#!/usr/bin/env bash

# scarches v4.0.1
# 
# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
# Intuitive.
# 
# The component may contain files which fall under a different license. The
# authors of this component should specify the license in the header of such
# files, or include a separate license file detailing the licenses of all included
# files.
# 
# Component authors:
#  * Vladimir Shitov (author)
#  * Dorien Roosen (maintainer)

set -e

if [ -z "$VIASH_TEMP" ]; then
  VIASH_TEMP=${VIASH_TEMP:-$VIASH_TMPDIR}
  VIASH_TEMP=${VIASH_TEMP:-$VIASH_TEMPDIR}
  VIASH_TEMP=${VIASH_TEMP:-$VIASH_TMP}
  VIASH_TEMP=${VIASH_TEMP:-$TMPDIR}
  VIASH_TEMP=${VIASH_TEMP:-$TMP}
  VIASH_TEMP=${VIASH_TEMP:-$TEMPDIR}
  VIASH_TEMP=${VIASH_TEMP:-$TEMP}
  VIASH_TEMP=${VIASH_TEMP:-/tmp}
fi

# define helper functions
# ViashQuote: put quotes around non flag values
# $1     : unquoted string
# return : possibly quoted string
# examples:
#   ViashQuote --foo      # returns --foo
#   ViashQuote bar        # returns 'bar'
#   Viashquote --foo=bar  # returns --foo='bar'
function ViashQuote {
  if [[ "$1" =~ ^-+[a-zA-Z0-9_\-]+=.+$ ]]; then
    echo "$1" | sed "s#=\(.*\)#='\1'#"
  elif [[ "$1" =~ ^-+[a-zA-Z0-9_\-]+$ ]]; then
    echo "$1"
  else
    echo "'$1'"
  fi
}
# ViashRemoveFlags: Remove leading flag
# $1     : string with a possible leading flag
# return : string without possible leading flag
# examples:
#   ViashRemoveFlags --foo=bar  # returns bar
function ViashRemoveFlags {
  echo "$1" | sed 's/^--*[a-zA-Z0-9_\-]*=//'
}
# ViashSourceDir: return the path of a bash file, following symlinks
# usage   : ViashSourceDir ${BASH_SOURCE[0]}
# $1      : Should always be set to ${BASH_SOURCE[0]}
# returns : The absolute path of the bash file
function ViashSourceDir {
  local source="$1"
  while [ -h "$source" ]; do
    local dir="$( cd -P "$( dirname "$source" )" >/dev/null 2>&1 && pwd )"
    source="$(readlink "$source")"
    [[ $source != /* ]] && source="$dir/$source"
  done
  cd -P "$( dirname "$source" )" >/dev/null 2>&1 && pwd
}
# ViashFindTargetDir: return the path of the '.build.yaml' file, following symlinks
# usage   : ViashFindTargetDir 'ScriptPath'
# $1      : The location from where to start the upward search
# returns : The absolute path of the '.build.yaml' file
function ViashFindTargetDir {
  local source="$1"
  while [[ "$source" != "" && ! -e "$source/.build.yaml" ]]; do
    source=${source%/*}
  done
  echo $source
}
# see https://en.wikipedia.org/wiki/Syslog#Severity_level
VIASH_LOGCODE_EMERGENCY=0
VIASH_LOGCODE_ALERT=1
VIASH_LOGCODE_CRITICAL=2
VIASH_LOGCODE_ERROR=3
VIASH_LOGCODE_WARNING=4
VIASH_LOGCODE_NOTICE=5
VIASH_LOGCODE_INFO=6
VIASH_LOGCODE_DEBUG=7
VIASH_VERBOSITY=$VIASH_LOGCODE_NOTICE

# ViashLog: Log events depending on the verbosity level
# usage: ViashLog 1 alert Oh no something went wrong!
# $1: required verbosity level
# $2: display tag
# $3+: messages to display
# stdout: Your input, prepended by '[$2] '.
function ViashLog {
  local required_level="$1"
  local display_tag="$2"
  shift 2
  if [ $VIASH_VERBOSITY -ge $required_level ]; then
    >&2 echo "[$display_tag]" "$@"
  fi
}

# ViashEmergency: log events when the system is unstable
# usage: ViashEmergency Oh no something went wrong.
# stdout: Your input, prepended by '[emergency] '.
function ViashEmergency {
  ViashLog $VIASH_LOGCODE_EMERGENCY emergency "$@"
}

# ViashAlert: log events when actions must be taken immediately (e.g. corrupted system database)
# usage: ViashAlert Oh no something went wrong.
# stdout: Your input, prepended by '[alert] '.
function ViashAlert {
  ViashLog $VIASH_LOGCODE_ALERT alert "$@"
}

# ViashCritical: log events when a critical condition occurs
# usage: ViashCritical Oh no something went wrong.
# stdout: Your input, prepended by '[critical] '.
function ViashCritical {
  ViashLog $VIASH_LOGCODE_CRITICAL critical "$@"
}

# ViashError: log events when an error condition occurs
# usage: ViashError Oh no something went wrong.
# stdout: Your input, prepended by '[error] '.
function ViashError {
  ViashLog $VIASH_LOGCODE_ERROR error "$@"
}

# ViashWarning: log potentially abnormal events
# usage: ViashWarning Something may have gone wrong.
# stdout: Your input, prepended by '[warning] '.
function ViashWarning {
  ViashLog $VIASH_LOGCODE_WARNING warning "$@"
}

# ViashNotice: log significant but normal events
# usage: ViashNotice This just happened.
# stdout: Your input, prepended by '[notice] '.
function ViashNotice {
  ViashLog $VIASH_LOGCODE_NOTICE notice "$@"
}

# ViashInfo: log normal events
# usage: ViashInfo This just happened.
# stdout: Your input, prepended by '[info] '.
function ViashInfo {
  ViashLog $VIASH_LOGCODE_INFO info "$@"
}

# ViashDebug: log all events, for debugging purposes
# usage: ViashDebug This just happened.
# stdout: Your input, prepended by '[debug] '.
function ViashDebug {
  ViashLog $VIASH_LOGCODE_DEBUG debug "$@"
}

# find source folder of this component
VIASH_META_RESOURCES_DIR=`ViashSourceDir ${BASH_SOURCE[0]}`

# find the root of the built components & dependencies
VIASH_TARGET_DIR=`ViashFindTargetDir $VIASH_META_RESOURCES_DIR`

# define meta fields
VIASH_META_NAME="scarches"
VIASH_META_FUNCTIONALITY_NAME="scarches"
VIASH_META_EXECUTABLE="$VIASH_META_RESOURCES_DIR/$VIASH_META_NAME"
VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
VIASH_META_TEMP_DIR="$VIASH_TEMP"



# initialise variables
VIASH_MODE='run'
VIASH_ENGINE_ID='docker'

######## Helper functions for setting up Docker images for viash ########
# expects: ViashDockerBuild

# ViashDockerInstallationCheck: check whether Docker is installed correctly
#
# examples:
#   ViashDockerInstallationCheck
function ViashDockerInstallationCheck {
  ViashDebug "Checking whether Docker is installed"
  if [ ! command -v docker &> /dev/null ]; then
    ViashCritical "Docker doesn't seem to be installed. See 'https://docs.docker.com/get-docker/' for instructions."
    exit 1
  fi

  ViashDebug "Checking whether the Docker daemon is running"
  local save=$-; set +e
  local docker_version=$(docker version --format '{{.Client.APIVersion}}' 2> /dev/null)
  local out=$?
  [[ $save =~ e ]] && set -e
  if [ $out -ne 0 ]; then
    ViashCritical "Docker daemon does not seem to be running. Try one of the following:"
    ViashCritical "- Try running 'dockerd' in the command line"
    ViashCritical "- See https://docs.docker.com/config/daemon/"
    exit 1
  fi
}

# ViashDockerRemoteTagCheck: check whether a Docker image is available 
# on a remote. Assumes `docker login` has been performed, if relevant.
#
# $1                  : image identifier with format `[registry/]image[:tag]`
# exit code $?        : whether or not the image was found
# examples:
#   ViashDockerRemoteTagCheck python:latest
#   echo $?                                     # returns '0'
#   ViashDockerRemoteTagCheck sdaizudceahifu
#   echo $?                                     # returns '1'
function ViashDockerRemoteTagCheck {
  docker manifest inspect $1 > /dev/null 2> /dev/null
}

# ViashDockerLocalTagCheck: check whether a Docker image is available locally
#
# $1                  : image identifier with format `[registry/]image[:tag]`
# exit code $?        : whether or not the image was found
# examples:
#   docker pull python:latest
#   ViashDockerLocalTagCheck python:latest
#   echo $?                                     # returns '0'
#   ViashDockerLocalTagCheck sdaizudceahifu
#   echo $?                                     # returns '1'
function ViashDockerLocalTagCheck {
  [ -n "$(docker images -q $1)" ]
}

# ViashDockerPull: pull a Docker image
#
# $1                  : image identifier with format `[registry/]image[:tag]`
# exit code $?        : whether or not the image was found
# examples:
#   ViashDockerPull python:latest
#   echo $?                                     # returns '0'
#   ViashDockerPull sdaizudceahifu
#   echo $?                                     # returns '1'
function ViashDockerPull {
  ViashNotice "Checking if Docker image is available at '$1'"
  if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
    docker pull $1 && return 0 || return 1
  else
    local save=$-; set +e
    docker pull $1 2> /dev/null > /dev/null
    local out=$?
    [[ $save =~ e ]] && set -e
    if [ $out -ne 0 ]; then
      ViashWarning "Could not pull from '$1'. Docker image doesn't exist or is not accessible."
    fi
    return $out
  fi
}

# ViashDockerPush: push a Docker image
#
# $1                  : image identifier with format `[registry/]image[:tag]`
# exit code $?        : whether or not the image was found
# examples:
#   ViashDockerPush python:latest
#   echo $?                                     # returns '0'
#   ViashDockerPush sdaizudceahifu
#   echo $?                                     # returns '1'
function ViashDockerPush {
  ViashNotice "Pushing image to '$1'"
  local save=$-; set +e
  local out
  if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
    docker push $1
    out=$?
  else
    docker push $1 2> /dev/null > /dev/null
    out=$?
  fi
  [[ $save =~ e ]] && set -e
  if [ $out -eq 0 ]; then
    ViashNotice "Container '$1' push succeeded."
  else
    ViashError "Container '$1' push errored. You might not be logged in or have the necessary permissions."
  fi
  return $out
}

# ViashDockerPullElseBuild: pull a Docker image, else build it
#
# $1                  : image identifier with format `[registry/]image[:tag]`
# ViashDockerBuild    : a Bash function which builds a docker image, takes image identifier as argument.
# examples:
#   ViashDockerPullElseBuild mynewcomponent
function ViashDockerPullElseBuild {
  local save=$-; set +e
  ViashDockerPull $1
  local out=$?
  [[ $save =~ e ]] && set -e
  if [ $out -ne 0 ]; then
    ViashDockerBuild $@
  fi
}

