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Add VariantSimilarity integration test.
Also refactored reusable integration test helper code.
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95 changes: 95 additions & 0 deletions
95
src/test/java/com/google/cloud/genomics/dataflow/pipelines/IntegrationTestHelper.java
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| /* | ||
| * Copyright (C) 2015 Google Inc. | ||
| * | ||
| * 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.dataflow.pipelines; | ||
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| import java.io.BufferedReader; | ||
| import java.io.IOException; | ||
| import java.io.Writer; | ||
| import java.nio.channels.Channels; | ||
| import java.security.GeneralSecurityException; | ||
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| import org.junit.Assert; | ||
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| import com.google.api.services.storage.Storage; | ||
| import com.google.cloud.dataflow.sdk.options.GcsOptions; | ||
| import com.google.cloud.dataflow.sdk.options.PipelineOptionsFactory; | ||
| import com.google.cloud.dataflow.sdk.util.GcsUtil; | ||
| import com.google.cloud.dataflow.sdk.util.Transport; | ||
| import com.google.cloud.dataflow.sdk.util.gcsfs.GcsPath; | ||
| import com.google.cloud.genomics.dataflow.utils.GenomicsOptions; | ||
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| public class IntegrationTestHelper { | ||
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| // Test configuration constants | ||
| final String API_KEY = System.getenv("GOOGLE_API_KEY"); | ||
| final String TEST_PROJECT = System.getenv("TEST_PROJECT"); | ||
| final String TEST_OUTPUT_GCS_FOLDER = System.getenv("TEST_OUTPUT_GCS_FOLDER"); | ||
| final String TEST_STAGING_GCS_FOLDER = System.getenv("TEST_STAGING_GCS_FOLDER"); | ||
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| // Variant test configuration constants | ||
| static final String PLATINUM_GENOMES_DATASET = "3049512673186936334"; | ||
| static final String PLATINUM_GENOMES_BRCA1_REFERENCES = "chr17:41196311:41277499"; | ||
| static final int PLATINUM_GENOMES_NUMBER_OF_SAMPLES = 17; | ||
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| GenomicsOptions popts = PipelineOptionsFactory.create().as(GenomicsOptions.class); | ||
| GcsUtil gcsUtil; | ||
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| public IntegrationTestHelper() { | ||
| Assert.assertNotNull("You must set the GOOGLE_API_KEY environment variable for this test.", API_KEY); | ||
| Assert.assertNotNull("You must set the TEST_PROJECT environment variable for this test.", TEST_PROJECT); | ||
| Assert.assertNotNull("You must set the TEST_OUTPUT_GCS_FOLDER environment variable for this test.", TEST_OUTPUT_GCS_FOLDER); | ||
| Assert.assertNotNull("You must set the TEST_STAGING_GCS_FOLDER environment variable for this test.", TEST_STAGING_GCS_FOLDER); | ||
| Assert.assertTrue("TEST_OUTPUT_GCS_FOLDER must end with '/'", TEST_OUTPUT_GCS_FOLDER.endsWith("/")); | ||
| Assert.assertTrue("TEST_OUTPUT_GCS_FOLDER must start with 'gs://'", TEST_OUTPUT_GCS_FOLDER.startsWith("gs://")); | ||
| Assert.assertTrue("TEST_STAGING_GCS_FOLDER must start with 'gs://'", TEST_STAGING_GCS_FOLDER.startsWith("gs://")); | ||
| // we don't care how TEST_STAGING_GCS_FOLDER ends, so no check for it. | ||
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| popts.setApiKey(API_KEY); | ||
| gcsUtil = new GcsUtil.GcsUtilFactory().create(popts); | ||
| } | ||
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| /** | ||
| * Make sure we can get to the output. | ||
| * | ||
| * Also write a sentinel value to the file. This protects against the possibility of prior | ||
| * test output causing a newly failing test to appear to succeed. | ||
| */ | ||
| public void touchOutput(String outputPath) throws IOException { | ||
| try (Writer writer = Channels.newWriter(gcsUtil.create(GcsPath.fromUri(outputPath), "text/plain"), "UTF-8")) { | ||
| writer.write("output will go here"); | ||
| } | ||
| } | ||
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| /** | ||
| * Open test output for reading. | ||
| */ | ||
| public BufferedReader openOutput(String outputPath) throws IOException { | ||
| return new BufferedReader(Channels.newReader(gcsUtil.open(GcsPath.fromUri(outputPath)), "UTF-8")); | ||
| } | ||
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| /** | ||
| * Delete test output. | ||
| */ | ||
| public void deleteOutput(String outputPath) throws IOException, GeneralSecurityException { | ||
| // boilerplate | ||
| GcsPath path = GcsPath.fromUri(outputPath); | ||
| GcsOptions gcsOptions = (GcsOptions)popts.as(GcsOptions.class); | ||
| Storage storage = Transport.newStorageClient(gcsOptions).build(); | ||
| // do the actual work | ||
| storage.objects().delete(path.getBucket(), path.getObject()).execute(); | ||
| } | ||
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| } |
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