Merge pull request #105 from medizininformatik-initiative/release-1.0…

….0.4

Release Version 1.0.0.4

.github/workflows/ci.yml

@@ -94,6 +94,10 @@ jobs:
     - name: Release
       uses: softprops/action-gh-release@v1
       with:
-        files: feasibility-dsf-process/target/feasibility-dsf-process-*.jar
+        draft: true
+        generate_release_notes: true
+        files: |
+          feasibility-dsf-process/target/feasibility-dsf-process-*.jar
+          feasibility-dsf-process/target/feasibility-dsf-process-*.jar.sha256
         name: "Feasibility DSF Process - v${{ steps.prep.outputs.version }}"
 

feasibility-dsf-process/pom.xml

@@ -85,19 +85,25 @@
         <dependency>
             <groupId>org.testcontainers</groupId>
             <artifactId>testcontainers</artifactId>
-            <version>1.18.3</version>
+            <version>${testcontainers.version}</version>
             <scope>test</scope>
         </dependency>
         <dependency>
             <groupId>org.testcontainers</groupId>
             <artifactId>nginx</artifactId>
-            <version>1.18.3</version>
+            <version>${testcontainers.version}</version>
+            <scope>test</scope>
+        </dependency>
+        <dependency>
+            <groupId>org.testcontainers</groupId>
+            <artifactId>toxiproxy</artifactId>
+            <version>${testcontainers.version}</version>
             <scope>test</scope>
         </dependency>
         <dependency>
             <groupId>org.testcontainers</groupId>
             <artifactId>junit-jupiter</artifactId>
-            <version>1.18.3</version>
+            <version>${testcontainers.version}</version>
             <scope>test</scope>
         </dependency>
         <dependency>
@@ -178,6 +184,23 @@
                 </executions>
             </plugin>
 
+            <plugin>
+                <groupId>net.nicoulaj.maven.plugins</groupId>
+                    <artifactId>checksum-maven-plugin</artifactId>
+                    <executions>
+                        <execution>
+                            <goals>
+                                <goal>artifacts</goal>
+                            </goals>
+                        </execution>
+                    </executions>
+                <configuration>
+                    <algorithms>
+                        <algorithm>SHA-256</algorithm>
+                    </algorithms>
+                </configuration>
+            </plugin>
+
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-dependency-plugin</artifactId>

feasibility-dsf-process/src/main/java/de/medizininformatik_initiative/feasibility_dsf_process/client/flare/FlareWebserviceClientImpl.java

@@ -3,6 +3,7 @@
 import org.apache.http.client.HttpClient;
 import org.apache.http.client.methods.HttpGet;
 import org.apache.http.client.methods.HttpPost;
+import org.apache.http.client.methods.HttpUriRequest;
 import org.apache.http.entity.ByteArrayEntity;
 import org.apache.http.impl.client.BasicResponseHandler;
 import org.apache.http.message.BasicHeader;
@@ -11,6 +12,7 @@
 import java.net.URI;
 
 import static ca.uhn.fhir.rest.api.Constants.HEADER_CONTENT_TYPE;
+import static java.lang.String.format;
 
 /**
  * Client for communicating with a Flare instance.
@@ -31,19 +33,28 @@ public int requestFeasibility(byte[] structuredQuery) throws IOException, Interr
         req.setEntity(new ByteArrayEntity(structuredQuery));
         req.setHeader(new BasicHeader(HEADER_CONTENT_TYPE, "application/sq+json"));
 
-        var response = httpClient.execute(req, new BasicResponseHandler());
+        var response = sendRequest(req);
 
         return Integer.parseInt(response);
     }
 
-    private URI resolve(String path) {
-        return flareBaseUrl.resolve((flareBaseUrl.getPath() + path).replaceAll("//", "/"));
-    }
-
     @Override
     public void testConnection() throws IOException {
         var req = new HttpGet(resolve("/cache/stats"));
 
