re-pkg as o.h.cli, add case_app module

.travis.yml

@@ -6,14 +6,16 @@ jdk:
 scala:
   - 2.11.8
 
-script: sbt ++$TRAVIS_SCALA_VERSION clean compile
+script: sbt ++$TRAVIS_SCALA_VERSION clean coverageTest
 
 cache:
   directories:
   - $HOME/.ivy2/cache
   - $HOME/.sbt/boot/
   - $HOME/.zinc
 
+after_success: sbt ++$TRAVIS_SCALA_VERSION travis-report
+
 before_cache:
   # Tricks to avoid unnecessary cache updates
   - find $HOME/.ivy2 -name "ivydata-*.properties" -delete

README.md

@@ -1,5 +1,17 @@
 # spark-commands
 
-[![Maven Central](https://img.shields.io/maven-central/v/org.hammerlab/spark-commands_2.11.svg?maxAge=600)](http://search.maven.org/#search%7Cga%7C1%7Cspark-commands)
+[![Build Status](https://travis-ci.org/hammerlab/spark-commands.svg?branch=master)](https://travis-ci.org/hammerlab/spark-commands)
+[![Coverage Status](https://coveralls.io/repos/github/hammerlab/spark-commands/badge.svg)](https://coveralls.io/github/hammerlab/spark-commands)
+
+Interfaces for creating CLI-runnable and testable commands/apps, with [Spark](http://spark.apache.org/)-based and non-Spark flavors.
+
+## args4j
+[![Maven Central](https://img.shields.io/maven-central/v/org.hammerlab.cli/args4j_2.11.svg?maxAge=600)](http://search.maven.org/#search%7Cga%7C1%7Chammerlab%20args4j)
+
+
+## case-app
+[![Maven Central](https://img.shields.io/maven-central/v/org.hammerlab.cli/case-app_2.11.svg?maxAge=600)](http://search.maven.org/#search%7Cga%7C1%7Chammerlab%20case-app)
+
+
+
 
-Interfaces for creating CLI-runnable and testable Spark commands/apps.

src/main/scala/org/hammerlab/commands/Args.scala → args4j/src/main/scala/org/hammerlab/cli/args4j/Args.scala

@@ -1,8 +1,9 @@
-package org.hammerlab.commands
+package org.hammerlab.cli.args4j
 
 import org.apache.spark.SparkContext
 import org.bdgenomics.utils.cli.Args4jBase
 
-trait Args extends Args4jBase {
+trait Args
+  extends Args4jBase {
   def validate(sc: SparkContext): Unit = {}
 }

src/main/scala/org/hammerlab/commands/Command.scala → args4j/src/main/scala/org/hammerlab/cli/args4j/Command.scala

@@ -1,4 +1,4 @@
-package org.hammerlab.commands
+package org.hammerlab.cli.args4j
 
 import grizzled.slf4j.Logging
 import org.bdgenomics.utils.cli.Args4j
@@ -21,7 +21,12 @@ abstract class Command[T <: Args: Manifest]
    *
    * @param args the command line arguments.
    */
-  def run(args: Array[String]): Unit = run(Args4j[T](args))
+  def run(args: Array[String]): Unit =
+    Args4j[T](args) match {
+      case Left(args) ⇒ run(args)
+      case _ ⇒
+    }
+
   def run(args: String*): Unit = run(args.toArray)
 
   def run(args: T): Unit

args4j/src/main/scala/org/hammerlab/cli/args4j/SparkCommand.scala

@@ -0,0 +1,39 @@
+package org.hammerlab.cli.args4j
+
+import org.apache.spark.SparkContext
+import org.hammerlab.spark.{ SparkConfBase, confs }
+
+abstract class SparkCommand[T <: Args: Manifest]
+  extends Command[T]
+    with SparkConfBase
+    with confs.Kryo {
+
+  override def run(args: T): Unit = {
+    val sc = createSparkContext()
+    try {
+      args.validate(sc)
+      run(args, sc)
+    } finally {
+      sc.stop()
+    }
+  }
+
+  def run(args: T, sc: SparkContext): Unit
+
+  /**
+   * Return a spark context.
+   *
+   * Typically, most properties are set through config file / cmd-line.
+   * @return
+   */
+  private def createSparkContext(): SparkContext = {
+    val conf = makeSparkConf
+
+    conf.getOption("spark.app.name") match {
+      case Some(cmdLineName) => conf.setAppName(s"$cmdLineName: $name")
+      case _ => conf.setAppName(name)
+    }
+
+    new SparkContext(conf)
+  }
+}

