Feature/spark hdp 2.3.2.3.1.0.0 78

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"
 
@@ -53,15 +53,15 @@ 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"
 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

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)
   }
-}
+}

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)
   }
-}
+}