Merge pull request #104 from viash-io/develop

Viash 0.5.9

CHANGELOG.md

@@ -1,3 +1,35 @@
+# Viash 0.5.9
+
+## NEW FEATURES
+
+* `viash run`: A long running Viash component can be interrupted by pressing 
+  CTRL-C or by sending it an `INT` or `SIGINT` signal.
+
+* `DockerPlatform`: Automatically add a few labels based on metadata to Dockerfile.
+
+* `DockerPlatform`: Added value `target_image_source` for setting the source of 
+  the target image. This is used for defining labels in the dockerfile.
+  Example:
+  ```yaml
+  target_image_source: https://github.com/foo/bar
+  ```
+
+## MINOR CHANGES
+
+* `viash ns list`: Added `--format yaml/json` argument to be able to return the
+  output as a json as well. Useful for when `jq` is installed but `yq` is not. Example:
+  ```
+    viash ns list -p docker -f json | jq '.[] | .info.config'
+  ```
+
+* `viash config view`: Same as above.
+
+## DEPRECATION
+
+* `CLI`: Deprecated `-P` flag use `-p` intead.
+
+* `DockerPlatform`: Deprecated `version` value.
+
 # Viash 0.5.8
 
 ## NEW FUNCTIONALITY

build.sbt

@@ -1,6 +1,6 @@
 name := "viash"
 
-version := "0.5.8"
+version := "0.5.9"
 
 scalaVersion := "2.12.10"
 

src/main/scala/com/dataintuitive/viash/CLIConf.scala

@@ -31,13 +31,6 @@ trait ViashCommand {
       "In addition, the path to a platform yaml file can also be specified.",
     required = false
   )
-  val platformid = opt[String](
-    short = 'P',
-    default = None,
-    descr = "[deprecated] passthrough option for platform.",
-    required = false,
-    hidden = true
-  )
   val config = trailArg[String](
     descr = "A viash config file (example: config.vsh.yaml). This argument can also be a script with the config as a header.",
     default = Some("config.vsh.yaml"),
@@ -86,13 +79,6 @@ trait ViashNs {
     default = None,
     required = false
   )
-  val platformid = opt[String](
-    short = 'P',
-    descr = "[deprecated] passthrough option for platform.",
-    default = None,
-    required = false,
-    hidden = true
-  )
   val parallel = opt[Boolean](
     name = "parallel",
     short = 'l',
@@ -231,6 +217,13 @@ class CLIConf(arguments: Seq[String]) extends ScallopConf(arguments) {
            |  viash config view config.vsh.yaml
            |
            |Arguments:""".stripMargin)
+      val format = choice(
+        name = "format",
+        short = 'f',
+        default = Some("yaml"),
+        choices = List("yaml", "json"),
+        descr = "Which output format to use."
+      )
     }
     val inject = new Subcommand("inject") with ViashCommand {
       banner(
@@ -322,6 +315,13 @@ class CLIConf(arguments: Seq[String]) extends ScallopConf(arguments) {
            |  viash ns list [-n nmspc] [-s src] [-p docker]
            |
            |Arguments:""".stripMargin)
+      val format = choice(
+        name = "format",
+        short = 'f',
+        default = Some("yaml"),
+        choices = List("yaml", "json"),
+        descr = "Which output format to use."
+      )
     }
 
     addSubcommand(build)

src/main/scala/com/dataintuitive/viash/Main.scala

@@ -35,7 +35,7 @@ object Main {
       internalMain(args)
     } catch {
       case e: Exception => 
-        System.err.println(e.getMessage())
+        System.err.println(e)
         System.exit(1)
     }
   }
@@ -88,16 +88,17 @@ object Main {
           append = cli.namespace.test.append()
         )
       case List(cli.namespace, cli.namespace.list) =>
-        val configs = readConfigs(cli.namespace.test, modifyFun = false)
+        val configs = readConfigs(cli.namespace.list, modifyFun = false)
         ViashNamespace.list(
-          configs = configs
+          configs = configs,
+          cli.namespace.list.format()
         )
       case List(cli.config, cli.config.view) =>
         val config = Config.readOnly(
           configPath = cli.config.view.config(),
           configMods = cli.config.view.config_mods()
         )
-        ViashConfig.view(config)
+        ViashConfig.view(config, cli.config.view.format())
       case List(cli.config, cli.config.inject) =>
         val config = Config.readOnly(
           configPath = cli.config.inject.config(),
@@ -115,7 +116,7 @@ object Main {
   ): Config = {
     Config.read(
       configPath = subcommand.config(),
-      platform = subcommand.platform.toOption | subcommand.platformid.toOption,
+      platform = subcommand.platform.toOption,
       modifyFun = modifyFun,
       configMods = subcommand.config_mods()
     )
@@ -132,7 +133,7 @@ object Main {
     val sourceDir = Paths.get(source)
 
