run

#!/bin/sh

set -u

config=$(cat -)
file=$(echo "$config" | jq -r '."source"')
resources=$(echo "$config" | jq -r '."resources"')
workdir=$(echo "$config" | jq -r '."workdir"')
language=$(echo "$config" | jq -r '."natural_language"')
nextflow_arguments=$(echo "$config" | jq -r '."nextflow_arguments"')

title="Nextflow"
if [ "$language" = "nl" ]; then
  empty="Lege oplossing"
  run_fail="Nextflow run is gefaald"
  file_not_found="Bestand is niet gevonden"
  dir_not_found="Folder is niet gevonden"
  file_check="Bestaan van bestand controleren"
  directory_check="Bestaan van folder controleren"
else
  empty="Empty submission"
  run_fail="Nextflow run failed"
  file_not_found="File not found"
  dir_not_found="Directory not found"
  file_check="Checking file existence"
  directory_check="Checking directory existence"
fi

echo '{ "command": "start-judgement" }'
echo "{ \"command\": \"start-tab\", \"title\": \"$title\" }"

if [ -s "$file" ]; then
  linter_out=$(mktemp)
  nextflow-linter -report="json:$linter_out" -rulesetfiles=rulesets/general.xml -sourcefiles="$file" > /dev/null
  jq --compact-output --monochrome-output '.packages[].files[].violations[] | .command = "annotate-code" | .column = 0 | .row = .lineNumber | .text = .message | .type = if .priority == 1 then "error" elif .priority == 2 then "warning" else "info" end | del(.ruleName, .priority, .lineNumber, .sourceLine, .message)' "$linter_out"
  rm "$linter_out"

  if [ -d "$resources/bin" ]; then
    export PATH="$resources/bin:$PATH"
  fi

  if ! err=$(nextflow -quiet run "$file" $nextflow_arguments); then
    # strip out submission filename
    err=$(echo "$err" | sed "s|$file|<code>|")
    # annotate code with the error if possible
    echo "$err" \
      | sed -nE 's/^.+cause: ([^"]+) @ line ([0-9]+), column ([0-9]+).+$/{ "text": "\1", "row": \2, "column": \3 }/p' \
      | jq '. | .command = "annotate-code" | .row -=1 | .type = "error"'
    jq --null-input --compact-output --monochrome-output \
      --arg description "$err" \
      '{ "command": "append-message", "message": { "format": "callout-danger", "description": $description } }'
    echo "{ \"command\": \"escalate-status\", \"status\": { \"enum\": \"wrong\", \"human\": \"$run_fail\" } }"
  fi

  filename="$resources/files.json"
  if [ -f "$filename" ]; then
    echo '{ "command": "close-tab" }'
    echo "{ \"command\": \"start-tab\", \"title\": \"Files\" }"
    jq --compact-output '.[]' "$filename" | while read -r fileinfo; do
      type=$(echo "$fileinfo" | jq -r '."type"')
      path="$workdir/$(echo "$fileinfo" | jq -r '."path"')"
      echo '{ "command": "start-context" }'
      if [ "$type" = "file" ]; then
        echo "{ \"command\": \"start-testcase\", \"description\": \"$file_check\" }"
        echo "{ \"command\": \"start-test\", \"expected\": \"$path\" }"
        if [ -f "$path" ]; then
          echo "{ \"command\": \"close-test\", \"generated\": \"$path\", \"status\": { \"enum\": \"correct\" } }"
        else
          echo "{ \"command\": \"close-test\", \"generated\": \"\", \"status\": { \"enum\": \"wrong\", \"human\": \"$file_not_found\" } }"
        fi
        echo '{ "command": "close-testcase" }'

      elif [ "$type" = "directory" ]; then
        echo "{ \"command\": \"start-testcase\", \"description\": \"$directory_check\" }"
        echo "{ \"command\": \"start-test\", \"expected\": \"$path\" }"
        if [ -d "$path" ]; then
          echo "{ \"command\": \"close-test\", \"generated\": \"$path\", \"status\": { \"enum\": \"correct\" } }"
        else
          echo "{ \"command\": \"close-test\", \"generated\": \"\", \"status\": { \"enum\": \"wrong\", \"human\": \"$dir_not_found\" } }"
        fi
        echo '{ "command": "close-testcase" }'
      fi
      echo '{ "command": "close-context" }'
    done
  fi
else
  echo "{ \"command\": \"escalate-status\", \"status\": { \"enum\": \"wrong\", \"human\": \"$empty\" } } "
fi

echo '{ "command": "close-tab" }'
echo '{ "command": "close-judgement" }'