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pulling changes from googlegenomics #1

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Merged
merged 4 commits into from
Mar 16, 2016
Merged

pulling changes from googlegenomics #1

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c85f705
Bump utils-java.
deflaux Mar 14, 2016
c22e1f1
Merge pull request #175 from deflaux/master
deflaux Mar 14, 2016
e61b791
[maven-release-plugin] prepare release google-genomics-dataflow-v1bet…
deflaux Mar 14, 2016
db6397b
[maven-release-plugin] prepare for next development iteration
deflaux Mar 14, 2016
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Binary file removed lib/alpn-boot-8.1.3.v20150130.jar
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Binary file added lib/alpn-boot-8.1.7.v20160121.jar
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6 changes: 3 additions & 3 deletions pom.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,7 @@
<groupId>com.google.cloud.genomics</groupId>
<artifactId>google-genomics-dataflow</artifactId>
<packaging>jar</packaging>
<version>v1beta2-0.21-SNAPSHOT</version>
<version>v1beta2-0.22-SNAPSHOT</version>

<organization>
<name>Google</name>
Expand Down Expand Up @@ -127,7 +127,7 @@
<dependency>
<groupId>com.google.cloud.genomics</groupId>
<artifactId>google-genomics-utils</artifactId>
<version>v1beta2-0.42</version>
<version>v1beta2-0.43</version>
<exclusions>
<!-- Exclude an old version of guava which is being pulled
in by a transitive dependency google-api-client 1.19.0 -->
Expand Down Expand Up @@ -248,7 +248,7 @@
<jdk>[1.8, 1.9)</jdk>
</activation>
<properties>
<alpn.jar>${basedir}/lib/alpn-boot-8.1.3.v20150130.jar</alpn.jar>
<alpn.jar>${basedir}/lib/alpn-boot-8.1.7.v20160121.jar</alpn.jar>
</properties>
</profile>
</profiles>
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16 changes: 8 additions & 8 deletions src/test/java/com/google/cloud/genomics/dataflow/pipelines/VariantSimilarityITCase.java
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Expand Up @@ -40,15 +40,15 @@
* - a Google Cloud project name in TEST_PROJECT,
* - a Cloud Storage folder path in TEST_OUTPUT_GCS_FOLDER to store temporary test outputs,
* - a Cloud Storage folder path in TEST_STAGING_GCS_FOLDER to store temporary files,
*
*
* Cloud Storage folder paths should be of the form "gs://bucket/folder/"
*
* When doing e.g. mvn install, you can skip integration tests using:
* mvn install -DskipITs
*
* To run one test:
* mvn -Dit.test=VariantSimilarityITCase#testLocal verify
*
* mvn -Dit.test=VariantSimilarityITCase#testStreamingLocal verify
*
* See also http://maven.apache.org/surefire/maven-failsafe-plugin/examples/single-test.html
*/
public class VariantSimilarityITCase {
Expand All @@ -72,10 +72,10 @@ public class VariantSimilarityITCase {
new GraphResult("NA12892", -7.64, 2.1),
new GraphResult("NA12893", 5.18, -1.18)
};

static String outputPrefix;
static IntegrationTestHelper helper;

@BeforeClass
public static void setUpBeforeClass() throws Exception {
helper = new IntegrationTestHelper();
Expand Down Expand Up @@ -138,11 +138,11 @@ public void testStreamingCloud() throws IOException, GeneralSecurityException {
};
testBase(ARGS);
}

private void testBase(String[] ARGS) throws IOException, GeneralSecurityException {
// Run the pipeline.
VariantSimilarity.main(ARGS);

// Download the pipeline results.
List<GraphResult> results = Lists.newArrayList();
for (GcsPath path : helper.gcsUtil.expand(GcsPath.fromUri(outputPrefix + "*"))) {
Expand All @@ -154,7 +154,7 @@ private void testBase(String[] ARGS) throws IOException, GeneralSecurityExceptio

// Check the pipeline results.
assertEquals(helper.PLATINUM_GENOMES_NUMBER_OF_SAMPLES, results.size());

assertThat(results,
CoreMatchers.allOf(CoreMatchers.hasItems(EXPECTED_RESULT)));
}
Expand Down