
- com.b2international.snowowl.fhir.core.request.valueset,
- com.b2international.snowowl.fhir.core.search,
- org.linuxforhealth.fhir.core,
- org.linuxforhealth.fhir.core.util.handler,
- org.linuxforhealth.fhir.exception,
- org.linuxforhealth.fhir.model.annotation,
- org.linuxforhealth.fhir.model.builder,
- org.linuxforhealth.fhir.model.config,
- org.linuxforhealth.fhir.model.format,
- org.linuxforhealth.fhir.model.generator.exception,
- org.linuxforhealth.fhir.model.parser.exception,
- org.linuxforhealth.fhir.model.r5.annotation,
- org.linuxforhealth.fhir.model.r5.constraint.spi,
- org.linuxforhealth.fhir.model.r5.exception,
- org.linuxforhealth.fhir.model.r5.generator,
- org.linuxforhealth.fhir.model.r5.parser,
- org.linuxforhealth.fhir.model.r5.resource,
- org.linuxforhealth.fhir.model.r5.type,
- org.linuxforhealth.fhir.model.r5.type.code,
- org.linuxforhealth.fhir.model.r5.util,
- org.linuxforhealth.fhir.model.r5.visitor,
- org.linuxforhealth.fhir.model.ucum.util,
- org.linuxforhealth.fhir.model.util
-Import-Package: jakarta.validation;version="3.0.2",
+ com.b2international.snowowl.fhir.core.request.valueset
+Import-Package: com.b2international.fhir;version="0.1.0",
+ com.b2international.fhir.r5.operations;version="0.1.0",
+ jakarta.validation;version="3.0.2",
  jakarta.validation.constraints;version="3.0.2",
- org.slf4j
+ org.hl7.fhir.exceptions;version="6.3.25",
+ org.hl7.fhir.r4.model.codesystems;version="6.3.25",
+ org.hl7.fhir.r5.model;version="6.3.25",
+ org.hl7.fhir.utilities.xhtml;version="6.3.25",
+ org.slf4j;version="2.0.0"
 Require-Bundle: org.eclipse.core.runtime;bundle-version="3.9.0",
  com.b2international.snowowl.core;visibility:=reexport,
- org.apache.commons.lang3;bundle-version="3.14.0",
  io.swagger.core.v3.swagger-annotations.jakarta;bundle-version="2.2.20"
 Bundle-ClassPath: .
 Bundle-ActivationPolicy: lazy

fhir/com.b2international.snowowl.fhir.core/src/com/b2international/snowowl/fhir/core/FhirDates.java

@@ -0,0 +1,91 @@
+/*
+ * Copyright 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.
+ * 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.
+ */
+package com.b2international.snowowl.fhir.core;
+
+import java.util.Date;
+
+import org.hl7.fhir.r5.model.CanonicalType;
+import org.hl7.fhir.r5.model.DateTimeType;
+import org.hl7.fhir.r5.model.InstantType;
+import org.hl7.fhir.r5.model.Resource;
+
+import com.b2international.commons.CompareUtils;
+import com.b2international.snowowl.core.ResourceURI;
+
+/**
+ * @since 9.3
+ */
+public class FhirModelHelpers {
+
+	public static final String OID_PREFIX = "urn:oid:";
+	
+	public static ResourceURI resourceUriFrom(Resource resource) {
+		return ResourceURI.of(resource.getResourceType().name().toLowerCase() + "s", resource.getId());
+	}
+	
+	public static DateTimeType toDateTimeElement(Long date) {
+		return toDateTimeElement(date == null ? null : new Date(date));
+	}
+	
+	public static DateTimeType toDateTimeElement(Date date) {
+		if (date == null) {
+			return null;
+		} else {
+			var dateElement = new DateTimeType(date);
+			dateElement.setTimeZoneZulu(true);
+			return dateElement;
+		}
+	}
+	
+	public static InstantType toInstantElement(Long date) {
+		return toInstantElement(date == null ? null : new Date(date));
+	}
+	
+	public static InstantType toInstantElement(Date date) {
+		if (date == null) {
+			return null;
+		} else {
+			var instantElement = new InstantType(date);
+			instantElement.setTimeZoneZulu(true);
+			return instantElement;
+		}
+	}
+	
+	public static final boolean isOid(CanonicalType system) {
+		return system != null & isOid(system.getValue());
+	}
+	
+	public static final boolean isOid(String system) {
+		return system != null && system.startsWith(OID_PREFIX);
+	}
+
+	public static String getSystemWithoutOidPrefix(CanonicalType system) {
+		return getSystemWithoutOidPrefix(system == null ? null : system.getValue());
+	}
+	
+	public static String getSystemWithoutOidPrefix(String system) {
+		if (CompareUtils.isEmpty(system)) {
+			return "";
+		}
+		
+		if (isOid(system)) {
+			return system.substring(OID_PREFIX.length());
+		}
+		
+		return system;
+	}
+	
+}