/*
Copyright 2014 Google Inc. All rights reserved.
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
*/
package com.google.cloud.genomics.api.client.commands.align;
import com.beust.jcommander.internal.Lists;
import com.google.api.client.util.store.MemoryDataStoreFactory;
import com.google.api.services.genomics.GenomicsScopes;
import com.google.api.services.genomics.model.AlignReadGroupSetsRequest;
import com.google.api.services.genomics.model.AlignReadGroupSetsResponse;
import com.google.api.services.genomics.model.Dataset;
import com.google.api.services.genomics.model.Job;
import com.google.cloud.genomics.api.client.commands.CommandTest;
import org.junit.Test;
import org.junit.runner.RunWith;
import org.junit.runners.JUnit4;
import org.mockito.Mockito;
import static org.junit.Assert.assertTrue;
@RunWith(JUnit4.class)
public class AlignInterleavedFastqsCommandTest extends CommandTest {
@Test
public void testScopes() throws Exception {
assertTrue(new AlignInterleavedFastqsCommand().getScopes()
.contains(GenomicsScopes.DEVSTORAGE_READ_WRITE));
}
@Test
public void testAlign() throws Exception {
AlignInterleavedFastqsCommand command = new AlignInterleavedFastqsCommand();
command.setDataStoreFactory(new MemoryDataStoreFactory());
command.fastqFiles = Lists.newArrayList("uri1");
command.datasetId = "abc";
// Get the dataset
Mockito.when(datasets.get("abc")).thenReturn(datasetGet);
Mockito.when(datasetGet.execute()).thenReturn(
new Dataset().setId("abc").setName("1kg"));
// Import them
Mockito.when(readsets.align(Mockito.any(AlignReadGroupSetsRequest.class)))
.thenReturn(readsetAlign);
Mockito.when(readsetAlign.execute()).thenReturn(
new AlignReadGroupSetsResponse().setJobId("8675309"));
// Get the job
Mockito.when(jobs.get("8675309")).thenReturn(jobGet);
Mockito.when(jobGet.execute()).thenReturn(
new Job().setDetailedStatus("description1").setImportedIds(Lists.newArrayList("r1")));
command.handleRequest(genomics);
String output = outContent.toString();
assertTrue(output, output.contains("read group sets into: 1kg"));
assertTrue(output, output.contains("Aligning job:"));
assertTrue(output, output.contains("description1"));
}
}