Fix json formatter for real and test cases

VEuPathDB · May 11, 2023 · 9068bc8 · 9068bc8
1 parent e035df2
commit 9068bc8
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Showing 3 changed files with 25 additions and 8 deletions.
diff --git a/src/main/java/org/veupathdb/service/eda/ss/model/db/FilteredResultFactory.java b/src/main/java/org/veupathdb/service/eda/ss/model/db/FilteredResultFactory.java
@@ -195,6 +195,7 @@ public static void produceTabularSubsetFromFile(Study study, Entity outputEntity
       )) {
         long rowsConsumed = 0L;
         long rowsSkipped = 0L;
+        resultConsumer.begin();
         while (resultStreamer.hasNext()) {
           if (rowsSkipped > reportConfig.getOffset()) {
             resultConsumer.consumeRow(resultStreamer.next());
@@ -206,6 +207,7 @@ public static void produceTabularSubsetFromFile(Study study, Entity outputEntity
             break;
           }
         }
+        resultConsumer.end();
         LOG.info("Completed processing file-based subsetting request");
       } catch (Exception e) {
         throw new RuntimeException("Failed to write result", e);

diff --git a/src/main/java/org/veupathdb/service/eda/ss/model/tabular/TabularResponses.java b/src/main/java/org/veupathdb/service/eda/ss/model/tabular/TabularResponses.java
@@ -142,13 +142,18 @@ public void end() throws IOException {
     private boolean _firstWritten = false;
 
     @Override
-    public void consumeRow(byte[][] values) throws IOException {
+    public void begin() throws IOException {
       _outputStream.write('[');
+    }
+
+    @Override
+    public void consumeRow(byte[][] values) throws IOException {
       if (_firstWritten) {
         _outputStream.write(',');
       } else {
         _firstWritten = true;
       }
+      _outputStream.write('[');
       for (int i = 0; i < values.length; i++) {
         if (i != 0) {
           _outputStream.write(',');
@@ -164,7 +169,11 @@ public void consumeRow(byte[][] values) throws IOException {
         }
       }
       _outputStream.write(']');
-      _outputStream.write(NEW_LINE_BYTES);
+    }
+
+    @Override
+    public void end() throws IOException {
+      _outputStream.write(']');
     }
   };
 

diff --git a/src/test/java/org/veupathdb/service/eda/ss/model/tabular/TabularResponsesTest.java b/src/test/java/org/veupathdb/service/eda/ss/model/tabular/TabularResponsesTest.java
@@ -21,11 +21,14 @@ public void testJsonBinaryFormatter() throws IOException {
     input[2] = "klmno".getBytes(StandardCharsets.UTF_8);
     input[3] = "pqrst".getBytes(StandardCharsets.UTF_8);
     input[4] = "uvwxy".getBytes(StandardCharsets.UTF_8);
+    formatter.begin();
     formatter.consumeRow(input);
     formatter.consumeRow(input);
-    String[] outputRows = output.toString().split("\n");
-    Assertions.assertEquals(5, new JSONArray(outputRows[0]).length());
-    Assertions.assertEquals(5, new JSONArray(outputRows[1]).length());
+    formatter.end();
+    JSONArray arr = new JSONArray(output.toString());
+    Assertions.assertEquals(2, arr.length());
+    Assertions.assertEquals(arr.getJSONArray(0).length(), 5);
+    Assertions.assertEquals(arr.getJSONArray(1).length(), 5);
   }
 
   @Test
@@ -39,11 +42,14 @@ public void testJsonBinaryFormatterEscapeChars() throws IOException {
     input[2] = "klmn/".getBytes(StandardCharsets.UTF_8);
     input[3] = "pqrst".getBytes(StandardCharsets.UTF_8);
     input[4] = "uvwxy".getBytes(StandardCharsets.UTF_8);
+    formatter.begin();
     formatter.consumeRow(input);
     formatter.consumeRow(input);
-    String[] outputRows = output.toString().split("\n");
-    Assertions.assertEquals(5, new JSONArray(outputRows[0]).length()); // Make sure it can be parsed as josn
-    Assertions.assertEquals(5, new JSONArray(outputRows[1]).length());
+    formatter.end();
+    JSONArray arr = new JSONArray(output.toString());;
+    Assertions.assertEquals(2, arr.length());
+    Assertions.assertEquals(arr.getJSONArray(0).length(), 5);
+    Assertions.assertEquals(arr.getJSONArray(1).length(), 5);
   }
 
 }