Amb 962 write transformer with one extension fml

docker/Transformation-Engine/src/main/java/nhsd/fhir/converter/service/mapping/Converter.java

@@ -0,0 +1,24 @@
+package nhsd.fhir.converter.service.mapping;
+
+import ca.uhn.fhir.context.FhirVersionEnum;
+import org.hl7.fhir.convertors.conv30_40.VersionConvertor_30_40;
+import org.hl7.fhir.dstu3.model.Resource;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.springframework.stereotype.Component;
+
+@Component
+public class Converter {
+    private final VersionConvertor_30_40 converter;
+
+    public Converter(VersionConvertor_30_40 converter) {
+        this.converter = converter;
+    }
+
+    public IBaseResource convert(IBaseResource resource, FhirVersionEnum version) {
+        if (FhirVersionEnum.R4 == version) {
+            return converter.convertResource((org.hl7.fhir.r4.model.Resource) resource);
+        } else {
+            return converter.convertResource((Resource) resource);
+        }
+    }
+}

docker/Transformation-Engine/src/main/java/nhsd/fhir/converter/service/mapping/ConverterService.java

@@ -0,0 +1,36 @@
+package nhsd.fhir.converter.service.mapping;
+
+import ca.uhn.fhir.context.FhirVersionEnum;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.springframework.http.MediaType;
+import org.springframework.stereotype.Service;
+import org.xml.sax.SAXException;
+
+import javax.xml.parsers.ParserConfigurationException;
+import java.io.IOException;
+
+@Service
+public class ConverterService {
+
+    private final Converter converter;
+    private final Transformer transformer;
+    private final FhirParser fhirParser;
+
+    public ConverterService(Converter converter, Transformer transformer, FhirParser fhirParser) {
+        this.converter = converter;
+        this.transformer = transformer;
+        this.fhirParser = fhirParser;
+    }
+
+    public String convert(String resource, MediaType mediaType, FhirVersionEnum fhirVersion) throws ParserConfigurationException, IOException, SAXException {
+        Class<? extends IBaseResource> resourceType = ResourceTypeFactory.createResourceType(resource, mediaType, fhirVersion);
+
+        IBaseResource fhirResource = fhirParser.parse(resource, resourceType, mediaType);
+        IBaseResource converted = converter.convert(fhirResource, fhirVersion);
+        IBaseResource transformed = transformer.transform(converted);
+
+        FhirVersionEnum outVersion = fhirVersion == FhirVersionEnum.R4 ? FhirVersionEnum.DSTU3 : FhirVersionEnum.R4;
+
+        return fhirParser.encode(transformed, mediaType, outVersion);
+    }
+}

docker/Transformation-Engine/src/main/java/nhsd/fhir/converter/service/mapping/FhirConfig.java

@@ -0,0 +1,46 @@
+package nhsd.fhir.converter.service.mapping;
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.parser.IParser;
+import org.hl7.fhir.convertors.advisors.impl.BaseAdvisor_30_40;
+import org.hl7.fhir.convertors.conv30_40.VersionConvertor_30_40;
+import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.Configuration;
+
+@Configuration
+public class FhirConfig {
+    @Bean
+    public FhirContext stu3FhirContext() {
+        return FhirContext.forDstu3();
+    }
+
+    @Bean
+    public FhirContext r4FhirContext() {
+        return FhirContext.forR4();
+    }
+
+    @Bean
+    public IParser stu3XmlParser(FhirContext stu3FhirContext) {
+        return stu3FhirContext.newXmlParser();
+    }
+
+    @Bean
+    public IParser stu3JsonParser(FhirContext stu3FhirContext) {
+        return stu3FhirContext.newJsonParser();
+    }
+
+    @Bean
+    public IParser r4XmlParser(FhirContext r4FhirContext) {
+        return r4FhirContext.newXmlParser();
+    }
+
+    @Bean
+    public IParser r4JsonParser(FhirContext r4FhirContext) {
+        return r4FhirContext.newJsonParser();
+    }
+
+    @Bean
+    public VersionConvertor_30_40 Converter30To40() {
+        return new VersionConvertor_30_40(new BaseAdvisor_30_40());
+    }
+}

docker/Transformation-Engine/src/main/java/nhsd/fhir/converter/service/mapping/FhirParser.java

