100-refactor-and-change-filter-expansion (#102)

reworked Query Building, added more tests, restructured crtdl processing --------- Signed-off-by: Lucas Triefenbach <[email protected]> Co-authored-by: Julian Gründner <[email protected]> Co-authored-by: Bastian Schaffer <[email protected]>
medizininformatik-initiative · Nov 4, 2024 · d8f4211 · d8f4211
1 parent f60f8e5
commit d8f4211
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Showing 95 changed files with 39,707 additions and 2,618 deletions.
diff --git a/pom.xml b/pom.xml
@@ -24,7 +24,28 @@
         <ontology-tag>v3.0.0-alpha</ontology-tag>
     </properties>
 
+
+
     <dependencies>
+
+        <dependency>
+            <groupId>org.assertj</groupId>
+            <artifactId>assertj-core</artifactId>
+            <scope>test</scope>
+        </dependency>
+
+        <dependency>
+            <groupId>com.squareup.okhttp3</groupId>
+            <artifactId>okhttp</artifactId>
+            <scope>test</scope>
+        </dependency>
+
+        <dependency>
+            <groupId>com.squareup.okhttp3</groupId>
+            <artifactId>mockwebserver</artifactId>
+            <scope>test</scope>
+        </dependency>
+
         <!-- https://mvnrepository.com/artifact/ca.uhn.hapi.fhir/hapi-fhir-base -->
         <dependency>
             <groupId>ca.uhn.hapi.fhir</groupId>
@@ -39,6 +60,11 @@
             <version>${Hapi.version}</version>
         </dependency>
 
+        <dependency>
+            <groupId>com.fasterxml.jackson.datatype</groupId>
+            <artifactId>jackson-datatype-jsr310</artifactId>
+        </dependency>
+
         <dependency>
             <groupId>ca.uhn.hapi.fhir</groupId>
             <artifactId>hapi-fhir-structures-r4</artifactId>
@@ -97,6 +123,8 @@
             <groupId>org.slf4j</groupId>
             <artifactId>slf4j-api</artifactId>
         </dependency>
+
+
         <dependency>
             <groupId>org.springframework.boot</groupId>
             <artifactId>spring-boot-autoconfigure</artifactId>
@@ -152,13 +180,33 @@
             <artifactId>spring-security-oauth2-client</artifactId>
         </dependency>
 
+        <dependency>
+            <groupId>ch.qos.logback</groupId>
+            <artifactId>logback-classic</artifactId>
+        </dependency>
+
         <!-- https://mvnrepository.com/artifact/org.codehaus.mojo/exec-maven-plugin -->
         <dependency>
             <groupId>org.codehaus.mojo</groupId>
             <artifactId>exec-maven-plugin</artifactId>
             <version>3.1.0</version>
         </dependency>
 
+        <!-- Mockito Core -->
+        <dependency>
+            <groupId>org.mockito</groupId>
+            <artifactId>mockito-core</artifactId>
+
+            <scope>test</scope>
+        </dependency>
+
+        <!-- Mockito JUnit Jupiter Extension -->
+        <dependency>
+            <groupId>org.mockito</groupId>
+            <artifactId>mockito-junit-jupiter</artifactId>
+            <scope>test</scope>
+        </dependency>
+
     </dependencies>
 
     <profiles>

diff --git a/src/main/java/de/medizininformatikinitiative/torch/BundleCreator.java b/src/main/java/de/medizininformatikinitiative/torch/BundleCreator.java
@@ -15,6 +15,9 @@
 
 @Component
 
+/**
+ * Bundle creator for collecting Resources by patient into bundles for export
+ */
 
 public class BundleCreator {
     private static final Logger logger = LoggerFactory.getLogger(BundleCreator.class);
@@ -23,7 +26,7 @@ public class BundleCreator {
     @Autowired
     FhirContext context;
 
-    org.hl7.fhir.r4.model.Bundle.HTTPVerb method=Bundle.HTTPVerb.PUT;
+    org.hl7.fhir.r4.model.Bundle.HTTPVerb method = Bundle.HTTPVerb.PUT;
 
     public BundleCreator() {
 

diff --git a/src/main/java/de/medizininformatikinitiative/torch/CdsStructureDefinitionHandler.java b/src/main/java/de/medizininformatikinitiative/torch/CdsStructureDefinitionHandler.java
@@ -1,7 +1,5 @@
 package de.medizininformatikinitiative.torch;
 
