Initial commit

.github/workflows/unittests.yaml

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+name: unit tests
+
+on: [push, pull_request]
+
+jobs:
+ test:
+ runs-on: ubuntu-latest
+ steps:
+ - name: Checkout
+ uses: actions/checkout@v2
+ with:
+ fetch-depth: 0
+ - name: Setup Scala
+ uses: olafurpg/setup-scala@v12
+ with:
+ java-version: [email protected]
+ - name: Unit Tests
+ run: |
+ set -e
+ ./mill _.test

.gitignore

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+.idea
+.idea_modules
+out
+jars

LICENSE

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+The MIT License
+
+Copyright (c) 2022 Fulcrum Genomics LLC
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.

README.md

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+[![unit tests](https:/fulcrumgenomics/scala-mill-skeleton/actions/workflows/unittests.yaml/badge.svg)](https:/fulcrumgenomics/scala-mill-skeleton/actions/workflows/unittests.yaml)
+[![License](https://img.shields.io/badge/license-MIT-blue.svg)](https:/fulcrumgenomics/fgbio/blob/main/LICENSE)
+[![Language](https://img.shields.io/badge/language-scala-brightgreen.svg)](http://www.scala-lang.org/)
+
+
+A skeleton repository a Scala-based [fgbio][fgbio-link]-like command-line toolkit.
+
+## Why this repo?
+
+This the starting point for [Fulcrum Genomics][fulcrum-genomics-link] projects that contain Scala-based 
+[fgbio][fgbio-link]-like tools.
+Using this infrastructure, you can add quickly add your own tools to a stand-alone toolkit:
+
+- add your own tools to `tools/src/main/scala/com/client/tools` (see `ExampleTool.scala` contained therein)
+
+## Building & Testing
+
+This repo uses [mill](https://com-lihaoyi.github.io/mill/mill/Intro_to_Mill.html) as it's build system.
+
+To run unit tests:
+
+```console
+./mill _.test
+```
+
+To build an executable JAR at `./jars/<FIXME>-tools.jar`:
+
+```console
+./mill _.deployLocal
+```
+
+To set up this project for IntelliJ, run:
+
+```console
+mill mill.scalalib.GenIdea/idea
+```
+
+
+[fgbio-link]: https:/fulcrumgenomics/fgbio
+[fulcrum-genomics-link]: https://www.fulcrumgenomics.com
+

