From 911f1bdfd6f33d2c812972d87a7dd826b585eaed Mon Sep 17 00:00:00 2001
From: Frank Austin Nothaft <fnothaft@alumni.stanford.edu>
Date: Wed, 6 Jul 2016 15:06:36 -0400
Subject: [PATCH] [ADAM-1006] Split uberjar out to adam-assembly submodule.

---
 adam-assembly/pom.xml                       | 182 ++++++++++++++++++++
 adam-cli/pom.xml                            |  30 ----
 bin/adam-submit                             |   6 +-
 distribution/src/main/assembly/assembly.xml |   4 +-
 pom.xml                                     |   7 +
 5 files changed, 194 insertions(+), 35 deletions(-)
 create mode 100644 adam-assembly/pom.xml

diff --git a/adam-assembly/pom.xml b/adam-assembly/pom.xml
new file mode 100644
index 0000000000..931b001fde
--- /dev/null
+++ b/adam-assembly/pom.xml
@@ -0,0 +1,182 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+  <modelVersion>4.0.0</modelVersion>
+  <parent>
+    <groupId>org.bdgenomics.adam</groupId>
+    <artifactId>adam-parent_2.10</artifactId>
+    <version>0.19.1-SNAPSHOT</version>
+    <relativePath>../pom.xml</relativePath>
+  </parent>
+
+  <artifactId>adam-assembly_2.10</artifactId>
+  <packaging>jar</packaging>
+  <name>ADAM_2.10: Assembly</name>
+  <properties>
+    <timestamp>${maven.build.timestamp}</timestamp>
+    <maven.build.timestamp.format>yyyy-MM-dd</maven.build.timestamp.format>
+  </properties>
+  <build>
+    <plugins>
+      <plugin>
+        <groupId>org.codehaus.mojo</groupId>
+        <artifactId>templating-maven-plugin</artifactId>
+        <executions>
+          <execution>
+            <id>filter-src</id>
+            <goals>
+              <goal>filter-sources</goal>
+            </goals>
+          </execution>
+        </executions>
+      </plugin>
+      <plugin>
+        <groupId>pl.project13.maven</groupId>
+        <artifactId>git-commit-id-plugin</artifactId>
+        <executions>
+          <execution>
+            <goals>
+              <goal>revision</goal>
+            </goals>
+          </execution>
+        </executions>
+      </plugin>
+      <plugin>
+        <groupId>org.apache.maven.plugins</groupId>
+        <artifactId>maven-shade-plugin</artifactId>
+        <configuration>
+          <createDependencyReducedPom>false</createDependencyReducedPom>
+          <filters>
+            <filter>
+              <artifact>*:*</artifact>
+              <excludes>
+                <exclude>META-INF/*.SF</exclude>
+                <exclude>META-INF/*.DSA</exclude>
+                <exclude>META-INF/*.RSA</exclude>
+              </excludes>
+            </filter>
+          </filters>
+        </configuration>
+        <executions>
+          <execution>
+            <phase>package</phase>
+            <goals>
+              <goal>shade</goal>
+            </goals>
+            <configuration>
+              <transformers>
+                <transformer implementation="org.apache.maven.plugins.shade.resource.ServicesResourceTransformer"/>
+              </transformers>
+            </configuration>
+          </execution>
+        </executions>
+      </plugin>
+      <!-- disable surefire -->
+      <plugin>
+        <groupId>org.apache.maven.plugins</groupId>
+        <artifactId>maven-surefire-plugin</artifactId>
+        <configuration>
+          <skipTests>true</skipTests>
+        </configuration>
+      </plugin>
+      <!-- enable scalatest -->
+      <plugin>
+        <groupId>org.scalatest</groupId>
+        <artifactId>scalatest-maven-plugin</artifactId>
+        <configuration>
+          <reportsDirectory>${project.build.directory}/surefire-reports</reportsDirectory>
+          <junitxml>.</junitxml>
+          <filereports>ADAMTestSuite.txt</filereports>
+          <!--
+              As explained here: http://stackoverflow.com/questions/1660441/java-flag-to-enable-extended-serialization-debugging-info
+              The second option allows us better debugging for serialization-based errors.
+          -->
+          <argLine>-Xmx1024m -Dsun.io.serialization.extendedDebugInfo=true</argLine>
+          <stdout>F</stdout>
+        </configuration>
+        <executions>
+          <execution>
+            <id>test</id>