-        httpClient.execute(req, new BasicResponseHandler());
+        sendRequest(req);
+    }
+
+    private URI resolve(String path) {
+        return flareBaseUrl.resolve((flareBaseUrl.getPath() + path).replaceAll("//", "/"));
+    }
+
+    private String sendRequest(HttpUriRequest req) throws IOException {
+        try {
+            return httpClient.execute(req, new BasicResponseHandler());
+        } catch (IOException e) {
+            throw new IOException(
+                    format("Error sending %s request to flare webservice url '%s'.", req.getMethod(), req.getURI()), e);
+        }
     }
 }

feasibility-dsf-process/src/main/java/de/medizininformatik_initiative/feasibility_dsf_process/client/flare/FlareWebserviceClientSpringConfig.java

@@ -99,7 +99,11 @@ private FlareWebserviceClient createFlareClient(HttpClient httpClient) {
     public HttpClient flareHttpClient(@Qualifier("base-client") SSLContext sslContext,
                                       EvaluationSettingsProvider evaluationSettingsProvider) {
         if (EvaluationStrategy.STRUCTURED_QUERY == evaluationSettingsProvider.evaluationStrategy()) {
-            HttpClientBuilder builder = new TlsClientFactory(null, sslContext).getNativeHttpClientBuilder();
+            TlsClientFactory clientFactory = new TlsClientFactory(null, sslContext);
+            clientFactory.setConnectTimeout(connectTimeout);
+            clientFactory.setConnectionRequestTimeout(connectTimeout);
+            clientFactory.setSocketTimeout(connectTimeout);
+            HttpClientBuilder builder = clientFactory.getNativeHttpClientBuilder();
 
             BasicCredentialsProvider credentialsProvider = new BasicCredentialsProvider();
 

feasibility-dsf-process/src/main/java/de/medizininformatik_initiative/feasibility_dsf_process/service/EvaluateCqlMeasure.java

@@ -14,6 +14,8 @@
 
 import java.util.Objects;
 
+import static de.medizininformatik_initiative.feasibility_dsf_process.variables.ConstantsFeasibility.MEASURE_REPORT_PERIOD_END;
+import static de.medizininformatik_initiative.feasibility_dsf_process.variables.ConstantsFeasibility.MEASURE_REPORT_PERIOD_START;
 import static de.medizininformatik_initiative.feasibility_dsf_process.variables.ConstantsFeasibility.VARIABLE_MEASURE_ID;
 import static de.medizininformatik_initiative.feasibility_dsf_process.variables.ConstantsFeasibility.VARIABLE_MEASURE_REPORT;
 
@@ -52,8 +54,8 @@ protected void doExecute(DelegateExecution execution, Variables variables) {
     private MeasureReport executeEvaluateMeasure(String measureId) {
         logger.debug("Evaluate measure {}", measureId);
         return storeClient.operation().onInstance("Measure/" + measureId).named("evaluate-measure")
-                .withParameter(Parameters.class, "periodStart", new DateType(1900, 1, 1))
-                .andParameter("periodEnd", new DateType(2100, 1, 1))
+                .withParameter(Parameters.class, "periodStart", new DateType(MEASURE_REPORT_PERIOD_START))
+                .andParameter("periodEnd", new DateType(MEASURE_REPORT_PERIOD_END))
                 .useHttpGet()
                 .returnResourceType(MeasureReport.class)
                 .execute();

feasibility-dsf-process/src/main/java/de/medizininformatik_initiative/feasibility_dsf_process/service/EvaluateStructuredQueryMeasure.java

