Refactor FhirController

Author: Lucas0T

pom.xml

@@ -190,6 +190,10 @@
             <artifactId>mockito-junit-jupiter</artifactId>
             <scope>test</scope>
         </dependency>
+        <dependency>
+            <groupId>org.springframework.boot</groupId>
+            <artifactId>spring-boot-starter-validation</artifactId>
+        </dependency>
 
     </dependencies>
 

src/main/java/de/medizininformatikinitiative/torch/Torch.java

@@ -2,15 +2,9 @@
 
 import org.springframework.boot.SpringApplication;
 import org.springframework.boot.autoconfigure.SpringBootApplication;
-import org.springframework.context.annotation.ComponentScan;
 
 
 @SpringBootApplication
-@ComponentScan(basePackages = {
-        "de.medizininformatikinitiative.torch.config",
-        "de.medizininformatikinitiative.torch.rest",
-        "de.medizininformatikinitiative.torch.service"
-})
 public class Torch {
 
     public static void main(String[] args) {

src/main/java/de/medizininformatikinitiative/torch/model/crtdl/ExtractDataParameters.java

@@ -0,0 +1,7 @@
+package de.medizininformatikinitiative.torch.model.crtdl;
+
+import java.util.List;
+
+public record ExtractDataParameters(Crtdl crtdl, List<String> patientIds) {
+}
+

src/main/java/de/medizininformatikinitiative/torch/rest/ExtractDataParametersParser.java

@@ -0,0 +1,92 @@
+package de.medizininformatikinitiative.torch.rest;
+
+import ca.uhn.fhir.context.FhirContext;
+import ca.uhn.fhir.parser.DataFormatException;
+import com.fasterxml.jackson.databind.ObjectMapper;
+import de.medizininformatikinitiative.torch.model.crtdl.Crtdl;
+import de.medizininformatikinitiative.torch.model.crtdl.ExtractDataParameters;
+import org.hl7.fhir.r4.model.Base64BinaryType;
+import org.hl7.fhir.r4.model.Parameters;
+import org.springframework.stereotype.Component;
+
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;
+
+import static java.util.Objects.requireNonNull;
+
+@Component
+public class ExtractDataParametersParser {
+
+    private final FhirContext fhirContext;
+    private final ObjectMapper objectMapper;
+
+    public ExtractDataParametersParser(FhirContext fhirContext, ObjectMapper objectMapper) {
+        this.fhirContext = requireNonNull(fhirContext);
+        this.objectMapper = requireNonNull(objectMapper);
+    }
+
+    /**
+     * Parses the CRDTL content from a byte array.
+     *
+     * @param content the byte array containing the CRDTL content
+     * @return the parsed Crtdl object
+     * @throws IOException if there is an error during parsing
+     */
+    private Crtdl parseCrtdlContent(byte[] content) throws IOException {
+        return objectMapper.readValue(content, Crtdl.class);
+    }
+
+    /**
+     * Parses a FHIR {@link Parameters} resource containing CRTDL data and optional patient IDs.
+     *
+     * <p>The input must be a valid JSON representation of a Parameters resource
+     * that includes:
+     * <ul>
+     *     <li>A parameter named {@code crtdl} with a {@code base64Binary} value containing the CRTDL content.</li>
+     *     <li>Optional parameters named {@code patient} with {@code string} values for patient IDs.</li>
+     * </ul>
+     *
+     * @param body the JSON string representing a FHIR Parameters resource
+     * @return an {@link ExtractDataParameters} containing the parsed CRTDL content and patient IDs
+     * @throws IllegalArgumentException if the input cannot be parsed as a valid Parameters
+     *                                  resource, the Parameters resource is empty, no crtdl
+     *                                  parameter with base64 encoded content is found, or the
+     *                                  CRTDL content cannot be read due to an IOException
+     */
+    public ExtractDataParameters parseParameters(String body) {
+        Parameters parameters;
+        try {
+            parameters = fhirContext.newJsonParser().parseResource(Parameters.class, body);
+        } catch (DataFormatException e) {
+            throw new IllegalArgumentException("Input is not a valid Parameters Resource", e);
+        }
+        if (parameters.isEmpty()) {
+            throw new IllegalArgumentException("Empty Parameters resource provided");
+        }
+        try {
+            byte[] crtdlContent = null;
+            List<String> patientIds = new ArrayList<>();
+
+            for (var parameter : parameters.getParameter()) {
+                if (parameter.hasValue()) {
+                    var value = parameter.getValue();
+                    if ("crtdl".equals(parameter.getName()) && value.hasType("base64Binary")) {
+                        crtdlContent = ((Base64BinaryType) parameter.getValue()).getValue();
+                    }
+                    if ("patient".equals(parameter.getName()) && value.hasType("string")) {
+                        patientIds.add(value.primitiveValue());
+                    }
+                }
+            }
+            if (crtdlContent == null) {
+                throw new IllegalArgumentException("No base64 encoded CRDTL content found in Parameters resource");
+            }
+            // Process crtdl content, potentially using patientIds
+            return new ExtractDataParameters(parseCrtdlContent(crtdlContent), patientIds);
+        } catch (IOException e) {
+            throw new IllegalArgumentException("Reading CRTDL Failed with IO Exception", e);
+        }
+    }
+}
+