# ViashDockerSetup: create a Docker image, according to specified docker setup strategy
#
# $1          : image identifier with format `[registry/]image[:tag]`
# $2          : docker setup strategy, see DockerSetupStrategy.scala
# examples:
#   ViashDockerSetup mynewcomponent alwaysbuild
function ViashDockerSetup {
  local image_id="$1"
  local setup_strategy="$2"
  if [ "$setup_strategy" == "alwaysbuild" -o "$setup_strategy" == "build" -o "$setup_strategy" == "b" ]; then
    ViashDockerBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
  elif [ "$setup_strategy" == "alwayspull" -o "$setup_strategy" == "pull" -o "$setup_strategy" == "p" ]; then
    ViashDockerPull $image_id
  elif [ "$setup_strategy" == "alwayspullelsebuild" -o "$setup_strategy" == "pullelsebuild" ]; then
    ViashDockerPullElseBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
  elif [ "$setup_strategy" == "alwayspullelsecachedbuild" -o "$setup_strategy" == "pullelsecachedbuild" ]; then
    ViashDockerPullElseBuild $image_id $(ViashDockerBuildArgs "$engine_id")
  elif [ "$setup_strategy" == "alwayscachedbuild" -o "$setup_strategy" == "cachedbuild" -o "$setup_strategy" == "cb" ]; then
    ViashDockerBuild $image_id $(ViashDockerBuildArgs "$engine_id")
  elif [[ "$setup_strategy" =~ ^ifneedbe ]]; then
    local save=$-; set +e
    ViashDockerLocalTagCheck $image_id
    local outCheck=$?
    [[ $save =~ e ]] && set -e
    if [ $outCheck -eq 0 ]; then
      ViashInfo "Image $image_id already exists"
    elif [ "$setup_strategy" == "ifneedbebuild" ]; then
      ViashDockerBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
    elif [ "$setup_strategy" == "ifneedbecachedbuild" ]; then
      ViashDockerBuild $image_id $(ViashDockerBuildArgs "$engine_id")
    elif [ "$setup_strategy" == "ifneedbepull" ]; then
      ViashDockerPull $image_id
    elif [ "$setup_strategy" == "ifneedbepullelsebuild" ]; then
      ViashDockerPullElseBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
    elif [ "$setup_strategy" == "ifneedbepullelsecachedbuild" ]; then
      ViashDockerPullElseBuild $image_id $(ViashDockerBuildArgs "$engine_id")
    else
      ViashError "Unrecognised Docker strategy: $setup_strategy"
      exit 1
    fi
  elif [ "$setup_strategy" == "push" -o "$setup_strategy" == "forcepush" -o "$setup_strategy" == "alwayspush" ]; then
    ViashDockerPush "$image_id"
  elif [ "$setup_strategy" == "pushifnotpresent" -o "$setup_strategy" == "gentlepush" -o "$setup_strategy" == "maybepush" ]; then
    local save=$-; set +e
    ViashDockerRemoteTagCheck $image_id
    local outCheck=$?
    [[ $save =~ e ]] && set -e
    if [ $outCheck -eq 0 ]; then
      ViashNotice "Container '$image_id' exists, doing nothing."
    else
      ViashNotice "Container '$image_id' does not yet exist."
      ViashDockerPush "$image_id"
    fi
  elif [ "$setup_strategy" == "donothing" -o "$setup_strategy" == "meh" ]; then
    ViashNotice "Skipping setup."
  else
    ViashError "Unrecognised Docker strategy: $setup_strategy"
    exit 1
  fi
}

# ViashDockerCheckCommands: Check whether a docker container has the required commands
#
# $1                  : image identifier with format `[registry/]image[:tag]`
# $@                  : commands to verify being present
# examples:
#   ViashDockerCheckCommands bash:4.0 bash ps foo
function ViashDockerCheckCommands {
  local image_id="$1"
  shift 1
  local commands="$@"
  local save=$-; set +e
  local missing # mark 'missing' as local in advance, otherwise the exit code of the command will be missing and always be '0'
  missing=$(docker run --rm --entrypoint=sh "$image_id" -c "for command in $commands; do command -v \$command >/dev/null 2>&1; if [ \$? -ne 0 ]; then echo \$command; exit 1; fi; done")
  local outCheck=$?
  [[ $save =~ e ]] && set -e
  if [ $outCheck -ne 0 ]; then
  	ViashError "Docker container '$image_id' does not contain command '$missing'."
  	exit 1
  fi
}

# ViashDockerBuild: build a docker image
# $1                               : image identifier with format `[registry/]image[:tag]`
# $...                             : additional arguments to pass to docker build
# $VIASH_META_TEMP_DIR             : temporary directory to store dockerfile & optional resources in
# $VIASH_META_NAME                 : name of the component
# $VIASH_META_RESOURCES_DIR        : directory containing the resources
# $VIASH_VERBOSITY                 : verbosity level
# exit code $?                     : whether or not the image was built successfully
function ViashDockerBuild {
  local image_id="$1"
  shift 1

  # create temporary directory to store dockerfile & optional resources in
  local tmpdir=$(mktemp -d "$VIASH_META_TEMP_DIR/dockerbuild-$VIASH_META_NAME-XXXXXX")
  local dockerfile="$tmpdir/Dockerfile"
  function clean_up {
    rm -rf "$tmpdir"
  }
  trap clean_up EXIT

  # store dockerfile and resources
  ViashDockerfile "$VIASH_ENGINE_ID" > "$dockerfile"

  # generate the build command
  local docker_build_cmd="docker build -t '$image_id' $@ '$VIASH_META_RESOURCES_DIR' -f '$dockerfile'"

  # build the container
  ViashNotice "Building container '$image_id' with Dockerfile"
  ViashInfo "$docker_build_cmd"
  local save=$-; set +e
  if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
    eval $docker_build_cmd
  else
    eval $docker_build_cmd &> "$tmpdir/docker_build.log"
  fi

  # check exit code
  local out=$?
  [[ $save =~ e ]] && set -e
  if [ $out -ne 0 ]; then
    ViashError "Error occurred while building container '$image_id'"
    if [ $VIASH_VERBOSITY -lt $VIASH_LOGCODE_INFO ]; then
      ViashError "Transcript: --------------------------------"
      cat "$tmpdir/docker_build.log"
      ViashError "End of transcript --------------------------"
    fi
    exit 1
  fi
}

######## End of helper functions for setting up Docker images for viash ########

# ViashDockerFile: print the dockerfile to stdout
# $1    : engine identifier
# return : dockerfile required to run this component
# examples:
#   ViashDockerFile
function ViashDockerfile {
  local engine_id="$1"

  if [[ "$engine_id" == "docker" ]]; then
    cat << 'VIASHDOCKER'
FROM pytorch/pytorch:2.9.1-cuda12.8-cudnn9-runtime
ENTRYPOINT []
RUN pip install --upgrade pip && \
  pip install --upgrade --no-cache-dir "anndata~=0.12.7" "awkward" "mudata~=0.3.2" "scvi-tools[cuda]~=1.4.1" && \
  python -c 'exec("try:\n  import zarr; from importlib.metadata import version\nexcept ModuleNotFoundError:\n  exit(0)\nelse:  assert int(version(\"zarr\").partition(\".\")[0]) > 2")'

LABEL org.opencontainers.image.authors="Vladimir Shitov, Dorien Roosen"
LABEL org.opencontainers.image.description="Companion container for running component integrate scarches"
LABEL org.opencontainers.image.created="2026-02-04T09:06:08Z"
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
LABEL org.opencontainers.image.version="v4.0.1"

VIASHDOCKER
  fi
}

# ViashDockerBuildArgs: return the arguments to pass to docker build
# $1    : engine identifier
# return : arguments to pass to docker build
function ViashDockerBuildArgs {
  local engine_id="$1"

  if [[ "$engine_id" == "docker" ]]; then
    echo ""
  fi
}

# ViashAbsolutePath: generate absolute path from relative path
# borrowed from https://stackoverflow.com/a/21951256
# $1     : relative filename
# return : absolute path
# examples:
#   ViashAbsolutePath some_file.txt   # returns /path/to/some_file.txt
#   ViashAbsolutePath /foo/bar/..     # returns /foo
function ViashAbsolutePath {
  local thePath
  local parr
  local outp
  local len
  if [[ ! "$1" =~ ^/ ]]; then
    thePath="$PWD/$1"
  else
    thePath="$1"
  fi
  echo "$thePath" | (
    IFS=/
    read -a parr
    declare -a outp
    for i in "${parr[@]}"; do
      case "$i" in
      ''|.) continue ;;
      ..)
        len=${#outp[@]}
        if ((len==0)); then
          continue
        else
          unset outp[$((len-1))]
        fi
        ;;
      *)
        len=${#outp[@]}
        outp[$len]="$i"
      ;;
      esac
    done
    echo /"${outp[*]}"
  )
}
# ViashDockerAutodetectMount: auto configuring docker mounts from parameters
# $1                             : The parameter value
# returns                        : New parameter
# $VIASH_DIRECTORY_MOUNTS        : Added another parameter to be passed to docker
# $VIASH_DOCKER_AUTOMOUNT_PREFIX : The prefix to be used for the automounts
# examples:
#   ViashDockerAutodetectMount /path/to/bar      # returns '/viash_automount/path/to/bar'
#   ViashDockerAutodetectMountArg /path/to/bar   # returns '--volume="/path/to:/viash_automount/path/to"'
function ViashDockerAutodetectMount {
  local abs_path=$(ViashAbsolutePath "$1")
  local mount_source
  local base_name
  if [ -d "$abs_path" ]; then
    mount_source="$abs_path"
    base_name=""
  else
    mount_source=`dirname "$abs_path"`
    base_name=`basename "$abs_path"`
  fi
  local mount_target="$VIASH_DOCKER_AUTOMOUNT_PREFIX$mount_source"
  if [ -z "$base_name" ]; then
    echo "$mount_target"
  else
    echo "$mount_target/$base_name"
  fi
}
function ViashDockerAutodetectMountArg {
  local abs_path=$(ViashAbsolutePath "$1")
  local mount_source
  local base_name
  if [ -d "$abs_path" ]; then
    mount_source="$abs_path"
    base_name=""
  else
    mount_source=`dirname "$abs_path"`
    base_name=`basename "$abs_path"`
  fi
  local mount_target="$VIASH_DOCKER_AUTOMOUNT_PREFIX$mount_source"
  ViashDebug "ViashDockerAutodetectMountArg $1 -> $mount_source -> $mount_target"
  echo "--volume=\"$mount_source:$mount_target\""
}
function ViashDockerStripAutomount {
  local abs_path=$(ViashAbsolutePath "$1")
  echo "${abs_path#$VIASH_DOCKER_AUTOMOUNT_PREFIX}"
}
# initialise variables
VIASH_DIRECTORY_MOUNTS=()

# configure default docker automount prefix if it is unset
if [ -z "${VIASH_DOCKER_AUTOMOUNT_PREFIX+x}" ]; then
  VIASH_DOCKER_AUTOMOUNT_PREFIX="/viash_automount"
fi

