ALS-6511: Fix pfb file writing issues

hms-dbmi · Jul 23, 2024 · 741aed8 · 741aed8
1 parent e0f9fad
commit 741aed8
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Showing 6 changed files with 17 additions and 4 deletions.
diff --git a/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/AsyncResult.java b/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/AsyncResult.java
@@ -32,6 +32,10 @@ public byte[] readAllBytes() {
         }
     }
 
+	public void closeWriter() {
+		stream.closeWriter();
+	}
+
 	public static enum Status{
 		SUCCESS {
 			@Override

diff --git a/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/PfbProcessor.java b/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/PfbProcessor.java
@@ -56,6 +56,7 @@ public void runQuery(Query query, AsyncResult result) {
                     }).collect(Collectors.toList());
                     result.appendResults(fieldValuesPerPatient);
                 });
+        result.closeWriter();
     }
 
     private Map<String, Map<Integer, String>> buildResult(AsyncResult result, Query query, TreeSet<Integer> ids) {

diff --git a/...essing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/ResultStoreStream.java b/...essing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/ResultStoreStream.java
@@ -108,4 +108,7 @@ public long estimatedSize() {
 		return writer.getFile().length();
 	}
 
+	public void closeWriter() {
+		writer.close();
+	}
 }
diff --git a/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/io/CsvWriter.java b/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/io/CsvWriter.java
@@ -3,6 +3,7 @@
 import java.io.File;
 import java.io.FileWriter;
 import java.io.IOException;
+import java.io.UncheckedIOException;
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.List;
@@ -50,7 +51,11 @@ public File getFile() {
     }
 
     @Override
-    public void close() throws IOException {
-        fileWriter.close();
+    public void close() {
+        try {
+            fileWriter.close();
+        } catch (IOException e) {
+            throw new UncheckedIOException(e);
+        }
     }
 }
diff --git a/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/io/ResultWriter.java b/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/io/ResultWriter.java
@@ -11,5 +11,5 @@ public interface ResultWriter {
 
     File getFile();
 
-    void close() throws IOException;
+    void close();
 }
diff --git a/service/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/service/QueryService.java b/service/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/service/QueryService.java
@@ -137,7 +137,7 @@ private AsyncResult initializeResult(Query query) throws ClassNotFoundException,
 
 		ResultWriter writer;
         if (ResultType.DATAFRAME_PFB.equals(query.getExpectedResultType())) {
-            writer = new PfbWriter(File.createTempFile("result-" + query.getId(), ".avro"));
+            writer = new PfbWriter(File.createTempFile("result-" + System.nanoTime(), ".avro"));
         } else {
             writer = new CsvWriter(File.createTempFile("result-" + System.nanoTime(), ".sstmp"));
         }