Merge pull request #91 from medizininformatik-initiative/84-use-a-tra…

…nsaction-bundle-to-create-measure-and-library-resource

Use a Transaction Bundle to Create Measure and Library Resource

mii-process-feasibility-docker-test-setup/docker-compose.yml

@@ -551,7 +551,7 @@ services:
 
   # ---- DIC-2 - FHIR Data Store ----------------------------------------------
   dic-2-store:
-    image: samply/blaze:0.22.3
+    image: samply/blaze:0.24
     restart: on-failure
     healthcheck:
       test: [ "CMD", "curl", "http://localhost:8080/health" ]
@@ -739,7 +739,7 @@ services:
 
   # ---- DIC-3 - FHIR Data Store ----------------------------------------------
   dic-3-store:
-    image: samply/blaze:0.22.3
+    image: samply/blaze:0.24
     restart: on-failure
     healthcheck:
       test: [ "CMD", "curl", "http://localhost:8080/health" ]

mii-process-feasibility/src/main/java/de/medizininformatik_initiative/process/feasibility/service/StoreFeasibilityResources.java

@@ -1,27 +1,32 @@
 package de.medizininformatik_initiative.process.feasibility.service;
 
-import ca.uhn.fhir.rest.api.MethodOutcome;
 import ca.uhn.fhir.rest.client.api.IGenericClient;
-import de.medizininformatik_initiative.process.feasibility.variables.ConstantsFeasibility;
 import dev.dsf.bpe.v1.ProcessPluginApi;
 import dev.dsf.bpe.v1.activity.AbstractServiceDelegate;
 import dev.dsf.bpe.v1.variables.Variables;
 import org.camunda.bpm.engine.delegate.DelegateExecution;
-import org.hl7.fhir.instance.model.api.IIdType;
+import org.hl7.fhir.r4.model.Bundle;
+import org.hl7.fhir.r4.model.IdType;
 import org.hl7.fhir.r4.model.Library;
 import org.hl7.fhir.r4.model.Measure;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.InitializingBean;
 
+import java.util.ArrayList;
 import java.util.Objects;
+import java.util.regex.Pattern;
 
-import static de.medizininformatik_initiative.process.feasibility.variables.ConstantsFeasibility.VARIABLE_LIBRARY;
-import static de.medizininformatik_initiative.process.feasibility.variables.ConstantsFeasibility.VARIABLE_MEASURE;
+import static de.medizininformatik_initiative.process.feasibility.variables.ConstantsFeasibility.*;
+import static java.nio.charset.StandardCharsets.UTF_8;
+import static org.hl7.fhir.r4.model.Bundle.BundleType.TRANSACTION;
+import static org.hl7.fhir.r4.model.Bundle.HTTPVerb.POST;
 
 public class StoreFeasibilityResources extends AbstractServiceDelegate implements InitializingBean {
 
     private static final Logger logger = LoggerFactory.getLogger(StoreFeasibilityResources.class);
+    private static final Pattern MEASURE_URL_PATTERN = Pattern.compile("(.+)/Measure/(.+)");
+    private static final Pattern LIBRARY_URL_PATTERN = Pattern.compile("urn:uuid:(.+)");
 
     private final IGenericClient storeClient;
     private final FeasibilityResourceCleaner cleaner;
@@ -49,21 +54,43 @@ protected void doExecute(DelegateExecution execution, Variables variables) {
         cleaner.cleanLibrary(library);
         cleaner.cleanMeasure(measure);
 
-        var libraryRes = storeLibraryResource(library);
-        var measureRes = storeMeasureResource(measure, libraryRes.getId());
+        fixCanonical(measure, library);
 
-        variables.setString(ConstantsFeasibility.VARIABLE_MEASURE_ID, measureRes.getId().getIdPart());
+        var transactionResponse = storeResources(measure, library);
+
+        variables.setString(VARIABLE_MEASURE_ID, extractMeasureId(transactionResponse));
+    }
+
+    private void fixCanonical(Measure measure, Library library) {
+        var measureUrlMatcher = MEASURE_URL_PATTERN.matcher(measure.getUrl());
+        var libraryUrlMatcher = LIBRARY_URL_PATTERN.matcher(library.getUrl());
+        if (measureUrlMatcher.find() && libraryUrlMatcher.find()) {
+            var base = measureUrlMatcher.group(1);
+            var measureId = measureUrlMatcher.group(2);
+            var libraryId = libraryUrlMatcher.group(1);
+            var libraryUrl = base + "/Library/" + libraryId;
+            measure.setLibrary(new ArrayList<>());
+            measure.addLibrary(libraryUrl);
+            library.setUrl(libraryUrl);
+            library.setName(libraryId);
+            library.setVersion("1.0.0");
+            var data = new String(library.getContent().get(0).getData(), UTF_8);
+            var rest = data.split("\n", 2)[1];
+            var newData = "library \"%s\" version '1.0.0'\n".formatted(libraryId) + rest;
+            library.getContent().get(0).setData(newData.getBytes(UTF_8));
+        }
     }
 