# initialise docker variables
VIASH_DOCKER_RUN_ARGS=(-i --rm)


# ViashHelp: Display helpful explanation about this executable
function ViashHelp {
  echo "scarches v4.0.1"
  echo ""
  echo "Performs reference mapping with scArches"
  echo ""
  echo "Inputs:"
  echo "    Arguments related to the input (query) dataset"
  echo ""
  echo "    -i, --input"
  echo "        type: file, required parameter, file must exist"
  echo "        Input h5mu file to use as a query"
  echo ""
  echo "    --layer"
  echo "        type: string"
  echo "        Layer to be used for scArches, if .X is not to be used."
  echo ""
  echo "    --modality"
  echo "        type: string"
  echo "        default: rna"
  echo "        Which modality from the input MuData file to process."
  echo ""
  echo "    --input_obs_batch"
  echo "        type: string"
  echo "        Name of the .obs column with batch information."
  echo ""
  echo "    --input_obs_label"
  echo "        type: string"
  echo "        Name of the .obs column with celltype information."
  echo ""
  echo "    --input_var_gene_names"
  echo "        type: string"
  echo "        Name of the .var column with gene names, if the var .index is not to be"
  echo "        used."
  echo ""
  echo "    --input_obs_size_factor"
  echo "        type: string"
  echo "        Key in adata.obs for size factor information. Instead of using library"
  echo "        size as a size factor,"
  echo "        the provided size factor column will be used as offset in the mean of"
  echo "        the likelihood."
  echo "        Assumed to be on linear scale."
  echo ""
  echo "    --input_obs_categorical_covariate"
  echo "        type: string, multiple values allowed"
  echo "        Keys in adata.obs that correspond to categorical data. These covariates"
  echo "        can be added in"
  echo "        addition to the batch covariate and are also treated as nuisance factors"
  echo "        (i.e., the model tries to minimize their effects on the latent space)."
  echo "        Thus, these should not be used for biologically-relevant factors that"
  echo "        you do _not_ want to correct for."
  echo "        Important: the order of the categorical covariates matters and should"
  echo "        match the order of the covariates in the trained reference model."
  echo ""
  echo "    --input_obs_continuous_covariate"
  echo "        type: string, multiple values allowed"
  echo "        Keys in adata.obs that correspond to continuous data. These covariates"
  echo "        can be added in"
  echo "        addition to the batch covariate and are also treated as nuisance factors"
  echo "        (i.e., the model tries to minimize their effects on the latent space)."
  echo "        Thus, these should not be"
  echo "        used for biologically-relevant factors that you do _not_ want to correct"
  echo "        for."
  echo "        Important: the order of the continuous covariates matters and should"
  echo "        match the order of the covariates in the trained reference model."
  echo ""
  echo "    --sanitize_ensembl_ids"
  echo "        type: boolean"
  echo "        default: true"
  echo "        Whether to sanitize ensembl ids by removing version numbers."
  echo ""
  echo "Reference:"
  echo "    -r, --reference"
  echo "        type: file, required parameter, file must exist"
  echo "        Path to the directory with reference model or a web link."
  echo ""
  echo "    --reference_class"
  echo "        type: string"
  echo "        example: SCANVI"
  echo "        For legacy models; the type of model (where the type of model was not"
  echo "        saved with it; e.g. when they were generated with scvi-tools versions <"
  echo "        0.15)."
  echo ""
  echo "Outputs:"
  echo "    -o, --output"
  echo "        type: file, required parameter, output, file must exist"
  echo "        Output h5mu file."
  echo ""
  echo "    --model_output"
  echo "        type: file, output, file must exist"
  echo "        default: model"
  echo "        Output directory for model"
  echo ""
  echo "    --obsm_output"
  echo "        type: string"
  echo "        default: X_integrated_scanvi"
  echo "        In which .obsm slot to store the resulting integrated embedding."
  echo ""
  echo "    --obs_output_predictions"
  echo "        type: string"
  echo "        default: scanvi_pred"
  echo "        In which .obs slot to store the resulting label predictions. Only"
  echo "        relevant if a scANVI model was provided."
  echo ""
  echo "    --obs_output_probabilities"
  echo "        type: string"
  echo "        default: scanvi_proba"
  echo "        In which .obs slot to store the probabilities of the label predictions."
  echo "        Only relevant if a scANVI model was provided."
  echo ""
  echo "    --output_compression"
  echo "        type: string"
  echo "        example: gzip"
  echo "        choices: [ gzip, lzf ]"
  echo "        Compression format to use for the output AnnData and/or Mudata objects."
  echo "        By default no compression is applied."
  echo ""
  echo "Early stopping arguments:"
  echo "    --early_stopping"
  echo "        type: boolean"
  echo "        Whether to perform early stopping with respect to the validation set."
  echo ""
  echo "    --early_stopping_monitor"
  echo "        type: string"
  echo "        default: elbo_validation"
  echo "        choices: [ elbo_validation, reconstruction_loss_validation,"
  echo "kl_local_validation ]"
  echo "        Metric logged during validation set epoch."
  echo ""
  echo "    --early_stopping_patience"
  echo "        type: integer"
  echo "        default: 45"
  echo "        min: 1"
  echo "        Number of validation epochs with no improvement after which training"
  echo "        will be stopped."
  echo ""
  echo "    --early_stopping_min_delta"
  echo "        type: double"
  echo "        default: 0.0"
  echo "        min: 0.0"
  echo "        Minimum change in the monitored quantity to qualify as an improvement,"
  echo "        i.e. an absolute change of less than min_delta, will count as no"
  echo "        improvement."
  echo ""
  echo "Learning parameters:"
  echo "    --max_epochs"
  echo "        type: integer"
  echo "        Number of passes through the dataset, defaults to (20000 / number of"
  echo "        cells) * 400 or 400; whichever is smallest."
  echo ""
  echo "    --reduce_lr_on_plateau"
  echo "        type: boolean"
  echo "        default: true"
  echo "        Whether to monitor validation loss and reduce learning rate when"
  echo "        validation set \`lr_scheduler_metric\` plateaus."
  echo ""
  echo "    --lr_factor"
  echo "        type: double"
  echo "        default: 0.6"
  echo "        min: 0.0"
  echo "        Factor to reduce learning rate."
  echo ""
  echo "    --lr_patience"
  echo "        type: double"
  echo "        default: 30.0"
  echo "        min: 0.0"
  echo "        Number of epochs with no improvement after which learning rate will be"
  echo "        reduced."
  echo ""
  echo "Viash built in Computational Requirements:"
  echo "    ---cpus=INT"
  echo "        Number of CPUs to use"
  echo "    ---memory=STRING"
  echo "        Amount of memory to use. Examples: 4GB, 3MiB."
  echo ""
  echo "Viash built in Docker:"
  echo "    ---setup=STRATEGY"
  echo "        Setup the docker container. Options are: alwaysbuild, alwayscachedbuild, ifneedbebuild, ifneedbecachedbuild, alwayspull, alwayspullelsebuild, alwayspullelsecachedbuild, ifneedbepull, ifneedbepullelsebuild, ifneedbepullelsecachedbuild, push, pushifnotpresent, donothing."
  echo "        Default: ifneedbepullelsecachedbuild"
  echo "    ---dockerfile"
  echo "        Print the dockerfile to stdout."
  echo "    ---docker_run_args=ARG"
  echo "        Provide runtime arguments to Docker. See the documentation on \`docker run\` for more information."
  echo "    ---docker_image_id"
  echo "        Print the docker image id to stdout."
  echo "    ---debug"
  echo "        Enter the docker container for debugging purposes."
  echo ""
  echo "Viash built in Engines:"
  echo "    ---engine=ENGINE_ID"
  echo "        Specify the engine to use. Options are: docker, native."
  echo "        Default: docker"
}

