12 cql cohort extraction

.gitignore

@@ -15,6 +15,7 @@
 log/
 target/
 output
+ontology
 dependencies
 package.json
 fhirpkg.lock.json

docker-compose.yml

@@ -2,7 +2,7 @@ services:
   torch-data-store:
     image: "samply/blaze:0.30"
     environment:
-      BASE_URL: "http://torch-data-store:8080"
+      BASE_URL: "http://localhost:8082"
       JAVA_TOOL_OPTIONS: "-Xmx2g"
       LOG_LEVEL: "info"
     ports:
@@ -30,7 +30,7 @@ services:
     restart: unless-stopped
     image: nginxinc/nginx-unprivileged:1.25.5-alpine
     ports:
-      - ${PORT_TORCH_NGINX:-127.0.0.1:8080}:8080
+      - ${PORT_TORCH_NGINX:-127.0.0.1:80}:8080
     volumes:
       - ./nginx.conf.template:/etc/nginx/nginx.conf.template
       - ./start-nginx.sh:/start-nginx.sh

pom.xml

@@ -21,6 +21,7 @@
         <maven.compiler.release>21</maven.compiler.release>
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
         <Hapi.version>6.2.5</Hapi.version>
+        <ontology-tag>v3.0.0-test.9</ontology-tag>
     </properties>
 
     <dependencies>
@@ -140,8 +141,115 @@
             <scope>test</scope>
         </dependency>
 
+        <dependency>
+            <groupId>org.projectlombok</groupId>
+            <artifactId>lombok</artifactId>
+            <scope>provided</scope>
+        </dependency>
+
+        <dependency>
+            <groupId>de.medizininformatik-initiative</groupId>
+            <artifactId>sq2cql</artifactId>
+            <version>v0.5.0-alpha.1</version>
+        </dependency>
+
     </dependencies>
 
+    <profiles>
+        <profile>
+            <id>download-ontology</id>
+            <activation>
+                <activeByDefault>false</activeByDefault>
+            </activation>
+            <build>
+                <plugins>
+                    <plugin>
+                        <groupId>org.codehaus.mojo</groupId>
+                        <artifactId>exec-maven-plugin</artifactId>
+                        <version>3.1.0</version>
+                        <executions>
+                            <execution>
+                                <id>delete-ontology-directories</id>
+                                <phase>generate-resources</phase>
+                                <goals>
+                                    <goal>exec</goal>
+                                </goals>
+                                <configuration>
+                                    <executable>rm</executable>
+                                    <arguments>
+                                        <argument>-rf</argument>
+                                        <argument>ontology</argument>
+                                    </arguments>
+                                </configuration>
+                            </execution>
+
+                            <execution>
+                                <id>create-ontology-directory</id>
+                                <phase>generate-resources</phase>
+                                <goals>
+                                    <goal>exec</goal>
+                                </goals>
+                                <configuration>
+                                    <executable>mkdir</executable>
+                                    <arguments>
+                                        <argument>ontology</argument>
+                                    </arguments>
+                                </configuration>
+                            </execution>
+
+                            <execution>
+                                <id>download-ontology-mapping</id>
+                                <phase>generate-resources</phase>
+                                <goals>
+                                    <goal>exec</goal>
+                                </goals>
+                                <configuration>
+                                    <executable>curl</executable>
+                                    <arguments>
+                                        <argument>-L</argument>
+                                        <argument>https://github.com/medizininformatik-initiative/fhir-ontology-generator/raw/${ontology-tag}/example/fdpg-ontology/mapping.zip</argument>
+                                        <argument>-o</argument>
+                                        <argument>ontology/mapping.zip</argument>
+                                    </arguments>
+                                </configuration>
+                            </execution>
+
+                            <execution>
+                                <id>unpack-ontology-mapping</id>
+                                <phase>generate-resources</phase>
+                                <goals>
+                                    <goal>exec</goal>
+                                </goals>
+                                <configuration>
+                                    <executable>unzip</executable>
+                                    <arguments>
+                                        <argument>-jod</argument>
+                                        <argument>ontology/</argument>
+                                        <argument>ontology/mapping.zip</argument>
+                                    </arguments>
+                                </configuration>
+                            </execution>
+
+                            <execution>
+                                <id>delete-zip-files</id>
+                                <phase>generate-resources</phase>
+                                <goals>
+                                    <goal>exec</goal>
+                                </goals>
+                                <configuration>
+                                    <executable>rm</executable>
+                                    <arguments>
+                                        <argument>ontology/mapping.zip</argument>
+                                    </arguments>
+                                </configuration>
+                            </execution>
+                        </executions>
+                    </plugin>
+                </plugins>
+            </build>
+        </profile>
+    </profiles>
+
     <build>
         <finalName>torch</finalName>
         <plugins>

