FROM ubuntu
# Install requirements fot the flask app
RUN apt-get clean && apt-get update && DEBIAN_FRONTEND=noninteractive apt-get upgrade -y && DEBIAN_FRONTEND=noninteractive apt-get install -y
    python3
    python3-pip
    r-base
    r-base-dev
    r-cran-rgl
    mutt
    git
    texlive-fonts-recommended

# Install requirements fot the flask app
RUN pip3 install -r ./requirements.txt

@app.route('/send', methods=['POST'])
def send():
    path = os.path.dirname(os.path.realpath(__file__))
    script = path + '/generate_pdf.sh'
    address = str(request.form['email'])
    start_date = convert_date(str(request.form['start_date']))
    end_date = convert_date(str(request.form['end_date']))
    command = [script, start_date, end_date, address]
    subprocess.run(command)
    return json.dumps({
        'status': 'OK',
        'message': 'The action is completed'
    })

#!/bin/bash
start_date="$1"
end_date="$2"
address="$3"
DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
report_name=""$DIR/my_document.pdf""
R -e "rmarkdown::render('$DIR/generate_document.Rmd', output_file = $report_name)" --args "$start_date" "$end_date"
report_name="$DIR/my_document.pdf"
echo | mutt -s "Generated document" -a $report_name -- "$address"
out=$(rm $report_name)

where.clause <- paste0("time >= '",
                       start.date,
                       "' AND time <= '",
                       as.character(as.Date(end.date) + days(1)),
                       "'")
con <- influxdbr::influx_connection(host = "localhost",
                                    port = 8086,
                                    user = "root",
                                    pass = "root")
select.query <- paste0(
  'id, name, surname, car, employment_status'
)
rows <- influx_select(con, db = 'my_db', select.query, from = 'workers',
                         where = where.clause)
rows <- as.data.frame(rows, stringsAsFactors = FALSE)
if(is.data.frame(rows) && nrow(rows) == 0) {
  cat('No data could be obtained from the database.', sep = 'n')
  knitr::knit_exit()
}

....
label: unnamed-chunk-4 (with options)
List of 3
 $ echo   : logi FALSE
 $ message: logi FALSE
 $ warning: logi FALSE

Success: (204) No Content
/app/generate_pdf.sh: line 8:    58 Killed
....