# initialise array
VIASH_POSITIONAL_ARGS=''

while [[ $# -gt 0 ]]; do
    case "$1" in
        -h|--help)
            ViashHelp
            exit
            ;;
        ---v|---verbose)
            let "VIASH_VERBOSITY=VIASH_VERBOSITY+1"
            shift 1
            ;;
        ---verbosity)
            VIASH_VERBOSITY="$2"
            shift 2
            ;;
        ---verbosity=*)
            VIASH_VERBOSITY="$(ViashRemoveFlags "$1")"
            shift 1
            ;;
        --version)
            echo "scarches v4.0.1"
            exit
            ;;
        --input)
            [ -n "$VIASH_PAR_INPUT" ] && ViashError Bad arguments for option \'--input\': \'$VIASH_PAR_INPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_INPUT="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --input. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --input=*)
            [ -n "$VIASH_PAR_INPUT" ] && ViashError Bad arguments for option \'--input=*\': \'$VIASH_PAR_INPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_INPUT=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        -i)
            [ -n "$VIASH_PAR_INPUT" ] && ViashError Bad arguments for option \'-i\': \'$VIASH_PAR_INPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_INPUT="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to -i. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --layer)
            [ -n "$VIASH_PAR_LAYER" ] && ViashError Bad arguments for option \'--layer\': \'$VIASH_PAR_LAYER\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_LAYER="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --layer. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --layer=*)
            [ -n "$VIASH_PAR_LAYER" ] && ViashError Bad arguments for option \'--layer=*\': \'$VIASH_PAR_LAYER\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_LAYER=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --modality)
            [ -n "$VIASH_PAR_MODALITY" ] && ViashError Bad arguments for option \'--modality\': \'$VIASH_PAR_MODALITY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MODALITY="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --modality. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --modality=*)
            [ -n "$VIASH_PAR_MODALITY" ] && ViashError Bad arguments for option \'--modality=*\': \'$VIASH_PAR_MODALITY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MODALITY=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --input_obs_batch)
            [ -n "$VIASH_PAR_INPUT_OBS_BATCH" ] && ViashError Bad arguments for option \'--input_obs_batch\': \'$VIASH_PAR_INPUT_OBS_BATCH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_INPUT_OBS_BATCH="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --input_obs_batch. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --input_obs_batch=*)
            [ -n "$VIASH_PAR_INPUT_OBS_BATCH" ] && ViashError Bad arguments for option \'--input_obs_batch=*\': \'$VIASH_PAR_INPUT_OBS_BATCH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_INPUT_OBS_BATCH=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --input_obs_label)
            [ -n "$VIASH_PAR_INPUT_OBS_LABEL" ] && ViashError Bad arguments for option \'--input_obs_label\': \'$VIASH_PAR_INPUT_OBS_LABEL\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_INPUT_OBS_LABEL="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --input_obs_label. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --input_obs_label=*)
            [ -n "$VIASH_PAR_INPUT_OBS_LABEL" ] && ViashError Bad arguments for option \'--input_obs_label=*\': \'$VIASH_PAR_INPUT_OBS_LABEL\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_INPUT_OBS_LABEL=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --input_var_gene_names)
            [ -n "$VIASH_PAR_INPUT_VAR_GENE_NAMES" ] && ViashError Bad arguments for option \'--input_var_gene_names\': \'$VIASH_PAR_INPUT_VAR_GENE_NAMES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_INPUT_VAR_GENE_NAMES="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --input_var_gene_names. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --input_var_gene_names=*)
            [ -n "$VIASH_PAR_INPUT_VAR_GENE_NAMES" ] && ViashError Bad arguments for option \'--input_var_gene_names=*\': \'$VIASH_PAR_INPUT_VAR_GENE_NAMES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_INPUT_VAR_GENE_NAMES=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --input_obs_size_factor)
            [ -n "$VIASH_PAR_INPUT_OBS_SIZE_FACTOR" ] && ViashError Bad arguments for option \'--input_obs_size_factor\': \'$VIASH_PAR_INPUT_OBS_SIZE_FACTOR\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_INPUT_OBS_SIZE_FACTOR="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --input_obs_size_factor. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --input_obs_size_factor=*)
            [ -n "$VIASH_PAR_INPUT_OBS_SIZE_FACTOR" ] && ViashError Bad arguments for option \'--input_obs_size_factor=*\': \'$VIASH_PAR_INPUT_OBS_SIZE_FACTOR\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_INPUT_OBS_SIZE_FACTOR=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --input_obs_categorical_covariate)
            if [ -z "$VIASH_PAR_INPUT_OBS_CATEGORICAL_COVARIATE" ]; then
              VIASH_PAR_INPUT_OBS_CATEGORICAL_COVARIATE="$2"
            else
              VIASH_PAR_INPUT_OBS_CATEGORICAL_COVARIATE="$VIASH_PAR_INPUT_OBS_CATEGORICAL_COVARIATE;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --input_obs_categorical_covariate. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --input_obs_categorical_covariate=*)
            if [ -z "$VIASH_PAR_INPUT_OBS_CATEGORICAL_COVARIATE" ]; then
              VIASH_PAR_INPUT_OBS_CATEGORICAL_COVARIATE=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_INPUT_OBS_CATEGORICAL_COVARIATE="$VIASH_PAR_INPUT_OBS_CATEGORICAL_COVARIATE;"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        --input_obs_continuous_covariate)
            if [ -z "$VIASH_PAR_INPUT_OBS_CONTINUOUS_COVARIATE" ]; then
              VIASH_PAR_INPUT_OBS_CONTINUOUS_COVARIATE="$2"
            else
              VIASH_PAR_INPUT_OBS_CONTINUOUS_COVARIATE="$VIASH_PAR_INPUT_OBS_CONTINUOUS_COVARIATE;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --input_obs_continuous_covariate. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --input_obs_continuous_covariate=*)
            if [ -z "$VIASH_PAR_INPUT_OBS_CONTINUOUS_COVARIATE" ]; then
              VIASH_PAR_INPUT_OBS_CONTINUOUS_COVARIATE=$(ViashRemoveFlags "$1")
            else
              VIASH_PAR_INPUT_OBS_CONTINUOUS_COVARIATE="$VIASH_PAR_INPUT_OBS_CONTINUOUS_COVARIATE;"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
        --sanitize_ensembl_ids)
            [ -n "$VIASH_PAR_SANITIZE_ENSEMBL_IDS" ] && ViashError Bad arguments for option \'--sanitize_ensembl_ids\': \'$VIASH_PAR_SANITIZE_ENSEMBL_IDS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SANITIZE_ENSEMBL_IDS="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --sanitize_ensembl_ids. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --sanitize_ensembl_ids=*)
            [ -n "$VIASH_PAR_SANITIZE_ENSEMBL_IDS" ] && ViashError Bad arguments for option \'--sanitize_ensembl_ids=*\': \'$VIASH_PAR_SANITIZE_ENSEMBL_IDS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_SANITIZE_ENSEMBL_IDS=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --reference)
            [ -n "$VIASH_PAR_REFERENCE" ] && ViashError Bad arguments for option \'--reference\': \'$VIASH_PAR_REFERENCE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_REFERENCE="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --reference. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --reference=*)
            [ -n "$VIASH_PAR_REFERENCE" ] && ViashError Bad arguments for option \'--reference=*\': \'$VIASH_PAR_REFERENCE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_REFERENCE=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        -r)
            [ -n "$VIASH_PAR_REFERENCE" ] && ViashError Bad arguments for option \'-r\': \'$VIASH_PAR_REFERENCE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_REFERENCE="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to -r. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --reference_class)
            [ -n "$VIASH_PAR_REFERENCE_CLASS" ] && ViashError Bad arguments for option \'--reference_class\': \'$VIASH_PAR_REFERENCE_CLASS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_REFERENCE_CLASS="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --reference_class. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --reference_class=*)
            [ -n "$VIASH_PAR_REFERENCE_CLASS" ] && ViashError Bad arguments for option \'--reference_class=*\': \'$VIASH_PAR_REFERENCE_CLASS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_REFERENCE_CLASS=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --output)
            [ -n "$VIASH_PAR_OUTPUT" ] && ViashError Bad arguments for option \'--output\': \'$VIASH_PAR_OUTPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTPUT="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --output. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --output=*)
            [ -n "$VIASH_PAR_OUTPUT" ] && ViashError Bad arguments for option \'--output=*\': \'$VIASH_PAR_OUTPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTPUT=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        -o)
            [ -n "$VIASH_PAR_OUTPUT" ] && ViashError Bad arguments for option \'-o\': \'$VIASH_PAR_OUTPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTPUT="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to -o. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --model_output)
            [ -n "$VIASH_PAR_MODEL_OUTPUT" ] && ViashError Bad arguments for option \'--model_output\': \'$VIASH_PAR_MODEL_OUTPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MODEL_OUTPUT="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --model_output. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --model_output=*)
            [ -n "$VIASH_PAR_MODEL_OUTPUT" ] && ViashError Bad arguments for option \'--model_output=*\': \'$VIASH_PAR_MODEL_OUTPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MODEL_OUTPUT=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --obsm_output)
            [ -n "$VIASH_PAR_OBSM_OUTPUT" ] && ViashError Bad arguments for option \'--obsm_output\': \'$VIASH_PAR_OBSM_OUTPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OBSM_OUTPUT="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --obsm_output. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --obsm_output=*)
            [ -n "$VIASH_PAR_OBSM_OUTPUT" ] && ViashError Bad arguments for option \'--obsm_output=*\': \'$VIASH_PAR_OBSM_OUTPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OBSM_OUTPUT=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --obs_output_predictions)
            [ -n "$VIASH_PAR_OBS_OUTPUT_PREDICTIONS" ] && ViashError Bad arguments for option \'--obs_output_predictions\': \'$VIASH_PAR_OBS_OUTPUT_PREDICTIONS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OBS_OUTPUT_PREDICTIONS="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --obs_output_predictions. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --obs_output_predictions=*)
            [ -n "$VIASH_PAR_OBS_OUTPUT_PREDICTIONS" ] && ViashError Bad arguments for option \'--obs_output_predictions=*\': \'$VIASH_PAR_OBS_OUTPUT_PREDICTIONS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OBS_OUTPUT_PREDICTIONS=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --obs_output_probabilities)
            [ -n "$VIASH_PAR_OBS_OUTPUT_PROBABILITIES" ] && ViashError Bad arguments for option \'--obs_output_probabilities\': \'$VIASH_PAR_OBS_OUTPUT_PROBABILITIES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OBS_OUTPUT_PROBABILITIES="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --obs_output_probabilities. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --obs_output_probabilities=*)
            [ -n "$VIASH_PAR_OBS_OUTPUT_PROBABILITIES" ] && ViashError Bad arguments for option \'--obs_output_probabilities=*\': \'$VIASH_PAR_OBS_OUTPUT_PROBABILITIES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OBS_OUTPUT_PROBABILITIES=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --output_compression)
            [ -n "$VIASH_PAR_OUTPUT_COMPRESSION" ] && ViashError Bad arguments for option \'--output_compression\': \'$VIASH_PAR_OUTPUT_COMPRESSION\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTPUT_COMPRESSION="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --output_compression. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --output_compression=*)
            [ -n "$VIASH_PAR_OUTPUT_COMPRESSION" ] && ViashError Bad arguments for option \'--output_compression=*\': \'$VIASH_PAR_OUTPUT_COMPRESSION\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_OUTPUT_COMPRESSION=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --early_stopping)
            [ -n "$VIASH_PAR_EARLY_STOPPING" ] && ViashError Bad arguments for option \'--early_stopping\': \'$VIASH_PAR_EARLY_STOPPING\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_EARLY_STOPPING="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --early_stopping. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --early_stopping=*)
            [ -n "$VIASH_PAR_EARLY_STOPPING" ] && ViashError Bad arguments for option \'--early_stopping=*\': \'$VIASH_PAR_EARLY_STOPPING\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_EARLY_STOPPING=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --early_stopping_monitor)
            [ -n "$VIASH_PAR_EARLY_STOPPING_MONITOR" ] && ViashError Bad arguments for option \'--early_stopping_monitor\': \'$VIASH_PAR_EARLY_STOPPING_MONITOR\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_EARLY_STOPPING_MONITOR="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --early_stopping_monitor. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --early_stopping_monitor=*)
            [ -n "$VIASH_PAR_EARLY_STOPPING_MONITOR" ] && ViashError Bad arguments for option \'--early_stopping_monitor=*\': \'$VIASH_PAR_EARLY_STOPPING_MONITOR\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_EARLY_STOPPING_MONITOR=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --early_stopping_patience)
            [ -n "$VIASH_PAR_EARLY_STOPPING_PATIENCE" ] && ViashError Bad arguments for option \'--early_stopping_patience\': \'$VIASH_PAR_EARLY_STOPPING_PATIENCE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_EARLY_STOPPING_PATIENCE="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --early_stopping_patience. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --early_stopping_patience=*)
            [ -n "$VIASH_PAR_EARLY_STOPPING_PATIENCE" ] && ViashError Bad arguments for option \'--early_stopping_patience=*\': \'$VIASH_PAR_EARLY_STOPPING_PATIENCE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_EARLY_STOPPING_PATIENCE=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --early_stopping_min_delta)
            [ -n "$VIASH_PAR_EARLY_STOPPING_MIN_DELTA" ] && ViashError Bad arguments for option \'--early_stopping_min_delta\': \'$VIASH_PAR_EARLY_STOPPING_MIN_DELTA\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_EARLY_STOPPING_MIN_DELTA="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --early_stopping_min_delta. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --early_stopping_min_delta=*)
            [ -n "$VIASH_PAR_EARLY_STOPPING_MIN_DELTA" ] && ViashError Bad arguments for option \'--early_stopping_min_delta=*\': \'$VIASH_PAR_EARLY_STOPPING_MIN_DELTA\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_EARLY_STOPPING_MIN_DELTA=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --max_epochs)
            [ -n "$VIASH_PAR_MAX_EPOCHS" ] && ViashError Bad arguments for option \'--max_epochs\': \'$VIASH_PAR_MAX_EPOCHS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MAX_EPOCHS="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --max_epochs. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --max_epochs=*)
            [ -n "$VIASH_PAR_MAX_EPOCHS" ] && ViashError Bad arguments for option \'--max_epochs=*\': \'$VIASH_PAR_MAX_EPOCHS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_MAX_EPOCHS=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --reduce_lr_on_plateau)
            [ -n "$VIASH_PAR_REDUCE_LR_ON_PLATEAU" ] && ViashError Bad arguments for option \'--reduce_lr_on_plateau\': \'$VIASH_PAR_REDUCE_LR_ON_PLATEAU\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_REDUCE_LR_ON_PLATEAU="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --reduce_lr_on_plateau. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --reduce_lr_on_plateau=*)
            [ -n "$VIASH_PAR_REDUCE_LR_ON_PLATEAU" ] && ViashError Bad arguments for option \'--reduce_lr_on_plateau=*\': \'$VIASH_PAR_REDUCE_LR_ON_PLATEAU\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_REDUCE_LR_ON_PLATEAU=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --lr_factor)
            [ -n "$VIASH_PAR_LR_FACTOR" ] && ViashError Bad arguments for option \'--lr_factor\': \'$VIASH_PAR_LR_FACTOR\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_LR_FACTOR="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --lr_factor. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --lr_factor=*)
            [ -n "$VIASH_PAR_LR_FACTOR" ] && ViashError Bad arguments for option \'--lr_factor=*\': \'$VIASH_PAR_LR_FACTOR\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_LR_FACTOR=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        --lr_patience)
            [ -n "$VIASH_PAR_LR_PATIENCE" ] && ViashError Bad arguments for option \'--lr_patience\': \'$VIASH_PAR_LR_PATIENCE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_LR_PATIENCE="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --lr_patience. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        --lr_patience=*)
            [ -n "$VIASH_PAR_LR_PATIENCE" ] && ViashError Bad arguments for option \'--lr_patience=*\': \'$VIASH_PAR_LR_PATIENCE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_PAR_LR_PATIENCE=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        ---engine)
            VIASH_ENGINE_ID="$2"
            shift 2
            ;;
        ---engine=*)
            VIASH_ENGINE_ID="$(ViashRemoveFlags "$1")"
            shift 1
            ;;
        ---setup)
            VIASH_MODE='setup'
            VIASH_SETUP_STRATEGY="$2"
            shift 2
            ;;
        ---setup=*)
            VIASH_MODE='setup'
            VIASH_SETUP_STRATEGY="$(ViashRemoveFlags "$1")"
            shift 1
            ;;
        ---dockerfile)
            VIASH_MODE='dockerfile'
            shift 1
            ;;
        ---docker_run_args)
            VIASH_DOCKER_RUN_ARGS+=("$2")
            shift 2
            ;;
        ---docker_run_args=*)
            VIASH_DOCKER_RUN_ARGS+=("$(ViashRemoveFlags "$1")")
            shift 1
            ;;
        ---docker_image_id)
            VIASH_MODE='docker_image_id'
            shift 1
            ;;
        ---debug)
            VIASH_MODE='debug'
            shift 1
            ;;
        ---cpus)
            [ -n "$VIASH_META_CPUS" ] && ViashError Bad arguments for option \'---cpus\': \'$VIASH_META_CPUS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_META_CPUS="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to ---cpus. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        ---cpus=*)
            [ -n "$VIASH_META_CPUS" ] && ViashError Bad arguments for option \'---cpus=*\': \'$VIASH_META_CPUS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_META_CPUS=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        ---memory)
            [ -n "$VIASH_META_MEMORY" ] && ViashError Bad arguments for option \'---memory\': \'$VIASH_META_MEMORY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_META_MEMORY="$2"
            [ $# -lt 2 ] && ViashError Not enough arguments passed to ---memory. Use "--help" to get more information on the parameters. && exit 1
            shift 2
            ;;
        ---memory=*)
            [ -n "$VIASH_META_MEMORY" ] && ViashError Bad arguments for option \'---memory=*\': \'$VIASH_META_MEMORY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
            VIASH_META_MEMORY=$(ViashRemoveFlags "$1")
            shift 1
            ;;
        *)  # positional arg or unknown option
            # since the positional args will be eval'd, can we always quote, instead of using ViashQuote
            VIASH_POSITIONAL_ARGS="$VIASH_POSITIONAL_ARGS '$1'"
            [[ $1 == -* ]] && ViashWarning $1 looks like a parameter but is not a defined parameter and will instead be treated as a positional argument. Use "--help" to get more information on the parameters.
            shift # past argument
            ;;
    esac
done

