#!/bin/sh

# ===========================================================================
#
#                            PUBLIC DOMAIN NOTICE
#            National Center for Biotechnology Information (NCBI)
#
#  This software/database is a "United States Government Work" under the
#  terms of the United States Copyright Act.  It was written as part of
#  the author's official duties as a United States Government employee and
#  thus cannot be copyrighted.  This software/database is freely available
#  to the public for use. The National Library of Medicine and the U.S.
#  Government do not place any restriction on its use or reproduction.
#  We would, however, appreciate having the NCBI and the author cited in
#  any work or product based on this material.
#
#  Although all reasonable efforts have been taken to ensure the accuracy
#  and reliability of the software and data, the NLM and the U.S.
#  Government do not and cannot warrant the performance or results that
#  may be obtained by using this software or data. The NLM and the U.S.
#  Government disclaim all warranties, express or implied, including
#  warranties of performance, merchantability or fitness for any particular
#  purpose.
#
# ===========================================================================
#
# File Name:  test-eutils
#
# Author:  Jonathan Kans
#
# Version Creation Date:   3/12/19
#
# ==========================================================================

# Entrez Direct - EDirect

dir=`dirname "$0"`

cmd="-all"

verby=false
timey=false
failed=false
failures=""
repeats=1
START=0
END=0
DIFF=0

ColorSetup() {

  if [ -z "$TERM" ] || [ ! -t 2 ]
  then
    INIT=""
  elif command -v tput >/dev/null
  then
    INIT="$(tput init)"
  else
    # assume ANSI
    escape="$(printf '\033')"
    INIT="${escape}[0m"
  fi
}

ColorSetup

while [ $# -gt 0 ]
do
  case "$1" in
    -all | -alive | -einfo | -esearch | -elink | -efetch | -esummary )
      cmd="$1"
      shift
      ;;
    all | alive | einfo | esearch | elink | efetch | esummary )
      cmd="$1"
      shift
      ;;
    -verbose )
      verby=true
      shift
      ;;
    -timer | -timed )
      timey=true
      shift
      ;;
    -repeat | -repeats )
      shift
      if [ $# -gt 0 ]
      then
        repeats="$1"
        shift
        if [ "$repeats" -lt 1 ]
        then
          repeats=1
        fi
        if [ "$repeats" -gt 100 ]
        then
          repeats=1
        fi
      fi
      ;;
    -h | -help | --help )
      cat <<EOF
USAGE: $0
       [ -all | -alive | -esearch | -elink | -efetch | -esummary ]
       [ -verbose ]
       [ -repeats # ]

EXAMPLE: test-eutils -alive
EOF
      exit 0
      ;;
    -* | * )
      exec >&2
      echo "$0: Unrecognized option $1"
      exit 1
      ;;
  esac
done

MarkFailure() {
  fails="$1"
  res="$2"
  if [ "$failed" != true ]
  then
    if [ "$verby" = true ]
    then
      echo ""
      echo "FAILURE"
      echo ""
    fi
    failed=true
  fi
  if [ "$verby" = true ]
  then
    echo ""
    echo "$fails"
    echo ""
    echo "$res"
    echo ""
  fi
  failures=$(printf '%s\n\n  %s' "$failures" "$fails")
}

DoStart() {
  DIFF=0
  START=$(perl -MTime::HiRes -e 'printf("%.0f\n",Time::HiRes::time()*1000)')
}

DoStop() {
  END=$(perl -MTime::HiRes -e 'printf("%.0f\n",Time::HiRes::time()*1000)')
  DIFF=$(($END - $START))
}

DoTime() {
  if [ "$timey" = true ]
  then
    echo " $DIFF"
  fi
}

DoAlive() {
  for i in $(seq 1 $repeats)
  do
    sleep 1
    DoStart
    size=0
    res=$(
      nquire -get https://eutils.ncbi.nlm.nih.gov/entrez/eutils einfo.fcgi
    )
    if [ -n "$res" ]
    then
      size=${#res}
    fi
    DoStop
    tst=$(
      echo "$res" | xtract -pattern DbList -sep "\n" -element DbName |
      sort | uniq | tr '\n' ' '
    )
    case "$tst" in
      *" mesh "* )
        printf "${INIT}."
        ;;
      * )
        fails="nquire -get https://eutils.ncbi.nlm.nih.gov/entrez/eutils einfo.fcgi"
        MarkFailure "$fails" "$res"
        printf "${INIT}x"
        ;;
    esac
    DoTime
    if [ "$size" -ne 1341 ]
    then
      echo "($size)"
    fi
  done