@@ -13,7 +13,6 @@
 import org.hl7.fhir.r4.model.MeasureReport.MeasureReportGroupComponent;
 import org.hl7.fhir.r4.model.MeasureReport.MeasureReportGroupPopulationComponent;
 import org.hl7.fhir.r4.model.Period;
-import org.joda.time.LocalDate;
 import org.springframework.beans.factory.InitializingBean;
 
 import java.io.IOException;
@@ -23,6 +22,8 @@
 
 import static de.medizininformatik_initiative.feasibility_dsf_process.variables.ConstantsFeasibility.CODESYSTEM_MEASURE_POPULATION;
 import static de.medizininformatik_initiative.feasibility_dsf_process.variables.ConstantsFeasibility.CODESYSTEM_MEASURE_POPULATION_VALUE_INITIAL_POPULATION;
+import static de.medizininformatik_initiative.feasibility_dsf_process.variables.ConstantsFeasibility.MEASURE_REPORT_PERIOD_END;
+import static de.medizininformatik_initiative.feasibility_dsf_process.variables.ConstantsFeasibility.MEASURE_REPORT_PERIOD_START;
 import static de.medizininformatik_initiative.feasibility_dsf_process.variables.ConstantsFeasibility.VARIABLE_LIBRARY;
 import static de.medizininformatik_initiative.feasibility_dsf_process.variables.ConstantsFeasibility.VARIABLE_MEASURE;
 import static de.medizininformatik_initiative.feasibility_dsf_process.variables.ConstantsFeasibility.VARIABLE_MEASURE_REPORT;
@@ -78,8 +79,8 @@ private MeasureReport buildMeasureReport(String measureRef, int feasibility) {
                 .setDate(new Date())
                 .setMeasure(measureRef)
                 .setPeriod(new Period()
-                        .setStart(new LocalDate(1900, 1, 1).toDate())
-                        .setEnd(new LocalDate(2100, 1, 1).toDate()));
+                        .setStart(MEASURE_REPORT_PERIOD_START)
+                        .setEnd(MEASURE_REPORT_PERIOD_END));
 
         var populationGroup = new MeasureReportGroupPopulationComponent()
                 .setCount(feasibility)

feasibility-dsf-process/src/main/java/de/medizininformatik_initiative/feasibility_dsf_process/service/ObfuscateEvaluationResult.java

@@ -5,12 +5,23 @@
 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.r4.model.CodeableConcept;
+import org.hl7.fhir.r4.model.Coding;
 import org.hl7.fhir.r4.model.MeasureReport;
+import org.hl7.fhir.r4.model.MeasureReport.MeasureReportGroupPopulationComponent;
+import org.hl7.fhir.r4.model.Period;
 import org.springframework.beans.factory.InitializingBean;
 
 import java.util.Objects;
 
+import static de.medizininformatik_initiative.feasibility_dsf_process.variables.ConstantsFeasibility.CODESYSTEM_MEASURE_POPULATION;
+import static de.medizininformatik_initiative.feasibility_dsf_process.variables.ConstantsFeasibility.CODESYSTEM_MEASURE_POPULATION_VALUE_INITIAL_POPULATION;
+import static de.medizininformatik_initiative.feasibility_dsf_process.variables.ConstantsFeasibility.MEASURE_REPORT_PERIOD_END;
+import static de.medizininformatik_initiative.feasibility_dsf_process.variables.ConstantsFeasibility.MEASURE_REPORT_PERIOD_START;
 import static de.medizininformatik_initiative.feasibility_dsf_process.variables.ConstantsFeasibility.VARIABLE_MEASURE_REPORT;
+import static java.lang.String.format;
+import static org.hl7.fhir.r4.model.MeasureReport.MeasureReportStatus.COMPLETE;
+import static org.hl7.fhir.r4.model.MeasureReport.MeasureReportType.SUMMARY;
 
 public class ObfuscateEvaluationResult extends AbstractServiceDelegate
         implements InitializingBean {
@@ -31,15 +42,42 @@ public void afterPropertiesSet() throws Exception {
     @Override
     protected void doExecute(DelegateExecution execution, Variables variables) {
         var measureReport = (MeasureReport) variables.getResource(VARIABLE_MEASURE_REPORT);
-        variables.setResource(VARIABLE_MEASURE_REPORT, obfuscateFeasibilityCount(measureReport));
+
+        if (measureReport.getStatus() == COMPLETE) {
+            variables.setResource(VARIABLE_MEASURE_REPORT, obfuscateFeasibilityCount(measureReport));
+        } else {
+            throw new RuntimeException(format("Expected status '%s' but actually is '%s' for measure report (id '%s').",
+                    COMPLETE, measureReport.getStatus(), measureReport.getId()));
+        }
     }
 