+            <goals>
+              <goal>test</goal>
+            </goals>
+          </execution>
+        </executions>
+      </plugin>
+      <plugin>
+        <groupId>org.codehaus.mojo</groupId>
+        <artifactId>build-helper-maven-plugin</artifactId>
+        <executions>
+          <execution>
+            <id>add-source</id>
+            <phase>generate-sources</phase>
+            <goals>
+              <goal>add-source</goal>
+            </goals>
+            <configuration>
+              <sources>
+                <source>src/main/scala</source>
+              </sources>
+            </configuration>
+          </execution>
+          <execution>
+            <id>add-test-source</id>
+            <phase>generate-test-sources</phase>
+            <goals>
+              <goal>add-test-source</goal>
+            </goals>
+            <configuration>
+              <sources>
+                <source>src/test/scala</source>
+              </sources>
+            </configuration>
+          </execution>
+        </executions>
+      </plugin>
+    </plugins>
+  </build>
+  <dependencies>
+    <dependency>
+      <groupId>org.bdgenomics.adam</groupId>
+      <artifactId>adam-cli_2.10</artifactId>
+    </dependency>
+  </dependencies>
+  <profiles>
+    <profile>
+      <id>default</id>
+      <activation>
+        <activeByDefault>true</activeByDefault>
+      </activation>
+      <build>
+        <plugins>
+          <plugin>
+            <groupId>org.scalatest</groupId>
+            <artifactId>scalatest-maven-plugin</artifactId>
+            <configuration>
+              <tagsToExclude>org.bdgenomics.adam.util.NetworkConnected,org.bdgenomics.adam.util.S3Test</tagsToExclude>
+            </configuration>
+          </plugin>
+        </plugins>
+      </build>
+    </profile>
+    <profile>
+      <id>network-connected</id>
+      <activation>
+        <property>
+          <name>networkconnected</name>
+        </property>
+      </activation>
+      <build>
+        <plugins>
+          <plugin>
+            <groupId>org.scalatest</groupId>
+            <artifactId>scalatest-maven-plugin</artifactId>
+            <configuration>
+              <tagsToExclude>org.bdgenomics.adam.util.S3Test</tagsToExclude>
+              <tagsToInclude>org.bdgenomics.adam.util.NetworkConnected</tagsToInclude>
+            </configuration>
+          </plugin>
+        </plugins>
+      </build>
+    </profile>
+  </profiles>
+</project>
diff --git a/adam-cli/pom.xml b/adam-cli/pom.xml
index 8570941c9b..9a46b680f5 100644
--- a/adam-cli/pom.xml
+++ b/adam-cli/pom.xml
@@ -40,36 +40,6 @@
           </execution>
         </executions>
       </plugin>
-      <plugin>
-        <groupId>org.apache.maven.plugins</groupId>
-        <artifactId>maven-shade-plugin</artifactId>
-        <configuration>
-          <createDependencyReducedPom>false</createDependencyReducedPom>
-          <filters>
-            <filter>
-              <artifact>*:*</artifact>
-              <excludes>
-                <exclude>META-INF/*.SF</exclude>
-                <exclude>META-INF/*.DSA</exclude>
-                <exclude>META-INF/*.RSA</exclude>
-              </excludes>
-            </filter>
-          </filters>
-        </configuration>
-        <executions>
-          <execution>
-            <phase>package</phase>
-            <goals>
-              <goal>shade</goal>
-            </goals>
-            <configuration>
-              <transformers>
-                <transformer implementation="org.apache.maven.plugins.shade.resource.ServicesResourceTransformer"/>
-              </transformers>
-            </configuration>
-          </execution>
-        </executions>
-      </plugin>
       <!-- disable surefire -->
       <plugin>
         <groupId>org.apache.maven.plugins</groupId>
diff --git a/bin/adam-submit b/bin/adam-submit
index e38e1a2de4..5d80f27647 100755
--- a/bin/adam-submit
+++ b/bin/adam-submit
@@ -57,17 +57,17 @@ ADAM_CLI_JAR=
 if [ -d "$SCRIPT_DIR/repo" ]; then
   ASSEMBLY_DIR="$SCRIPT_DIR/repo"
 else
-  ASSEMBLY_DIR="$SCRIPT_DIR/adam-cli/target"
+  ASSEMBLY_DIR="$SCRIPT_DIR/adam-assembly/target"
 fi
 