  for i in $(seq 1 $repeats)
  do
    sleep 1
    DoStart
    size=0
    res=$(
      nquire -get https://eutils.ncbi.nlm.nih.gov/entrez/eutils elink.fcgi -dbfrom pubmed -db pubmed -id 2539356
    )
    if [ -n "$res" ]
    then
      size=${#res}
    fi
    DoStop
    num=$(
      echo "$res" | tr '\n' ' ' | xtract -pattern LinkSet -num "Link/Id"
    )
    if [ -z "$num" ] || [ "$num" -lt 100 ]
    then
      fails="nquire -get https://eutils.ncbi.nlm.nih.gov/entrez/eutils elink.fcgi -dbfrom pubmed -db pubmed -id 2539356"
      MarkFailure "$fails" "$res"
      printf "${INIT}x"
    else
      printf "${INIT}."
    fi
    DoTime
  done

  for i in $(seq 1 $repeats)
  do
    sleep 1
    DoStart
    size=0
    res=$(
      nquire -get https://eutils.ncbi.nlm.nih.gov/entrez/eutils efetch.fcgi -db pubmed -id 2539356 -rettype native -retmode xml
    )
    if [ -n "$res" ]
    then
      size=${#res}
    fi
    DoStop
    tst=$(
      echo "$res" | tr '\n' ' '
    )
    case "$tst" in
      *"Tn3 transposon inserts at a reduced frequency"* )
        printf "${INIT}."
        ;;
      * )
        fails="nquire -get https://eutils.ncbi.nlm.nih.gov/entrez/eutils efetch.fcgi -db pubmed -id 2539356 -rettype native -retmode xml"
        MarkFailure "$fails" "$res"
        printf "${INIT}x"
        ;;
    esac
    DoTime
    if [ "$size" -ne 13931 ]
    then
      echo "($size)"
    fi
  done

  for i in $(seq 1 $repeats)
  do
    sleep 1
    DoStart
    size=0
    res=$(
      nquire -get https://eutils.ncbi.nlm.nih.gov/entrez/eutils esummary.fcgi -db pubmed -id 2539356 -version 2.0
    )
    if [ -n "$res" ]
    then
      size=${#res}
    fi
    DoStop
    tst=$(
      echo "$res" | tr '\n' ' '
    )
    case "$tst" in
      *"Nucleotide sequences required for Tn3 transposition immunity"* )
        printf "${INIT}."
        ;;
      * )
        fails="nquire -get https://eutils.ncbi.nlm.nih.gov/entrez/eutils esummary.fcgi -db pubmed -id 2539356 -version 2.0"
        MarkFailure "$fails" "$res"
        printf "${INIT}x"
        ;;
    esac
    DoTime
  done

  for i in $(seq 1 $repeats)
  do
    sleep 1
    DoStart
    size=0
    res=$(
      nquire -get https://eutils.ncbi.nlm.nih.gov/entrez/eutils esearch.fcgi -db pubmed -term "tn3 transposition immunity"
    )
    if [ -n "$res" ]
    then
      size=${#res}
    fi
    DoStop
    tst=$(
      echo "$res" | tr '\n' ' '
    )
    case "$tst" in
      *"QueryTranslation>tn3"* )
        printf "${INIT}."
        ;;
      * )
        fails="nquire -get https://eutils.ncbi.nlm.nih.gov/entrez/eutils esearch.fcgi -db pubmed -term \"tn3 transposition immunity\""
        MarkFailure "$fails" "$res"
        printf "${INIT}x"
        ;;
    esac
    DoTime
    if [ "$size" -ne 1589 ]
    then
      echo "($size)"
    fi
  done
  printf "${INIT}\n"
}

DoInfo() {
  for i in $(seq 1 $repeats)
  do
    DoStart
    res=$(
      einfo -db all
    )
    DoStop
    tst=$(
      echo "$res" | xtract -pattern DbInfo -sep "\n" -element DbName |
      sort | uniq | tr '\n' ' '
    )
    case "$tst" in
      *" mesh "* )
        printf "${INIT}."
        ;;
      * )
        fails="einfo -db all"
        MarkFailure "$fails" "$res"
        printf "${INIT}x"
        ;;
    esac
    DoTime
  done
  printf "${INIT}\n"
}

DoSearch() {
  while read db qy
  do
    for i in $(seq 1 $repeats)
    do
      DoStart
      res=$(
        esearch -db "$db" -query "$qy" < /dev/null
      )
      DoStop
      num=$(
        echo "$res" | xtract -pattern ENTREZ_DIRECT -element Count
      )
      if [ -z "$num" ] || [ "$num" -lt 1 ]
      then
        fails=$(echo "esearch -db \"$db\" -query \"$qy\"")
        MarkFailure "$fails" "$res"
        printf "${INIT}x"
      else
        printf "${INIT}."
      fi
      DoTime
    done
  done < "$dir/help/tst-esearch.txt"
  printf "${INIT}\n"
}