     private MeasureReport obfuscateFeasibilityCount(MeasureReport measureReport) {
-        var obfuscatedFeasibilityCount = obfuscator.obfuscate(measureReport.getGroupFirstRep().
-                getPopulationFirstRep().getCount());
+        var obfuscatedFeasibilityCount = obfuscator.obfuscate(extractInitialPopulation(measureReport).getCount());
+
+        var obfuscatedMeasureReport = new MeasureReport()
+                .setStatus(COMPLETE)
+                .setType(SUMMARY)
+                .setMeasure(measureReport.getMeasure())
+                .setPeriod(new Period()
+                        .setStart(MEASURE_REPORT_PERIOD_START)
+                        .setEnd(MEASURE_REPORT_PERIOD_END));
+
+        obfuscatedMeasureReport.getGroupFirstRep().getPopulationFirstRep()
+                .setCode(new CodeableConcept().addCoding(new Coding().setSystem(CODESYSTEM_MEASURE_POPULATION)
+                        .setCode(CODESYSTEM_MEASURE_POPULATION_VALUE_INITIAL_POPULATION)))
+                .setCount(obfuscatedFeasibilityCount);
 
-        var obfuscatedMeasureReport = measureReport.copy();
-        obfuscatedMeasureReport.getGroupFirstRep().getPopulationFirstRep().setCount(obfuscatedFeasibilityCount);
         return obfuscatedMeasureReport;
     }
+
+    private MeasureReportGroupPopulationComponent extractInitialPopulation(MeasureReport measureReport) {
+        return measureReport.getGroupFirstRep().getPopulation().stream()
+                .filter((p) -> p.getCode().getCoding().stream()
+                        .anyMatch((c) -> c.getSystem().equals(CODESYSTEM_MEASURE_POPULATION) && c.getCode()
+                                .equals(CODESYSTEM_MEASURE_POPULATION_VALUE_INITIAL_POPULATION)))
+                .findFirst()
+                .orElseThrow(() -> new RuntimeException(
+                        format("Missing population with coding '%s' in measure report (id '%s').",
+                                CODESYSTEM_MEASURE_POPULATION_VALUE_INITIAL_POPULATION, measureReport.getId())));
+    }
 }

feasibility-dsf-process/src/main/java/de/medizininformatik_initiative/feasibility_dsf_process/variables/ConstantsFeasibility.java

@@ -1,5 +1,9 @@
 package de.medizininformatik_initiative.feasibility_dsf_process.variables;
 
+import org.joda.time.LocalDate;
+
+import java.util.Date;
+
 public interface ConstantsFeasibility {
     String VARIABLE_MEASURE = "measure";
     String VARIABLE_LIBRARY = "library";
@@ -23,4 +27,7 @@ public interface ConstantsFeasibility {
 
     String FEASIBILITY_REQUEST_PROCESS_ID = "medizininformatik-initiativede_feasibilityRequest";
     String FEASIBILITY_EXECUTE_PROCESS_ID = "medizininformatik-initiativede_feasibilityExecute";
+
+    Date MEASURE_REPORT_PERIOD_START = new LocalDate(1900, 1, 1).toDate();
+    Date MEASURE_REPORT_PERIOD_END = new LocalDate(2100, 1, 1).toDate();
 }

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

@@ -2,7 +2,6 @@
 
 import org.testcontainers.containers.GenericContainer;
 import org.testcontainers.containers.Network;
-import org.testcontainers.junit.jupiter.Container;
 import org.testcontainers.utility.DockerImageName;
 
 import java.net.URL;
@@ -13,26 +12,27 @@ public abstract class FlareWebserviceClientImplBaseIT {
 
     protected static final Network DEFAULT_CONTAINER_NETWORK = Network.newNetwork();
 
