VcfToBqTask unit tests

build.gradle

@@ -60,6 +60,7 @@ test {
   // Print test results
   testLogging {
     events "passed", "skipped", "failed"
+    showStandardStreams = true
   }
   testLogging.showStandardStreams = true
 }

src/test/java/com/google/gcp_variant_transforms/library/LibraryTestModule.java

@@ -12,5 +12,6 @@ protected void configure() {
     bind(VcfParser.class).to(VcfParserImpl.class);
     bind(BigQueryRowGenerator.class).to(BigQueryRowGeneratorImpl.class);
     bind(VariantToBqUtils.class).to(VariantToBqUtilsImpl.class);
+    bind(SchemaGenerator.class).to(SchemaGeneratorImpl.class);
   }
 }

src/test/java/com/google/gcp_variant_transforms/task/VcfToBqTaskTest.java

@@ -0,0 +1,96 @@
+// Copyright 2020 Google LLC
+
+package com.google.gcp_variant_transforms.task;
+
+import static com.google.common.truth.Truth.assertThat;
+import static org.mockito.Mockito.doNothing;
+import static org.mockito.Mockito.doReturn;
+import static org.mockito.Mockito.spy;
+import static org.mockito.Mockito.verify;
+
+import com.google.api.services.bigquery.model.TableSchema;
+import com.google.common.collect.ImmutableList;
+import com.google.gcp_variant_transforms.beam.PipelineRunner;
+import com.google.gcp_variant_transforms.library.HeaderReader;
+import com.google.gcp_variant_transforms.library.VcfParser;
+import com.google.gcp_variant_transforms.library.SchemaGenerator;
+import com.google.gcp_variant_transforms.options.VcfToBqContext;
+import com.google.gcp_variant_transforms.options.VcfToBqOptions;
+import com.google.inject.Injector;
+import htsjdk.variant.vcf.VCFHeader;
+import java.io.IOException;
+import org.apache.beam.sdk.options.PipelineOptions;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.ArgumentCaptor;
+import org.mockito.Captor;
+import org.mockito.MockitoAnnotations;
+import org.mockito.Mock;
+
+/**
+ * Units tests for VcfToBqTask.java
+ */
+ public class VcfToBqTaskTest {
+  Injector spyInjector;
+  VcfToBqTask vcfToBqTask;
+  VcfToBqTask spyVcfToBqTask;
+
+  @Mock private PipelineRunner mockedPipelineRunner;
+  @Mock private VcfToBqOptions mockedVcfToBqOptions;
+  @Mock private VcfToBqContext mockedVcfToBqContext;
+  @Mock private VcfParser mockedVcfParser;
+  @Mock private HeaderReader mockedHeaderReader;
+  @Mock private SchemaGenerator mockedSchemaGenerator;
+  @Mock private VCFHeader mockedVcfHeader;
+  @Mock private TableSchema mockedTableSchema;
+
+  @Captor private ArgumentCaptor<PipelineOptions> argCaptorPipelineOptions;
+  @Captor private ArgumentCaptor<ImmutableList<String>> argCaptorImmutableList;
+
+  @Before
+  public void initializeSpyAndMocks() throws IOException{
+    MockitoAnnotations.initMocks(this);
+    vcfToBqTask = new VcfToBqTask(
+        mockedPipelineRunner, 
+        mockedHeaderReader, 
+        mockedVcfToBqContext,
+        mockedVcfParser,
+        mockedVcfToBqOptions,
+        mockedSchemaGenerator);
+    spyVcfToBqTask = spy(vcfToBqTask);
+  }
+
+  public void setUpRunBehaviors() throws IOException {
+    ImmutableList.Builder<String> headerLinesBuilder = new ImmutableList.Builder<String>();
+    for (int i = 0; i < 5; i++) {
+      headerLinesBuilder.add("##sampleHeaderLine=" + i);
+    }
+    ImmutableList<String> headerLines = headerLinesBuilder.build();
+    doReturn(headerLines).when(mockedHeaderReader).getHeaderLines();
+    doNothing().when(spyVcfToBqTask).setPipelineOptions(argCaptorPipelineOptions.capture());
+    doNothing().when(mockedVcfToBqContext).setHeaderLines(argCaptorImmutableList.capture());
+    doNothing().when(mockedPipelineRunner).runPipeline();
+  }
+
+  @Test
+  public void testVcfTaskConstructor_whenInitialize_thenNotNull() throws IOException {
+    assertThat(vcfToBqTask).isNotNull();
+    assertThat(spyVcfToBqTask).isNotNull();
+    }
+
+  @Test
+  public void testVcfTask_whenRun_thenVerifyCalls() throws IOException {
+    ImmutableList.Builder<String> headerLines = new ImmutableList.Builder<String>();
+    for (int i = 0; i < 5; i++) {
+      headerLines.add("##sampleHeaderLine=" + i);
+    }
+    setUpRunBehaviors();
+    spyVcfToBqTask.run();
+
+    verify(spyVcfToBqTask).setPipelineOptions(mockedVcfToBqOptions);
+    verify(mockedVcfToBqContext).setHeaderLines(headerLines.build());
+    verify(mockedVcfToBqContext).setVCFHeader(mockedVcfHeader);
+    verify(mockedVcfToBqContext).setBqSchema(mockedTableSchema);
+    verify(mockedPipelineRunner).runPipeline();
+  }
+}