Switch to arrays

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

@@ -0,0 +1,147 @@
+# ViashParseArgumentValue: Parse the value of an argument
+# 
+# This script is used by to parse the value of an argument and set
+# the corresponding environment variable.
+# 
+# If the argument is multiple: false:
+# 
+# * If the variable is already set, an error is thrown.
+# * If the value is equal to UNDEFINED, it is replaced with
+#   @@VIASH_UNDEFINED@@.
+# * If the value is quoted, the quotes are removed.
+#
+# If the argument is multiple: true:
+#
+# * If the value is equal to UNDEFINED, it is replaced with
+#   @@VIASH_UNDEFINED@@.
+# * If the value is quoted, the quotes are removed.
+# * If the value is a list of values, the values are split by semicolons.
+# * If the value contains escaped characters '"\;, they are unescaped.
+#
+# Arguments:
+# $1: The name of an argument (used for error messages)
+# $2: The name of the environment variable to set
+# $3: Whether the argument can be passed multiple times (true/false)
+# $4: The value of the argument
+# return: None, but sets the environment variable
+# 
+# Examples:
+#
+# ViashParseArgumentValue "--input" "par_input" "true" "'UNDEFINED'" "false"
+#
+# See ViashParseArgumentValue.test.sh for additional examples.
+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} & ${value@Q}"
+      exit 1
+    fi
+
+    value=$(ViashParseSingleString "$value")
+
+    # set the variable
+    declare -g "$env_name=${value}"
+  else
+    local -n prev_values="$env_name"
+
+    local new_values=()
+    readarray -t "new_values" < <(ViashParseMultipleStringAsArray "$value")
+
+    local combined_values=( "${prev_values[@]}" "${new_values[@]}" )
+
+    # if length is larger than 1 and some element is @@VIASH_UNDEFINED@@, throw error
+    if [ ${#combined_values[@]} -gt 1 ]; then
+      for element in "${combined_values[@]}"; do
+        if [ "$element" == "@@VIASH_UNDEFINED@@" ]; then
+          ViashError "Argument '${flag}': If argument value 'UNDEFINED' is passed, no other values should be provided.\nFound: ${combined_values@Q}"
+          exit 1
+        fi
+      done
+    fi
+
+    declare -g -a "$env_name=(\"\${combined_values[@]}\")"
+  fi
+}
+
+function ViashParseSingleString() {
+  local value="$1"
+
+  # if value is equal to UNDEFINED, replace with @@VIASH_UNDEFINED@@
+  if [ "$value" == "UNDEFINED" ]; then
+    value="@@VIASH_UNDEFINED@@"
+  fi
+
+  # if value is quoted, remove the quotes
+  if [[ "$value" =~ ^\".*\"$ ]]; then
+    value="${value:1:${#value}-2}"
+  elif [[ "$value" =~ ^\'.*\'$ ]]; then
+    value="${value:1:${#value}-2}"
+  fi
+
+  echo "$value"
+}
+
+function ViashParseMultipleStringAsArray() {
+  local value="$1"
+
+  # if value is equal to UNDEFINED, replace with @@VIASH_UNDEFINED@@
+  if [ "$value" == "UNDEFINED" ]; then
+    value="@@VIASH_UNDEFINED@@"
+  fi
+
+  # escape slashes
+  value="${value//\\\\/@@VIASH_ESCAPE_SLASH@@}"
+  # escape semicolons
+  value="${value//\\;/@@VIASH_ESCAPE_SEMICOLON@@}"
+  # escape quotes
+  value="${value//\\\"/@@VIASH_ESCAPE_QUOTE@@}"
+  # escape single quotes
+  value="${value//\\\'/@@VIASH_ESCAPE_SINGLE_QUOTE@@}"
+
+  local gawk_script="
+    BEGIN {
+      FPAT = \"([^;]+)|(\\\"[^\\\"]+\\\")|('[^']+')\";
+    }
+
+    {
+      for (i = 1; i <= NF; i++) {
+        field = \$i;
+
+        # if field is equal to 'UNDEFINED_ITEM', replace it with @@VIASH_UNDEFINED_ITEM@@
+        if (field == \"UNDEFINED_ITEM\") {
+          field = \"@@VIASH_UNDEFINED_ITEM@@\";
+        }
+
+        # Remove leading and trailing double quotes.
+        if (field ~ /^\".*\"$/) {
+          gsub(/^\"|\"$/, \"\", field);
+        } else if (field ~ /^'.*'$/) {
+          gsub(/^'|'$/, \"\", field);
+        }
+
+        # Unescape escaped characters
+        gsub(/@@VIASH_ESCAPE_SINGLE_QUOTE@@/, \"'\", field);
+        gsub(/@@VIASH_ESCAPE_QUOTE@@/, \"\\\"\", field);
+        gsub(/@@VIASH_ESCAPE_SEMICOLON@@/, \";\", field);
+        gsub(/@@VIASH_ESCAPE_SLASH@@/, \"\\\\\", field);
+
+        # Output each field on a separate line.
+        print field;
+      }
+    }
+  "
+
+  echo "${value}" | awk "$gawk_script"
+}