-import ca.uhn.fhir.context.FhirContext;
-import ca.uhn.fhir.context.RuntimeResourceDefinition;
 import de.medizininformatikinitiative.torch.util.ResourceReader;
 import org.hl7.fhir.r4.model.CanonicalType;
 import org.hl7.fhir.r4.model.StructureDefinition;
@@ -12,14 +10,20 @@
 import java.util.HashMap;
 import java.util.List;
 
+/**
+ * Structure for loading and serving the CDS structrue definitions
+ */
+
 @Component
 public class CdsStructureDefinitionHandler {
 
-    public FhirContext ctx;
+
     private HashMap<String, StructureDefinition> definitionsMap = new HashMap<>();
+    protected ResourceReader resourceReader;
 
-    public CdsStructureDefinitionHandler(String fileDirectory) {
+    public CdsStructureDefinitionHandler(String fileDirectory, ResourceReader resourceReader) {
         try {
+            this.resourceReader = resourceReader;
             processDirectory(fileDirectory);
         } catch (IOException e) {
             throw new RuntimeException(e);
@@ -34,7 +38,7 @@ public CdsStructureDefinitionHandler(String fileDirectory) {
      * @throws IOException
      */
     public void readStructureDefinition(String filePath) throws IOException {
-        StructureDefinition structureDefinition = (StructureDefinition) ResourceReader.readResource(filePath);
+        StructureDefinition structureDefinition = (StructureDefinition) resourceReader.readResource(filePath);
         definitionsMap.put(structureDefinition.getUrl(), structureDefinition);
     }
 
@@ -66,15 +70,12 @@ public StructureDefinition getDefinition(List<CanonicalType> urls) {
         }
         return null;
     }
+
     public StructureDefinition.StructureDefinitionSnapshotComponent getSnapshot(String url) {
         return (definitionsMap.get(url)).getSnapshot();
 
     }
 
-    public RuntimeResourceDefinition getStandardDefinition(String url) {
-        return ctx.getResourceDefinition(String.valueOf(definitionsMap.get(url).getResourceType()));
-
-    }
 
     /**
      * Reads all JSON files in a directory and stores their StructureDefinitions in the definitionsMap

diff --git a/src/main/java/de/medizininformatikinitiative/torch/ConsentHandler.java b/src/main/java/de/medizininformatikinitiative/torch/ConsentHandler.java
@@ -4,10 +4,11 @@
 import com.fasterxml.jackson.databind.JsonNode;
 import com.fasterxml.jackson.databind.ObjectMapper;
 import de.medizininformatikinitiative.torch.exceptions.PatientIdNotFoundException;
-import de.medizininformatikinitiative.torch.util.*;
+import de.medizininformatikinitiative.torch.model.fhir.Query;
+import de.medizininformatikinitiative.torch.model.fhir.QueryParams;
 import de.medizininformatikinitiative.torch.service.DataStore;
+import de.medizininformatikinitiative.torch.util.*;
 import org.hl7.fhir.r4.model.*;
-import org.jetbrains.annotations.NotNull;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
@@ -20,6 +21,9 @@
 import java.io.IOException;
 import java.util.*;
 