src/main/java/de/medizininformatikinitiative/torch/config/AppConfig.java

@@ -7,21 +7,37 @@
 import de.medizininformatikinitiative.torch.CdsStructureDefinitionHandler;
 import de.medizininformatikinitiative.torch.DataStore;
 import de.medizininformatikinitiative.torch.ResourceTransformer;
+import de.medizininformatikinitiative.torch.cql.*;
 import de.medizininformatikinitiative.torch.rest.CapabilityStatementController;
 import de.medizininformatikinitiative.torch.util.ElementCopier;
 import de.medizininformatikinitiative.torch.util.Redaction;
 import de.medizininformatikinitiative.torch.util.ResultFileManager;
+import de.numcodex.sq2cql.Translator;
+import de.numcodex.sq2cql.model.Mapping;
+import de.numcodex.sq2cql.model.MappingContext;
+import de.numcodex.sq2cql.model.MappingTreeBase;
+import de.numcodex.sq2cql.model.MappingTreeModuleRoot;
 import org.springframework.beans.factory.annotation.Qualifier;
 import org.springframework.beans.factory.annotation.Value;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
+import org.springframework.context.annotation.Lazy;
 import org.springframework.http.client.reactive.ReactorClientHttpConnector;
 import org.springframework.web.reactive.function.client.WebClient;
 import reactor.netty.http.client.HttpClient;
 import reactor.netty.resources.ConnectionProvider;
 
+import java.io.File;
+import java.io.IOException;
+import java.util.Arrays;
+import java.util.Map;
 import java.util.concurrent.ExecutorService;
 import java.util.concurrent.Executors;
+import java.util.function.Function;
+import java.util.stream.Collectors;
+import java.util.stream.Stream;
+
+import static java.util.Map.entry;
 
 @Configuration
 public class AppConfig {
@@ -63,6 +79,81 @@ public DataStore dataStore(@Qualifier("fhirClient") WebClient client, FhirContex
         return new DataStore(client, context);
     }
 
+    @Value("${torch.mappingsFile}")
+    private String mappingsFile;
+
+    @Value("${torch.conceptTreeFile}")
+    private String conceptTreeFile;
+
+    @Lazy
+    @Bean
+    Translator createCqlTranslator(@Qualifier("translation") ObjectMapper jsonUtil) throws IOException {
+        var mappings = jsonUtil.readValue(new File(mappingsFile), Mapping[].class);
+        var mappingTreeBase = new MappingTreeBase(Arrays.stream(jsonUtil.readValue(new File(conceptTreeFile), MappingTreeModuleRoot[].class)).toList());
+
+        return Translator.of(MappingContext.of(
+                Stream.of(mappings)
+                        .collect(Collectors.toMap(Mapping::key, Function.identity(), (a, b) -> a)),
+                mappingTreeBase,
+                Map.ofEntries(entry("http://fhir.de/CodeSystem/bfarm/icd-10-gm", "icd10"),
+                        entry("mii.abide", "abide"),
+                        entry("http://fhir.de/CodeSystem/bfarm/ops", "ops"),
+                        entry("http://dicom.nema.org/resources/ontology/DCM", "dcm"),
+                        entry("https://www.medizininformatik-initiative.de/fhir/core/modul-person/CodeSystem/Vitalstatus", "vitalstatus"),
+                        entry("http://loinc.org", "loinc"),
+                        entry("https://fhir.bbmri.de/CodeSystem/SampleMaterialType", "sample"),
+                        entry("http://fhir.de/CodeSystem/bfarm/atc", "atc"),
+                        entry("http://snomed.info/sct", "snomed"),
+                        entry("http://terminology.hl7.org/CodeSystem/condition-ver-status", "cvs"),
+                        entry("http://hl7.org/fhir/administrative-gender", "gender"),
+                        entry("urn:oid:1.2.276.0.76.5.409", "urn409"),
+                        entry(
+                                "https://www.netzwerk-universitaetsmedizin.de/fhir/CodeSystem/ecrf-parameter-codes",
+                                "numecrf"),
+                        entry("urn:iso:std:iso:3166", "iso3166"),
+                        entry("https://www.netzwerk-universitaetsmedizin.de/fhir/CodeSystem/frailty-score",
+                                "frailtyscore"),
+                        entry("http://terminology.hl7.org/CodeSystem/consentcategorycodes", "consentcategory"),
+                        entry("urn:oid:2.16.840.1.113883.3.1937.777.24.5.3", "consent"),
+                        entry("http://hl7.org/fhir/sid/icd-o-3", "icdo3"),
+                        entry("http://hl7.org/fhir/consent-provision-type", "provisiontype"))));
+    }
+
+    @Qualifier("cql")
+    @Lazy
+    @Bean
+    QueryTranslator createCqlQueryTranslator(
+            Translator sq2cqlTranslator,
+            @Qualifier("translation") ObjectMapper jsonUtil) {
+        return new CqlQueryTranslator(sq2cqlTranslator, jsonUtil);
+    }
+
+
+    @Bean
+    FhirConnector createFhirConnector(@Value("${torch.fhir.url}") String fhirUrl) {
+        return new FhirConnector(fhirContext().newRestfulGenericClient(fhirUrl));
+    }
+
+    @Bean
+    FhirHelper createFhirHelper(FhirContext fhirContext) {
+        return new FhirHelper(fhirContext);
+    }
+
+    @Bean
+    CqlClient createCqlQueryClient(
+            FhirConnector fhirConnector,
+            FhirHelper fhirHelper
+    ) {
+
+        return new CqlClient(fhirConnector, fhirHelper);
+    }
+
+    @Qualifier("translation")
+    @Bean
+    ObjectMapper createTranslationObjectMapper() {
+        return new ObjectMapper();
+    }
+
     @Bean
     public ElementCopier elementCopier(CdsStructureDefinitionHandler cds) {
         return new ElementCopier(cds);