     // create regex for filtering platform ids
-    val platformStr = (subcommand.platform.toOption | subcommand.platformid.toOption).getOrElse(".*")
+    val platformStr = (subcommand.platform.toOption).getOrElse(".*")
 
     // find *.vsh.* files and parse as config
     val scriptFiles = find(sourceDir, (path, attrs) => {

src/main/scala/com/dataintuitive/viash/ViashConfig.scala

@@ -22,33 +22,39 @@ import com.dataintuitive.viash.helpers.IO
 
 import java.nio.file.{Files, Paths}
 import io.circe.syntax.EncoderOps
-import io.circe.yaml.Printer
+import io.circe.{Json, Printer => JsonPrinter}
+import io.circe.yaml.{Printer => YamlPrinter}
 
 import scala.sys.process.Process
 import com.dataintuitive.viash.platforms.DebugPlatform
 
 object ViashConfig {
-  private val printer = Printer(
+  private val yamlPrinter = YamlPrinter(
     preserveOrder = true,
     dropNullKeys = true,
-    mappingStyle = Printer.FlowStyle.Block,
+    mappingStyle = YamlPrinter.FlowStyle.Block,
     splitLines = true,
-    stringStyle = Printer.StringStyle.DoubleQuoted
+    stringStyle = YamlPrinter.StringStyle.DoubleQuoted
   )
+  private val jsonPrinter = JsonPrinter.spaces2.copy(dropNullValues = true)
 
-  def view(config: Config) {
-    val json = config.asJson
-    val configYamlStr = printer.pretty(json)
-    println(configYamlStr)
+  private def printJson(json: Json, format: String): Unit = {
+    val str = format match {
+      case "yaml" => yamlPrinter.pretty(json)
+      case "json" => jsonPrinter.print(json)
+    }
+    println(str)
+  }
+
+  def view(config: Config, format: String): Unit = {
+    printJson(config.asJson, format)
   }
 
-  def viewMany(configs: List[Config]) {
-    val json = configs.asJson
-    val configYamlStr = printer.pretty(json)
-    println(configYamlStr)
+  def viewMany(configs: List[Config], format: String): Unit = {
+    printJson(configs.asJson, format)
   }
 
-  def inject(config: Config) {
+  def inject(config: Config): Unit = {
     val fun = config.functionality
 
     // check if config has a main script

src/main/scala/com/dataintuitive/viash/ViashNamespace.scala

@@ -159,7 +159,7 @@ object ViashNamespace {
     }
   }
 
-  def list(configs: List[Config]) {
-    ViashConfig.viewMany(configs)
+  def list(configs: List[Config], format: String = "yaml") {
+    ViashConfig.viewMany(configs, format)
   }
 }

src/main/scala/com/dataintuitive/viash/platforms/DockerPlatform.scala

@@ -45,6 +45,7 @@ case class DockerPlatform(
   setup_strategy: DockerSetupStrategy = IfNeedBePullElseCachedBuild,
   privileged: Boolean = false,
   run_args: OneOrMore[String] = Nil,
+  target_image_source: Option[String] = None,
   oType: String = "docker",
 
   // setup variables
@@ -54,15 +55,10 @@ case class DockerPlatform(
   yum: Option[YumRequirements] = None,
   r: Option[RRequirements] = None,
   python: Option[PythonRequirements] = None,
-  docker: Option[DockerRequirements] = None,
-
-  // deprecated
-  version: Option[Version] = None
+  docker: Option[DockerRequirements] = None
 ) extends Platform {
   override val hasSetup = true
 