# parse positional parameters
eval set -- $VIASH_POSITIONAL_ARGS


if   [ "$VIASH_ENGINE_ID" == "native" ]  ; then
  VIASH_ENGINE_TYPE='native'
elif   [ "$VIASH_ENGINE_ID" == "docker" ]  ; then
  VIASH_ENGINE_TYPE='docker'
else
  ViashError "Engine '$VIASH_ENGINE_ID' is not recognized. Options are: docker, native."
  exit 1
fi

if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
  # check if docker is installed properly
  ViashDockerInstallationCheck

  # determine docker image id
  if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/integrate/scarches:v4.0.1'
  fi

  # print dockerfile
  if [ "$VIASH_MODE" == "dockerfile" ]; then
    ViashDockerfile "$VIASH_ENGINE_ID"
    exit 0

  elif [ "$VIASH_MODE" == "docker_image_id" ]; then
    echo "$VIASH_DOCKER_IMAGE_ID"
    exit 0
  
  # enter docker container
  elif [[ "$VIASH_MODE" == "debug" ]]; then
    VIASH_CMD="docker run --entrypoint=bash ${VIASH_DOCKER_RUN_ARGS[@]} -v '$(pwd)':/pwd --workdir /pwd -t $VIASH_DOCKER_IMAGE_ID"
    ViashNotice "+ $VIASH_CMD"
    eval $VIASH_CMD
    exit 

  # build docker image
  elif [ "$VIASH_MODE" == "setup" ]; then
    ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" "$VIASH_SETUP_STRATEGY"
    ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bash'
    exit 0
  fi

  # check if docker image exists
  ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" ifneedbepullelsecachedbuild
  ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'bash'
fi

# setting computational defaults

# helper function for parsing memory strings
function ViashMemoryAsBytes {
  local memory=`echo "$1" | tr '[:upper:]' '[:lower:]' | tr -d '[:space:]'`
  local memory_regex='^([0-9]+)([kmgtp]i?b?|b)$'
  if [[ $memory =~ $memory_regex ]]; then
    local number=${memory/[^0-9]*/}
    local symbol=${memory/*[0-9]/}
    
    case $symbol in
      b)      memory_b=$number ;;
      kb|k)   memory_b=$(( $number * 1000 )) ;;
      mb|m)   memory_b=$(( $number * 1000 * 1000 )) ;;
      gb|g)   memory_b=$(( $number * 1000 * 1000 * 1000 )) ;;
      tb|t)   memory_b=$(( $number * 1000 * 1000 * 1000 * 1000 )) ;;
      pb|p)   memory_b=$(( $number * 1000 * 1000 * 1000 * 1000 * 1000 )) ;;
      kib|ki)   memory_b=$(( $number * 1024 )) ;;
      mib|mi)   memory_b=$(( $number * 1024 * 1024 )) ;;
      gib|gi)   memory_b=$(( $number * 1024 * 1024 * 1024 )) ;;
      tib|ti)   memory_b=$(( $number * 1024 * 1024 * 1024 * 1024 )) ;;
      pib|pi)   memory_b=$(( $number * 1024 * 1024 * 1024 * 1024 * 1024 )) ;;
    esac
    echo "$memory_b"
  fi
}
# compute memory in different units
if [ ! -z ${VIASH_META_MEMORY+x} ]; then
  VIASH_META_MEMORY_B=`ViashMemoryAsBytes $VIASH_META_MEMORY`
  # do not define other variables if memory_b is an empty string
  if [ ! -z "$VIASH_META_MEMORY_B" ]; then
    VIASH_META_MEMORY_KB=$(( ($VIASH_META_MEMORY_B+999) / 1000 ))
    VIASH_META_MEMORY_MB=$(( ($VIASH_META_MEMORY_KB+999) / 1000 ))
    VIASH_META_MEMORY_GB=$(( ($VIASH_META_MEMORY_MB+999) / 1000 ))
    VIASH_META_MEMORY_TB=$(( ($VIASH_META_MEMORY_GB+999) / 1000 ))
    VIASH_META_MEMORY_PB=$(( ($VIASH_META_MEMORY_TB+999) / 1000 ))
    VIASH_META_MEMORY_KIB=$(( ($VIASH_META_MEMORY_B+1023) / 1024 ))
    VIASH_META_MEMORY_MIB=$(( ($VIASH_META_MEMORY_KIB+1023) / 1024 ))
    VIASH_META_MEMORY_GIB=$(( ($VIASH_META_MEMORY_MIB+1023) / 1024 ))
    VIASH_META_MEMORY_TIB=$(( ($VIASH_META_MEMORY_GIB+1023) / 1024 ))
    VIASH_META_MEMORY_PIB=$(( ($VIASH_META_MEMORY_TIB+1023) / 1024 ))
  else
    # unset memory if string is empty
    unset $VIASH_META_MEMORY_B
  fi
fi
# unset nproc if string is empty
if [ -z "$VIASH_META_CPUS" ]; then
  unset $VIASH_META_CPUS
fi


# check whether required parameters exist
if [ -z ${VIASH_PAR_INPUT+x} ]; then
  ViashError '--input' is a required argument. Use "--help" to get more information on the parameters.
  exit 1
fi
if [ -z ${VIASH_PAR_REFERENCE+x} ]; then
  ViashError '--reference' is a required argument. Use "--help" to get more information on the parameters.
  exit 1
fi
if [ -z ${VIASH_PAR_OUTPUT+x} ]; then
  ViashError '--output' is a required argument. Use "--help" to get more information on the parameters.
  exit 1
fi
if [ -z ${VIASH_META_NAME+x} ]; then
  ViashError 'name' is a required argument. Use "--help" to get more information on the parameters.
  exit 1
fi
if [ -z ${VIASH_META_FUNCTIONALITY_NAME+x} ]; then
  ViashError 'functionality_name' is a required argument. Use "--help" to get more information on the parameters.
  exit 1
fi
if [ -z ${VIASH_META_RESOURCES_DIR+x} ]; then
  ViashError 'resources_dir' is a required argument. Use "--help" to get more information on the parameters.
  exit 1
fi
if [ -z ${VIASH_META_EXECUTABLE+x} ]; then
  ViashError 'executable' is a required argument. Use "--help" to get more information on the parameters.
  exit 1
fi
if [ -z ${VIASH_META_CONFIG+x} ]; then
  ViashError 'config' is a required argument. Use "--help" to get more information on the parameters.
  exit 1
fi
if [ -z ${VIASH_META_TEMP_DIR+x} ]; then
  ViashError 'temp_dir' is a required argument. Use "--help" to get more information on the parameters.
  exit 1
fi

# filling in defaults
if [ -z ${VIASH_PAR_MODALITY+x} ]; then
  VIASH_PAR_MODALITY="rna"
fi
if [ -z ${VIASH_PAR_SANITIZE_ENSEMBL_IDS+x} ]; then
  VIASH_PAR_SANITIZE_ENSEMBL_IDS="true"
fi
if [ -z ${VIASH_PAR_MODEL_OUTPUT+x} ]; then
  VIASH_PAR_MODEL_OUTPUT="model"
fi
if [ -z ${VIASH_PAR_OBSM_OUTPUT+x} ]; then
  VIASH_PAR_OBSM_OUTPUT="X_integrated_scanvi"
fi
if [ -z ${VIASH_PAR_OBS_OUTPUT_PREDICTIONS+x} ]; then
  VIASH_PAR_OBS_OUTPUT_PREDICTIONS="scanvi_pred"
fi
if [ -z ${VIASH_PAR_OBS_OUTPUT_PROBABILITIES+x} ]; then
  VIASH_PAR_OBS_OUTPUT_PROBABILITIES="scanvi_proba"
fi
if [ -z ${VIASH_PAR_EARLY_STOPPING_MONITOR+x} ]; then
  VIASH_PAR_EARLY_STOPPING_MONITOR="elbo_validation"
fi
if [ -z ${VIASH_PAR_EARLY_STOPPING_PATIENCE+x} ]; then
  VIASH_PAR_EARLY_STOPPING_PATIENCE="45"
fi
if [ -z ${VIASH_PAR_EARLY_STOPPING_MIN_DELTA+x} ]; then
  VIASH_PAR_EARLY_STOPPING_MIN_DELTA="0.0"
fi
if [ -z ${VIASH_PAR_REDUCE_LR_ON_PLATEAU+x} ]; then
  VIASH_PAR_REDUCE_LR_ON_PLATEAU="true"
fi
if [ -z ${VIASH_PAR_LR_FACTOR+x} ]; then
  VIASH_PAR_LR_FACTOR="0.6"
fi
if [ -z ${VIASH_PAR_LR_PATIENCE+x} ]; then
  VIASH_PAR_LR_PATIENCE="30.0"
fi

# check whether required files exist
if [ ! -z "$VIASH_PAR_INPUT" ] && [ ! -e "$VIASH_PAR_INPUT" ]; then
  ViashError "Input file '$VIASH_PAR_INPUT' does not exist."
  exit 1
fi
if [ ! -z "$VIASH_PAR_REFERENCE" ] && [ ! -e "$VIASH_PAR_REFERENCE" ]; then
  ViashError "Input file '$VIASH_PAR_REFERENCE' does not exist."
  exit 1
fi