src/main/java/de/medizininformatikinitiative/torch/cql/CqlClient.java

@@ -0,0 +1,49 @@
+package de.medizininformatikinitiative.torch.cql;
+
+import lombok.extern.slf4j.Slf4j;
+import org.hl7.fhir.r4.model.Bundle;
+import org.hl7.fhir.r4.model.ListResource;
+import org.hl7.fhir.r4.model.MeasureReport;
+import org.hl7.fhir.r4.model.Parameters;
+import reactor.core.publisher.Mono;
+
+import java.io.IOException;
+import java.util.List;
+import java.util.Objects;
+import java.util.UUID;
+
+
+@Slf4j
+public class CqlClient {
+    private final FhirConnector fhirConnector;
+    private final FhirHelper fhirHelper;
+
+    public CqlClient(FhirConnector fhirConnector,
+                     FhirHelper fhirHelper) {
+        this.fhirConnector = Objects.requireNonNull(fhirConnector);
+        this.fhirHelper = fhirHelper;
+    }
+
+
+    public Mono<List<String>> getPatientListByCql(String cqlQuery) {
+
+        var libraryUri = "urn:uuid" + UUID.randomUUID();
+        var measureUri = "urn:uuid" + UUID.randomUUID();
+        MeasureReport measureReport;
+
+        try {
+            Bundle bundle = fhirHelper.createBundle(cqlQuery, libraryUri, measureUri);
+            fhirConnector.transmitBundle(bundle);
+
+            Parameters params = fhirHelper.getListExecutionParams();
+            params.setParameter("measure", measureUri);
+            measureReport = fhirConnector.evaluateMeasure(measureUri, params);
+
+            var subjectListId = measureReport.getGroupFirstRep().getPopulationFirstRep().getSubjectResults().getReferenceElement().getIdPart();
+            return Mono.just(fhirConnector.searchAndExtractIds(subjectListId));
+        } catch (IOException e) {
+            throw new RuntimeException(e);
+        }
+
+    }
+}

src/main/java/de/medizininformatikinitiative/torch/cql/CqlQueryTranslator.java

@@ -0,0 +1,38 @@
+package de.medizininformatikinitiative.torch.cql;
+
+import com.fasterxml.jackson.core.JsonProcessingException;
+import com.fasterxml.jackson.databind.ObjectMapper;
+import de.medizininformatikinitiative.torch.model.ccdl.StructuredQuery;
+import de.numcodex.sq2cql.Translator;
+import lombok.NonNull;
+import lombok.RequiredArgsConstructor;
+
+/**
+ * A translator for translating a {@link de.medizininformatikinitiative.torch.model.ccdl.StructuredQuery} into its CQL representation.
+ */
+@RequiredArgsConstructor
+public class CqlQueryTranslator implements QueryTranslator {
+
+    @NonNull
+    private final Translator translator;
+
+    @NonNull
+    private final ObjectMapper jsonUtil;
+
+    @Override
+    public String translate(StructuredQuery query) throws QueryTranslationException {
+        de.numcodex.sq2cql.model.structured_query.StructuredQuery structuredQuery;
+        try {
+            structuredQuery = jsonUtil.readValue(jsonUtil.writeValueAsString(query),
+                    de.numcodex.sq2cql.model.structured_query.StructuredQuery.class);
+        } catch (JsonProcessingException e) {
+            throw new QueryTranslationException("cannot encode/decode structured query as JSON", e);
+        }
+
+        try {
+            return translator.toCql(structuredQuery).print();
+        } catch (Exception e) {
+            throw new QueryTranslationException("cannot translate structured query to CQL format", e);
+        }
+    }
+}