args4j/src/test/scala/org/hammerlab/cli/args4j/SparkCommandTest.scala

@@ -0,0 +1,67 @@
+package org.hammerlab.cli.args4j
+
+import com.esotericsoftware.kryo.Kryo
+import org.apache.spark.SparkContext
+import org.apache.spark.serializer.KryoRegistrator
+import org.hammerlab.paths.Path
+import org.hammerlab.test.Suite
+import org.kohsuke.args4j.Argument
+
+class SparkCommandTest
+  extends Suite {
+  test("command") {
+    val outFile = tmpPath()
+
+    TestCommand.main(
+      Array(
+        outFile.toString
+      )
+    )
+
+    outFile
+      .lines
+      .toList should be(
+      List(
+        "8mb",
+        "org.hammerlab.cli.args4j.TestRegistrar"
+      )
+    )
+  }
+}
+
+class TestArgs
+  extends Args {
+  @Argument(required = true)
+  var outFile: String = _
+}
+
+class TestRegistrar
+  extends KryoRegistrator {
+  override def registerClasses(kryo: Kryo): Unit = {}
+}
+
+import org.hammerlab.spark.test.suite.TestConfs
+
+object TestCommand
+  extends SparkCommand[TestArgs]
+    with TestConfs {
+
+  override def name: String = "test"
+  override def description: String = "test command"
+
+  sparkConf(
+    "spark.kryoserializer.buffer" → "8mb"
+  )
+
+  override def registrar = classOf[TestRegistrar]
+
+  override def run(args: TestArgs, sc: SparkContext): Unit = {
+    val conf = sc.getConf
+    Path(args.outFile).writeLines(
+      List(
+        conf.get("spark.kryoserializer.buffer"),
+        conf.get("spark.kryo.registrator")
+      )
+    )
+  }
+}

build.sbt

@@ -1,9 +1,33 @@
-name := "spark-commands"
-version := "1.0.4"
 
-providedDeps += spark.value
+val defaults = Seq(
+  organization := "org.hammerlab.cli",
+  deps ++= Seq(
+    slf4j,
+    spark_util % "1.3.0"
+  )
+) ++ addSparkDeps
 
-deps ++= Seq(
-  libs.value('bdg_utils_cli),
-  libs.value('slf4j)
+lazy val args4j = project.settings(
+  defaults,
+  version := "1.1.0-SNAPSHOT",
+  deps += bdg_utils_cli % "0.3.0",
+  testDeps += Parent.autoImport.args4j
 )
+
+lazy val case_app = project.settings(
+  defaults,
+  name := "case-app",
+  version := "1.0.0-SNAPSHOT",
+  deps ++= Seq(
+    Parent.autoImport.case_app,
+    io % "1.2.0",
+    paths % "1.2.0"
+  )
+)
+
+lazy val cli_root =
+  rootProject(
+    "cli-root",
+    args4j,
+    case_app
+  )

case_app/src/main/scala/org/hammerlab/cli/app/App.scala

@@ -0,0 +1,34 @@
+package org.hammerlab.cli.app
+
+import caseapp.core.Messages
+import caseapp.{ CaseApp, Parser, RemainingArgs }
+import grizzled.slf4j.Logging
+
+abstract class App[Args : Parser : Messages]
+  extends CaseApp[Args]
+    with Logging {
+
+  final override def run(options: Args, remainingArgs: RemainingArgs): Unit =
+    remainingArgs match {
+      case RemainingArgs(args, Nil) ⇒
+        run(
+          options,
+          args
+        )
+      case RemainingArgs(args, unparsed) ⇒
+        throw new IllegalArgumentException(
+          s"Unparsed arguments: ${unparsed.mkString(" ")}"
+        )
+    }
+
+  def done(): Unit = {}
+
+  final def run(options: Args, remainingArgs: Seq[String]): Unit =
+    try {
+      _run(options, remainingArgs)
+    } finally {
+      done()
+    }
+
+  protected def _run(options: Args, remainingArgs: Seq[String]): Unit
+}

case_app/src/main/scala/org/hammerlab/cli/app/IndexingApp.scala

@@ -0,0 +1,36 @@
+package org.hammerlab.cli.app
+
+import caseapp.Parser
+import caseapp.core.Messages
+import org.hammerlab.io.Printer
+import org.hammerlab.paths.Path
+
+trait OutPathArgs {
+  def out: Option[Path]
+}
+
+/**
+ * Interface for apps that take a [[Path]] and "index" it in some way, generating an output file that is by default
+ * named by appending an extension to the input path.
+ *
+ * @param defaultSuffix if [[OutPathArgs.out]] is empty, construct an output path by appending this string to the argument
+ *                      value [[PathApp.path]].
+ */
+abstract class IndexingApp[Args <: OutPathArgs : Parser : Messages](defaultSuffix: String)
+  extends PathApp[Args] {
+  implicit var printer: Printer = _
+
+  override def init(options: Args): Unit = {
+    printer =
+      Printer(
+        options
+          .out
+          .getOrElse(
+            path + defaultSuffix
+          )
+      )
+  }
+
+  override def close(): Unit =
+    printer.close()
+}

case_app/src/main/scala/org/hammerlab/cli/app/PathApp.scala

@@ -0,0 +1,33 @@
+package org.hammerlab.cli.app
+
+import java.io.Closeable
+
+import caseapp.Parser
+import caseapp.core.Messages
+import org.hammerlab.paths.Path
+
+abstract class PathApp[Args : Parser : Messages]
+  extends App[Args]
+    with Closeable {
+
+  @transient implicit var path: Path = _
+
+  def init(options: Args): Unit = {}
+  def close(): Unit = {}
+
+  final protected override def _run(options: Args, args: Seq[String]): Unit = {
+    if (args.size != 1) {
+      throw new IllegalArgumentException(
+        s"Exactly one argument (a BAM file path) is required"
+      )
+    }
+
+    path = Path(args.head)
+
+    init(options)
+    run(options)
+    close()
+  }
+
+  protected def run(options: Args): Unit
+}