Merge pull request #12 from DataBiosphere/aj-1327-get-objects

Author: yuliadub

cli/src/test/java/bio/terra/pfb/JavaPfbCommandTest.java

@@ -34,7 +34,7 @@ public void restoreStreams() {
   @Test
   void invalidFilePath() {
     testCommandStringMatches(
-        List.of("show", "-i invalid/file/path"), errContent, "(No such file or directory)");
+        List.of("show", "-i invalid/file/path"), errContent, "Error reading PFB Value object");
   }
 
   @Test

library/src/main/java/bio/terra/pfb/PfbReader.java

@@ -48,20 +48,32 @@ public static String showMetadata(String fileLocation) throws IOException {
   }
 
   public static List<String> show(String fileLocation) throws IOException {
-    GenericDatumReader<GenericRecord> datumReader = new GenericDatumReader<>();
-    URL url = isValidUrl(fileLocation);
-    GenericRecord genericRecord = null;
     List<String> data = new ArrayList<>();
-    try (InputStream in =
-            url != null ? readFromSignedUrl(url.toString()) : readFromLocalFile(fileLocation);
-        DataFileStream<GenericRecord> reader = new DataFileStream<>(in, datumReader)) {
-      // Skip Metadata Object, which should always appear first
-      reader.next(genericRecord);
-      while (reader.hasNext()) {
-        genericRecord = reader.next(genericRecord);
-        data.add(convertEnum(genericRecord.toString()));
+
+    try (DataFileStream<GenericRecord> records = PfbReader.getGenericRecordsStream(fileLocation)) {
+      while (records.hasNext()) {
+        data.add(convertEnum(records.next().toString()));
       }
       return data;
+    } catch (IOException e) {
+      throw new InvalidPfbException("Error reading PFB Value object");
+    }
+  }
+
+  /** DataFileStream implements Closeable and must be closed by the client code. */
+  public static DataFileStream<GenericRecord> getGenericRecordsStream(String fileLocation)
+      throws IOException {
+    GenericDatumReader<GenericRecord> datumReader = new GenericDatumReader<>();
+    URL url = isValidUrl(fileLocation);
+    try {
+      InputStream in =
+          url != null ? readFromSignedUrl(url.toString()) : readFromLocalFile(fileLocation);
+      var reader = new DataFileStream<>(in, datumReader);
+      // advance past metadata
+      reader.next();
+      return reader;
+    } catch (Exception e) {
+      throw new InvalidPfbException("Error reading PFB Value object");
     }
   }
 

library/src/test/java/bio/terra/pfb/PfbReaderTest.java

@@ -3,7 +3,9 @@
 import static bio.terra.pfb.utils.CompareOutputUtils.FileExtension.JSON;
 import static bio.terra.pfb.utils.CompareOutputUtils.FileExtension.TXT;
 import static bio.terra.pfb.utils.CompareOutputUtils.PfbCommandType.*;
+import static org.junit.jupiter.api.Assertions.assertThrows;
 
+import bio.terra.pfb.exceptions.InvalidPfbException;
 import bio.terra.pfb.utils.CompareOutputUtils;
 import java.io.IOException;
 import java.util.List;
@@ -48,6 +50,21 @@ void showMetadata(String fileName) throws IOException {
     CompareOutputUtils.assertJavaPfbIsPyPFB(fileName, SHOW_METADATA, "", JSON);
   }
 
+  @ParameterizedTest
+  @MethodSource("provideTestFiles")
+  void getGenericRecordsStream(String fileName) throws IOException {
+    CompareOutputUtils.testDataStream(fileName);
+  }
+
+  @Test
+  @MethodSource("provideTestFiles")
+  void getGenericRecordsStreamError() throws IOException {
+    assertThrows(
+        InvalidPfbException.class,
+        () -> CompareOutputUtils.testDataStream("noFile.txt"),
+        "Error reading PFB Value object");
+  }
+
   @ParameterizedTest
   @MethodSource("provideTestFiles")
   void showTest(String fileName) throws IOException {

library/src/test/java/bio/terra/pfb/utils/CompareOutputUtils.java

@@ -3,6 +3,7 @@
 import static bio.terra.pfb.utils.CompareOutputUtils.FileExtension.JSON;
 import static org.hamcrest.MatcherAssert.assertThat;
 import static org.hamcrest.Matchers.equalTo;
+import static org.junit.jupiter.api.Assertions.assertNotNull;
 
 import bio.terra.pfb.PfbReader;
 import java.io.IOException;
@@ -51,6 +52,11 @@ public static void compareJSONLineByLine(
     }
   }
 
+  public static void testDataStream(String fileName) throws IOException {
+    String avroFilePath = getAvroFilePath(fileName, "");
+    assertNotNull(PfbReader.getGenericRecordsStream(avroFilePath));
+  }
+
   public enum PfbCommandType {
     SHOW_SCHEMA("showSchema"),
     SHOW_METADATA("showMetadata"),