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Author: Olivier Sallou
Last-Update: 2018-04-23 14:51:06
Description: Remove Google cloud storage
Forwarded: not-needed
--- a/src/main/java/picard/nio/GoogleStorageUtils.java
+++ b/src/main/java/picard/nio/GoogleStorageUtils.java
@@ -25,14 +25,6 @@
package picard.nio;
-import com.google.cloud.storage.StorageOptions;
-import com.google.cloud.storage.contrib.nio.CloudStorageConfiguration;
-import com.google.cloud.storage.contrib.nio.CloudStorageFileSystemProvider;
-import com.google.api.client.util.Strings;
-import com.google.api.gax.retrying.RetrySettings;
-import com.google.cloud.http.HttpTransportOptions;
-import org.threeten.bp.Duration;
-
/**
* This class serves as a connection to google's implementation of nio support for GCS housed files.
*
@@ -50,42 +42,6 @@
class GoogleStorageUtils {
public static void initialize() {
- // requester pays support is currently not configured
- CloudStorageFileSystemProvider.setDefaultCloudStorageConfiguration(GoogleStorageUtils.getCloudStorageConfiguration(20, null));
- CloudStorageFileSystemProvider.setStorageOptions(GoogleStorageUtils.setGenerousTimeouts(StorageOptions.newBuilder()).build());
}
- /** The config we want to use. **/
- private static CloudStorageConfiguration getCloudStorageConfiguration(int maxReopens, String requesterProject) {
- CloudStorageConfiguration.Builder builder = CloudStorageConfiguration.builder()
- // if the channel errors out, re-open up to this many times
- .maxChannelReopens(maxReopens);
- if (!Strings.isNullOrEmpty(requesterProject)) {
- // enable requester pays and indicate who pays
- builder = builder.autoDetectRequesterPays(true).userProject(requesterProject);
- }
-
- // this causes the gcs filesystem to treat files that end in a / as a directory
- // true is the default but this protects against future changes in behavior
- builder.usePseudoDirectories(true);
- return builder.build();
- }
-
- private static StorageOptions.Builder setGenerousTimeouts(StorageOptions.Builder builder) {
- return builder
- .setTransportOptions(HttpTransportOptions.newBuilder()
- .setConnectTimeout(120_000)
- .setReadTimeout(120_000)
- .build())
- .setRetrySettings(RetrySettings.newBuilder()
- .setMaxAttempts(15)
- .setMaxRetryDelay(Duration.ofMillis(256_000L))
- .setTotalTimeout(Duration.ofMillis(4000_000L))
- .setInitialRetryDelay(Duration.ofMillis(1000L))
- .setRetryDelayMultiplier(2.0)
- .setInitialRpcTimeout(Duration.ofMillis(180_000L))
- .setRpcTimeoutMultiplier(1.0)
- .setMaxRpcTimeout(Duration.ofMillis(180_000L))
- .build());
- }
}
--- a/src/main/java/picard/fingerprint/FingerprintChecker.java
+++ b/src/main/java/picard/fingerprint/FingerprintChecker.java
@@ -24,7 +24,7 @@
package picard.fingerprint;
-import com.google.cloud.storage.contrib.nio.SeekableByteChannelPrefetcher;
+//import com.google.cloud.storage.contrib.nio.SeekableByteChannelPrefetcher;
import com.google.common.annotations.VisibleForTesting;
import htsjdk.samtools.SAMFileHeader;
import htsjdk.samtools.SAMReadGroupRecord;
@@ -469,11 +469,7 @@
}
private static final Function<SeekableByteChannel, SeekableByteChannel> seekableChannelFunction = (chan) -> {
- try {
- return SeekableByteChannelPrefetcher.addPrefetcher(1, chan);
- } catch (IOException e) {
- throw new RuntimeException("Trouble wrapping seekable stream with prefetcher.", e);
- }
+ throw new RuntimeException("Trouble wrapping seekable stream with prefetcher.");
};
/**
|