+import static de.medizininformatikinitiative.torch.model.fhir.QueryParams.EMPTY;
+import static de.medizininformatikinitiative.torch.model.fhir.QueryParams.stringValue;
+
 /**
  * The {@code ConsentHandler} class is responsible for managing and verifying patient consents
  * within the Torch application.
@@ -49,21 +53,21 @@ public class ConsentHandler {
     /**
      * Constructs a new {@code ConsentHandler} with the specified dependencies.
      *
-     * @param dataStore                    The {@link DataStore} service for Server Calls.
-     * @param mapper                       The {@link ConsentCodeMapper} for mapping consent codes.
-     * @param profilePath                  The file system path to the consent profile mapping configuration.
+     * @param dataStore                     The {@link DataStore} service for Server Calls.
+     * @param mapper                        The {@link ConsentCodeMapper} for mapping consent codes.
+     * @param profilePath                   The file system path to the consent profile mapping configuration.
      * @param cdsStructureDefinitionHandler The {@link CdsStructureDefinitionHandler} for handling structure definitions.
+     * @param objectMapper
      * @throws IOException If an error occurs while reading the mapping profile file.
      */
     @Autowired
-    public ConsentHandler(DataStore dataStore, ConsentCodeMapper mapper, String profilePath, CdsStructureDefinitionHandler cdsStructureDefinitionHandler) throws IOException {
+    public ConsentHandler(DataStore dataStore, ConsentCodeMapper mapper, String profilePath, CdsStructureDefinitionHandler cdsStructureDefinitionHandler, FhirContext ctx, ObjectMapper objectMapper) throws IOException {
         this.dataStore = dataStore;
         this.mapper = mapper;
-        this.ctx = ResourceReader.ctx;
-        this.fhirPathBuilder = new FhirPathBuilder(cdsStructureDefinitionHandler);
+        this.ctx = ctx;
+        this.fhirPathBuilder = new FhirPathBuilder(new Slicing(cdsStructureDefinitionHandler, ctx));
         this.cdsStructureDefinitionHandler = cdsStructureDefinitionHandler;
         this.consentProcessor = new ConsentProcessor(ctx);
-        ObjectMapper objectMapper = new ObjectMapper();
         mappingProfiletoDateField = objectMapper.readTree(new File(profilePath).getAbsoluteFile());
     }
 
@@ -77,8 +81,8 @@ public ConsentHandler(DataStore dataStore, ConsentCodeMapper mapper, String prof
      * @param consentInfo A map containing consent information structured by patient ID and consent codes.
      * @return {@code true} if the resource complies with the consents; {@code false} otherwise.
      */
-    public Boolean checkConsent(@NotNull DomainResource resource, Map<String, Map<String, List<Period>>> consentInfo) {
-        logger.trace("Checking Consent for {}", resource.getResourceType());
+    public Boolean checkConsent(DomainResource resource, Map<String, Map<String, List<Period>>> consentInfo) {
+        logger.trace("Checking Consent for {} {}", resource.getResourceType(), resource.getId());
         Iterator<CanonicalType> profileIterator = resource.getMeta().getProfile().iterator();
         JsonNode fieldValue = null;
         StructureDefinition.StructureDefinitionSnapshotComponent snapshot = null;
@@ -100,7 +104,7 @@ public Boolean checkConsent(@NotNull DomainResource resource, Map<String, Map<St
         }
 
         if (fieldValue == null) {
-            logger.warn("No matching profile found for resource of type: {}", resource.getResourceType());
+            logger.warn("No matching profile found for resource {} of type: {}", resource.getId(), resource.getResourceType());
             return false;
         }
 
@@ -133,7 +137,7 @@ public Boolean checkConsent(@NotNull DomainResource resource, Map<String, Map<St
                 try {
                     patientID = ResourceUtils.getPatientId(resource);
                 } catch (PatientIdNotFoundException e) {
-                    logger.warn("Resource does not Contain any Patient Reference {}", resource.getIdElement());
+                    logger.warn("Resource {} does not Contain any Patient Reference ", resource.getIdElement());
                     return false;
                 }
 
@@ -163,7 +167,8 @@ public Boolean checkConsent(@NotNull DomainResource resource, Map<String, Map<St
                     return true;
                 }
             }
-            logger.debug("No valid consent period found for any value.");
+            logger.warn("No valid consent period found for any value.");
+            logger.debug("No valid consent period found for any value in Resource {}", resource.getIdElement());
             return false;  // No matching consent period found
         }
     }
@@ -178,19 +183,22 @@ public Boolean checkConsent(@NotNull DomainResource resource, Map<String, Map<St
      * @param batch A list of patient IDs to process in this batch.
      * @return A {@link Flux} emitting maps containing consent information structured by patient ID and consent codes.
      */
-    public Flux<Map<String, Map<String, List<Period>>>> buildingConsentInfo(String key, @NotNull List<String> batch) {
+    public Flux<Map<String, Map<String, List<Period>>>> buildingConsentInfo(String key, List<String> batch) {
+        Objects.requireNonNull(batch, "Patient batch cannot be null");
         // Retrieve the relevant codes for the given key
         Set<String> codes = mapper.getRelevantCodes(key);
 