build.sc

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+import java.text.SimpleDateFormat
+import java.util.Date
+import java.util.jar.Attributes.Name.{IMPLEMENTATION_VERSION => ImplementationVersion}
+import scala.sys.process.Process
+import scala.util.{Failure, Success, Try}
+import mill._, scalalib._, publish._
+import coursier.maven.MavenRepository
+
+/** Base trait for build modules. */
+trait CommonModule extends SbtModule {
+ def deployLocal(assembly: PathRef, jarName:String) = {
+ os.makeDir.all(os.pwd / 'jars)
+ println(s"Copying artifact ${assembly.path} to jars / $jarName")
+ os.copy(assembly.path, os.pwd / 'jars / jarName, replaceExisting=true)
+ }
+
+ override def repositories: Seq[coursier.Repository] = super.repositories ++ Seq(
+ MavenRepository("https://oss.sonatype.org/content/repositories/public"),
+ MavenRepository("https://oss.sonatype.org/content/repositories/snapshots"),
+ MavenRepository("https://jcenter.bintray.com/"),
+ MavenRepository("https://artifactory.broadinstitute.org/artifactory/libs-snapshot/")
+ )
+}
+
+/** A base trait for versioning modules. */
+trait ReleaseModule extends JavaModule {
+ /** Execute Git arguments and return the standard output. */
+ private def git(args: String*): String = os.proc("git", args).call().out.string.trim
+
+ /** Get the commit hash at the HEAD of this branch. */
+ private def gitHead: String = git("rev-parse", "HEAD")
+
+ /** Get the commit shorthash at the HEAD of this branch .*/
+ private def shortHash: String = gitHead.take(7)
+
+ /** If the Git repository is left in a dirty state. */
+ private def dirty: Boolean = git("status", "--porcelain").nonEmpty
+
+ private def today: String = new SimpleDateFormat("yyyyMMdd").format(new Date())
+
+ /** The implementation version. */
+ private def implementationVersion = T input {
+ val prefix = s"${today}-${shortHash}"
+ if (dirty) s"${prefix}-dirty" else prefix
+ }
+
+ /** The version string `Target`. */
+ def version = T input { println(implementationVersion()) }
+
+ /** The JAR manifest. */
+ override def manifest = T { super.manifest().add(ImplementationVersion.toString -> implementationVersion()) }
+}
+
+
+object tools extends CommonModule with PublishModule with ReleaseModule {
+ def scalaVersion = "2.13.8"
+ def mainClass = Some("com.client.cmdline.ClientMain")
+ def artifactName = "client-tools"
+ def gitHash = Process("git rev-parse --short HEAD").lineStream.head
+ def publishVersion = s"0.0.1-${gitHash}-SNAPSHOT"
+ def pomSettings = PomSettings(
+ description = artifactName(),
+ organization = "com.client",
+ url = "https:/fulcrumgenomics/client-tools",
+ licenses = Seq(new License(id="Private", name="Private", url="n/a", isOsiApproved=false, isFsfLibre=false, distribution="no")),
+ versionControl = VersionControl.github("fulcrumgenomics", "scala-mill-skeleton"),
+ developers = Seq(
+ Developer("tfenne", "Tim Fennell", "https:/tfenne"),
+ Developer("nh13", "Nils Homer", "https:/nh13"),
+ )
+ )
+
+ private val orgsToExclude = Seq(
+ "org.apache.ant",
+ "gov.nih.nlm.ncbi",
+ "org.testng",
+ "com.google.cloud.genomics"
+ )
+
+ def ivyDeps = Agg(
+ ivy"org.scala-lang:scala-compiler:${scalaVersion()}",
+ ivy"mysql:mysql-connector-java:5.1.24",
+ ivy"com.fulcrumgenomics:commons_2.13:1.1.0",
+ ivy"com.fulcrumgenomics:sopt_2.13:1.1.0",
+ ivy"com.fulcrumgenomics:fgbio_2.13:1.4.0-61dde53-SNAPSHOT".excludeOrg(orgsToExclude:_*),
+ )
+
+ object test extends Tests {
+ def ivyDeps = Agg(ivy"org.scalatest::scalatest:3.1.0")
+ def testFrameworks = Seq("org.scalatest.tools.Framework")
+
+ // run mill tools.test.singleTest com.client.x.y.x.TestClassName
+ def singleTest(args: String*) = T.command {
+ super.runMain("org.scalatest.run", args: _*)
+ }
+ }
+
+ def javacOptions = Seq("-source", "1.8", "-target", "1.8")
+
+ def deployLocal = T { super.deployLocal(assembly(), "client-tools.jar") }
+}

mill

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+#!/usr/bin/env sh
+
+# This is a wrapper script, that automatically download mill from GitHub release pages
+# You can give the required mill version with MILL_VERSION env variable
+# If no version is given, it falls back to the value of DEFAULT_MILL_VERSION
+DEFAULT_MILL_VERSION=0.10.1
+
+set -e
+
+if [ -z "$MILL_VERSION" ] ; then
+ if [ -f ".mill-version" ] ; then
+ MILL_VERSION="$(head -n 1 .mill-version 2> /dev/null)"
+ elif [ -f "mill" ] && [ "$BASH_SOURCE" != "mill" ] ; then
+ MILL_VERSION=$(grep -F "DEFAULT_MILL_VERSION=" "mill" | head -n 1 | cut -d= -f2)
+ else
+ MILL_VERSION=$DEFAULT_MILL_VERSION
+ fi
+fi
+
+if [ "x${XDG_CACHE_HOME}" != "x" ] ; then
+ MILL_DOWNLOAD_PATH="${XDG_CACHE_HOME}/mill/download"
+else
+ MILL_DOWNLOAD_PATH="${HOME}/.cache/mill/download"
+fi
+MILL_EXEC_PATH="${MILL_DOWNLOAD_PATH}/${MILL_VERSION}"
+
+version_remainder="$MILL_VERSION"
+MILL_MAJOR_VERSION="${version_remainder%%.*}"; version_remainder="${version_remainder#*.}"
+MILL_MINOR_VERSION="${version_remainder%%.*}"; version_remainder="${version_remainder#*.}"
+
+if [ ! -x "$MILL_EXEC_PATH" ] ; then
+ mkdir -p $MILL_DOWNLOAD_PATH
+ if [ "$MILL_MAJOR_VERSION" -gt 0 ] || [ "$MILL_MINOR_VERSION" -ge 5 ] ; then
+ ASSEMBLY="-assembly"
+ fi
+ DOWNLOAD_FILE=$MILL_EXEC_PATH-tmp-download
+ MILL_DOWNLOAD_URL="https:/lihaoyi/mill/releases/download/${MILL_VERSION%%-*}/$MILL_VERSION${ASSEMBLY}"
+ curl --fail -L -o "$DOWNLOAD_FILE" "$MILL_DOWNLOAD_URL"
+ chmod +x "$DOWNLOAD_FILE"
+ mv "$DOWNLOAD_FILE" "$MILL_EXEC_PATH"
+ unset DOWNLOAD_FILE
+ unset MILL_DOWNLOAD_URL
+fi
+
+unset MILL_DOWNLOAD_PATH
+unset MILL_VERSION
+
+exec $MILL_EXEC_PATH "$@"