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

@@ -0,0 +1,97 @@
+# ViashRenderJsonKeyValue: renders a key-value pair in JSON format
+#
+# Arguments:
+# $1: The key
+# $2: The type of the value (string, boolean, boolean_true, boolean_false, file, double, integer)
+# $3: Whether the value can be passed multiple times (true/false)
+# $4+: The value(s) of the key
+# return: prints the key-value pair in JSON format
+#
+# Examples:
+#
+# ViashRenderJsonKeyValue "input" "string" "false" "file.txt"
+# ViashRenderJsonKeyValue "input" "string" "true" "file1.txt" "file2.txt"
+function ViashRenderJsonKeyValue {
+  local key="$1"
+  local type="$2"
+  local multiple="$3"
+  shift 3
+
+  local out="  \"${key}\":"
+
+  # Handle null case
+  if [ $# -eq 1 ] && [ "$1" == "@@VIASH_UNDEFINED@@" ]; then
+    out+=" null"
+    echo "$out"
+    return
+  fi
+
+  # Handle multiple values (array)
+  if [ "$multiple" == "true" ]; then
+    out+=" ["
+    local first=true
+    while [ $# -gt 0 ]; do
+      if [ "$first" == "false" ]; then
+        out+=","
+      fi
+      first=false
+
+      if [ "$1" == "@@VIASH_UNDEFINED_ITEM@@" ]; then
+        out+=" null"
+      elif [ "$type" == "string" ] || [ "$type" == "file" ]; then
+        out+=" $(ViashRenderJsonQuotedValue "$key" "$1")"
+      elif [ "$type" == "boolean" ] || [ "$type" == "boolean_true" ] || [ "$type" == "boolean_false" ]; then
+        out+=" $(ViashRenderJsonBooleanValue "$key" "$1")"
+      else
+        out+=" $(ViashRenderJsonUnquotedValue "$key" "$1")"
+      fi
+      shift
+    done
+    out+=" ]"
+  else
+    # Handle single value
+    out+=" "
+    if [ "$1" == "@@VIASH_UNDEFINED_ITEM@@" ]; then
+      out+="null"
+    elif [ "$type" == "string" ] || [ "$type" == "file" ]; then
+      out+="$(ViashRenderJsonQuotedValue "$key" "$1")"
+    elif [ "$type" == "boolean" ] || [ "$type" == "boolean_true" ] || [ "$type" == "boolean_false" ]; then
+      out+="$(ViashRenderJsonBooleanValue "$key" "$1")"
+    else
+      out+="$(ViashRenderJsonUnquotedValue "$key" "$1")"
+    fi
+  fi
+
+  echo "$out"
+}
+
+function ViashRenderJsonQuotedValue {
+  local key="$1"
+  local value="$2"
+  # escape backslashes, quotes, and newlines for JSON
+  echo "$value" | \
+    sed 's#\\#\\\\#g' | \
+    sed 's#"#\\"#g' | \
+    sed ':a;N;$!ba;s/\n/\\n/g' | \
+    sed 's#^#"#g;s#$#"#g'
+}
+
+function ViashRenderJsonBooleanValue {
+  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
+}
+
+function ViashRenderJsonUnquotedValue {
+  local key="$1"
+  local value="$2"
+  echo "$value"
+}