         logger.trace("Starting to build consent info for key: {} with batch size: {}", key, batch.size());
-
+        QueryParams consentParams = EMPTY.appendParam("_profile", stringValue("https://www.medizininformatik-initiative.de/fhir/modul-consent/StructureDefinition/mii-pr-consent-einwilligung"));
+        consentParams = consentParams.appendParam(BatchUtils.queryElements("Consent"), QueryParams.stringValue(String.join(",", batch)));
         // Fetch resources using a bounded elastic scheduler for offloading blocking HTTP I/O
-        return dataStore.getResources("Consent", FhirSearchBuilder.getConsent(batch))
+        Query query = new Query("Consent", consentParams);
+        return dataStore.getResources(query)
                 .subscribeOn(Schedulers.boundedElastic())  // Offload the HTTP requests
                 .doOnSubscribe(subscription -> logger.debug("Fetching resources for batch: {}", batch))
                 .doOnNext(resource -> logger.trace("Resource fetched for ConsentBuild: {}", resource.getIdElement().getIdPart()))
                 .onErrorResume(e -> {
-                    logger.error("Error fetching resources for parameters: {}", FhirSearchBuilder.getConsent(batch), e);
+                    logger.error("Error fetching resources for parameters: {}", query, e);
                     return Flux.empty();
                 })
 
@@ -244,12 +252,13 @@ public Flux<Map<String, Map<String, List<Period>>>> buildingConsentInfo(String k
      * @return A {@link Flux} emitting updated maps of consent information.
      */
     public Flux<Map<String, Map<String, List<Period>>>> updateConsentPeriodsByPatientEncounters(
-            Flux<Map<String, Map<String, List<Period>>>> consentInfoFlux, @NotNull List<String> batch) {
-
-        logger.info("Starting to update consent info with batch size: {}", batch.size());
-
+            Flux<Map<String, Map<String, List<Period>>>> consentInfoFlux, List<String> batch) {
+        Objects.requireNonNull(batch, "Patient batch cannot be null");
+        logger.debug("Starting to update consent info with batch size: {}", batch.size());
+        QueryParams encounterParams = EMPTY.appendParam("_profile", stringValue("https://www.medizininformatik-initiative.de/fhir/core/modul-fall/StructureDefinition/KontaktGesundheitseinrichtung"));
+        encounterParams = encounterParams.appendParam(BatchUtils.queryElements("Encounter"), QueryParams.stringValue(String.join(",", batch)));
         // Step 1: Fetch all encounters for the batch of patients
-        Flux<Encounter> allEncountersFlux = dataStore.getResources("Encounter", FhirSearchBuilder.getEncounter(batch))
+        Flux<Encounter> allEncountersFlux = dataStore.getResources(new Query("Encounter", encounterParams))
                 .subscribeOn(Schedulers.boundedElastic())
                 .cast(Encounter.class)
                 .doOnSubscribe(subscription -> logger.debug("Fetching encounters for batch: {}", batch))
@@ -289,7 +298,7 @@ public Flux<Map<String, Map<String, List<Period>>>> updateConsentPeriodsByPatien
                     List<Encounter> patientEncounters = (List<Encounter>) encountersByPatientMap.get(patientId);
 
                     if (patientEncounters == null || patientEncounters.isEmpty()) {
-                        logger.info("No encounters found for patient {}", patientId);
+                        logger.warn("No encounters found for patient {}", patientId);
                         // No encounters for this patient, return the consent info as is
                         return Mono.just(patientConsentInfo);
                     }
@@ -312,8 +321,8 @@ public Flux<Map<String, Map<String, List<Period>>>> updateConsentPeriodsByPatien
      * @param encounters         A list of {@link Encounter} resources associated with the patient.
      */
     private void updateConsentPeriodsByPatientEncounters(
-            Map<String, List<Period>> patientConsentInfo, @NotNull List<Encounter> encounters) {
-
+            Map<String, List<Period>> patientConsentInfo, List<Encounter> encounters) {
+        Objects.requireNonNull(encounters, "Encounters list cannot be null");
         for (Encounter encounter : encounters) {
             Period encounterPeriod = encounter.getPeriod();