tools/src/main/scala/com/client/cmdline/ClientMain.scala

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+package com.client.cmdline
+
+import com.fulcrumgenomics.cmdline.FgBioMain
+
+/**
+ * Main program that loads everything up and runs the appropriate sub-command
+ */
+object ClientMain {
+ /** The main method */
+ def main(args: Array[String]): Unit = new ClientMain().makeItSoAndExit(args)
+}
+
+class ClientMain extends FgBioMain {
+
+ /** The name of the toolkit, used in printing usage and status lines. */
+ override def name: String = "client-tools"
+
+ /** The packages we wish to include in our command line **/
+ override protected def packageList: List[String] =
+ List[String]("com.client")
+}

tools/src/main/scala/com/client/cmdline/ClientTool.scala

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+package com.client.cmdline
+
+import com.fulcrumgenomics.cmdline.FgBioTool
+import com.fulcrumgenomics.commons.util.LazyLogging
+
+/** All tools should extend this. */
+trait ClientTool extends FgBioTool with LazyLogging

tools/src/main/scala/com/client/cmdline/ClpGroups.scala

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+package com.client.cmdline
+
+import com.fulcrumgenomics.sopt.cmdline.ClpGroup
+
+/** Groups for organizing command line programs for display. */
+object ClpGroups {
+
+ class _All extends ClpGroup {
+ override val name: String = "All tools"
+ override val description: String = "All tools."
+ }
+
+ final val All = classOf[_All]
+}

tools/src/main/scala/com/client/tools/ExampleTool.scala

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+package com.client.tools
+
+
+import com.fulcrumgenomics.sopt.clp
+import com.client.cmdline.{ClpGroups, ClientTool}
+
+@clp(group=ClpGroups.All, description=
+ """
+ |Trivial example tool to make sure build system is working.
+ """)
+class ExampleTool() extends ClientTool {
+
+ override def execute(): Unit = {
+ System.err.println("Hello World!")
+ }
+}

tools/src/test/scala/com/client/UnitSpec.scala

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+package com.client
+
+import org.scalatest.flatspec.AnyFlatSpec
+import org.scalatest.matchers.should.Matchers
+
+/** Base class for unit tests. */
+class UnitSpec extends AnyFlatSpec with Matchers {}

tools/src/test/scala/com/client/cmdline/ClpTests.scala

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+package com.client.cmdline
+
+import com.client.UnitSpec
+import com.fulcrumgenomics.commons.util.CaptureSystemStreams
+
+/** Some basic test for the CLP classes. */
+class ClpTests extends UnitSpec with CaptureSystemStreams {
+
+ "ClientTool" should "should print hello world" in {
+ val (output, _, _) = captureItAll { () =>
+ new ClientMain().makeItSo("ExampleTool".split(' ')) shouldBe 0
+ }
+ output shouldBe "Hello World!\n"
+ }
+}