Merge eceaea9 into b0ac086

bigdatagenomics · Feb 5, 2018 · 549e010 · 549e010
2 parents b0ac086 + eceaea9
commit 549e010
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Showing 9 changed files with 24 additions and 186 deletions.
diff --git a/assembly/pom.xml b/assembly/pom.xml
@@ -3,12 +3,12 @@
   <modelVersion>4.0.0</modelVersion>
   <parent>
     <groupId>org.bdgenomics.cannoli</groupId>
-    <artifactId>cannoli-parent_2.10</artifactId>
+    <artifactId>cannoli-parent-spark2_2.11</artifactId>
     <version>0.2.0-SNAPSHOT</version>
     <relativePath>../pom.xml</relativePath>
   </parent>
 
-  <artifactId>cannoli-assembly_2.10</artifactId>
+  <artifactId>cannoli-assembly-spark2_2.11</artifactId>
   <packaging>jar</packaging>
   <name>Cannoli_${scala.version.prefix}: Assembly</name>
   <properties>
@@ -52,7 +52,7 @@
   <dependencies>
     <dependency>
       <groupId>org.bdgenomics.cannoli</groupId>
-      <artifactId>cannoli-cli_${scala.version.prefix}</artifactId>
+      <artifactId>cannoli-cli-spark2_${scala.version.prefix}</artifactId>
       <scope>compile</scope>
     </dependency>
   </dependencies>

diff --git a/cli/pom.xml b/cli/pom.xml
@@ -3,12 +3,12 @@
   <modelVersion>4.0.0</modelVersion>
   <parent>
     <groupId>org.bdgenomics.cannoli</groupId>
-    <artifactId>cannoli-parent_2.10</artifactId>
+    <artifactId>cannoli-parent-spark2_2.11</artifactId>
     <version>0.2.0-SNAPSHOT</version>
     <relativePath>../pom.xml</relativePath>
   </parent>
 
-  <artifactId>cannoli-cli_2.10</artifactId>
+  <artifactId>cannoli-cli-spark2_2.11</artifactId>
   <packaging>jar</packaging>
   <name>Cannoli_${scala.version.prefix}: CLI</name>
   <properties>
@@ -74,17 +74,17 @@
     </dependency>
     <dependency>
       <groupId>org.bdgenomics.adam</groupId>
-      <artifactId>adam-cli_${scala.version.prefix}</artifactId>
+      <artifactId>adam-cli-spark2_${scala.version.prefix}</artifactId>
       <scope>compile</scope>
     </dependency>
     <dependency>
       <groupId>org.bdgenomics.cannoli</groupId>
-      <artifactId>cannoli-core_${scala.version.prefix}</artifactId>
+      <artifactId>cannoli-core-spark2_${scala.version.prefix}</artifactId>
       <scope>compile</scope>
     </dependency>
     <dependency>
       <groupId>org.bdgenomics.utils</groupId>
-      <artifactId>utils-misc_${scala.version.prefix}</artifactId>
+      <artifactId>utils-misc-spark2_${scala.version.prefix}</artifactId>
       <type>test-jar</type>
       <scope>test</scope>
     </dependency>

diff --git a/core/pom.xml b/core/pom.xml
@@ -3,12 +3,12 @@
   <modelVersion>4.0.0</modelVersion>
   <parent>
     <groupId>org.bdgenomics.cannoli</groupId>
-    <artifactId>cannoli-parent_2.10</artifactId>
+    <artifactId>cannoli-parent-spark2_2.11</artifactId>
     <version>0.2.0-SNAPSHOT</version>
     <relativePath>../pom.xml</relativePath>
   </parent>
 
-  <artifactId>cannoli-core_2.10</artifactId>
+  <artifactId>cannoli-core-spark2_2.11</artifactId>
   <packaging>jar</packaging>
   <name>Cannoli_${scala.version.prefix}: Core</name>
 
@@ -49,12 +49,12 @@
     </dependency>
     <dependency>
       <groupId>org.bdgenomics.adam</groupId>
-      <artifactId>adam-core_${scala.version.prefix}</artifactId>
+      <artifactId>adam-core-spark2_${scala.version.prefix}</artifactId>
       <scope>compile</scope>
     </dependency>
     <dependency>
       <groupId>org.bdgenomics.utils</groupId>
-      <artifactId>utils-misc_${scala.version.prefix}</artifactId>
+      <artifactId>utils-misc-spark2_${scala.version.prefix}</artifactId>
       <type>test-jar</type>
       <scope>test</scope>
     </dependency>

diff --git a/distribution/pom.xml b/distribution/pom.xml
@@ -3,12 +3,12 @@
   <modelVersion>4.0.0</modelVersion>
   <parent>
     <groupId>org.bdgenomics.cannoli</groupId>
-    <artifactId>cannoli-parent_2.10</artifactId>
+    <artifactId>cannoli-parent-spark2_2.11</artifactId>
     <version>0.2.0-SNAPSHOT</version>
     <relativePath>../pom.xml</relativePath>
   </parent>
 