DoLink() {
  while read db tg id
  do
    for i in $(seq 1 $repeats)
    do
      DoStart
      res=$(
        elink -db "$db" -target "$tg" -id "$id"
      )
      DoStop
      num=$(
        echo "$res" | xtract -pattern ENTREZ_DIRECT -element Count
      )
      if [ -z "$num" ] || [ "$num" -lt 1 ]
      then
        fails=$(echo "elink -db \"$db\" -target \"$tg\" -id \"$id\"")
        MarkFailure "$fails" "$res"
        printf "${INIT}x"
      else
        printf "${INIT}."
      fi
      DoTime
    done
  done < "$dir/help/tst-elink.txt"
  printf "${INIT}\n"
}

DoFetch() {
  while read db ft id mt
  do
    for i in $(seq 1 $repeats)
    do
      DoStart
      res=$(
        efetch -db "$db" -id "$id" -format "$ft"
      )
      DoStop
      tst=$(
        echo "$res" | tr '\n' ' '
      )
      case "$tst" in
        *"$mt"* )
          printf "${INIT}."
          ;;
        * )
          fails=$(echo "efetch -db \"$db\" -id \"$id\" -format \"$ft\"")
          MarkFailure "$fails" "$res"
          printf "${INIT}x"
          ;;
      esac
      DoTime
    done
  done < "$dir/help/tst-efetch.txt"
  printf "${INIT}\n"
}

DoSummary() {
  while read db id
  do
    for i in $(seq 1 $repeats)
    do
      DoStart
      res=$(
        esummary -db "$db" -id "$id"
      )
      DoStop
      tst=$(
        echo "$res" | xtract -pattern DocumentSummary -element DocumentSummary/Id
      )
      if [ -z "$tst" ] || [ "$tst" != "$id" ]
      then
        fails=$(echo "esummary -db \"$db\" -id \"$id\"")
        MarkFailure "$fails" "$res"
        printf "${INIT}x"
      else
        printf "${INIT}."
      fi
      DoTime
    done
  done < "$dir/help/tst-esummary.txt"

  # special tests for dbVar summary, since IDs are reconstructed weekly
  DoStart
  res=$(
    esearch -db dbvar -query "study [OT] AND case_set [STYPE]" |
    efetch -format docsum -start 1 -stop 1
  )
  DoStop
  tst=$(
    echo "$res" | xtract -pattern DocumentSummary -element Study_type
  )
  if [ -z "$tst" ] || [ "$tst" != "Case-Set" ]
  then
    fails=$(echo "esearch -db dbvar -query \"study AND case_set\"")
    MarkFailure "$fails" "$res"
    printf "${INIT}x"
  else
    printf "${INIT}."
  fi
  DoTime

  DoStart
  query="pathogenic [CLIN] AND germline [ALLELE_ORIGIN]"
  query="$query AND nstd102 [ACC] AND brca1 [GENE_NAME]"
  query="$query AND copy_number_variation [VT] AND variant [OT]"
  res=$( esearch -db dbvar -query "$query" |
         efetch -format docsum -start 1 -stop 1 )
  DoStop
  tst=$(
    echo "$res" | xtract -pattern DocumentSummary -first dbVarGene/name
  )
  if [ "$tst" != "BRCA1" ]
  then
    fails=$(echo "esearch -db dbvar -query \"nstd102 AND brca1\"")
    MarkFailure "$fails" "$res"
    printf "${INIT}x"
  else
    printf "${INIT}."
  fi
  DoTime

  printf "${INIT}\n"
}

DoCmd() {

  case "$cmd" in
    -all | all )
      echo "alive"
      DoAlive
      echo "einfo"
      DoInfo
      echo "esearch"
      DoSearch
      echo "elink"
      DoLink
      echo "efetch"
      DoFetch
      echo "esummary"
      DoSummary
      ;;
    -alive | alive )
      DoAlive
      ;;
    -einfo | einfo )
      DoInfo
      ;;
    -esearch | esearch )
      DoSearch
      ;;
    -elink | elink )
      DoLink
      ;;
    -efetch | efetch )
      DoFetch
      ;;
    -esummary | esummary )
      DoSummary
      ;;
    * )
      break
      ;;
  esac

  seconds_end=$(date "+%s")
  seconds=$((seconds_end - seconds_start))

  echo "${INIT}"
  echo "Elapsed time $seconds seconds"
  echo ""
}

seconds_start=$(date "+%s")

echo ""
ver=$( einfo -help | head -n 1 | sed 's/einfo //g' )
int=$( einfo -help | grep internal )
if [ -n "$int" ]
then
  echo "Int EDirect $ver"
else
  echo "EDirect $ver"
fi
echo ""

DoCmd

if [ "$failed" = true ]
then
  export EXTERNAL_EDIRECT=true
  export NQUIRE_TIMEOUT=1
  seconds_start=$(date "+%s")

  echo ""
  if [ -n "$int" ]
  then
    echo "Ext EDirect $ver"
    echo ""

    DoCmd
  fi
fi

if [ "$failed" = true ]
then
  echo ""
  echo "Failure in test-eutils commands:"
  echo "$failures"
  echo ""
  exit 1
fi

echo "Successful completion"