diff --git a/build.sbt b/build.sbt index 35c6753d..24bb2d65 100644 --- a/build.sbt +++ b/build.sbt @@ -4,13 +4,13 @@ import scala.util.Properties name := """bdg-sequila""" -version := "0.5.5-spark-2.4.2-SNAPSHOT" +version := "0.5.5-spark-2.3.2.3.1.0.0-78" organization := "org.biodatageeks" scalaVersion := "2.11.8" -val DEFAULT_SPARK_2_VERSION = "2.4.2" +val DEFAULT_SPARK_2_VERSION = "2.3.2.3.1.0.0-78" val DEFAULT_HADOOP_VERSION = "2.6.5" @@ -26,20 +26,20 @@ libraryDependencies += "org.apache.spark" % "spark-core_2.11" % sparkVersion libraryDependencies += "org.apache.spark" % "spark-sql_2.11" % sparkVersion libraryDependencies += "org.apache.spark" %% "spark-hive" % sparkVersion -libraryDependencies += "org.apache.spark" %% "spark-hive-thriftserver" % "2.4.0" +libraryDependencies += "org.apache.spark" %% "spark-hive-thriftserver" % sparkVersion -libraryDependencies += "com.holdenkarau" % "spark-testing-base_2.11" % "2.4.0_0.11.0" % "test" excludeAll ExclusionRule(organization = "javax.servlet") excludeAll (ExclusionRule("org.apache.hadoop")) +libraryDependencies += "com.holdenkarau" % "spark-testing-base_2.11" % "2.3.2_0.11.0" % "test" excludeAll ExclusionRule(organization = "javax.servlet") excludeAll (ExclusionRule("org.apache.hadoop")) //libraryDependencies += "org.apache.spark" %% "spark-hive" % "2.0.0" % "test" -libraryDependencies += "org.bdgenomics.adam" %% "adam-core-spark2" % "0.25.0" -libraryDependencies += "org.bdgenomics.adam" %% "adam-apis-spark2" % "0.25.0" -libraryDependencies += "org.bdgenomics.adam" %% "adam-cli-spark2" % "0.25.0" +libraryDependencies += "org.bdgenomics.adam" %% "adam-core-spark2" % "0.24.0" excludeAll (ExclusionRule("org.apache.hadoop")) +libraryDependencies += "org.bdgenomics.adam" %% "adam-apis-spark2" % "0.24.0" excludeAll (ExclusionRule("org.apache.hadoop")) +libraryDependencies += "org.bdgenomics.adam" %% "adam-cli-spark2" % "0.24.0" excludeAll (ExclusionRule("org.apache.hadoop")) libraryDependencies += "org.scala-lang" % "scala-library" % "2.11.8" libraryDependencies += "org.rogach" %% "scallop" % "3.1.2" -libraryDependencies += "org.hammerlab.bdg-utils" %% "cli" % "0.3.0" +libraryDependencies += "org.hammerlab.bdg-utils" %% "cli" % "0.3.0" excludeAll (ExclusionRule("org.apache.hadoop")) libraryDependencies += "com.github.samtools" % "htsjdk" % "2.19.0" @@ -53,7 +53,7 @@ libraryDependencies += "org.apache.logging.log4j" % "log4j-api" % "2.11.0" libraryDependencies += "com.intel.gkl" % "gkl" % "0.8.5-1-darwin-SNAPSHOT" libraryDependencies += "com.intel.gkl" % "gkl" % "0.8.5-1-linux-SNAPSHOT" -libraryDependencies += "org.hammerlab.bam" %% "load" % "1.2.0-M1" +libraryDependencies += "org.hammerlab.bam" %% "load" % "1.2.0-M1" excludeAll (ExclusionRule("org.apache.hadoop")) libraryDependencies += "de.ruedigermoeller" % "fst" % "2.57" libraryDependencies += "org.apache.commons" % "commons-lang3" % "3.7" @@ -61,7 +61,7 @@ libraryDependencies += "org.eclipse.jetty" % "jetty-servlet" % "9.3.24.v20180605 libraryDependencies += "org.apache.derby" % "derbyclient" % "10.14.2.0" -libraryDependencies += "org.biodatageeks" % "bdg-performance_2.11" % "0.2-SNAPSHOT" excludeAll (ExclusionRule("org.apache.hadoop")) +//libraryDependencies += "org.biodatageeks" % "bdg-performance_2.11" % "0.2-spark-2.3.3-SNAPSHOT" excludeAll (ExclusionRule("org.apache.hadoop")) libraryDependencies += "org.disq-bio" % "disq" % "0.3.0" @@ -94,7 +94,7 @@ resolvers ++= Seq( "Job Server Bintray" at "https://dl.bintray.com/spark-jobserver/maven", "zsibio-snapshots" at "http://zsibio.ii.pw.edu.pl/nexus/repository/maven-snapshots/", "spring" at "http://repo.spring.io/libs-milestone/", - "Cloudera" at "https://repository.cloudera.com/content/repositories/releases/", + "confluent" at "http://packages.confluent.io/maven/", "Hortonworks" at "http://repo.hortonworks.com/content/repositories/releases/" ) @@ -117,10 +117,12 @@ assemblyMergeStrategy in assembly := { case PathList("com", xs@_*) => MergeStrategy.first case PathList("shadeio", xs@_*) => MergeStrategy.first + case PathList(ps @ _*) if ps.last endsWith ".class" => MergeStrategy.first case PathList("au", xs@_*) => MergeStrategy.first case ("META-INF/org/apache/logging/log4j/core/config/plugins/Log4j2Plugins.dat") => MergeStrategy.first case ("images/ant_logo_large.gif") => MergeStrategy.first + case "overview.html" => MergeStrategy.rename case "mapred-default.xml" => MergeStrategy.last case "about.html" => MergeStrategy.rename diff --git a/src/main/scala/org/biodatageeks/hive/ThriftServerPageSeq.scala b/src/main/scala/org/biodatageeks/hive/ThriftServerPageSeq.scala index 89202383..af784621 100644 --- a/src/main/scala/org/biodatageeks/hive/ThriftServerPageSeq.scala +++ b/src/main/scala/org/biodatageeks/hive/ThriftServerPageSeq.scala @@ -170,4 +170,4 @@ private[ui] class ThriftServerPageSeq(parent: ThriftServerTabSeq) extends WebUIP } UIUtils.listingTable(headers, generateDataRow, data, fixedWidth = true) } -} +} \ No newline at end of file diff --git a/src/main/scala/org/biodatageeks/hive/ThriftServerSessionPageSeq.scala b/src/main/scala/org/biodatageeks/hive/ThriftServerSessionPageSeq.scala index ca86f951..b71aaf93 100644 --- a/src/main/scala/org/biodatageeks/hive/ThriftServerSessionPageSeq.scala +++ b/src/main/scala/org/biodatageeks/hive/ThriftServerSessionPageSeq.scala @@ -181,4 +181,4 @@ private[ui] class ThriftServerSessionPageSeq(parent: ThriftServerTabSeq) } UIUtils.listingTable(headers, generateDataRow, data, fixedWidth = true) } -} +} \ No newline at end of file