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rcannoodrcannood
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add argument to bash script
1 parent 51f6fa2 commit 9a56fce

2 files changed

Lines changed: 98 additions & 13 deletions

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‎src/main/scala/io/viash/config/resources/BashScript.scala‎

Lines changed: 8 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -33,6 +33,14 @@ case class BashScript(
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is_executable: Option[Boolean] = Some(true),
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parent: Option[URI] = None,
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@description("""Whether to use jq for JSON parameter parsing and store multiple-value arguments as Bash arrays.
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| - `true`: Use jq for JSON parsing. Arguments with `multiple: true` are stored as Bash arrays (e.g. `par_input=("a" "b" "c")`). Requires jq to be installed.
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| - `false`: Use the built-in JSON parser. Arguments with `multiple: true` are stored as separator-delimited strings (e.g. `par_input="a;b;c"`), using the argument's `multiple_sep` (default `";"`).
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| - Not specified (default): Same behavior as `false`, but a deprecation warning is shown at build time indicating that the default will change to `true` in a future version of Viash.""")
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@example("use_jq: true", "yaml")
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@since("Viash 0.10.0")
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use_jq: Option[Boolean] = None,
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@description("Specifies the resource as a Bash script.")
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`type`: String = "bash_script"
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) extends Script {

‎src/main/scala/io/viash/languages/Bash.scala‎

Lines changed: 90 additions & 13 deletions
Original file line numberDiff line numberDiff line change
@@ -17,10 +17,10 @@
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package io.viash.languages
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import io.viash.helpers.Resources
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import io.viash.helpers.{Resources, Logger}
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import io.viash.config.arguments._
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import io.viash.config.Config
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import io.viash.config.resources.ScriptInjectionMods
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import io.viash.config.resources.{ScriptInjectionMods, BashScript}
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object Bash extends Language {
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val id: String = "bash"
@@ -29,29 +29,102 @@ object Bash extends Language {
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val commentStr: String = "#"
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val executor: Seq[String] = Seq("bash")
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val viashParseJsonCode: String = Resources.read("languages/bash/ViashParseJson.sh")
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val viashParseJsonCompatCode: String = Resources.read("languages/bash/ViashParseJsonCompatibility.sh")
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private val logger = Logger("Bash")
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def generateInjectionMods(argsMetaAndDeps: Map[String, List[Argument[_]]], config: Config): ScriptInjectionMods = {
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val fullCode = s"""${viashParseJsonCode}
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// Determine use_jq setting from the BashScript resource
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val useJq = config.resources.collectFirst {
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case bs: BashScript => bs.use_jq
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}.flatten
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useJq match {
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case Some(true) =>
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generateJqInjectionMods(argsMetaAndDeps)
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case Some(false) =>
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generateCompatInjectionMods(argsMetaAndDeps)
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case None =>
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logger.warn(
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"Deprecation warning: 'use_jq' is not set for bash_script resource. " +
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"Currently defaulting to compatibility mode (built-in parser, separator-delimited strings for multiple-value arguments). " +
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"In a future version of Viash, the default will change to 'use_jq: true', " +
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"which requires jq to be installed. " +
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"Please set 'use_jq: true' or 'use_jq: false' explicitly in your bash_script resource to silence this warning."
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)
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generateCompatInjectionMods(argsMetaAndDeps)
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}
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}
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/**
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* Generate injection mods for compatibility mode:
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* Uses the built-in bash JSON parser, then converts multiple-value
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* arguments from bash arrays to separator-delimited strings.
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*/
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private def generateCompatInjectionMods(argsMetaAndDeps: Map[String, List[Argument[_]]]): ScriptInjectionMods = {
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val parseCode = s"""${viashParseJsonCompatCode}
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# Parse JSON parameters
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_viash_json_content=$$(cat "$$VIASH_WORK_PARAMS")
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ViashParseJsonBash <<< "$$_viash_json_content"
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"""
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// Convert multiple-value arguments from arrays to IFS-separated strings
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val multipleArgs = argsMetaAndDeps.toList.flatMap { case (_, args) =>
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args.collect {
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case arg if arg.multiple =>
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val sep = arg.multiple_sep
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s"""${arg.par}="$$(IFS='${sep}'; printf '%s' "$${${arg.par}[*]}")""""
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}
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}
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val fullCode = if (multipleArgs.nonEmpty) {
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parseCode + "\n# Convert arrays to separator-delimited strings for compatibility\n" +
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multipleArgs.mkString("\n") + "\n"
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} else {
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parseCode
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}
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ScriptInjectionMods(params = fullCode)
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}
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/**
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* Generate injection mods for jq mode:
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* Uses jq to parse JSON and populate bash variables directly.
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* Multiple-value arguments are stored as bash arrays.
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*/
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private def generateJqInjectionMods(argsMetaAndDeps: Map[String, List[Argument[_]]]): ScriptInjectionMods = {
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val parseCode = s"""${viashParseJsonCode}
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# Parse JSON parameters using jq
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_viash_json_content=$$(cat "$$VIASH_WORK_PARAMS")
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ViashParseJsonBash <<< "$$_viash_json_content"
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"""
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ScriptInjectionMods(params = parseCode)
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}
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def generateConfigInjectMods(argsMetaAndDeps: Map[String, List[Argument[_]]], config: Config): ScriptInjectionMods = {
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// Determine use_jq setting from the BashScript resource
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val useJq = config.resources.collectFirst {
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case bs: BashScript => bs.use_jq
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}.flatten
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val useArrays = useJq.contains(true)
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val parSet = argsMetaAndDeps.flatMap { case (_, params) =>
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params.map { par =>
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val value = getExampleValue(par)
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val value = getExampleValue(par, useArrays)
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if (par.multiple) {
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// For multiple values, create a bash array
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val values = value match {
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case v if v.isEmpty => ""
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case v => v
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if (useArrays) {
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// jq mode: bash array
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val values = value match {
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case v if v.isEmpty => ""
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case v => v
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}
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s"""${par.par}=($values)"""
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} else {
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// compat mode: IFS-separated string
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s"""${par.par}='$value'"""
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}
54-
s"""${par.par}=($values)"""
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} else {
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s"""${par.par}='$value'"""
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}
@@ -62,11 +135,15 @@ ViashParseJsonBash <<< "$$_viash_json_content"
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ScriptInjectionMods(params = paramsCode)
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}
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private def getExampleValue(arg: Argument[_]): String = {
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private def getExampleValue(arg: Argument[_], useArrays: Boolean = true): String = {
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val values = getArgumentValues(arg)
67-
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68141
if (arg.multiple) {
69-
values.map(v => s"'$v'").mkString(" ")
142+
if (useArrays) {
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values.map(v => s"'$v'").mkString(" ")
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} else {
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values.mkString(arg.multiple_sep)
146+
}
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} else {
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values.headOption.getOrElse("")
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}

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