Switch to arrays

src/main/resources/io/viash/helpers/bashutils/ViashParseArgumentValue.sh

@@ -0,0 +1,34 @@
+function ViashParseArgumentValue {
+  local flag="$1"
+  local env_name="$2"
+  local multiple="$3"
+  local value="$4"
+
+  if [ $# -lt 4 ]; then
+    ViashError "Not enough arguments passed to ${flag}. Use '--help' to get more information on the parameters."
+    exit 1
+  fi
+
+  if [ "$multiple" == "false" ]; then
+    # check whether the variable is already set
+    if [ ! -z ${!env_name+x} ]; then
+      local -n prev_value="$env_name"
+      ViashError "Pass only one argument to argument '${flag}'. Found: ${prev_value@Q} & ${value@Q}"
+      exit 1
+    fi
+
+    # set the variable
+    declare -g "$env_name=${value}"
+  else
+    local new_values
+
+    local -n prev_values="$env_name"
+
+    # todo: allow escaping the delimiter
+    readarray -d ';' -t new_values < <(printf '%s' "$value")
+
+    combined_values=( "${prev_values[@]}" "${new_values[@]}" )
+
+    declare -g -a "$env_name=(\"\${combined_values[@]}\")"
+  fi
+}

src/main/resources/io/viash/helpers/bashutils/ViashRenderYaml.sh

@@ -0,0 +1,75 @@
+function ViashRenderYamlQuotedValue {
+  local key="$1"
+  local value="$2"
+  # escape quotes, backslashes and newlines, and then surround by quotes
+  echo "$value" | \
+    sed 's#\\#\\\\#g' | \
+    sed 's#"#\\"#g' | \
+    sed ':a;N;$!ba;s/\n/\\n/g' | \
+    sed 's#^#"#g;s#$#"#g'
+}
+
+function ViashRenderYamlBooleanValue {
+  local key="$1"
+  local value="$2"
+  # convert to lowercase
+  value=$(echo "$value" | tr '[:upper:]' '[:lower:]')
+  if [[ "$value" == "true" || "$value" == "yes" ]]; then
+    echo "true"
+  elif [[ "$value" == "false" || "$value" == "no" ]]; then
+    echo "false"
+  else
+    echo "Argument '$key' has to be a boolean, but got '$value'. Use '--help' to get more information on the parameters."
+  fi
+}
+
+# can be infinite too
+function ViashRenderYamlUnquotedValue {
+  local key="$1"
+  local value="$2"
+  echo "$value"
+}
+
+function ViashRenderYamlKeyValue {
+  local key="$1"
+  local type="$2"
+  local multiple="$3"
+  shift 3
+
+  local out="  ${key}: "
+
+  if [ "$1" == "UNDEFINED" ]; then
+    out+="null"
+    echo "$out"
+    return
+  fi
+
+  if [ "$multiple" == "true" ]; then
+    out+="["
+  fi
+
+  first_elem=1
+
+  for value in "$@"; do
+    if [ $first_elem -eq 1 ]; then
+      first_elem=0
+    else
+      out+=", "
+    fi
+    if [ "$value" == "UNDEFINED_ITEM" ]; then
+      out+="null"
+    elif [[ "$type" == "string" || "$type" == "file" ]]; then
+      out+="$(ViashRenderYamlQuotedValue "$key" "$value")"
+    elif [[ "$type" == "boolean" || "$type" == "boolean_true" || "$type" == "boolean_false" ]]; then
+      out+="$(ViashRenderYamlBooleanValue "$key" "$value")"
+    else
+      out+="$(ViashRenderYamlUnquotedValue "$key" "$value")"
+    fi
+  done
+
+  if [ "$multiple" == "true" ]; then
+    out+="]"
+  fi
+
+  echo "$out"
+}