-    private MethodOutcome storeLibraryResource(Library library) {
-        logger.info("Store Library `{}`", library.getId());
-        return storeClient.create().resource(library).execute();
+    private Bundle storeResources(Measure measure, Library library) {
+        logger.info("Store Measure `{}` and Library `{}`", measure.getId(), library.getUrl());
+
+        Bundle bundle = new Bundle().setType(TRANSACTION);
+        bundle.addEntry().setResource(measure).getRequest().setMethod(POST).setUrl("Measure");
+        bundle.addEntry().setResource(library).getRequest().setMethod(POST).setUrl("Library");
+        return storeClient.transaction().withBundle(bundle).execute();
     }
 
-    private MethodOutcome storeMeasureResource(Measure measure, IIdType libraryId) {
-        logger.info("Store Measure `{}`", measure.getId());
-        measure.getLibrary().clear();
-        measure.addLibrary("Library/" + libraryId.getIdPart());
-        return storeClient.create().resource(measure).execute();
+    private String extractMeasureId(Bundle transactionResponse) {
+        return new IdType(transactionResponse.getEntryFirstRep().getResponse().getLocation()).getIdPart();
     }
 }

mii-process-feasibility/src/test/java/de/medizininformatik_initiative/process/feasibility/Assertions.java

@@ -0,0 +1,19 @@
+package de.medizininformatik_initiative.process.feasibility;
+
+import org.hl7.fhir.r4.model.Base;
+import org.hl7.fhir.r4.model.Bundle;
+
+public interface Assertions {
+
+    static BaseAssert assertThat(Base actual) {
+        return new BaseAssert(actual);
+    }
+
+    static BundleAssert assertThat(Bundle actual) {
+        return new BundleAssert(actual);
+    }
+
+    static BundleEntryRequestComponentAssert assertThat(Bundle.BundleEntryRequestComponent actual) {
+        return new BundleEntryRequestComponentAssert(actual);
+    }
+}

mii-process-feasibility/src/test/java/de/medizininformatik_initiative/process/feasibility/BaseAssert.java

@@ -0,0 +1,20 @@
+package de.medizininformatik_initiative.process.feasibility;
+
+import org.assertj.core.api.AbstractAssert;
+import org.assertj.core.api.Condition;
+import org.hl7.fhir.r4.model.Base;
+
+public class BaseAssert extends AbstractAssert<BaseAssert, Base> {
+
+    protected BaseAssert(Base actual) {
+        super(actual, BaseAssert.class);
+    }
+
+    private static Condition<Base> deepEqualTo(Base expected) {
+        return new Condition<>(actual -> actual.equalsDeep(expected), "deep equal to " + expected);
+    }
+
+    public BaseAssert isDeepEqualTo(Base expected) {
+        return is(deepEqualTo(expected));
+    }
+}

mii-process-feasibility/src/test/java/de/medizininformatik_initiative/process/feasibility/BundleAssert.java

@@ -0,0 +1,20 @@
+package de.medizininformatik_initiative.process.feasibility;
+
+import org.assertj.core.api.AbstractAssert;
+import org.assertj.core.api.Condition;
+import org.hl7.fhir.r4.model.Bundle;
+
+public class BundleAssert extends AbstractAssert<BundleAssert, Bundle> {
+
+    protected BundleAssert(Bundle actual) {
+        super(actual, BundleAssert.class);
+    }
+
+    public BundleAssert hasType(String type) {
+        return has(type(type));
+    }
+
+    private static Condition<Bundle> type(String type) {
+        return new Condition<>(bundle -> bundle.getType().toCode().equals(type), "of type " + type);
+    }
+}

mii-process-feasibility/src/test/java/de/medizininformatik_initiative/process/feasibility/BundleEntryRequestComponentAssert.java