@@ -0,0 +1,60 @@
+package nhsd.fhir.converter.service.mapping;
+
+import ca.uhn.fhir.context.FhirVersionEnum;
+import ca.uhn.fhir.parser.IParser;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.springframework.http.MediaType;
+import org.springframework.stereotype.Component;
+
+@Component
+public class FhirParser {
+    private final IParser stu3JsonParser;
+    private final IParser r4JsonParser;
+    private final IParser stu3XmlParser;
+    private final IParser r4XmlParser;
+
+    public FhirParser(IParser stu3JsonParser, IParser r4JsonParser, IParser stu3XmlParser, IParser r4XmlParser) {
+        this.stu3JsonParser = stu3JsonParser;
+        this.r4JsonParser = r4JsonParser;
+        this.stu3XmlParser = stu3XmlParser;
+        this.r4XmlParser = r4XmlParser;
+    }
+
+    public <T extends IBaseResource> T parse(String resource, Class<T> resourceType, MediaType mediaType) {
+        boolean isR4 = resourceType.getName().contains("r4");
+
+        if (MediaType.APPLICATION_JSON == mediaType) {
+            if (isR4) {
+                return r4JsonParser.parseResource(resourceType, resource);
+            } else {
+                return stu3JsonParser.parseResource(resourceType, resource);
+            }
+        } else if (MediaType.APPLICATION_XML == mediaType) {
+            if (isR4) {
+                return r4XmlParser.parseResource(resourceType, resource);
+            } else {
+                return stu3XmlParser.parseResource(resourceType, resource);
+            }
+        }
+        throw new IllegalStateException("Invalid Content-Type");
+    }
+
+    public String encode(IBaseResource resource, MediaType mediaType, FhirVersionEnum fhirVersion) {
+        boolean isR4 = FhirVersionEnum.R4 == fhirVersion;
+
+        if (MediaType.APPLICATION_JSON == mediaType) {
+            if (isR4) {
+                return r4JsonParser.encodeResourceToString(resource);
+            } else {
+                return stu3JsonParser.encodeResourceToString(resource);
+            }
+        } else if (MediaType.APPLICATION_XML == mediaType) {
+            if (isR4) {
+                return r4XmlParser.encodeResourceToString(resource);
+            } else {
+                return stu3XmlParser.encodeResourceToString(resource);
+            }
+        }
+        throw new IllegalStateException("Invalid Accept header");
+    }
+}

docker/Transformation-Engine/src/main/java/nhsd/fhir/converter/service/mapping/ResourceTypeFactory.java

@@ -0,0 +1,50 @@
+package nhsd.fhir.converter.service.mapping;
+
+import ca.uhn.fhir.context.FhirVersionEnum;
+import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.hl7.fhir.r4.model.MedicationRequest;
+import org.hl7.fhir.r4.model.MedicationStatement;
+import org.json.JSONObject;
+import org.springframework.http.MediaType;
+import org.springframework.stereotype.Component;
+import org.w3c.dom.Document;
+import org.xml.sax.InputSource;
+import org.xml.sax.SAXException;
+
+import javax.xml.parsers.DocumentBuilder;
+import javax.xml.parsers.DocumentBuilderFactory;
+import javax.xml.parsers.ParserConfigurationException;
+import java.io.IOException;
+import java.io.StringReader;
+
+@Component
+public class ResourceTypeFactory {
+    public static Class<? extends IBaseResource> createResourceType(String fhirResource, MediaType mediaType, FhirVersionEnum fhirVersion) throws ParserConfigurationException, IOException, SAXException {
+        String resourceType = getResourceType(fhirResource, mediaType);
+        switch (resourceType) {
+            case "MedicationRequest":
+                return FhirVersionEnum.R4 == fhirVersion ?
+                        MedicationRequest.class
+                        : org.hl7.fhir.dstu3.model.MedicationRequest.class;
+            case "MedicationStatement":
+                return FhirVersionEnum.R4 == fhirVersion ?
+                        MedicationStatement.class
+                        : org.hl7.fhir.dstu3.model.MedicationStatement.class;
+        }
+        throw new IllegalStateException("Resource not supported");
+    }
+
+    private static String getResourceType(final String fhirSchema, MediaType mediaType) throws ParserConfigurationException, IOException, SAXException {
+        if ("xml".equals(mediaType.getSubtype())) {
+            DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
+            DocumentBuilder builder = factory.newDocumentBuilder();
+            Document doc = builder.parse(new InputSource(new StringReader(fhirSchema)));
+
+            return doc.getFirstChild().getNodeName();
+        } else {
+            JSONObject json = new JSONObject(fhirSchema);
+
+            return json.getString("resourceType");
+        }
+    }
+}

docker/Transformation-Engine/src/main/java/nhsd/fhir/converter/service/mapping/Transformer.java

