#!/bin/sh

c_red="\033[1;31m"
c_green="\033[1;32m"
c_yellow="\033[1;33m"
c_blue="\033[1;34m"
c_magenta="\033[1;35m"
c_cyan="\033[1;36m"
c_reset="\033[0m"

CLINVAR_URL="https://www.ncbi.nlm.nih.gov/clinvar/"
CLINVAR_RESULTS_XPATH="/html/body/div/div/form/div[1]/div[5]/div/div[5]/div/table/tbody"
CLINVAR_DESC_XPATH="/html/body/div[3]/main/div[4]/div"
CLINVAR_EVID_XPATH="/html/body/div[2]/div[2]/div[3]/table/tbody"
FZF_CMD="fzf --ansi -m --tabstop=1 --bind change:top --layout=reverse --delimiter="\t""

usage() {
  printf "Usage: %bclinvar %bsearch-query%b\n" $c_green $c_yellow $c_reset
}

if [ "$#" -eq 0 ] ; then
  usage
  exit 1
fi


awk_parse_results='
BEGIN{
  RS="</tr[^>]*>"
  FS="</?td[^>]*>"
  OFS="\t"
  c_red="\033[1;31m"
  c_green="\033[1;32m"
  c_yellow="\033[1;33m"
  c_blue="\033[1;34m"
  c_magenta="\033[1;35m"
  c_reset="\033[0m"
}
function getmut(str, res) {
  res=gensub(/^.*<span class="ui-button-text">(.*)<\/span>.*$/,"\\1","g",str)
  gsub(/&gt;/,">",res)
  return striptag(res)
}
function striptag(str) {
  gsub(/<[^>]*>/,"",str)
  return str
}
function getpath(str) {
  str=striptag(str)
  if(str~/[pP]athogenic/)
    str=c_yellow str c_reset
  if(str~/[bB]enign/)
    str=c_magenta str c_reset
  return str
}
$16~/VCV[0-9]+/{
  mut=getmut($4)
  if(mut~/^NM/)
    print mut, getpath($12), $16 
}
'

awk_parse_evidence='
BEGIN{
  RS="</tr[^>]*>"
  FS="</?td[^>]*>"
  OFS="\t"
  c_red="\033[1;31m"
  c_green="\033[1;32m"
  c_yellow="\033[1;33m"
  c_blue="\033[1;34m"
  c_magenta="\033[1;35m"
  c_reset="\033[0m"
}
function striptag(str) {
  gsub(/<[^>]*>/,"",str)
  return str
}
!done[$4]{
  done[$4]++
  gsub(/<br\/>/, " ")
  gsub(/\n/, " ", $16)
  if($8~/[pP]athogenic/)
    $8 = c_yellow $8 c_reset
  if($8~/[bB]enign/)
    $8 = c_magenta $8 c_reset
  print $8, $10, $12, $16, $4
  print $4, striptag($26) > "/dev/stderr"
}
'

preview() {
  id=$(echo "$*" | awk '{id=$NF; gsub(/^VCV/, "", id); print int(id+0)}')
  curl -s -L "$CLINVAR_URL/variation/$id" \
        --compressed \
    | xmllint --html --xpath "$CLINVAR_DESC_XPATH" - 2>/dev/null \
    | w3m -dump -T text/html -O utf-8 \
    | sed 's/^Help/-------/'
       
  exit 0
}

evid() {
  id=$(echo "$*" | awk '{id=$NF; gsub(/^VCV/, "", id); print int(id+0)}')
  export EVID_DESC_OUT="evid-$id"
  trap "rm $EVID_DESC_OUT" EXIT

  curl -s -L "$CLINVAR_URL/variation/$id/evidence/" \
        --compressed \
    | xmllint --html --xpath "$CLINVAR_EVID_XPATH" - 2>/dev/null \
    | awk "$awk_parse_evidence" 2> $EVID_DESC_OUT \
    | column -t -s $'\t' \
    | $FZF_CMD --preview "sh $0 -VV $EVID_DESC_OUT {}"

  exit 0
}

evid_desc() {
  db=$1
  shift
  id=$(echo "%s" "$*" | awk '{print $NF}')
  grep "$id" "$db" | awk -F'\t' '{print $2}' | fmt
}

[ "$1" == "-U" ] && preview "$2"
[ "$1" == "-V" ] && evid "$2"
[ "$1" == "-VV" ] && evid_desc "$2" "$3"

# do search
results=$(curl -s -L "$CLINVAR_URL" \
               -G --data-urlencode "EntrezSystem2.PEntrez.clinVar.clinVar_Entrez_ResultsPanel.Entrez_DisplayBar.PageSize=200" \
               -G --data-urlencode "term=$*" \
               --compressed )

parsed_results=$(printf "%s" "$results" | xmllint --html --xpath "$CLINVAR_RESULTS_XPATH" - 2>/dev/null | awk "$awk_parse_results")

if [ "$(printf "%s" "$parsed_results" | wc -l)" -eq 0 ] ; then
  parsed_results=$(printf "%s" "$results" | xmllint --html --xpath "/html/body/div[3]/main/div[3]/div/div/dl/dd[5]" - 2>/dev/null | sed 's/<[^>]*>//g')
fi

# Main menu
while : ; do
  id=$(printf "%s" "$parsed_results" | column -t -s $'\t' | $FZF_CMD --preview "sh $0 -U {}" | awk '{print $NF}')

  [ "$id" = "" ] && exit 0
  [ "$id" = "0" ] && exit 0
  # xdg-open "$CLINVAR_URL/variation/$id"
  sh $0 -V $id
done