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

@@ -0,0 +1,38 @@
+
+# ViashRenderPythonValue 'string' "false" "${VIASH_META_NAME[@]:-@@VIASH_UNDEFINED@@}"
+function ViashRenderPythonValue {
+  local type="$1"
+  local multiple="$2"
+  shift 2
+
+  if [ $# -eq 1 ] && [ "$1" == "@@VIASH_UNDEFINED@@" ]; then
+    echo "None"
+    return
+  fi
+
+  local out=""
+
+  if [ "$multiple" == "true" ]; then
+    out+="["
+  fi
+  while [ $# -gt 0 ]; do
+    if [ "$1" == "@@VIASH_UNDEFINED_ITEM@@" ]; then
+      out+="None"
+    elif [ "$type" == "string" ] || [ "$type" == "file" ]; then
+      # render it as r'...' but escape single quotes
+      out+=$(echo "$1" | sed "s/'/\\\'/g" | sed "s/^/r\'/;s/$/\'/")
+    elif [ "$type" == "boolean" ] || [ "$type" == "boolean_true" ] || [ "$type" == "boolean_false" ]; then
+      out+="$1"
+    else
+      out+="$1"
+    fi
+    if [ "$multiple" == "true" ] && [ $# -gt 1 ]; then
+      out+=", "
+    fi
+    shift
+  done
+  if [ "$multiple" == "true" ]; then
+    out+="]"
+  fi
+  echo "$out"
+}

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

@@ -0,0 +1,79 @@
+# ViashRenderYamlKeyValue: renders a key-value pair in YAML format
+#
+# Arguments:
+# $1: The key
+# $2: The type of the value (string, boolean, boolean_true, boolean_false, file, double, integer)
+# $3: Whether the value can be passed multiple times (true/false)
+# $4+: The value(s) of the key
+# return: prints the key-value pair in YAML format
+#
+# Examples:
+#
+# ViashRenderYamlKeyValue "input" "string" "false" "file.txt"
+# ViashRenderYamlKeyValue "input" "string" "true" "file1.txt" "file2.txt"
+function ViashRenderYamlKeyValue {
+  local key="$1"
+  local type="$2"
+  local multiple="$3"
+  shift 3
+
+  local out="  ${key}:"
+
+  if [ $# -eq 1 ] && [ "$1" == "@@VIASH_UNDEFINED@@" ]; then
+    out+=" null"
+    echo "$out"
+    return
+  fi
+
+  while [ $# -gt 0 ]; do
+    if [ "$multiple" == "true" ]; then
+      out+=$'\n    - '
+    else
+      out+=" "
+    fi
+    if [ "$1" == "@@VIASH_UNDEFINED_ITEM@@" ]; then
+      out+="null"
+    elif [ "$type" == "string" ] || [ "$type" == "file" ]; then
+      out+="$(ViashRenderYamlQuotedValue "$key" "$1")"
+    elif [ "$type" == "boolean" ] || [ "$type" == "boolean_true" ] || [ "$type" == "boolean_false" ]; then
+      out+="$(ViashRenderYamlBooleanValue "$key" "$1")"
+    else
+      out+="$(ViashRenderYamlUnquotedValue "$key" "$1")"
+    fi
+    shift
+  done
+
+  echo "$out"
+}
+
+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"
+}