# check whether parameters values are of the right type
if [[ -n "$VIASH_PAR_SANITIZE_ENSEMBL_IDS" ]]; then
  if ! [[ "$VIASH_PAR_SANITIZE_ENSEMBL_IDS" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--sanitize_ensembl_ids' has to be a boolean. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_EARLY_STOPPING" ]]; then
  if ! [[ "$VIASH_PAR_EARLY_STOPPING" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--early_stopping' has to be a boolean. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_EARLY_STOPPING_PATIENCE" ]]; then
  if ! [[ "$VIASH_PAR_EARLY_STOPPING_PATIENCE" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--early_stopping_patience' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
  if [[ $VIASH_PAR_EARLY_STOPPING_PATIENCE -lt 1 ]]; then
    ViashError '--early_stopping_patience' has be more than or equal to 1. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_EARLY_STOPPING_MIN_DELTA" ]]; then
  if ! [[ "$VIASH_PAR_EARLY_STOPPING_MIN_DELTA" =~ ^[-+]?(\.[0-9]+|[0-9]+(\.[0-9]*)?)([eE][-+]?[0-9]+)?$ ]]; then
    ViashError '--early_stopping_min_delta' has to be a double. Use "--help" to get more information on the parameters.
    exit 1
  fi
  if command -v bc &> /dev/null; then
    if ! [[ `echo $VIASH_PAR_EARLY_STOPPING_MIN_DELTA '>=' 0.0 | bc` -eq 1 ]]; then
      ViashError '--early_stopping_min_delta' has be more than or equal to 0.0. Use "--help" to get more information on the parameters.
      exit 1
    fi
  elif command -v awk &> /dev/null; then
    if ! [[ `awk -v n1=$VIASH_PAR_EARLY_STOPPING_MIN_DELTA -v n2=0.0 'BEGIN { print (n1 >= n2) ? "1" : "0" }'` -eq 1 ]]; then
      ViashError '--early_stopping_min_delta' has be more than or equal to 0.0. Use "--help" to get more information on the parameters.
      exit 1
    fi
  else
    ViashWarning '--early_stopping_min_delta' specifies a minimum value but the value was not verified as neither \'bc\' or \`awk\` are present on the system.
  fi
fi
if [[ -n "$VIASH_PAR_MAX_EPOCHS" ]]; then
  if ! [[ "$VIASH_PAR_MAX_EPOCHS" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError '--max_epochs' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_REDUCE_LR_ON_PLATEAU" ]]; then
  if ! [[ "$VIASH_PAR_REDUCE_LR_ON_PLATEAU" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
    ViashError '--reduce_lr_on_plateau' has to be a boolean. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_PAR_LR_FACTOR" ]]; then
  if ! [[ "$VIASH_PAR_LR_FACTOR" =~ ^[-+]?(\.[0-9]+|[0-9]+(\.[0-9]*)?)([eE][-+]?[0-9]+)?$ ]]; then
    ViashError '--lr_factor' has to be a double. Use "--help" to get more information on the parameters.
    exit 1
  fi
  if command -v bc &> /dev/null; then
    if ! [[ `echo $VIASH_PAR_LR_FACTOR '>=' 0.0 | bc` -eq 1 ]]; then
      ViashError '--lr_factor' has be more than or equal to 0.0. Use "--help" to get more information on the parameters.
      exit 1
    fi
  elif command -v awk &> /dev/null; then
    if ! [[ `awk -v n1=$VIASH_PAR_LR_FACTOR -v n2=0.0 'BEGIN { print (n1 >= n2) ? "1" : "0" }'` -eq 1 ]]; then
      ViashError '--lr_factor' has be more than or equal to 0.0. Use "--help" to get more information on the parameters.
      exit 1
    fi
  else
    ViashWarning '--lr_factor' specifies a minimum value but the value was not verified as neither \'bc\' or \`awk\` are present on the system.
  fi
fi
if [[ -n "$VIASH_PAR_LR_PATIENCE" ]]; then
  if ! [[ "$VIASH_PAR_LR_PATIENCE" =~ ^[-+]?(\.[0-9]+|[0-9]+(\.[0-9]*)?)([eE][-+]?[0-9]+)?$ ]]; then
    ViashError '--lr_patience' has to be a double. Use "--help" to get more information on the parameters.
    exit 1
  fi
  if command -v bc &> /dev/null; then
    if ! [[ `echo $VIASH_PAR_LR_PATIENCE '>=' 0.0 | bc` -eq 1 ]]; then
      ViashError '--lr_patience' has be more than or equal to 0.0. Use "--help" to get more information on the parameters.
      exit 1
    fi
  elif command -v awk &> /dev/null; then
    if ! [[ `awk -v n1=$VIASH_PAR_LR_PATIENCE -v n2=0.0 'BEGIN { print (n1 >= n2) ? "1" : "0" }'` -eq 1 ]]; then
      ViashError '--lr_patience' has be more than or equal to 0.0. Use "--help" to get more information on the parameters.
      exit 1
    fi
  else
    ViashWarning '--lr_patience' specifies a minimum value but the value was not verified as neither \'bc\' or \`awk\` are present on the system.
  fi
fi
if [[ -n "$VIASH_META_CPUS" ]]; then
  if ! [[ "$VIASH_META_CPUS" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError 'cpus' has to be an integer. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_META_MEMORY_B" ]]; then
  if ! [[ "$VIASH_META_MEMORY_B" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError 'memory_b' has to be a long. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_META_MEMORY_KB" ]]; then
  if ! [[ "$VIASH_META_MEMORY_KB" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError 'memory_kb' has to be a long. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_META_MEMORY_MB" ]]; then
  if ! [[ "$VIASH_META_MEMORY_MB" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError 'memory_mb' has to be a long. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_META_MEMORY_GB" ]]; then
  if ! [[ "$VIASH_META_MEMORY_GB" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError 'memory_gb' has to be a long. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_META_MEMORY_TB" ]]; then
  if ! [[ "$VIASH_META_MEMORY_TB" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError 'memory_tb' has to be a long. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_META_MEMORY_PB" ]]; then
  if ! [[ "$VIASH_META_MEMORY_PB" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError 'memory_pb' has to be a long. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_META_MEMORY_KIB" ]]; then
  if ! [[ "$VIASH_META_MEMORY_KIB" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError 'memory_kib' has to be a long. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_META_MEMORY_MIB" ]]; then
  if ! [[ "$VIASH_META_MEMORY_MIB" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError 'memory_mib' has to be a long. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_META_MEMORY_GIB" ]]; then
  if ! [[ "$VIASH_META_MEMORY_GIB" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError 'memory_gib' has to be a long. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_META_MEMORY_TIB" ]]; then
  if ! [[ "$VIASH_META_MEMORY_TIB" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError 'memory_tib' has to be a long. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi
if [[ -n "$VIASH_META_MEMORY_PIB" ]]; then
  if ! [[ "$VIASH_META_MEMORY_PIB" =~ ^[-+]?[0-9]+$ ]]; then
    ViashError 'memory_pib' has to be a long. Use "--help" to get more information on the parameters.
    exit 1
  fi
fi

# check whether value is belongs to a set of choices
if [ ! -z "$VIASH_PAR_OUTPUT_COMPRESSION" ]; then
  VIASH_PAR_OUTPUT_COMPRESSION_CHOICES=("gzip;lzf")
  IFS=';'
  set -f
  if ! [[ ";${VIASH_PAR_OUTPUT_COMPRESSION_CHOICES[*]};" =~ ";$VIASH_PAR_OUTPUT_COMPRESSION;" ]]; then
    ViashError '--output_compression' specified value of \'$VIASH_PAR_OUTPUT_COMPRESSION\' is not in the list of allowed values. Use "--help" to get more information on the parameters.
    exit 1
  fi
  set +f
  unset IFS
fi

if [ ! -z "$VIASH_PAR_EARLY_STOPPING_MONITOR" ]; then
  VIASH_PAR_EARLY_STOPPING_MONITOR_CHOICES=("elbo_validation;reconstruction_loss_validation;kl_local_validation")
  IFS=';'
  set -f
  if ! [[ ";${VIASH_PAR_EARLY_STOPPING_MONITOR_CHOICES[*]};" =~ ";$VIASH_PAR_EARLY_STOPPING_MONITOR;" ]]; then
    ViashError '--early_stopping_monitor' specified value of \'$VIASH_PAR_EARLY_STOPPING_MONITOR\' is not in the list of allowed values. Use "--help" to get more information on the parameters.
    exit 1
  fi
  set +f
  unset IFS
fi

# create parent directories of output files, if so desired
if [ ! -z "$VIASH_PAR_OUTPUT" ] && [ ! -d "$(dirname "$VIASH_PAR_OUTPUT")" ]; then
  mkdir -p "$(dirname "$VIASH_PAR_OUTPUT")"
fi
if [ ! -z "$VIASH_PAR_MODEL_OUTPUT" ] && [ ! -d "$(dirname "$VIASH_PAR_MODEL_OUTPUT")" ]; then
  mkdir -p "$(dirname "$VIASH_PAR_MODEL_OUTPUT")"
fi

if  [ "$VIASH_ENGINE_ID" == "native" ]  ; then
  if [ "$VIASH_MODE" == "run" ]; then
    VIASH_CMD="bash"
  else
    ViashError "Engine '$VIASH_ENGINE_ID' does not support mode '$VIASH_MODE'."
    exit 1
  fi
fi

if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
  # detect volumes from file arguments
  VIASH_CHOWN_VARS=()
if [ ! -z "$VIASH_PAR_INPUT" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_INPUT")" )
  VIASH_PAR_INPUT=$(ViashDockerAutodetectMount "$VIASH_PAR_INPUT")
fi
if [ ! -z "$VIASH_PAR_REFERENCE" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_REFERENCE")" )
  VIASH_PAR_REFERENCE=$(ViashDockerAutodetectMount "$VIASH_PAR_REFERENCE")
fi
if [ ! -z "$VIASH_PAR_OUTPUT" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_OUTPUT")" )
  VIASH_PAR_OUTPUT=$(ViashDockerAutodetectMount "$VIASH_PAR_OUTPUT")
  VIASH_CHOWN_VARS+=( "$VIASH_PAR_OUTPUT" )
fi
if [ ! -z "$VIASH_PAR_MODEL_OUTPUT" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_MODEL_OUTPUT")" )
  VIASH_PAR_MODEL_OUTPUT=$(ViashDockerAutodetectMount "$VIASH_PAR_MODEL_OUTPUT")
  VIASH_CHOWN_VARS+=( "$VIASH_PAR_MODEL_OUTPUT" )
fi
if [ ! -z "$VIASH_META_RESOURCES_DIR" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_META_RESOURCES_DIR")" )
  VIASH_META_RESOURCES_DIR=$(ViashDockerAutodetectMount "$VIASH_META_RESOURCES_DIR")
fi
if [ ! -z "$VIASH_META_EXECUTABLE" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_META_EXECUTABLE")" )
  VIASH_META_EXECUTABLE=$(ViashDockerAutodetectMount "$VIASH_META_EXECUTABLE")
fi
if [ ! -z "$VIASH_META_CONFIG" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_META_CONFIG")" )
  VIASH_META_CONFIG=$(ViashDockerAutodetectMount "$VIASH_META_CONFIG")
fi
if [ ! -z "$VIASH_META_TEMP_DIR" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_META_TEMP_DIR")" )
  VIASH_META_TEMP_DIR=$(ViashDockerAutodetectMount "$VIASH_META_TEMP_DIR")
fi
  
  # get unique mounts
  VIASH_UNIQUE_MOUNTS=($(for val in "${VIASH_DIRECTORY_MOUNTS[@]}"; do echo "$val"; done | sort -u))
fi

if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
  # change file ownership
  function ViashPerformChown {
    if (( ${#VIASH_CHOWN_VARS[@]} )); then
      set +e
      VIASH_CMD="docker run --entrypoint=bash --rm ${VIASH_UNIQUE_MOUNTS[@]} $VIASH_DOCKER_IMAGE_ID -c 'chown $(id -u):$(id -g) --silent --recursive ${VIASH_CHOWN_VARS[@]}'"
      ViashDebug "+ $VIASH_CMD"
      eval $VIASH_CMD
      set -e
    fi
  }
  trap ViashPerformChown EXIT
fi

if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
  # helper function for filling in extra docker args
  if [ ! -z "$VIASH_META_MEMORY_B" ]; then
    VIASH_DOCKER_RUN_ARGS+=("--memory=${VIASH_META_MEMORY_B}")
  fi
  if [ ! -z "$VIASH_META_CPUS" ]; then
    VIASH_DOCKER_RUN_ARGS+=("--cpus=${VIASH_META_CPUS}")
  fi
fi

if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
  VIASH_CMD="docker run --entrypoint=bash ${VIASH_DOCKER_RUN_ARGS[@]} ${VIASH_UNIQUE_MOUNTS[@]} $VIASH_DOCKER_IMAGE_ID"
fi


# set dependency paths


ViashDebug "Running command: $(echo $VIASH_CMD)"
cat << VIASHEOF | eval $VIASH_CMD
set -e
tempscript=\$(mktemp "$VIASH_META_TEMP_DIR/viash-run-scarches-XXXXXX").py
function clean_up {
  rm "\$tempscript"
}
function interrupt {
  echo -e "\nCTRL-C Pressed..."
  exit 1
}
trap clean_up EXIT
trap interrupt INT SIGINT
cat > "\$tempscript" << 'VIASHMAIN'
import sys
import mudata
from anndata import AnnData
import scvi
import pandas as pd
import numpy as np
import torch
from tempfile import TemporaryDirectory
from pathlib import Path
import pickle

