Do not write empty ndjson

Author: Lucas0T

src/main/java/de/medizininformatikinitiative/torch/model/consent/PatientBatchWithConsent.java

@@ -26,6 +26,10 @@ public record PatientBatchWithConsent(Map<String, PatientResourceBundle> bundles
         bundles = Map.copyOf(bundles);
     }
 
+    public Boolean isEmpty() {
+        return bundles.values().stream().allMatch(PatientResourceBundle::isEmpty);
+    }
+
     public static PatientBatchWithConsent fromBatch(PatientBatch batch) {
         return new PatientBatchWithConsent(batch.ids().stream().collect(
                 Collectors.toMap(Function.identity(), PatientResourceBundle::new)), false);

src/main/java/de/medizininformatikinitiative/torch/util/ResultFileManager.java

@@ -20,13 +20,7 @@
 import java.nio.file.Paths;
 import java.nio.file.StandardOpenOption;
 import java.time.Duration;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Optional;
-import java.util.Set;
-import java.util.UUID;
+import java.util.*;
 import java.util.concurrent.ConcurrentHashMap;
 import java.util.stream.Stream;
 
@@ -156,7 +150,10 @@ public Mono<Path> initJobDir(String jobId) {
     public void saveBatchToNDJSON(String jobId, PatientBatchWithConsent batch) throws IOException {
         requireNonNull(jobId);
         requireNonNull(batch);
-
+        if (batch.isEmpty()) {
+            logger.trace("Attempted to save empty batch for jobId: {}", jobId);
+            return;
+        }
         var ndJsonFile = createNdJsonFile(jobId, batch);
 
         try (BufferedWriter out = Files.newBufferedWriter(ndJsonFile)) {

src/test/java/de/medizininformatikinitiative/torch/CdsBlackBoxIT.java

@@ -16,7 +16,6 @@
 
 import static de.medizininformatikinitiative.torch.TestUtils.nodeFromValueString;
 import static de.medizininformatikinitiative.torch.assertions.Assertions.assertThat;
-import static de.medizininformatikinitiative.torch.assertions.BundleAssertFactory.BUNDLE_ASSERT;
 import static org.assertj.core.api.Assertions.assertThat;
 
 /**
@@ -61,7 +60,7 @@ void testExamples() throws IOException {
         List<Bundle> coreBundles = statusResponse.coreBundleUrl().stream().flatMap(fileServerClient::fetchBundles).toList();
         List<Bundle> patientBundles = statusResponse.patientBundleUrls().stream().flatMap(fileServerClient::fetchBundles).toList();
 
-        assertThat(coreBundles).singleElement().asInstanceOf(BUNDLE_ASSERT).containsNEntries(0);
+        assertThat(coreBundles).isEmpty();
         assertThat(patientBundles).hasSize(3);
 
         // test if referenced IDs match the actual patient's IDs

src/test/java/de/medizininformatikinitiative/torch/CdsPerformanceBlackBoxIT.java

@@ -50,7 +50,7 @@ void testWithoutReferences() throws IOException {
         var coreBundles = statusResponse.coreBundleUrl().stream().flatMap(fileServerClient::fetchBundles).toList();
         var patientBundles = statusResponse.patientBundleUrls().stream().flatMap(fileServerClient::fetchBundles).toList();
 
-        assertThat(coreBundles).singleElement().asInstanceOf(BUNDLE_ASSERT).containsNEntries(0);
+        assertThat(coreBundles).isEmpty();
         assertThat(patientBundles).hasSize(25000);
     }
 

src/test/java/de/medizininformatikinitiative/torch/FileServerClient.java

@@ -22,7 +22,7 @@ public Stream<Bundle> fetchBundles(URI url) {
         // only use the path part of the URL here, because in the test setup the port of the file server isn't right
         var response = webClient.get().uri(url.getPath()).retrieve().bodyToMono(String.class).block();
         if (response == null) {
-            throw new RuntimeException("Error while feting NDJSON from " + url);
+            throw new RuntimeException("Error while fetching NDJSON from " + url);
         }
         return Stream.of(response.split("\n")).map(line -> context.newJsonParser().parseResource(Bundle.class, line));
     }

src/test/java/de/medizininformatikinitiative/torch/SpecificBlackBoxIT.java

@@ -18,7 +18,6 @@
 import java.util.Set;
 
 import static de.medizininformatikinitiative.torch.assertions.Assertions.assertThat;
-import static de.medizininformatikinitiative.torch.assertions.BundleAssertFactory.BUNDLE_ASSERT;
 import static org.assertj.core.api.Assertions.assertThat;
 
 /**
@@ -101,7 +100,7 @@ void testDoubleRefResolve() throws IOException {
         var coreBundles = statusResponse.coreBundleUrl().stream().flatMap(fileServerClient::fetchBundles).toList();
         var patientBundles = statusResponse.patientBundleUrls().stream().flatMap(fileServerClient::fetchBundles).toList();
 
-        assertThat(coreBundles).singleElement().asInstanceOf(BUNDLE_ASSERT).containsNEntries(0);
+        assertThat(coreBundles).isEmpty();
         assertThat(patientBundles).hasSize(1);
 
         executeStandardTests(patientBundles);
@@ -150,7 +149,7 @@ void testMustHaveResolve() throws IOException {
         var coreBundles = statusResponse.coreBundleUrl().stream().flatMap(fileServerClient::fetchBundles).toList();
         var patientBundles = statusResponse.patientBundleUrls().stream().flatMap(fileServerClient::fetchBundles).toList();
 
-        assertThat(coreBundles).singleElement().asInstanceOf(BUNDLE_ASSERT).containsNEntries(0);
+        assertThat(coreBundles).isEmpty();
         assertThat(patientBundles).hasSize(1);
 
         executeStandardTests(patientBundles);