@@ -0,0 +1,30 @@
+package de.medizininformatik_initiative.process.feasibility;
+
+import org.assertj.core.api.AbstractAssert;
+import org.assertj.core.api.Condition;
+import org.hl7.fhir.r4.model.Bundle;
+
+
+public class BundleEntryRequestComponentAssert extends AbstractAssert<BundleEntryRequestComponentAssert,
+        Bundle.BundleEntryRequestComponent> {
+
+    protected BundleEntryRequestComponentAssert(Bundle.BundleEntryRequestComponent actual) {
+        super(actual, BundleEntryRequestComponentAssert.class);
+    }
+
+    public BundleEntryRequestComponentAssert hasMethod(Bundle.HTTPVerb method) {
+        return has(method(method));
+    }
+
+    private static Condition<Bundle.BundleEntryRequestComponent> method(Bundle.HTTPVerb method) {
+        return new Condition<>(bundle -> bundle.getMethod() == method, "of method " + method);
+    }
+
+    public BundleEntryRequestComponentAssert hasUrl(String url) {
+        return has(url(url));
+    }
+
+    private static Condition<Bundle.BundleEntryRequestComponent> url(String url) {
+        return new Condition<>(bundle -> bundle.getUrl().equals(url), "of URL " + url);
+    }
+}

mii-process-feasibility/src/test/java/de/medizininformatik_initiative/process/feasibility/client/flare/FlareWebserviceClientImplBaseIT.java

@@ -12,7 +12,7 @@ public abstract class FlareWebserviceClientImplBaseIT {
 
     protected static final Network DEFAULT_CONTAINER_NETWORK = Network.newNetwork();
 
-    public static GenericContainer<?> fhirServer = new GenericContainer<>(DockerImageName.parse("samply/blaze:0.23.0"))
+    public static GenericContainer<?> fhirServer = new GenericContainer<>(DockerImageName.parse("samply/blaze:0.24"))
             .withExposedPorts(8080)
             .withNetwork(DEFAULT_CONTAINER_NETWORK)
             .withNetworkAliases("fhir-server")

mii-process-feasibility/src/test/java/de/medizininformatik_initiative/process/feasibility/client/store/StoreClientIT.java

@@ -53,7 +53,7 @@ public class StoreClientIT {
     private static final Network DEFAULT_CONTAINER_NETWORK = Network.newNetwork();
 
     @Container
-    public GenericContainer<?> fhirServer = new GenericContainer<>(DockerImageName.parse("samply/blaze:0.23.0"))
+    public GenericContainer<?> fhirServer = new GenericContainer<>(DockerImageName.parse("samply/blaze:0.24"))
             .withExposedPorts(8080)
             .withNetwork(DEFAULT_CONTAINER_NETWORK)
             .withNetworkAliases("fhir-server")

mii-process-feasibility/src/test/java/de/medizininformatik_initiative/process/feasibility/service/StoreFeasibilityResourcesTest.java

@@ -1,22 +1,21 @@
 package de.medizininformatik_initiative.process.feasibility.service;
 
-import ca.uhn.fhir.rest.api.MethodOutcome;
 import ca.uhn.fhir.rest.client.api.IGenericClient;
 import dev.dsf.bpe.v1.variables.Variables;
 import org.camunda.bpm.engine.delegate.DelegateExecution;
-import org.hl7.fhir.r4.model.IdType;
+import org.hl7.fhir.r4.model.Bundle;
 import org.hl7.fhir.r4.model.Library;
 import org.hl7.fhir.r4.model.Measure;
-import org.hl7.fhir.r4.model.Resource;
 import org.junit.jupiter.api.Test;
 import org.junit.jupiter.api.extension.ExtendWith;
-import org.mockito.Answers;
-import org.mockito.InjectMocks;
-import org.mockito.Mock;
+import org.mockito.*;
 import org.mockito.junit.jupiter.MockitoExtension;
 
+import static de.medizininformatik_initiative.process.feasibility.Assertions.assertThat;
 import static de.medizininformatik_initiative.process.feasibility.variables.ConstantsFeasibility.*;
-import static org.mockito.ArgumentMatchers.any;
+import static java.nio.charset.StandardCharsets.UTF_8;
+import static org.assertj.core.api.Assertions.assertThat;
+import static org.hl7.fhir.r4.model.Bundle.HTTPVerb.POST;
 import static org.mockito.Mockito.verify;
 import static org.mockito.Mockito.when;
 
@@ -32,6 +31,9 @@ public class StoreFeasibilityResourcesTest {
     @Mock
     private FeasibilityResourceCleaner cleaner;
 
+    @Captor
+    private ArgumentCaptor<Bundle> transactionBundleCaptor;
+
     @Mock
     private DelegateExecution execution;
 