@@ -0,0 +1,44 @@
+package nhsd.fhir.converter.service.mapping;
+
+import org.hl7.fhir.instance.model.api.IBaseResource;
+import org.hl7.fhir.r4.context.IWorkerContext;
+import org.hl7.fhir.r4.context.SimpleWorkerContext;
+import org.hl7.fhir.r4.model.StructureMap;
+import org.hl7.fhir.r4.utils.StructureMapUtilities;
+import org.springframework.stereotype.Component;
+
+import java.io.IOException;
+import java.io.InputStream;
+
+@Component
+public class Transformer {
+    static private String medicationRequestStu3ToR4Fml;
+    private final StructureMap structureMap;
+    private final StructureMapUtilities structureMapUtilities;
+
+    public Transformer() throws IOException {
+        IWorkerContext worker = new SimpleWorkerContext();
+        structureMapUtilities = new StructureMapUtilities(worker);
+        structureMap = structureMapUtilities.parse(medicationRequestStu3ToR4Fml, "src");
+    }
+
+    IBaseResource transform(IBaseResource resource) {
+        org.hl7.fhir.r4.model.Resource source = (org.hl7.fhir.r4.model.Resource) resource;
+        org.hl7.fhir.r4.model.Resource target = source.copy();
+
+        structureMapUtilities.transform("source", source, structureMap, target);
+
+        return target;
+    }
+
+    static {
+//        InputStream is = Transformer.class.getClassLoader().getResourceAsStream("fml/MedicationRequest/STU3_to_R4.fml");
+        InputStream is = Transformer.class.getClassLoader().getResourceAsStream("fml/MedicationRequest/extension.fml");
+        try {
+            medicationRequestStu3ToR4Fml = new String(is.readAllBytes());
+        } catch (IOException e) {
+            System.err.println("Can't load fml mapping file");
+        }
+
+    }
+}

docker/Transformation-Engine/src/main/resources/application.yml

@@ -0,0 +1,35 @@
+spring:
+  datasource:
+    url: 'jdbc:h2:file:./database/h2'
+    username: sa
+    password: null
+    driverClassName: org.h2.Driver
+    max-active: 15
+
+    # database connection pool size
+    hikari:
+      maximum-pool-size: 10
+  flyway:
+    check-location: false
+    baselineOnMigrate: true
+  jpa:
+    properties:
+      hibernate.format_sql: false
+      hibernate.show_sql: false
+      #      hibernate.dialect: org.hibernate.dialect.h2dialect
+      #      hibernate.hbm2ddl.auto: update
+      #      hibernate.jdbc.batch_size: 20
+      #      hibernate.cache.use_query_cache: false
+      #      hibernate.cache.use_second_level_cache: false
+      #      hibernate.cache.use_structured_entries: false
+      #      hibernate.cache.use_minimal_puts: false
+      ###    These settings will enable fulltext search with lucene
+      hibernate.search.enabled: true
+  #      hibernate.search.backend.type: lucene
+  #      hibernate.search.backend.analysis.configurer: ca.uhn.fhir.jpa.search.HapiLuceneAnalysisConfigurer
+  #      hibernate.search.backend.directory.type: local-filesystem
+  #      hibernate.search.backend.directory.root: target/lucenefiles
+  #      hibernate.search.backend.lucene_version: lucene_current
+  batch:
+    job:
+      enabled: false

docker/Transformation-Engine/src/main/resources/fml/MedicationRequest/STU3_to_R4.fml

@@ -0,0 +1,13 @@
+map "http://hl7.org/fhir/StructureMap/DomainResource3to4" = "R3 to R4 Conversions for DomainResource"
+
+uses "http://hl7.org/fhir/3.0/StructureDefinition/DomainResource" alias DomainResourceR3 as source
+uses "http://hl7.org/fhir/4.0/StructureDefinition/DomainResource" alias DomainResource as target
+
+//imports "http://hl7.org/fhir/StructureMap/*3to4"
+
+group DomainResource(source src : DomainResourceR3, target tgt : DomainResource)  {
+  src.status -> tgt.status;
+  //src.contained -> tgt.contained;
+  //src.extension -> tgt.extension;
+  //src.modifierExtension -> tgt.modifierExtension;
+}

docker/Transformation-Engine/src/main/resources/fml/MedicationRequest/extension.fml