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

@@ -30,41 +30,12 @@ object Bash {
   lazy val ViashRemoveFlags: String = readUtils("ViashRemoveFlags")
   lazy val ViashAbsolutePath: String = readUtils("ViashAbsolutePath")
   lazy val ViashDockerAutodetectMount: String = readUtils("ViashDockerAutodetectMount")
-  // backwards compatibility, for now
-  lazy val ViashAutodetectMount: String = ViashDockerAutodetectMount.replace("ViashDocker", "Viash")
   lazy val ViashSourceDir: String = readUtils("ViashSourceDir")
   lazy val ViashFindTargetDir: String = readUtils("ViashFindTargetDir")
   lazy val ViashDockerFuns: String = readUtils("ViashDockerFuns")
   lazy val ViashLogging: String = readUtils("ViashLogging")
-
-  def save(saveVariable: String, args: Seq[String]): String = {
-    saveVariable + "=\"$" + saveVariable + " " + args.mkString(" ") + "\""
-  }
-
-  // generate strings in the form of:
-  // SAVEVARIABLE="$SAVEVARIABLE $(Quote arg1) $(Quote arg2)"
-  def quoteSave(saveVariable: String, args: Seq[String]): String = {
-    saveVariable + "=\"$" + saveVariable +
-      args.map(" $(ViashQuote \"" + _ + "\")").mkString +
-      "\""
-  }
-
-  def argStore(name: String, plainName: String, store: String, argsConsumed: Int, storeUnparsed: Option[String]): String = {
-    val passStr =
-      if (storeUnparsed.isDefined) {
-        "\n            " + quoteSave(storeUnparsed.get, (1 to argsConsumed).map("$" + _))
-      } else {
-        ""
-      }
-    s"""         $name)
-       |            $plainName=$store$passStr
-       |            shift $argsConsumed
-       |            ;;""".stripMargin
-  }
-
-  def argStoreSed(name: String, plainName: String, storeUnparsed: Option[String]): String = {
-    argStore(name + "=*", plainName, "$(ViashRemoveFlags \"$1\")", 1, storeUnparsed)
-  }
+  lazy val ViashRenderYaml: String = readUtils("ViashRenderYaml")
+  lazy val ViashParseArgumentValue: String = readUtils("ViashParseArgumentValue")
 
   /** 
    * Access the parameters contents in a bash script,

src/main/scala/io/viash/runners/ExecutableRunner.scala

@@ -395,20 +395,14 @@ final case class ExecutableRunner(
     val detectMounts = args.flatMap {
       case arg: FileArgument if arg.multiple =>
         // resolve arguments with multiplicity different from singular args
-        val viash_temp = "VIASH_TEST_" + arg.plainName.toUpperCase()
         val chownIfOutput = if (arg.direction == Output) "\n    VIASH_CHOWN_VARS+=( \"$var\" )" else ""
         Some(
           s"""
             |if [ ! -z "$$${arg.VIASH_PAR}" ]; then
-            |  $viash_temp=()
-            |  IFS='${Bash.escapeString(arg.multiple_sep, quote = true)}'
-            |  for var in $$${arg.VIASH_PAR}; do
-            |    unset IFS
-            |    VIASH_DIRECTORY_MOUNTS+=( "$$(ViashDockerAutodetectMountArg "$$var")" )
-            |    var=$$(ViashDockerAutodetectMount "$$var")
-            |    $viash_temp+=( "$$var" )$chownIfOutput
+            |  for i in "$${!${arg.VIASH_PAR}[@]}"; do
+            |    VIASH_DIRECTORY_MOUNTS+=( "$$(ViashDockerAutodetectMountArg $${${arg.VIASH_PAR}[$$i]})" )
+            |    ${arg.VIASH_PAR}[$$i]=$$(ViashDockerAutodetectMount $${${arg.VIASH_PAR}[$$i]})
             |  done
-            |  ${arg.VIASH_PAR}=$$(IFS='${Bash.escapeString(arg.multiple_sep, quote = true)}' ; echo "$${$viash_temp[*]}")
             |fi""".stripMargin
         )
       case arg: FileArgument =>
@@ -455,17 +449,12 @@ final case class ExecutableRunner(
     val stripAutomounts = args.flatMap {
       case arg: FileArgument if arg.multiple && arg.direction == Input =>
         // resolve arguments with multiplicity different from singular args
-        val viash_temp = "VIASH_TEST_" + arg.plainName.toUpperCase()
         Some(
           s"""
             |  if [ ! -z "$$${arg.VIASH_PAR}" ]; then
-            |    unset $viash_temp
-            |    IFS='${Bash.escapeString(arg.multiple_sep, quote = true)}'
-            |    for var in $$${arg.VIASH_PAR}; do
-            |      unset IFS
-            |      ${BashWrapper.store("ViashDockerStripAutomount", viash_temp, "\"$(ViashDockerStripAutomount \"$var\")\"", Some(arg.multiple_sep)).mkString("\n    ")}
+            |    for i in "$${!${arg.VIASH_PAR}[@]}"; do
+            |      ${arg.VIASH_PAR}[i]=$$(ViashDockerStripAutomount "$${${arg.VIASH_PAR}[i]}")
             |    done
-            |    ${arg.VIASH_PAR}="$$$viash_temp"
             |  fi""".stripMargin
         )
       case arg: FileArgument =>