### VIASH START
# The following code has been auto-generated by Viash.
par = {
  'input': $( if [ ! -z ${VIASH_PAR_INPUT+x} ]; then echo "r'${VIASH_PAR_INPUT//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'layer': $( if [ ! -z ${VIASH_PAR_LAYER+x} ]; then echo "r'${VIASH_PAR_LAYER//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'modality': $( if [ ! -z ${VIASH_PAR_MODALITY+x} ]; then echo "r'${VIASH_PAR_MODALITY//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'input_obs_batch': $( if [ ! -z ${VIASH_PAR_INPUT_OBS_BATCH+x} ]; then echo "r'${VIASH_PAR_INPUT_OBS_BATCH//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'input_obs_label': $( if [ ! -z ${VIASH_PAR_INPUT_OBS_LABEL+x} ]; then echo "r'${VIASH_PAR_INPUT_OBS_LABEL//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'input_var_gene_names': $( if [ ! -z ${VIASH_PAR_INPUT_VAR_GENE_NAMES+x} ]; then echo "r'${VIASH_PAR_INPUT_VAR_GENE_NAMES//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'input_obs_size_factor': $( if [ ! -z ${VIASH_PAR_INPUT_OBS_SIZE_FACTOR+x} ]; then echo "r'${VIASH_PAR_INPUT_OBS_SIZE_FACTOR//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'input_obs_categorical_covariate': $( if [ ! -z ${VIASH_PAR_INPUT_OBS_CATEGORICAL_COVARIATE+x} ]; then echo "r'${VIASH_PAR_INPUT_OBS_CATEGORICAL_COVARIATE//\'/\'\"\'\"r\'}'.split(';')"; else echo None; fi ),
  'input_obs_continuous_covariate': $( if [ ! -z ${VIASH_PAR_INPUT_OBS_CONTINUOUS_COVARIATE+x} ]; then echo "r'${VIASH_PAR_INPUT_OBS_CONTINUOUS_COVARIATE//\'/\'\"\'\"r\'}'.split(';')"; else echo None; fi ),
  'sanitize_ensembl_ids': $( if [ ! -z ${VIASH_PAR_SANITIZE_ENSEMBL_IDS+x} ]; then echo "r'${VIASH_PAR_SANITIZE_ENSEMBL_IDS//\'/\'\"\'\"r\'}'.lower() == 'true'"; else echo None; fi ),
  'reference': $( if [ ! -z ${VIASH_PAR_REFERENCE+x} ]; then echo "r'${VIASH_PAR_REFERENCE//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'reference_class': $( if [ ! -z ${VIASH_PAR_REFERENCE_CLASS+x} ]; then echo "r'${VIASH_PAR_REFERENCE_CLASS//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'output': $( if [ ! -z ${VIASH_PAR_OUTPUT+x} ]; then echo "r'${VIASH_PAR_OUTPUT//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'model_output': $( if [ ! -z ${VIASH_PAR_MODEL_OUTPUT+x} ]; then echo "r'${VIASH_PAR_MODEL_OUTPUT//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'obsm_output': $( if [ ! -z ${VIASH_PAR_OBSM_OUTPUT+x} ]; then echo "r'${VIASH_PAR_OBSM_OUTPUT//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'obs_output_predictions': $( if [ ! -z ${VIASH_PAR_OBS_OUTPUT_PREDICTIONS+x} ]; then echo "r'${VIASH_PAR_OBS_OUTPUT_PREDICTIONS//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'obs_output_probabilities': $( if [ ! -z ${VIASH_PAR_OBS_OUTPUT_PROBABILITIES+x} ]; then echo "r'${VIASH_PAR_OBS_OUTPUT_PROBABILITIES//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'output_compression': $( if [ ! -z ${VIASH_PAR_OUTPUT_COMPRESSION+x} ]; then echo "r'${VIASH_PAR_OUTPUT_COMPRESSION//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'early_stopping': $( if [ ! -z ${VIASH_PAR_EARLY_STOPPING+x} ]; then echo "r'${VIASH_PAR_EARLY_STOPPING//\'/\'\"\'\"r\'}'.lower() == 'true'"; else echo None; fi ),
  'early_stopping_monitor': $( if [ ! -z ${VIASH_PAR_EARLY_STOPPING_MONITOR+x} ]; then echo "r'${VIASH_PAR_EARLY_STOPPING_MONITOR//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'early_stopping_patience': $( if [ ! -z ${VIASH_PAR_EARLY_STOPPING_PATIENCE+x} ]; then echo "int(r'${VIASH_PAR_EARLY_STOPPING_PATIENCE//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'early_stopping_min_delta': $( if [ ! -z ${VIASH_PAR_EARLY_STOPPING_MIN_DELTA+x} ]; then echo "float(r'${VIASH_PAR_EARLY_STOPPING_MIN_DELTA//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'max_epochs': $( if [ ! -z ${VIASH_PAR_MAX_EPOCHS+x} ]; then echo "int(r'${VIASH_PAR_MAX_EPOCHS//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'reduce_lr_on_plateau': $( if [ ! -z ${VIASH_PAR_REDUCE_LR_ON_PLATEAU+x} ]; then echo "r'${VIASH_PAR_REDUCE_LR_ON_PLATEAU//\'/\'\"\'\"r\'}'.lower() == 'true'"; else echo None; fi ),
  'lr_factor': $( if [ ! -z ${VIASH_PAR_LR_FACTOR+x} ]; then echo "float(r'${VIASH_PAR_LR_FACTOR//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'lr_patience': $( if [ ! -z ${VIASH_PAR_LR_PATIENCE+x} ]; then echo "float(r'${VIASH_PAR_LR_PATIENCE//\'/\'\"\'\"r\'}')"; else echo None; fi )
}
meta = {
  'name': $( if [ ! -z ${VIASH_META_NAME+x} ]; then echo "r'${VIASH_META_NAME//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'functionality_name': $( if [ ! -z ${VIASH_META_FUNCTIONALITY_NAME+x} ]; then echo "r'${VIASH_META_FUNCTIONALITY_NAME//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'resources_dir': $( if [ ! -z ${VIASH_META_RESOURCES_DIR+x} ]; then echo "r'${VIASH_META_RESOURCES_DIR//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'executable': $( if [ ! -z ${VIASH_META_EXECUTABLE+x} ]; then echo "r'${VIASH_META_EXECUTABLE//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'config': $( if [ ! -z ${VIASH_META_CONFIG+x} ]; then echo "r'${VIASH_META_CONFIG//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'temp_dir': $( if [ ! -z ${VIASH_META_TEMP_DIR+x} ]; then echo "r'${VIASH_META_TEMP_DIR//\'/\'\"\'\"r\'}'"; else echo None; fi ),
  'cpus': $( if [ ! -z ${VIASH_META_CPUS+x} ]; then echo "int(r'${VIASH_META_CPUS//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'memory_b': $( if [ ! -z ${VIASH_META_MEMORY_B+x} ]; then echo "int(r'${VIASH_META_MEMORY_B//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'memory_kb': $( if [ ! -z ${VIASH_META_MEMORY_KB+x} ]; then echo "int(r'${VIASH_META_MEMORY_KB//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'memory_mb': $( if [ ! -z ${VIASH_META_MEMORY_MB+x} ]; then echo "int(r'${VIASH_META_MEMORY_MB//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'memory_gb': $( if [ ! -z ${VIASH_META_MEMORY_GB+x} ]; then echo "int(r'${VIASH_META_MEMORY_GB//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'memory_tb': $( if [ ! -z ${VIASH_META_MEMORY_TB+x} ]; then echo "int(r'${VIASH_META_MEMORY_TB//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'memory_pb': $( if [ ! -z ${VIASH_META_MEMORY_PB+x} ]; then echo "int(r'${VIASH_META_MEMORY_PB//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'memory_kib': $( if [ ! -z ${VIASH_META_MEMORY_KIB+x} ]; then echo "int(r'${VIASH_META_MEMORY_KIB//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'memory_mib': $( if [ ! -z ${VIASH_META_MEMORY_MIB+x} ]; then echo "int(r'${VIASH_META_MEMORY_MIB//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'memory_gib': $( if [ ! -z ${VIASH_META_MEMORY_GIB+x} ]; then echo "int(r'${VIASH_META_MEMORY_GIB//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'memory_tib': $( if [ ! -z ${VIASH_META_MEMORY_TIB+x} ]; then echo "int(r'${VIASH_META_MEMORY_TIB//\'/\'\"\'\"r\'}')"; else echo None; fi ),
  'memory_pib': $( if [ ! -z ${VIASH_META_MEMORY_PIB+x} ]; then echo "int(r'${VIASH_META_MEMORY_PIB//\'/\'\"\'\"r\'}')"; else echo None; fi )
}
dep = {
  
}

### VIASH END

sys.path.append(meta["resources_dir"])
from setup_logger import setup_logger
from set_var_index import set_var_index
from compress_h5mu import write_h5ad_to_h5mu_with_compression

logger = setup_logger()


def _read_model_name_from_registry(model_path) -> str:
    """Read registry with information about the model, return the model name"""
    registry = scvi.model.base.BaseModelClass.load_registry(model_path)
    return registry["model_name"]


def _detect_base_model(model_path):
    """Read from the model's file which scvi_tools model it contains"""
    return getattr(scvi.model, _read_model_name_from_registry(model_path))


def _validate_obs_metadata_params(model_registry, model_name):
    """
    Validates .obs metadata par variables that are required by scvi-tools models.

    This function checks that necessary .obs metadata field names (batch, labels, size factors)
    specified in the model registry have the required corresponding parameters provided in the input.

    Parameters
    ----------
    model_registry : dict
        Dictionary containing model configuration and requirements.
    model_name : str
        Name of the model being validated.
    """

    # Maps the keys of the model registry to their corresponding par keys containing the .obs metadata
    registry_par_mapper = {
        "batch_key": "input_obs_batch",
        "labels_key": "input_obs_label",
        "size_factor_key": "input_obs_size_factor",
        "categorical_covariate_keys": "input_obs_categorical_covariate",
        "continuous_covariate_keys": "input_obs_continuous_covariate",
    }

    for registry_key, key in registry_par_mapper.items():
        model_registry_key = model_registry.get(registry_key)
        par_key = par[key]

        if model_registry_key and not par_key:
            if key != "input_obs_label" or not model_registry.get("unlabeled_category"):
                raise ValueError(
                    f"The provided {model_name} model requires \`--{key}\` to be provided."
                )

        elif par_key and not model_registry_key:
            logger.warning(
                f"\`--{key}\` was provided but is not used in the provided {model_name} model."
            )

        elif model_registry_key and par_key:
            if key in [
                "input_obs_categorical_covariate",
                "input_obs_continuous_covariate",
            ]:
                if len(par_key) != len(model_registry_key):
                    raise ValueError(
                        f"The number of provided covariates in \`--{key}\` ({par_key}) does not match the number of covariates used in the provided model ({model_registry_key})."
                    )


def _align_query_with_registry(adata_query, model_path):
    """
    Creates a qeury AnnData object with the expected structure and metadata fields that are aligned with the pre-trained reference model.

    Parameters
    ----------
    adata_query : AnnData
        The query AnnData object to be aligned with the model structure.
    model_path : str
        Path to the directory containing the pre-trained model.