@@ -0,0 +1,25 @@
+map "http://basic.test/medication-request" = "basic-test-medication-request"
+uses "http://hl7.org/fhir/StructureDefinition/MedicationRequest" alias MedicationRequest as source
+uses "http://hl7.org/fhir/StructureDefinition/MedicationRequest" alias MedicationRequest as target
+uses "http://hl7.org/fhir/StructureDefinition/CodeableConcept" alias CodeableConcept as source
+uses "http://hl7.org/fhir/StructureDefinition/CodeableConcept" alias CodeableConcept as target
+uses "http://hl7.org/fhir/StructureDefinition/Coding" alias Coding as source
+uses "http://hl7.org/fhir/StructureDefinition/Coding" alias Coding as target
+group MedicationRequest(source src : MedicationRequest, target tgt : MedicationRequest)  {
+    src.extension as ext where $this.url='https://fhir.nhs.uk/STU3/StructureDefinition/Extension-CareConnect-GPC-PrescriptionType-1'
+        -> tgt.extension as tgtext, tgtext.url='UPDATED DEFINITION HERE' then {
+        ext.value : CodeableConcept as vs -> tgtext.value = create('CodeableConcept') as vt then CodeableConceptPrescriptionType(vs, vt);
+     };
+   }
+group CodeableConceptPrescriptionType(source src : CodeableConcept, target tgt : CodeableConcept) {
+    // src.coding -> tgt.coding; the short form is only woking when you have a <<type>>
+    src.coding -> tgt.coding;
+    src.text as text -> tgt.text = text;
+}
+group Coding(source src : Coding, target tgt : Coding) <<type+>> {
+    src.system as system where $this='https://fhir.nhs.uk/STU3/CodeSystem/CareConnect-PrescriptionType-1' -> tgt.system = 'UPDATED CODESYSTEM HERE';
+    src.version as version -> tgt.version = version;
+    src.code as code -> tgt.code = code;
+    src.display as display -> tgt.display = display;
+    src.userSelected as userSelected -> tgt.userSelected = userSelected;
+}

docker/Transformation-Engine/src/test/java/nhsd/fhir/converter/controller/ConversionControllerTest.java

@@ -47,7 +47,7 @@ public void callConverterToConvert_R4_to_R3_json_json() throws Exception {
 
         //then
         assertEquals(responseEntity.getStatusCode(), HttpStatus.OK);
-        assertEquals(responseEntity.getBody(), staticR3Json);
+        assertEquals(responseEntity.getBody(), staticR3Json.trim());
     }
 
     @Test

docker/Transformation-Engine/src/test/java/nhsd/fhir/converter/service/transformers/BundleConverterTest.java → docker/Transformation-Engine/src/test/java/nhsd/fhir/converter/service/converter/BundleConverterTest.java

@@ -1,7 +1,6 @@
-package nhsd.fhir.converter.service.transformers;
+package nhsd.fhir.converter.service.converter;
 
 import ca.uhn.fhir.context.FhirVersionEnum;
-import nhsd.fhir.converter.service.converter.BundleConverter;
 import org.apache.commons.io.FileUtils;
 import org.custommonkey.xmlunit.XMLAssert;
 import org.custommonkey.xmlunit.XMLUnit;

docker/Transformation-Engine/src/test/java/nhsd/fhir/converter/service/transformers/MedicationRequestConverterTest.java → docker/Transformation-Engine/src/test/java/nhsd/fhir/converter/service/converter/MedicationRequestConverterTest.java

@@ -1,7 +1,6 @@
-package nhsd.fhir.converter.service.transformers;
+package nhsd.fhir.converter.service.converter;
 
 import ca.uhn.fhir.context.FhirVersionEnum;
-import nhsd.fhir.converter.service.converter.MedicationRequestConverter;
 import org.apache.commons.io.FileUtils;
 import org.json.JSONException;
 import org.json.JSONObject;

docker/Transformation-Engine/src/test/java/nhsd/fhir/converter/service/transformers/MedicationStatementConverterTest.java → docker/Transformation-Engine/src/test/java/nhsd/fhir/converter/service/converter/MedicationStatementConverterTest.java

@@ -1,7 +1,6 @@
-package nhsd.fhir.converter.service.transformers;
+package nhsd.fhir.converter.service.converter;
 
 import ca.uhn.fhir.context.FhirVersionEnum;
-import nhsd.fhir.converter.service.converter.MedicationStatementConverter;
 import org.apache.commons.io.FileUtils;
 import org.json.JSONObject;
 import org.junit.jupiter.api.BeforeEach;