/*
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;
import com.beust.jcommander.internal.Lists;
import com.google.api.client.googleapis.json.GoogleJsonResponseException;
import com.google.api.client.util.store.MemoryDataStoreFactory;
import com.google.api.services.genomics.GenomicsScopes;
import com.google.api.services.genomics.model.ExportReadGroupSetsRequest;
import com.google.api.services.genomics.model.ExportReadGroupSetsResponse;
import com.google.api.services.genomics.model.Job;
import com.google.api.services.genomics.model.ReadGroupSet;
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 ExportReadsCommandTest extends CommandTest {
@Test
public void testScopes() throws Exception {
assertTrue(new ExportReadsCommand().getScopes()
.contains(GenomicsScopes.DEVSTORAGE_READ_WRITE));
}
@Test
public void testExportReadsets() throws Exception {
ExportReadsCommand command = new ExportReadsCommand();
command.setDataStoreFactory(new MemoryDataStoreFactory());
command.readGroupSetIds = Lists.newArrayList("r1", "r2");
command.projectNumber = 3L;
command.exportUri = "exportme";
// Get the readsets
Mockito.when(readsets.get("r1")).thenReturn(readsetGet);
Mockito.when(readsets.get("r2")).thenReturn(readsetGet);
Mockito.when(readsetGet.execute()).thenReturn(
new ReadGroupSet().setName("name1"),
new ReadGroupSet().setName("name2"));
// Export them
Mockito.when(readsets.export(Mockito.any(ExportReadGroupSetsRequest.class)))
.thenReturn(readsetExport);
Mockito.when(readsetExport.execute()).thenReturn(
new ExportReadGroupSetsResponse().setJobId("8675309"));
// Get the job
Mockito.when(jobs.get("8675309")).thenReturn(jobGet);
Mockito.when(jobGet.execute()).thenReturn(new Job().setDetailedStatus("description1"));
command.handleRequest(genomics);
String output = outContent.toString();
assertTrue(output, output.contains("Exporting read group sets name1,name2"));
assertTrue(output, output.contains("Export job:"));
assertTrue(output, output.contains("description1"));
}
@Test
public void testExportReadsets_badIds() throws Exception {
ExportReadsCommand command = new ExportReadsCommand();
command.readGroupSetIds = Lists.newArrayList("bad");
// Get the readsets
Mockito.when(readsets.get(Mockito.anyString())).thenThrow(GoogleJsonResponseException.class);
command.handleRequest(genomics);
String output = outContent.toString();
assertTrue(output, output.contains("The read group set ID bad won't work"));
}
}