@@ -41,24 +43,72 @@ public class StoreFeasibilityResourcesTest {
     @InjectMocks
     private StoreFeasibilityResources service;
 
-    @Test
-    public void testDoExecute() {
-        var measure = new Measure();
-        var library = new Library();
-        library.getContentFirstRep().setContentType("text/cql");
-        when(variables.getResource(VARIABLE_MEASURE)).thenReturn(measure);
-        when(variables.getResource(VARIABLE_LIBRARY)).thenReturn(library);
+    // Creates a Measure like the Feasibility Backend will do.
+    private static Measure inputMeasure() {
+        return new Measure()
+                .setUrl("https://foo.de/Measure/9308b842-2bee-418b-b3bf-cc347541c1c3")
+                .addLibrary("urn:uuid:7942465b-513a-4812-a078-e72dfea97f43");
+    }
 
-        var libraryMethodOutcome = new MethodOutcome(new IdType(LIBRARY_ID));
-        var measureMethodOutcome = new MethodOutcome(new IdType(MEASURE_ID));
+    // Creates a Library like the Feasibility Backend will do.
+    private static Library inputLibrary() {
+        var library = new Library()
+                .setUrl("urn:uuid:7942465b-513a-4812-a078-e72dfea97f43")
+                .setName("Retrieve");
+        library.addContent().setContentType("text/cql").setData("""
+                library Retrieve version '1.0.0'
+                using FHIR version '4.0.0'
+                include FHIRHelpers version '4.0.0'
+                """.getBytes(UTF_8));
+        return library;
+    }
 
-        when(storeClient.create().resource(any(Resource.class)).execute())
-                .thenReturn(libraryMethodOutcome, measureMethodOutcome);
+    private static Measure outputMeasure() {
+        return new Measure()
+                .setUrl("https://foo.de/Measure/9308b842-2bee-418b-b3bf-cc347541c1c3")
+                .addLibrary("https://foo.de/Library/7942465b-513a-4812-a078-e72dfea97f43");
+    }
+
+    private static Library outputLibrary() {
+        var library = new Library()
+                .setUrl("https://foo.de/Library/7942465b-513a-4812-a078-e72dfea97f43")
+                .setName("7942465b-513a-4812-a078-e72dfea97f43")
+                .setVersion("1.0.0");
+        library.addContent().setContentType("text/cql").setData("""
+                library "7942465b-513a-4812-a078-e72dfea97f43" version '1.0.0'
+                using FHIR version '4.0.0'
+                include FHIRHelpers version '4.0.0'
+                """.getBytes(UTF_8));
+        return library;
+    }
+
+    @Test
+    public void testDoExecute() {
+        var inputMeasure = inputMeasure();
+        var inputLibrary = inputLibrary();
+        var transactionResponse = new Bundle();
+        transactionResponse.addEntry().getResponse().setLocation("Measure/" + MEASURE_ID);
+        inputLibrary.getContentFirstRep().setContentType("text/cql");
+        when(variables.getResource(VARIABLE_MEASURE)).thenReturn(inputMeasure);
+        when(variables.getResource(VARIABLE_LIBRARY)).thenReturn(inputLibrary);
+        when(storeClient.transaction().withBundle(transactionBundleCaptor.capture()).execute()).thenReturn(transactionResponse);
 
         service.doExecute(execution, variables);
 
-        verify(cleaner).cleanLibrary(library);
-        verify(cleaner).cleanMeasure(measure);
+        verify(cleaner).cleanLibrary(inputLibrary);
+        verify(cleaner).cleanMeasure(inputMeasure);
+        assertThat(transactionBundleCaptor.getValue()).hasType("transaction");
+        assertThat(transactionBundleCaptor.getValue().getEntry()).hasSize(2);
+        assertThat(transactionBundleCaptor.getValue().getEntry().get(0).getResource())
+                .isDeepEqualTo(outputMeasure());
+        assertThat(transactionBundleCaptor.getValue().getEntry().get(0).getRequest())
+                .hasMethod(POST)
+                .hasUrl("Measure");
+        assertThat(transactionBundleCaptor.getValue().getEntry().get(1).getResource())
+                .isDeepEqualTo(outputLibrary());
+        assertThat(transactionBundleCaptor.getValue().getEntry().get(1).getRequest())
+                .hasMethod(POST)
+                .hasUrl("Library");
         verify(variables).setString(VARIABLE_MEASURE_ID, MEASURE_ID);
     }
 }