-  <artifactId>cannoli-distribution_2.10</artifactId>
+  <artifactId>cannoli-distribution-spark2_2.11</artifactId>
   <packaging>pom</packaging>
   <name>Cannoli_${scala.version.prefix}: Distribution</name>
   <build>

diff --git a/pom.xml b/pom.xml
@@ -8,7 +8,7 @@
   </parent>
 
   <groupId>org.bdgenomics.cannoli</groupId>
-  <artifactId>cannoli-parent_2.10</artifactId>
+  <artifactId>cannoli-parent-spark2_2.11</artifactId>
   <version>0.2.0-SNAPSHOT</version>
   <packaging>pom</packaging>
   <name>Cannoli_${scala.version.prefix}</name>
@@ -17,10 +17,10 @@
   <inceptionYear>2017</inceptionYear>
 
   <properties>
-    <adam.version>0.23.0</adam.version>
-    <scala.version>2.10.6</scala.version>
-    <scala.version.prefix>2.10</scala.version.prefix>
-    <spark.version>1.6.3</spark.version>
+    <adam.version>0.24.0-SNAPSHOT</adam.version>
+    <scala.version>2.11.12</scala.version>
+    <scala.version.prefix>2.11</scala.version.prefix>
+    <spark.version>2.2.1</spark.version>
     <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
     <project.build.targetEncoding>UTF-8</project.build.targetEncoding>
     <maven.enforcer.maven-version>[3.1.1,)</maven.enforcer.maven-version>
@@ -349,27 +349,27 @@
     <dependencies>
       <dependency>
         <groupId>org.bdgenomics.adam</groupId>
-        <artifactId>adam-core_${scala.version.prefix}</artifactId>
+        <artifactId>adam-core-spark2_${scala.version.prefix}</artifactId>
         <version>${adam.version}</version>
       </dependency>
       <dependency>
         <groupId>org.bdgenomics.adam</groupId>
-        <artifactId>adam-cli_${scala.version.prefix}</artifactId>
+        <artifactId>adam-cli-spark2_${scala.version.prefix}</artifactId>
         <version>${adam.version}</version>
       </dependency>
       <dependency>
         <groupId>org.bdgenomics.cannoli</groupId>
-        <artifactId>cannoli-core_${scala.version.prefix}</artifactId>
+        <artifactId>cannoli-core-spark2_${scala.version.prefix}</artifactId>
         <version>${project.version}</version>
       </dependency>
       <dependency>
         <groupId>org.bdgenomics.cannoli</groupId>
-        <artifactId>cannoli-cli_${scala.version.prefix}</artifactId>
+        <artifactId>cannoli-cli-spark2_${scala.version.prefix}</artifactId>
         <version>${project.version}</version>
       </dependency>
       <dependency>
         <groupId>org.bdgenomics.utils</groupId>
-        <artifactId>utils-misc_${scala.version.prefix}</artifactId>
+        <artifactId>utils-misc-spark2_${scala.version.prefix}</artifactId>
         <version>${utils.version}</version>
         <type>test-jar</type>
       </dependency>

diff --git a/scripts/jenkins-test b/scripts/jenkins-test
@@ -37,61 +37,6 @@ then
     exit 1
 fi
 
-# this next line is supposed to fail
-set +e
-
-echo "Rewriting POM.xml files to Scala 2.10 and Spark 1 should error..."
-./scripts/move_to_spark_1.sh
-if [[ $? == 0 ]];
-then
-    echo "Running move_to_spark_1.sh when POMs are set up for Spark 1 should fail, but error code was 0 (success)."
-    exit 1
-fi
-
-./scripts/move_to_scala_2.10.sh
-if [[ $? == 0 ]];
-then
-    echo "Running move_to_scala_2.10.sh when POMs are set up for Scala 2.10 should fail, but error code was 0 (success)."
-    exit 1
-fi
-
-set -e
-
-# are we testing for spark 2.0.0? if so, we need to rewrite our poms first
-if [ ${SPARK_VERSION} == 2.0.0 ];
-then
-
-    echo "Rewriting POM.xml files for Spark 2."
-    ./scripts/move_to_spark_2.sh
-
-    # shouldn't be able to move to spark 2 twice
-    set +e
-    ./scripts/move_to_spark_2.sh
-    if [[ $? == 0 ]];
-    then
-        echo "We have already moved to Spark 2, so running move_to_spark_2.sh a second time should fail, but error code was 0 (success)."
-        exit 1
-    fi
-    set -e
-fi
-
-# are we testing for scala 2.11? if so, we need to rewrite our poms to 2.11 first
-if [ ${SCALAVER} == 2.11 ];
-then
-    echo "Rewriting POM.xml files for Scala 2.11."
-    ./scripts/move_to_scala_2.11.sh
-
-    # shouldn't be able to move to scala 2.11 twice
-    set +e
-    ./scripts/move_to_scala_2.11.sh
-    if [[ $? == 0 ]];
-    then
-        echo "We have already moved to Scala 2.11, so running move_to_scala_2.11.sh a second time should fail, but error code was 0 (success)."
-        exit 1
-    fi
-    set -e
-fi
-
 # print versions
 echo "Testing CANNOLI version ${VERSION} on Spark ${SPARK_VERSION} and Hadoop ${HADOOP_VERSION}"
 