-    @Container
-    public static GenericContainer<?> fhirServer = new GenericContainer<>(
-            DockerImageName.parse("samply/blaze:0.23.0"))
+    public static GenericContainer<?> fhirServer = new GenericContainer<>(DockerImageName.parse("samply/blaze:0.23.0"))
             .withExposedPorts(8080)
             .withNetwork(DEFAULT_CONTAINER_NETWORK)
             .withNetworkAliases("fhir-server")
             .withEnv("LOG_LEVEL", "debug");
 
-    @Container
-    public static GenericContainer<?> flare = new GenericContainer<>(
-            DockerImageName.parse("ghcr.io/medizininformatik-initiative/flare:2.1.0"))
+    public static GenericContainer<?> flare = new GenericContainer<>(DockerImageName.parse("ghcr.io/medizininformatik-initiative/flare:2.1.0"))
             .withExposedPorts(8080)
             .withNetwork(DEFAULT_CONTAINER_NETWORK)
             .withNetworkAliases("flare")
-            .withEnv(Map.of(
-                    "FLARE_FHIR_SERVER", "http://fhir-server:8080/fhir/"
-            ))
+            .withEnv(Map.of("FLARE_FHIR_SERVER", "http://fhir-server:8080/fhir/"))
             .withStartupTimeout(Duration.ofMinutes(5))
             .dependsOn(fhirServer);
 
+    static {
+        Runtime.getRuntime().addShutdownHook(new Thread(() -> {
+            flare.stop();
+            fhirServer.stop();
+        }));
+    }
+
     protected static URL getResource(final String name) {
         return FlareWebserviceClientImplBaseIT.class.getResource(name);
     }

feasibility-dsf-process/src/test/java/de/medizininformatik_initiative/feasibility_dsf_process/client/flare/FlareWebserviceClientImplTest.java

@@ -18,6 +18,8 @@
 import java.net.URISyntaxException;
 import java.time.Duration;
 
+import static jakarta.ws.rs.HttpMethod.POST;
+import static org.assertj.core.api.Assertions.assertThatThrownBy;
 import static org.junit.jupiter.api.Assertions.assertDoesNotThrow;
 import static org.junit.jupiter.api.Assertions.assertEquals;
 import static org.junit.jupiter.api.Assertions.assertThrows;
@@ -28,14 +30,16 @@
 @ExtendWith(MockitoExtension.class)
 public class FlareWebserviceClientImplTest {
 
-    private org.apache.http.client.HttpClient httpClient;
+    private HttpClient httpClient;
+    private URI flareBaseUrl;
     private FlareWebserviceClient flareWebserviceClient;
     @Captor ArgumentCaptor<HttpPost> postCaptor;
 
     @BeforeEach
     public void setUp() throws URISyntaxException {
         httpClient = mock(HttpClient.class);
-        flareWebserviceClient = new FlareWebserviceClientImpl(httpClient, new URI("http://localhost:5000/"));
+        flareBaseUrl = new URI("http://localhost:5000/");
+        flareWebserviceClient = new FlareWebserviceClientImpl(httpClient, flareBaseUrl);
     }
 
     @Test
@@ -134,4 +138,18 @@ void testOtherEvaluationStrategyFails() throws Exception {
 
         assertEquals("EVALUATION_STRATEGY is not set to 'structured-query'.", e.getMessage());
     }
+
+    @Test
+    void sendErrorGetsRethrownWithAdditionalInformation() throws Exception {
+        byte[] structuredQuery = "foo".getBytes();
+        IOException error = new IOException("error-151930");
+        when(httpClient.execute(any(HttpPost.class), any(BasicResponseHandler.class))).thenThrow(error);
+
+        assertThatThrownBy(() -> {
+            flareWebserviceClient.requestFeasibility(structuredQuery);
+        })
+            .hasMessage("Error sending %s request to flare webservice url '%s'.", POST,
+                    flareBaseUrl.resolve("/query/execute"))
+            .hasCause(error);
+    }
 }