    Returns
    -------
    AnnData
        A new AnnData object with structure and metadata aligned to match the
        requirements of the pre-trained model.
    """

    model = _detect_base_model(model_path)
    model_name = _read_model_name_from_registry(model_path)
    model_registry = model.load_registry(model_path)["setup_args"]
    _validate_obs_metadata_params(model_registry, model_name)

    # Sanitize gene names and set as index of the AnnData object
    # all scArches VAE models expect gene names to be in the .var index
    adata_query = set_var_index(
        adata_query, par["input_var_gene_names"], par["sanitize_ensembl_ids"]
    )

    # align layer
    query_layer = (
        adata_query.X if not par["layer"] else adata_query.layers[par["layer"]]
    )
    var_index = adata_query.var_names.tolist()
    obs_index = adata_query.obs_names.tolist()

    # align observations
    query_obs = {}

    ## batch_key, size_factor_key
    simple_mappings = {
        "batch_key": "input_obs_batch",  # relevant for AUTOZI, LinearSCVI, PEAKVI, SCANVI, SCVI, TOTALVI, MULTIVI, JaxSCVI
        "size_factor_key": "input_obs_size_factor",  # relevant for SCANVI, SCVI, TOTALVI, MULTIVI
    }

    for registry_key, par_key in simple_mappings.items():
        if model_registry.get(registry_key):
            query_obs[model_registry[registry_key]] = adata_query.obs[
                par[par_key]
            ].tolist()

    ## labels-key, relevant for AUTOZI, CondSCVI, LinearSCVI, PEAKVI, SCANVI, SCVI
    if model_registry.get("labels_key"):
        if par["input_obs_label"]:
            query_obs[model_registry["labels_key"]] = adata_query.obs[
                par["input_obs_label"]
            ].tolist()
        else:
            adata_query.obs[model_registry["labels_key"]] = model_registry[
                "unlabeled_category"
            ]
            query_obs[model_registry["labels_key"]] = adata_query.obs[
                model_registry["labels_key"]
            ].tolist()

    ## covariate keys
    covariate_mappings = {
        "categorical_covariate_keys": "input_obs_categorical_covariate",
        "continuous_covariate_keys": "input_obs_continuous_covariate",
    }
    for registry_key, par_key in covariate_mappings.items():
        if model_registry.get(registry_key):
            for covariate, par_covariate in zip(
                model_registry[registry_key], par[par_key]
            ):
                query_obs[covariate] = adata_query.obs[par_covariate].tolist()

    obs = pd.DataFrame(query_obs, index=obs_index)
    var = pd.DataFrame(index=var_index)

    aligned_query_anndata = AnnData(X=query_layer, obs=obs, var=var)
    if model_registry["layer"]:
        aligned_query_anndata.layers[model_registry["layer"]] = query_layer

    return aligned_query_anndata


def map_to_existing_reference(adata_query, model_path, check_val_every_n_epoch=1):
    """
    A function to map the query data to the reference atlas.

    Input:
        * adata_query: An AnnData object with the query
        * model_path: The reference model directory

    Output:
        * vae_query: the trained scvi_tools model
        * adata_query: The AnnData object with the query preprocessed for the mapping to the reference
    """
    model = _detect_base_model(model_path)

    # Keys of the AnnData query object need to match the exact keys in the reference model registry

    aligned_adata_query = _align_query_with_registry(adata_query, model_path)

    try:
        model.prepare_query_anndata(aligned_adata_query, model_path)
    except ValueError:
        logger.warning(
            "ValueError thrown when preparing adata for mapping. Clearing .varm field to prevent it"
        )
        aligned_adata_query.varm.clear()
        try:
            model.prepare_query_anndata(aligned_adata_query, model_path)
        except ValueError:
            raise ValueError(
                f"Could not perform model.prepare_model_anndata, likely because the model was trained with different var names then were found in the index. \\n\\nmodel var_names: {model.prepare_query_anndata(aligned_adata_query, model_path, return_reference_var_names=True).tolist()} \\n\\nquery data var_names: {aligned_adata_query.var_names.tolist()}  "
            )

    try:
        # Load query data into the model
        vae_query = model.load_query_data(
            aligned_adata_query, model_path, freeze_dropout=True
        )
    except KeyError:
        # Older models do not have the 'setup_method_name' key saved with the model.
        # Assume these were generated from an anndata object.
        model_torch = torch.load(
            f"{model_path}/model.pt", weights_only=False, map_location="cpu"
        )
        model_torch["attr_dict"]["registry_"]["setup_method_name"] = "setup_anndata"

        with TemporaryDirectory(dir=meta["temp_dir"]) as tempdir:
            temp_file_name = Path(tempdir) / "model.pt"
            torch.save(model_torch, temp_file_name)
            del model_torch
            vae_query = model.load_query_data(
                aligned_adata_query, tempdir, freeze_dropout=True
            )

    # Train scArches model for query mapping
    vae_query.train(
        max_epochs=par["max_epochs"],
        early_stopping=par["early_stopping"],
        early_stopping_monitor=par["early_stopping_monitor"],
        early_stopping_patience=par["early_stopping_patience"],
        early_stopping_min_delta=par["early_stopping_min_delta"],
        check_val_every_n_epoch=check_val_every_n_epoch,
        accelerator="auto",
    )

    return vae_query


def _convert_object_dtypes_to_strings(adata):
    """Convert object dtypes in .var and .obs to string to prevent error when saving file"""

    def convert_cols(df):
        object_cols = df.columns[df.dtypes == "object"]
        for col in object_cols:
            df[col] = df[col].astype(str)
        return df

    adata.var = convert_cols(adata.var)
    adata.obs = convert_cols(adata.obs)

    return adata


def _get_model_path(model_path: str):
    """Obtain path to the directory with reference model. If the proposed \`model_path\` is a .zip archive, unzip it. If nesessary, convert model to the new format

    Parameters
    ----------
    model_path : str
        Path to a directory, where to search for the model or to a zip file containing the model

    Returns
    -------
    Path to a directory with reference model in format of scvi-tools>=0.15
    """
    import os
    import zipfile
    import tempfile
    from pathlib import Path

    if os.path.isdir(model_path) and "model.pt" in os.listdir(model_path):
        # Probably, the \`model_path\` already contains model in the output format of scvi-tools>=0.15
        return model_path

    # The model either has old format or is a zip file downloaded from Zenodo
    new_directory = Path(tempfile.TemporaryDirectory().name)

    if zipfile.is_zipfile(model_path):
        with zipfile.ZipFile(model_path) as archive:
            archive.extractall(new_directory)
            model_dir = next(new_directory.glob("**/*.pt")).parent

    else:
        model_dir = next(Path(model_path).glob("**/*.pt")).parent

    if "model_params.pt" in os.listdir(model_dir):
        try:
            # The current approach is to store the class with the model in a registry
            model_class = _detect_base_model(model_dir)
        except ValueError:
            # Failed to load the registry, try
            with (model_dir / "attr.pkl").open("rb") as open_file:
                attrs = pickle.load(open_file)
            try:
                model_name = attrs["registry_"]["model_name"]
            except KeyError:
                # With older scvi-tools models, the model name was not stored with the model...
                model_name = par["reference_class"]
                if not model_name:
                    raise ValueError(
                        "Could not load reference model. This might be because it is a legacy model for which the model type was not saved with the model. Please provide it manually using the 'reference_class' argument."
                    )
                if not hasattr(scvi.model, model_name):
                    raise ValueError(
                        f"Requested to load legacy model using type {model_name}, but such a class does not exist in \`scvi.models\`."
                    )
            model_class = getattr(scvi.model, model_name)

        # The model is in the \`directory\`, but it was generated with scvi-tools<0.15
        # TODO: for new references (that could not be SCANVI based), we need to check the base class somehow. Reading registry does not work with models generated by scvi-tools<0.15
        # Here I assume that the reference model is for HLCA and thus is SCANVI based
        converted_model_path = os.path.join(model_dir, "converted")
        model_class.convert_legacy_save(model_dir, converted_model_path)
        return converted_model_path

    elif "model.pt" in os.listdir(model_dir):
        # Archive contained model in the new format, so just return the directory
        return model_dir

    else:
        raise ValueError(
            "Cannot find model in the provided reference path. Please, provide a path or a link to the directory with reference model. For HLCA use https://zenodo.org/record/6337966/files/HLCA_reference_model.zip"
        )


def main():
    logger.info("Reading %s, modality %s", par["input"], par["modality"])
    adata = mudata.read_h5ad(par["input"].strip(), mod=par["modality"])
    adata_query = adata.copy()

    model_path = _get_model_path(par["reference"])
    vae_query = map_to_existing_reference(adata_query, model_path=model_path)
    model_name = _read_model_name_from_registry(model_path)

    # Save info about the used model
    adata.uns["integration_method"] = model_name

    logger.info("Trying to write latent representation")
    output_key = par["obsm_output"].format(model_name=model_name)
    adata.obsm[output_key] = vae_query.get_latent_representation()

    # In addition to integrating the data, scANVI also performs label annotations
    if model_name == "SCANVI":
        adata.obs[par["obs_output_predictions"]] = vae_query.predict()
        adata.obs[par["obs_output_probabilities"]] = np.max(
            vae_query.predict(soft=True), axis=1
        )

    logger.info("Converting dtypes")
    adata = _convert_object_dtypes_to_strings(adata)

    logger.info(
        "Saving h5mu file to %s with compression %s",
        par["output"],
        par["output_compression"],
    )
    write_h5ad_to_h5mu_with_compression(
        par["output"], par["input"], par["modality"], adata, par["output_compression"]
    )

    logger.info("Saving model")
    vae_query.save(par["model_output"], overwrite=True)


if __name__ == "__main__":
    main()
VIASHMAIN
python -B "\$tempscript" &
wait "\$!"

VIASHEOF


if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
  # strip viash automount from file paths
  
  if [ ! -z "$VIASH_PAR_INPUT" ]; then
    VIASH_PAR_INPUT=$(ViashDockerStripAutomount "$VIASH_PAR_INPUT")
  fi
  if [ ! -z "$VIASH_PAR_REFERENCE" ]; then
    VIASH_PAR_REFERENCE=$(ViashDockerStripAutomount "$VIASH_PAR_REFERENCE")
  fi
  if [ ! -z "$VIASH_PAR_OUTPUT" ]; then
    VIASH_PAR_OUTPUT=$(ViashDockerStripAutomount "$VIASH_PAR_OUTPUT")
  fi
  if [ ! -z "$VIASH_PAR_MODEL_OUTPUT" ]; then
    VIASH_PAR_MODEL_OUTPUT=$(ViashDockerStripAutomount "$VIASH_PAR_MODEL_OUTPUT")
  fi
  if [ ! -z "$VIASH_META_RESOURCES_DIR" ]; then
    VIASH_META_RESOURCES_DIR=$(ViashDockerStripAutomount "$VIASH_META_RESOURCES_DIR")
  fi
  if [ ! -z "$VIASH_META_EXECUTABLE" ]; then
    VIASH_META_EXECUTABLE=$(ViashDockerStripAutomount "$VIASH_META_EXECUTABLE")
  fi
  if [ ! -z "$VIASH_META_CONFIG" ]; then
    VIASH_META_CONFIG=$(ViashDockerStripAutomount "$VIASH_META_CONFIG")
  fi
  if [ ! -z "$VIASH_META_TEMP_DIR" ]; then
    VIASH_META_TEMP_DIR=$(ViashDockerStripAutomount "$VIASH_META_TEMP_DIR")
  fi
fi


# check whether required files exist
if [ ! -z "$VIASH_PAR_OUTPUT" ] && [ ! -e "$VIASH_PAR_OUTPUT" ]; then
  ViashError "Output file '$VIASH_PAR_OUTPUT' does not exist."
  exit 1
fi
if [ ! -z "$VIASH_PAR_MODEL_OUTPUT" ] && [ ! -e "$VIASH_PAR_MODEL_OUTPUT" ]; then
  ViashError "Output file '$VIASH_PAR_MODEL_OUTPUT' does not exist."
  exit 1
fi


exit 0