-num_jars="$(ls -1 "$ASSEMBLY_DIR" | grep "^adam-cli_[0-9A-Za-z\.-]*\.jar$" | grep -v javadoc | wc -l)"
+num_jars="$(ls -1 "$ASSEMBLY_DIR" | grep "^adam-assembly_[0-9A-Za-z\.-]*\.jar$" | grep -v javadoc | wc -l)"
 if [ "$num_jars" -eq "0" ]; then
   echo "Failed to find ADAM cli assembly in $ASSEMBLY_DIR." 1>&2
   echo "You need to build ADAM before running this program." 1>&2
   exit 1
 fi
 
-ASSEMBLY_JARS="$(ls -1 "$ASSEMBLY_DIR" | grep "^adam-cli_[0-9A-Za-z\.-]*\.jar$" | grep -v javadoc || true)"
+ASSEMBLY_JARS="$(ls -1 "$ASSEMBLY_DIR" | grep "^adam-assembly_[0-9A-Za-z\.-]*\.jar$" | grep -v javadoc || true)"
 if [ "$num_jars" -gt "1" ]; then
   echo "Found multiple ADAM cli assembly jars in $ASSEMBLY_DIR:" 1>&2
   echo "$ASSEMBLY_JARS" 1>&2
diff --git a/distribution/src/main/assembly/assembly.xml b/distribution/src/main/assembly/assembly.xml
index d3e651f30d..1c5f1bd0a9 100644
--- a/distribution/src/main/assembly/assembly.xml
+++ b/distribution/src/main/assembly/assembly.xml
@@ -45,9 +45,9 @@
       <outputDirectory>javadocs</outputDirectory>
     </fileSet>
     <fileSet>
-      <directory>../adam-cli/target</directory>
+      <directory>../adam-assembly/target</directory>
       <includes>
-        <include>adam-cli_*.jar</include>
+        <include>adam-assembly_*.jar</include>
       </includes>
       <outputDirectory>repo</outputDirectory>
       <directoryMode>0755</directoryMode>
diff --git a/pom.xml b/pom.xml
index 6de697299e..4c1b6b1ec6 100644
--- a/pom.xml
+++ b/pom.xml
@@ -36,6 +36,7 @@
     <module>adam-core</module>
     <module>adam-apis</module>
     <module>adam-cli</module>
+    <module>adam-assembly</module>
   </modules>
 
   <licenses>
@@ -346,6 +347,11 @@
         <type>test-jar</type>
         <scope>test</scope>
       </dependency>
+      <dependency>
+        <groupId>org.bdgenomics.adam</groupId>
+        <artifactId>adam-cli_2.10</artifactId>
+        <version>${project.version}</version>
+      </dependency>
       <dependency>
         <groupId>org.bdgenomics.adam</groupId>
         <artifactId>adam-apis_2.10</artifactId>
@@ -566,6 +572,7 @@
         <module>adam-core</module>
         <module>adam-apis</module>
         <module>adam-cli</module>
+        <module>adam-assembly</module>
         <!-- distribution should be last -->
         <module>distribution</module>
       </modules>