-  assert(version.isEmpty, "docker platform: attribute 'version' is deprecated")
-
   override val requirements: List[Requirements] = {
     val x =
       setup :::
@@ -138,8 +134,26 @@ case class DockerPlatform(
   }
 
   private def processDockerSetup(functionality: Functionality) = {
+    // construct labels from metadata
+    val auth = functionality.authors match {
+      case Nil => Nil
+      case aut: List[Author] => List(s"""authors="${aut.mkString(", ")}"""")
+    }
+    /*val descr = functionality.description.map{ des => 
+      s"""org.opencontainers.image.description="${Bash.escape(des)}""""
+    }.toList*/
+
+    val descr = List(
+      s"""org.opencontainers.image.description="Companion container for running component ${functionality.namespace.map(_ + " ").getOrElse("")}${functionality.name}""""
+    )
+    val imageSource = target_image_source.map(des => s"""org.opencontainers.image.source="${Bash.escape(des)}"""").toList
+    val labelReq = DockerRequirements(label = auth ::: descr ::: imageSource)
+
+    val requirements2 = labelReq :: requirements
+
     // get dependencies
-    val runCommands = requirements.flatMap(_.dockerCommands)
+    val runCommands = requirements2.flatMap(_.dockerCommands)
+
 
     // don't draw defaults from functionality for the from image
     val fromImageInfo = Docker.getImageInfo(

src/main/scala/com/dataintuitive/viash/wrapper/BashWrapper.scala

@@ -123,21 +123,27 @@ object BashWrapper {
 
         // check whether the script can be written to a temprorary location or
         // whether it needs to be a specific path
-        val scriptSetup = 
+        val scriptSetup =
           s"""
             |tempscript=\\$$(mktemp "$$VIASH_TEMP/viash-run-${functionality.name}-XXXXXX")
             |function clean_up {
             |  rm "\\$$tempscript"
             |}
-            |trap clean_up EXIT""".stripMargin
+            |function interrupt {
+            |  echo -e "\\nCTRL-C Pressed..."
+            |  exit 1
+            |}
+            |trap clean_up EXIT
+            |trap interrupt INT SIGINT""".stripMargin
         val scriptPath = "\\$tempscript"
 
         s"""
           |set -e$scriptSetup
           |cat > "$scriptPath" << 'VIASHMAIN'
           |$escapedCode
           |VIASHMAIN$cdToResources$resourcesToPath
-          |${res.meta.command(scriptPath)}
+          |${res.meta.command(scriptPath)} &
+          |wait "\\$$!"
           |""".stripMargin
 
       // if we want to debug our code

src/test/scala/com/dataintuitive/viash/auxiliary/MainBuildAuxiliaryDockerTag.scala

@@ -42,10 +42,10 @@ class MainBuildAuxiliaryDockerTag extends FunSuite with BeforeAndAfterAll {
     val dockerout = Exec.run(Seq(executableBashTagFile.toString, "---dockerfile"))
     // we expect something basic like
     // FROM bash:5.0
-    //
+    // LABEL ...
     // RUN :
     // Allow for extra spaces just in case the format changes slightly format-wise but without functional differences
-    val regex = """^FROM bash:5\.0[\r\n\s]*RUN\s+:\s*$""".r
+    val regex = """^FROM bash:5\.0[\r\n\s]*.*""".r
     assert(regex.findFirstIn(dockerout).isDefined, regex.toString)
   }
 
@@ -75,10 +75,10 @@ class MainBuildAuxiliaryDockerTag extends FunSuite with BeforeAndAfterAll {
     val dockerout = Exec.run(Seq(executableBashTagFile.toString, "---dockerfile"))
     // we expect something basic like
     // FROM bash:3.2
-    //
+    // LABEL ...
     // RUN :
     // Allow for extra spaces just in case the format changes slightly format-wise but without functional differences
-    val regex = """^FROM bash:3\.2[\r\n\s]*RUN\s+:\s*$""".r
+    val regex = """^FROM bash:3\.2[\r\n\s]*.*""".r
     assert(regex.findFirstIn(dockerout).isDefined, regex.toString)
   }