@@ -128,20 +73,6 @@ set -x -v
 find ${CANNOLI_MVN_TMP_DIR}
 rm -rf ${CANNOLI_MVN_TMP_DIR}
 
-# and move our poms back to their original values
-# this will allow us to pass our porcelain test at the end
-if [ ${SPARK_VERSION} == 2.0.0 ];
-then
-
-    echo "Rewriting POM.xml files back to Spark 1."
-    ./scripts/move_to_spark_1.sh
-fi
-if [ ${SCALAVER} == 2.11 ];
-then
-    echo "Rewriting POM.xml files back to Scala 2.10."
-    ./scripts/move_to_scala_2.10.sh
-fi
-
 find . -name pom.xml \
     -exec sed -i.bak \
     -e "s:sun.io.serialization.extendedDebugInfo=true -Djava.io.tmpdir=${CANNOLI_MVN_TMP_DIR}:sun.io.serialization.extendedDebugInfo=true:g" \

diff --git a/scripts/move_to_scala_2.10.sh b/scripts/move_to_scala_2.10.sh
diff --git a/scripts/move_to_spark_1.sh b/scripts/move_to_spark_1.sh
diff --git a/scripts/release/release.sh b/scripts/release/release.sh
@@ -24,64 +24,6 @@ echo "releasing from ${commit} on branch ${branch}"
 
 git push origin ${branch}
 
-# do scala 2.10 release
-git checkout -b maint_2.10-${release} ${branch}
-mvn --batch-mode \
-  -P distribution \
-  -Dresume=false \
-  -Dtag=cannoli-parent_2.10-${release} \
-  -DreleaseVersion=${release} \
-  -DdevelopmentVersion=${devel} \
-  -DbranchName=cannoli_2.10-${release} \
-  release:clean \
-  release:prepare \
-  release:perform
-
-if [ $? != 0 ]; then
-  echo "Releasing Spark 1, Scala 2.10 version failed."
-  exit 1
-fi
-
-# do scala 2.11 release
-git checkout -b maint_2.11-${release} ${branch}
-./scripts/move_to_scala_2.11.sh
-git commit -a -m "Modifying pom.xml files for Spark 1, Scala 2.11 release."
-mvn --batch-mode \
-  -P distribution \
-  -Dresume=false \
-  -Dtag=cannoli-parent_2.11-${release} \
-  -DreleaseVersion=${release} \
-  -DdevelopmentVersion=${devel} \
-  -DbranchName=cannoli_2.11-${release} \
-  release:clean \
-  release:prepare \
-  release:perform
-
-if [ $? != 0 ]; then
-  echo "Releasing Spark 1, Scala 2.11 version failed."
-  exit 1
-fi
-
-# do spark 2, scala 2.10 release
-git checkout -b maint_spark2_2.10-${release} ${branch}
-./scripts/move_to_spark_2.sh
-git commit -a -m "Modifying pom.xml files for Spark 2, Scala 2.10 release."
-mvn --batch-mode \
-  -P distribution \
-  -Dresume=false \
-  -Dtag=cannoli-parent-spark2_2.10-${release} \
-  -DreleaseVersion=${release} \
-  -DdevelopmentVersion=${devel} \
-  -DbranchName=cannoli-spark2_2.10-${release} \
-  release:clean \
-  release:prepare \
-  release:perform
-
-if [ $? != 0 ]; then
-  echo "Releasing Spark 2, Scala 2.10 version failed."
-  exit 1
-fi
-
 # do spark 2, scala 2.11 release
 git checkout -b maint_spark2_2.11-${release} ${branch}
 ./scripts/move_to_spark_2.sh