ALS-7810: Attempt to fix parsing error

hms-dbmi · Nov 20, 2024 · 67b1b77 · 67b1b77
1 parent c5c3d77
commit 67b1b77
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Showing 2 changed files with 7 additions and 5 deletions.
diff --git a/...ng/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/upload/SignUrlService.java b/...ng/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/upload/SignUrlService.java
@@ -26,6 +26,8 @@ public class SignUrlService {
     private final int signedUrlExpiryMinutes;
     private final Region region;
 
+    private final S3Client s3;
+
     private static Logger log = LoggerFactory.getLogger(SignUrlService.class);
 
     @Autowired
@@ -37,13 +39,13 @@ public SignUrlService(
         this.bucketName = bucketName;
         this.signedUrlExpiryMinutes = signedUrlExpiryMinutes;
         this.region = Region.of(region);
-    }
 
-    public void uploadFile(File file, String objectKey) {
-        S3Client s3 = S3Client.builder()
-                .region(region)
+        s3 = S3Client.builder()
+                .region(this.region)
                 .build();
+    }
 
+    public void uploadFile(File file, String objectKey) {
         putS3Object(s3, bucketName, objectKey, file);
         s3.close();
     }

diff --git a/processing/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/processing/io/PfbWriterTest.java b/processing/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/processing/io/PfbWriterTest.java
@@ -28,7 +28,7 @@ public void writeValidPFB() {
         PfbWriter pfbWriter = new PfbWriter(new File("target/test-result.avro"), UUID.randomUUID().toString(), dictionaryService);
 
         Mockito.when(dictionaryService.getConcepts(List.of("patient_id", "\\demographics\\age\\", "\\phs123\\stroke\\")))
-                .thenReturn(List.of(new Concept("Categorical", "\\demographics\\age\\", "age", "AGE", "demographics", "patient age", Map.of("drs_uri", "a-drs.uri"))));
+                .thenReturn(List.of(new Concept("Categorical", "\\demographics\\age\\", "age", "AGE", null, "patient age", Map.of("drs_uri", "[\"a-drs.uri\", \"another-drs.uri\"]"))));
 
         pfbWriter.writeHeader(new String[] {"patient_id", "\\demographics\\age\\", "\\phs123\\stroke\\"});
         List<List<String>> nullableList = new ArrayList<>();